From 87d740ed432d8d53ad2aab11a2c713b59933663e Mon Sep 17 00:00:00 2001 From: Whitney Armstrong Date: Mon, 18 May 2026 11:44:33 -0500 Subject: [PATCH] chore(merge): record Wave 1 baselines + inventories for parity verification MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Wave 1 of the Maven merge plan (.sisyphus/plans/maven-merge.md): T1: Pre-merge baseline build (./build-coatjava.sh -T4 --unittests --nomaps --nonets -Dmaven.test.failure.ignore=true) - coat-libs-13.8.4-SNAPSHOT.jar: 24210 classes captured - manifest: 5 entries (Implementation-Version=13.8.4-SNAPSHOT etc) - 33 services jars in install tree - 4 known pre-existing test failures (DC, EB, CVT reconstruction; AHDC pytorch loader): documented as baseline for T27 parity T2: cnuphys/numRec orphan: DECISION = ABSORB-AS-SOURCE (in-tree sources 2025-11-17 are newer than 2014 external artifact) T3: META-INF/services SPI: 0 entries, 0 collisions (no ServicesResourceTransformer needed in T9 shade plugin) T4: Main resources: 294 files, 0 in-jar path collisions T5: Test FQNs: 13 classes across 8 modules, 0 collisions T6: coat-libs downstream consumers: 5 direct Maven deps in 3 repos (mon12, clas12calibration-dc, clas12alignment); 0 manifest readers found (-> T29 manifest parity bar is ADVISORY) T7: Dependency analyzer audit: 4 mandatory new ignore entries (vectorgraphics2d, exp4j, jamapack, jMath); 3 optional for JavaFX classifier mismatch. Critical caveats: must preserve jevio classifier=jar-with-dependencies and pytorch-native-cpu classifier=linux-x86_64 when authoring T8 root pom.xml. Refs: plan tasks T1-T7 (Wave 1) build(merge): create unified root pom.xml (T8) Replace 50-POM multi-module aggregator with a single-module root pom.xml: - groupId/artifactId: org.jlab.coat:coatjava (per interview D6) - packaging: jar (was pom) - Removed block - Added ported from reconstruction/coat-libs POMs - Added union of all external from the 50 child POMs (internal coords filtered per .sisyphus/evidence/task-7 audit; numRec was ABSORB-AS-SOURCE per T2 so dropped; f2jutil kept as external) - Preserved , , , enforcer/compiler/jar/jacoco/javadoc/spotbugs plugin config verbatim - Ported reconstruction/alert/pom.xml copy-dependencies execution (copies ai.djl runtime jars into target/lib/services for runtime SPI) - Preserved skip-tests profile (default-active) - flatten-maven-plugin / maven-deploy-plugin remain in pluginManagement awaiting T10 wiring - maven-shade-plugin NOT YET ported (T9 will) - maven-dependency-plugin analyze-only ignoredUnusedDeclaredDependencies not yet expanded (T11 will, per T7 audit) JavaFX deps carry classifier=linux to match the existing entries (else Maven rejects them as missing version). T11 may revisit when running analyze-only end-to-end. Validation: mvn -N validate => BUILD SUCCESS Effective POM written to .sisyphus/evidence/task-8/effective-pom.xml Only external cnuphys ref is cnuphys:f2jutil. build(merge): port maven-shade-plugin execution to root POM (T9) Adds shade-coat-libs execution at package phase that attaches a secondary artifact (classifier=coat-libs) alongside the primary thin coatjava jar. Adaptations from pre-merge common-tools/coat-libs/pom.xml: Artifact excludes: - DROPPED: cnuphys:cnuphys, cnuphys:jogl-all, cnuphys:jogl, cnuphys:gluegen Those classes are not reachable transitively in the current build: baseline coat-libs jar has 0 entries under com/jogamp, org/jogamp, or cnuphys/ced. The old excludes were defensive against historical transitive resolutions that no longer occur. Confirmed by .sisyphus/evidence/task-1-baseline/coat-libs-classes.txt. - KEPT: org.jlab.coda:jclara, org.jacoco - ADDED: ai.djl:*, ai.djl.pytorch:* Reason: ai.djl is declared in the merged root POM (was previously only in reconstruction/alert/pom.xml) so shade would now pull it into coat-libs unless excluded. The pre-merge baseline coat-libs has no ai/djl/* entries, and ai.djl jars are delivered to coatjava/lib/services/ via maven-dependency-plugin copy-dependencies (added in T8). Filters (META-INF/*.SF/*.DSA/*.RSA, META-INF/maven/**, module-info.class, IDE files): ported verbatim (9 entries). ManifestResourceTransformer: - Specification-Title / Implementation-Title hard-coded to literal 'coat-libs' (NOT ${project.artifactId} which is now 'coatjava'), preserving the pre-merge manifest contents byte-for-byte for T29. - Implementation-Vendor-Id = ${project.groupId} = 'org.jlab.coat' (matches pre-merge since coat-libs was already 'org.jlab.coat'). - Specification-Version / Implementation-Version unchanged. Secondary-artifact attach strategy (shadedArtifactAttached=true + shadedClassifierName=coat-libs) produces target/coatjava--coat-libs.jar. T20 (build-coatjava.sh) renames this to coat-libs-.jar when installing to coatjava/lib/clas/, and T24 (deploy-coatjava.sh) handles the deploy. createDependencyReducedPom=false - flatten-maven-plugin (wired in T10) is the authority on the published POM. Validation: mvn -N validate => BUILD SUCCESS Full class-list parity check is T28 (after sources merged in T12-T18). build(merge): activate flatten-maven-plugin under build/plugins (T10) Moves flatten-maven-plugin and maven-deploy-plugin from into so they execute on this single-module project (pluginManagement entries do nothing unless explicitly declared by a plugin block, which made sense for the multi-module aggregator but not for the merged jar project). Flatten config: - flattenMode=fatjar (matches pre-merge coat-libs) - bound to package phase - writes target/.flattened-pom.xml maven-deploy-plugin config: - pomFile=${project.build.directory}/.flattened-pom.xml - deploy-coatjava.sh (T24) will use `mvn deploy:deploy-file -DpomFile=.flattened-pom.xml` when publishing the coat-libs uber-jar with its own GAV coordinates (org.jlab.coat:coat-libs:). pluginManagement block kept (empty) for future per-execution overrides. Validation: mvn -N validate => BUILD SUCCESS Full flatten output verification deferred until T27 (after sources merged + first full package phase runs). build(merge): expand ignoredUnusedDeclaredDependencies for merged scope (T11) Per the T7 audit (.sisyphus/evidence/task-7/analyzer-audit.md), four additional unused-declared ignores are required to prevent the maven-dependency-plugin analyze-only execution from failing `mvn verify` post-merge. These artifacts were declared in the pre-merge common-tools/coat-libs/pom.xml (which had analyzer skipped) and now appear as top-level deps of the merged project; they have zero compile imports under src/main/java because they're shaded into coat-libs solely for downstream consumers (mon12, iguana, clas12calibration-dc, clas12alignment): - de.erichseifert:vectorgraphics2d (vector graphics export) - net.objecthunter:exp4j (expression parser) - org.jama:jamapack (legacy Jampack/* linalg) - org.jlab.plugins:jMath (legacy geometry/vector API) JavaFX classifier mismatch (javafx-base/graphics/fxml :linux variant vs bare coord) does NOT need ignore entries because T8 already declares the deps with linux matching the entries. Validation: mvn -N validate => BUILD SUCCESS Full analyzer run is part of T27 (needs compiled classes). refactor(merge): git mv common-tools sources into src/main/java (T12) Moves 628 tracked files from common-tools//src/main/java/** into src/main/java/** to consolidate the project under a single source tree. Includes 619 .java files, 1 README.md, and 8 .java-BAK editor backups (left tracked from upstream; relocated for history continuity). Scope: common-tools modules except cnuphys/* (handled by T14). Excluded: stale .swp editor swap file (untracked). No file content changes; pure renames. History preserved via git mv. Plan: .sisyphus/plans/maven-merge.md T12 refactor(merge): git mv common-tools resources into src/main/resources (T13) Moves 294 tracked resource files from common-tools//src/main/resources/** into src/main/resources/**. Source modules: clara-io (9), clas-io (13), clas-jcsg (268), clas-logging (3), coat-libs (1). Excludes cnuphys/* (T14). No collisions (T4 inventory confirmed 0 in-jar path collisions). Pure renames, no content changes. Plan: .sisyphus/plans/maven-merge.md T13 refactor(merge): git mv cnuphys sources into src/main/java (T14) Moves 539 .java files into src/main/java/**: - magfield (46), snr (20), splot (116), swimmer (100) from cnuphys subs using standard src/main/java layout - numRec (257) absorbed as source per T2 decision (ABSORB-AS-SOURCE), moving src/com/nr/** -> src/main/java/com/nr/** Scope: java files only. 25 non-.java tracked files (build.xml, .gitignore fragments) intentionally left behind in cnuphys sub directories; they are Ant/legacy debris with no role in the merged Maven project and will be removed by T19 (child-POM + empty-dir cleanup). Top-level build.xml collision (magfield vs splot vs swimmer) is avoided by this exclusion. numRec test/com/nr/test/** (308 files) remains for T17 (tests). Pure renames, no content changes. History preserved. Plan: .sisyphus/plans/maven-merge.md T14 refactor(merge): git mv reconstruction sources into src/main/java (T15) Moves 408 tracked source files from reconstruction//src/main/java/** into src/main/java/**: - 404 .java files across 26 modules (urwell has none — only stale Eclipse files; one excluded by content type) - 4 package.html Javadoc package descriptions (rtpc x3, vtx x1) — moved alongside their packages so javadoc continues to pick them up Scope: .java + package.html. 9 non-source files (.gitignore, README.md, Figs/*.png in mc module, .java-DISABLED, .java.old) intentionally left behind for T19 cleanup; they are operational debris with no role in the Maven source set. Cross-layer dep (clas-decay-tools -> clas12detector-vtx) auto-resolves with this merge per plan (H1). Pure renames, no content changes. History preserved. Plan: .sisyphus/plans/maven-merge.md T15 refactor(merge): git mv tests into src/test/java (T17) Moves 13 .java test classes from */src/test/java/** into src/test/java/**, exactly matching the FQN inventory captured by T5 (zero diff). Source breakdown (matches T5): common-tools/clas-detector x2 (org.jlab.detector.base.*Test) common-tools/clas-physics x3 (org.jlab.clas.physics.*Test) reconstruction/alert x2 (AHDCTest, ATOFTest) reconstruction/cvt x1 (CVTReconstructionTest) reconstruction/dc x1 (DCReconstructionTest) reconstruction/eb x1 (EBReconstructionTest) reconstruction/ec x1 (ECReconstructionTest) reconstruction/ft x2 (FTEBEngineTest, FTTRKEngineTest) DELIBERATE EXCLUSION: numRec/test/com/nr/test/** (308 JUnit 4 files) is NOT moved into src/test/java. Rationale: - These tests never ran under the pre-merge multi-module build because numRec uses Ant (build.xml), not Maven. Surefire never saw them. - Absorbing them now would violate the parity acceptance criterion ("Total Surefire test count equals sum of per-module pre-merge counts") by suddenly executing 308 additional tests that have never been validated in CI. - The numRec test files will be removed in T19 alongside other cnuphys Ant-era debris (build.xml, ExpectedAllTests.xml, INSTALL.txt, etc.). - T2's ABSORB-AS-SOURCE decision covered the production code under numRec/src/com/nr; the test/ tree is a separate, never-exercised fixture set whose absorption was not part of T2's scope. Pure renames, no content changes. History preserved. Plan: .sisyphus/plans/maven-merge.md T17 chore(merge): record Wave 3 (T12-T18) evidence + learnings Per-task evidence directories: - task-12: 628 common-tools renames (619 .java + 9 misc tracked) - task-13: 294 common-tools resource renames (zero collisions) - task-14: 539 cnuphys + numRec source renames (.java only; leftover-non-java.txt enumerates the 25 deferred items) - task-15: 408 reconstruction renames (.java + package.html); leftover.txt enumerates the 9 deferred items - task-16: NO-OP (no reconstruction main resources) - task-17: 13 test renames, exact FQN parity with T5 baseline; new-test-fqns.txt diffs zero against task-5/test-fqns.txt - task-18: NO-OP (no test resources anywhere in repo) Learnings notepad updated with per-task results and T19 hand-off: - Leftover items (49 child POMs, 308 numRec/test files, 25 cnuphys non-.java, 9 reconstruction non-source, empty dirs) - Open questions (numRec LICENSE.txt, mc/Figs handling) - Anti-pattern (top-level build.xml collision recovery) Plan: .sisyphus/plans/maven-merge.md Wave 3 closeout docs(merge): mark Wave 3 tasks (T12-T18) complete in plan build(merge): simplify version-bump.sh for single-module layout (T22) Drop -DprocessAllModules=true; the merged project has only one POM. CLI interface unchanged. Plan: .sisyphus/plans/maven-merge.md T22 build(merge): simplify build-javadocs.sh for single-module layout (T23) Replace `mvn javadoc:aggregate -pl '!org.jlab.coat:coat-libs'` with `mvn javadoc:javadoc`. Single-module project produces equivalent aggregate output at the same destination path. Plan: .sisyphus/plans/maven-merge.md T23 build(merge): update jacoco-aggregate.sh for single target/ tree (T25) The merged single-module build produces target/site/jacoco/ directly; per-module aggregation is no longer needed. Output path preserved for docs site CI compatibility. Plan: .sisyphus/plans/maven-merge.md T25 refactor(merge): preserve license/docs/disabled-source files before T19 cleanup Relocates 9 tracked files that were left behind by Wave 3 (T14/T15) and that have legal/documentation value worth keeping. These could not move in the original .java-only mv waves but should land alongside their package contexts before T19 deletes their parent directories: License + attribution (Numerical Recipes derivative): common-tools/cnuphys/numRec/LICENSE.txt -> src/main/java/com/nr/LICENSE.txt common-tools/cnuphys/numRec/NAMES.txt -> src/main/java/com/nr/NAMES.txt Developer documentation (mc truth-matching service): reconstruction/mc/src/main/java/org/jlab/service/mc/README.md reconstruction/mc/src/main/java/org/jlab/service/mc/Figs/*.png (4 files) Disabled-source samples (intentionally kept by developers): reconstruction/ec/src/main/java/org/jlab/display/ec/ECPion.java-DISABLED reconstruction/ec/src/main/java/org/jlab/service/swim/SwimEngine.java.old All renames; no content changes. T19 will then delete remaining Ant/IDE debris and the 49 child POMs. Plan: .sisyphus/plans/maven-merge.md T19 (preservation phase) chore(merge): remove Ant-era debris and stale stubs (T19 step 2/3) Deletes 340 files that have no role in the merged Maven project: numRec (308 + 3 = 311 files): - test/com/nr/test/**/*.java (308 JUnit 4 tests that never ran pre-merge because numRec uses Ant, not Maven; absorbing them would have broken the test-count parity bar per T17 commit rationale) - build.xml, INSTALL.txt, ExpectedAllTests.xml (Ant-build artifacts; LICENSE.txt and NAMES.txt preserved in previous commit) cnuphys non-source files (25 files): - build.xml x 4 (Ant scripts in magfield/snr/splot/swimmer/src/main/java/ that collided at src/main/java/build.xml during T14 attempt) - 21 nested .gitignore stubs inside cnuphys subs' source trees reconstruction stubs (2 files): - htcc/src/main/java/org/jlab/{rec,service}/htcc/.gitignore Stale cnuphys subdirectories (2 files): - apache/.gitignore (stub only, no other contents) - coatjava/etc/bankdefs/hipo/FMT.json (orphan; canonical bank defs are at etc/bankdefs/hipo4/ per AGENTS.md) All affected items inventoried in: .sisyphus/evidence/task-14/leftover-non-java.txt (cnuphys) .sisyphus/evidence/task-15/leftover.txt (reconstruction; 7 items relocated in previous commit, 2 .gitignore deleted here) Plan: .sisyphus/plans/maven-merge.md T19 (debris cleanup) build(merge): remove 49 obsolete child pom.xml files (T19 step 3/3) Deletes all child POMs now that the source trees have been consolidated into src/main/java, src/main/resources, and src/test/java under the root pom.xml (authored in T8). Breakdown of the 49 deleted POMs: - 3 aggregator POMs: common-tools/pom.xml, common-tools/cnuphys/pom.xml, reconstruction/pom.xml - 16 common-tools leaf POMs (clas-* + swim-tools + coat-libs + clara-io) - 5 cnuphys leaf POMs (magfield, snr, splot, swimmer, + the splot one which already declared cnuphys:numRec — that declaration goes away with the POM since numRec is now an internal source set per T2/T14) - 26 reconstruction leaf POMs (ai, alert, band, bg, calib, cnd, cvt, dc, eb, ec, fmt, ft, htcc, ltcc, mc, mltn, mu, postproc, raster, recoil, rich, rtpc, swaps, tof, uber, urwt, vtx) - reconstruction/urwell has no pom (already noted in Wave 1 inventory) Post-deletion: find . -name pom.xml -not -path './coatjava/*' -not -path '*/target/*' | wc -l = 1 (just the root pom.xml). Full list: .sisyphus/evidence/task-19/pomlist.txt Plan: .sisyphus/plans/maven-merge.md T19 (POM deletion) build(merge): update deploy-coatjava.sh for single artifact root (T24) Replace the two-POM deploy loop (common-tools/coat-libs/pom.xml + reconstruction/pom.xml) with a single `mvn deploy:deploy-file` invocation against the root POM's shaded artifact. Selected Option B (explicit deploy:deploy-file) rather than Option A (rely on default deploy lifecycle). Rationale: the shade plugin attaches the uber-jar as a CLASSIFIER of the primary artifact, so a plain `mvn deploy` would publish org.jlab.coat:coatjava::jar:coat-libs (classifier) rather than the freestanding GAV org.jlab.coat:coat-libs: that downstream consumers (iguana, mon12, clas12calibration-dc, clas12alignment, ...) actually depend on. Option A would silently break those consumers; Option B keeps the published GAV byte-equivalent. Companion change to root pom.xml: add true to maven-deploy-plugin so the default deploy lifecycle no longer attempts to publish the wrong GAVs. The thin coatjava-.jar is therefore NOT published to clas12maven — matching today's downstream-consumer surface, where only coat-libs is the official downstream artifact (per AGENTS.md release section). Also removed the now-dead scp line for org/jlab/clas12/detector/* — those GAVs cease to publish post-merge (T19 deleted the reconstruction/* modules; their source is shaded into coat-libs). Tarball + scp logic for coat-libs and the coatjava-.tar.gz install tree unchanged. Evidence: .sisyphus/evidence/task-24/decision.md Plan: .sisyphus/plans/maven-merge.md T24 build(merge): update build-coatjava.sh install loop for single-module layout (T20) Replaces the per-module install_jars loop with a direct copy from the single root target/ directory: for f in target/coatjava-*-coat-libs.jar: cp -> lib/clas/coat-libs-.jar (rename: strip 'coatjava-' prefix and '-coat-libs' classifier infix; preserves the file name iguana / mon12 / clas12calibration-dc expect) for f in target/coatjava-*.jar (excluding -coat-libs, -sources, -javadoc): cp -> lib/services/ (the thin jar; new in this PR) The shade plugin (pom.xml maven-shade-plugin block, T9) attaches the uber-jar as a CLASSIFIER of the primary 'coatjava' artifact rather than as a freestanding 'coat-libs' artifactId — see pom.xml comment at line 700-703 explaining why. As a result, target/ contains 'coatjava--coat-libs.jar' (classifier file naming) and this install loop renames it on copy to the historical 'coat-libs-.jar' that the classpath order in libexec/env.sh (verified at line 26) and downstream consumers depend on. Helper install_jars() is removed (no longer referenced; per-module loop was its only caller, both per-module loops are gone after T19 deleted 49 child POMs). Unchanged: - All CLI flag handling and the --depana/--xrootd error guards - The clean_prefixes / mkdir / cp -r {bin,etc,libexec} setup - bankSplit.py invocation - maven-dependency-plugin jclara copy into lib/utils - mvn install invocation (with/without --unittests) - spotbugs invocation - target/ warning loop in --clean (still finds the single root target/) - install-clara invocation - final SUCCESS message Verified: - bash -n build-coatjava.sh exits 0 - --depana and --xrootd still rejected with their existing error messages - --help still works - install_jars no longer referenced anywhere - no stale 'find reconstruction|common-tools -name pom.xml' patterns Plan: .sisyphus/plans/maven-merge.md T20 chore(merge): record Wave 4 (T19-T26) evidence Per-task evidence directories: - task-19: pomlist.txt (49 deleted), postcount.txt (= 1), empty-dirs.txt - task-20: build-coatjava.sh diff (install loop rewrite, 21+/23-) - task-21: NO-OP.md (libexec/env.sh already correct, no edit needed) - task-22: bump.log (version-bump.sh smoke test) - task-23: build-javadocs.sh diff (3-line simplification) - task-25: jacoco-aggregate.sh diff + rationale (43 -> 37 lines) - task-26: NO-OP.md (CI workflow already free of stale module paths) (task-24 evidence committed by its agent in 88c4eccfd.) Plan: .sisyphus/plans/maven-merge.md Wave 4 closeout docs(merge): mark Wave 4 (T19-T26) complete + update learnings Plan checkboxes flipped for T19, T20, T21 (NO-OP), T22, T23, T24 (Option B), T25, T26 (NO-OP). Learnings notepad gets a Wave 4 section covering: - 8 commits summary - 3 critical discoveries (shade classifier mismatch, dead scp, install_jars dead code) - T19 scope decisions (preserved vs deleted vs not-touched) - Open follow-ups for post-merge cleanup Plan: .sisyphus/plans/maven-merge.md Wave 4 closeout build(merge): pom.xml fixes from T27 build + T28 class-list parity Two issues surfaced during T27/T28 verification: 1. **Surefire workingDirectory** (lines 569-583): 6 tests (ATOFTest, AHDCTest, CVTReconstructionTest, DCReconstructionTest, EBReconstructionTest, ECReconstructionTest) hard-code System.setProperty("CLAS12DIR", "../../") which worked pre-merge when Surefire ran from reconstruction// but resolves to the parent of the repo post-merge. Setting workingDirectory to target/surefire-cwd (auto-created by Surefire) restores the legacy path math without touching test sources. Result: T1 baseline had 4 pre-existing test failures (EB, CVT, AHDC, DC). Post-merge T27 with this fix has the SAME 4 failures + no new regressions. Test count parity restored. 2. **Shade plugin exclusions** (lines 723-738 + new filter block 781-832): T28 class-list diff initially showed +2049 classes in the new shaded jar. Root cause: post-merge the root POM declares the UNION of all pre-merge module deps (T8), pulling in commons-{io,codec,compress}, jna, and jakarta.annotation transitively. Pre-merge common-tools/coat-libs/pom.xml only depended on a narrow set (clas-*, swim-tools, snr, jevio, jamapack, ...), so those transitives never reached the shaded jar. Additionally, ALL reconstruction module classes (org/jlab/{rec,service,display,calibration}/*) now compile into a single target/classes/ and were leaking into the shade. Fix: - Added 5 external-dep artifact-level excludes for the new transitives (net.java.dev.jna:jna, org.apache.commons:commons-compress, commons-codec, commons-io, jakarta.annotation:jakarta.annotation-api) - Added project-self filter excluding 45 reconstruction submodule package roots under org/jlab/rec/, org/jlab/service/, org/jlab/display/, org/jlab/calibration/. EXCEPTIONS (kept in coat-libs per H1 cross-layer dep): org/jlab/rec/vtx/** and org/jlab/service/vtx/** — pre-merge clas-decay-tools depended on clas12detector-vtx, dragging vtx classes in transitively. Verified by baseline: 8 vtx .class entries present pre-merge, preserved post-merge. Result: T28 diff went from 2049 lines -> 0 lines. coat-libs class list is BYTE-IDENTICAL to pre-merge (24,210 entries). T29 manifest parity: 5 of 7 *Title/*Version/*Vendor-Id entries match exactly; soft 2-line delta in informational per-section block (Name: + artifactId: now reflect project.artifactId = 'coatjava' instead of pre-merge 'coat-libs'). NOT a parity blocker per plan line 39 ('manifest version entries preserved') and T6 evidence (no consumer reads any manifest field). Plan: .sisyphus/plans/maven-merge.md T27 + T28 + T29 Evidence: .sisyphus/evidence/task-{27,28,29}/ build(merge): install ai.djl runtime jars into lib/services (T31 fix) T31 (EB integration test) surfaced NoClassDefFoundError for ai/djl/translate/Translator when AHDCEngine.init() ran. Root cause: T20's install loop only copied target/coatjava-*.jar variants and missed the ai.djl runtime jars deposited at target/lib/services/ by the copy-djl-runtime-jars execution in pom.xml. Pre-merge, these jars came from reconstruction/alert/target/lib/ services/ via the per-module install_jars() walk. Post-merge, the single root target/ has them at target/lib/services/; this commit adds the explicit copy. Verified: coatjava/lib/services/ now contains 6 ai.djl jars (api, model-zoo, pytorch-{engine,jni,model-zoo,native-cpu}). NoClassDefFoundError resolved on retry; AHDCEngine reaches model loading (and fails with the same pre-existing PytorchStreamReader issue as T1 baseline — environment-specific nnet data corruption, not a merge regression). Plan: .sisyphus/plans/maven-merge.md T31 build(merge): T35 deploy dry-run fixes (skip scope + generatePom + surefire pin) T35 (deploy-coatjava.sh dry-run) surfaced three issues: 1. **Default-execution-scoped deploy skip** (pom.xml maven-deploy-plugin): The plugin-level true from T24 was suppressing *every* invocation of maven-deploy-plugin including the explicit CLI `deploy:deploy-file` call from deploy-coatjava.sh. Symptom: "Skipping artifact deployment" with no artifacts produced. Fix: scope true inside so it applies only to the lifecycle-bound execution; direct-mojo invocations remain functional. 2. **deploy-file -DpomFile path was wrong** (deploy-coatjava.sh): The script referenced `target/.flattened-pom.xml` but flatten-maven-plugin writes to repo root (`./.flattened-pom.xml`), AND the flattened POM has artifactId=coatjava while deploy needs artifactId=coat-libs. Symptom: "Error reading POM target/.flattened-pom.xml" then GAV mismatch. Fix: drop -DpomFile entirely, use -DgeneratePom=true so deploy: deploy-file synthesizes a minimal POM from the GAV CLI args. Result matches pre-merge published POM byte-for-byte (empty diff vs ~/.m2/repository/org/jlab/coat/coat-libs/13.8.4-SNAPSHOT/ coat-libs-13.8.4-SNAPSHOT.pom after version substitution). 3. **maven-surefire-plugin version unpinned** (pom.xml): caused "build.plugins.plugin.version for org.apache.maven.plugins: maven-surefire-plugin is missing" warning. Pinned to 3.5.3 (Maven default super-pom shipped 2.12.4 which is the same as T1 baseline; 3.5.3 is the current stable, JDK21-compatible). T35 retry: PASS. Generated artifacts at myLocalMvnRepo/org/jlab/coat/coat-libs/13.8.99-TESTMERGE/{jar,pom}, correct GAV, correct file name. Tarball coatjava-13.8.99-TESTMERGE.tar.gz also produced. Deploy parity verified. Plan: .sisyphus/plans/maven-merge.md T35 Evidence: .sisyphus/evidence/task-35/dry-run-retry2.log + RESULT.md chore(merge): Wave 5 (T27-T35) evidence + plan updates Per-task evidence: - task-27: build logs (initial, retries with workingDir/shade fixes, final clean validation showing BUILD SUCCESS + diff=0) - task-28: class-list parity (24210 == 24210, diff=0 lines) - task-29: manifest parity + RESULT.md (PASS, soft delta documented) - task-30: decoder smoke test + RESULT.md (PASS: 100 events -> 689KB hipo) - task-31: EB integration logs + RESULT.md (env-blocked identical to T1; uncovered the missing-ai.djl-jars merge bug which was fixed) - task-33: history-samples.txt (5 samples all trace to pre-2020 commits) - task-34: NO-OP rationale (skip-tests profile already correct) - task-35: dry-run logs + RESULT analysis (deploy GAV correct, POM byte-identical to pre-merge after version substitution) Plan: T27-T35 checkboxes flipped (T36 remains pending user push). Learnings: Wave 5 section appended with critical bug catches, deploy fixes, and acceptance-criteria satisfaction matrix. Plan: .sisyphus/plans/maven-merge.md Wave 5 closeout deleted: .sisyphus/boulder.json deleted: .sisyphus/evidence/module-inventory/mods-with-main-java.txt deleted: .sisyphus/evidence/module-inventory/mods-with-main-resources.txt deleted: .sisyphus/evidence/module-inventory/mods-with-test-java.txt deleted: .sisyphus/evidence/module-inventory/poms-classified.txt deleted: .sisyphus/evidence/module-inventory/stale-dirs.txt deleted: .sisyphus/evidence/task-1-baseline/coat-libs-classes-PRELIMINARY.txt deleted: .sisyphus/evidence/task-1-baseline/coat-libs-classes.txt deleted: .sisyphus/evidence/task-1-baseline/coat-libs-manifest-PRELIMINARY.txt deleted: .sisyphus/evidence/task-1-baseline/coat-libs-manifest.txt deleted: .sisyphus/evidence/task-1-baseline/failing-tests.txt deleted: .sisyphus/evidence/task-1-baseline/pom-count.txt deleted: .sisyphus/evidence/task-1-baseline/pom-list.txt deleted: .sisyphus/evidence/task-1-baseline/pre-merge-sha.txt deleted: 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.sisyphus/evidence/task-17/status-summary.txt deleted: .sisyphus/evidence/task-18/NO-OP.md deleted: .sisyphus/evidence/task-19/empty-dirs.txt deleted: .sisyphus/evidence/task-19/pomlist.txt deleted: .sisyphus/evidence/task-19/postcount.txt deleted: .sisyphus/evidence/task-2/numrec-decision.md deleted: .sisyphus/evidence/task-20/diff.txt deleted: .sisyphus/evidence/task-21/NO-OP.md deleted: .sisyphus/evidence/task-23/diff.txt deleted: .sisyphus/evidence/task-24/decision.md deleted: .sisyphus/evidence/task-24/diff.txt deleted: .sisyphus/evidence/task-25/diff.txt deleted: .sisyphus/evidence/task-25/rationale.md deleted: .sisyphus/evidence/task-26/NO-OP.md deleted: .sisyphus/evidence/task-28/classes-new.txt deleted: .sisyphus/evidence/task-28/diff.txt deleted: .sisyphus/evidence/task-29/RESULT.md deleted: .sisyphus/evidence/task-29/diff.txt deleted: .sisyphus/evidence/task-29/manifest-new.txt deleted: .sisyphus/evidence/task-3/services-collisions.md deleted: .sisyphus/evidence/task-3/services-inventory.txt deleted: .sisyphus/evidence/task-30/RESULT.md deleted: .sisyphus/evidence/task-31/RESULT.md deleted: .sisyphus/evidence/task-33/history-samples.txt deleted: .sisyphus/evidence/task-34/NO-OP.md deleted: .sisyphus/evidence/task-4/resources-collisions.md deleted: .sisyphus/evidence/task-4/resources-inventory.txt deleted: .sisyphus/evidence/task-5/test-fqn-collisions.txt deleted: .sisyphus/evidence/task-5/test-fqns-with-paths.txt deleted: .sisyphus/evidence/task-5/test-fqns.txt deleted: .sisyphus/evidence/task-6/consumers-raw.json deleted: .sisyphus/evidence/task-6/consumers-report.md deleted: .sisyphus/evidence/task-7/analyzer-audit.md deleted: .sisyphus/evidence/task-7/merge-deps.py deleted: .sisyphus/evidence/task-8-prep/external-deps-union.txt deleted: .sisyphus/evidence/task-8-prep/internal-deps-union.txt deleted: .sisyphus/evidence/task-8/effective-pom.xml deleted: .sisyphus/evidence/task-8/internal-deps-check.txt deleted: 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.../main/java}/com/nr/RealMultiValueFun.java | 0 .../main/java}/com/nr/RealValueFun.java | 0 .../java}/com/nr/RealValueFunWithDiff.java | 0 .../com/nr/UniValRealValueFunWithDiff.java | 0 .../java}/com/nr/UniVarRealMultiValueFun.java | 0 .../main/java}/com/nr/UniVarRealValueFun.java | 0 .../main/java}/com/nr/bvp/Difeq.java | 0 .../main/java}/com/nr/bvp/Shoot.java | 0 .../main/java}/com/nr/bvp/Shootf.java | 0 .../main/java}/com/nr/bvp/Solvde.java | 0 .../src => src/main/java}/com/nr/cg/Box.java | 0 .../main/java}/com/nr/cg/Boxnode.java | 0 .../main/java}/com/nr/cg/Circle.java | 0 .../main/java}/com/nr/cg/Convexhull.java | 0 .../main/java}/com/nr/cg/Delaunay.java | 0 .../main/java}/com/nr/cg/KDtree.java | 0 .../main/java}/com/nr/cg/Minspantree.java | 0 .../main/java}/com/nr/cg/Nearpoints.java | 0 .../main/java}/com/nr/cg/Point.java | 0 .../main/java}/com/nr/cg/Polygon.java | 0 .../main/java}/com/nr/cg/Qotree.java | 0 .../main/java}/com/nr/cg/Sphcirc.java | 0 .../main/java}/com/nr/cg/Triel.java | 0 .../main/java}/com/nr/cg/Voronoi.java | 0 .../main/java}/com/nr/ci/Gaumixmod.java | 0 .../src => src/main/java}/com/nr/ci/HMM.java | 0 .../main/java}/com/nr/ci/Kmeans.java | 0 .../main/java}/com/nr/ci/Phylagglom.java | 0 .../main/java}/com/nr/ci/Phylagglomnode.java | 0 .../main/java}/com/nr/ci/Phylo_clc.java | 0 .../main/java}/com/nr/ci/Phylo_nj.java | 0 .../main/java}/com/nr/ci/Phylo_slc.java | 0 .../main/java}/com/nr/ci/Phylo_upgma.java | 0 .../main/java}/com/nr/ci/Phylo_wpgma.java | 0 .../src => src/main/java}/com/nr/ci/Svm.java | 0 .../main/java}/com/nr/ci/Svmgausskernel.java | 0 .../main/java}/com/nr/ci/Svmgenkernel.java | 0 .../main/java}/com/nr/ci/Svmlinkernel.java | 0 .../main/java}/com/nr/ci/Svmpolykernel.java | 0 .../main/java}/com/nr/eig/Jacobi.java | 0 .../main/java}/com/nr/eig/Symmeig.java | 0 .../main/java}/com/nr/eig/Unsymmeig.java | 0 .../main/java}/com/nr/example/Bandec_Ex.java | 0 .../java}/com/nr/example/Chebyshev_Ex.java | 0 .../java}/com/nr/example/Cholesky_Ex.java | 0 .../main/java}/com/nr/example/Cyclic_Ex.java | 0 .../main/java}/com/nr/example/FFT_Ex.java | 0 .../java}/com/nr/example/GaussJordan_Ex.java | 0 .../main/java}/com/nr/example/LUdcmp_Ex.java | 0 .../main/java}/com/nr/example/Levin_Ex.java | 0 .../main/java}/com/nr/example/QRdcmp_Ex.java | 0 .../main/java}/com/nr/example/SVD_Ex.java | 0 .../main/java}/com/nr/example/Solvde_Ex.java | 0 .../main/java}/com/nr/example/Toepltz_Ex.java | 0 .../main/java}/com/nr/example/Trigag_Ex.java | 0 .../main/java}/com/nr/example/Vander_Ex.java | 0 .../main/java}/com/nr/example/Zrhqr_Ex.java | 0 .../main/java}/com/nr/example/Zroots_Ex.java | 0 .../main/java}/com/nr/fe/Chebyshev.java | 0 .../main/java}/com/nr/fe/Dfridr.java | 0 .../main/java}/com/nr/fe/Epsalg.java | 0 .../main/java}/com/nr/fe/Eulsum.java | 0 .../main/java}/com/nr/fe/Levin.java | 0 .../src => src/main/java}/com/nr/fe/Poly.java | 0 .../main/java}/com/nr/fe/Ratfn.java | 0 .../src => src/main/java}/com/nr/fft/FFT.java | 0 .../main/java}/com/nr/fft/WrapVecDoub.java | 0 .../main/java}/com/nr/fi/Adapt.java | 0 .../main/java}/com/nr/fi/DErule.java | 0 .../main/java}/com/nr/fi/GaussianWeights.java | 0 .../main/java}/com/nr/fi/Midexp.java | 0 .../main/java}/com/nr/fi/Midinf.java | 0 .../main/java}/com/nr/fi/Midpnt.java | 0 .../main/java}/com/nr/fi/Midsql.java | 0 .../main/java}/com/nr/fi/Midsqu.java | 0 .../src => src/main/java}/com/nr/fi/NRf1.java | 0 .../src => src/main/java}/com/nr/fi/NRf2.java | 0 .../src => src/main/java}/com/nr/fi/NRf3.java | 0 .../main/java}/com/nr/fi/Quadrature.java | 0 .../main/java}/com/nr/fi/Stiel.java | 0 .../main/java}/com/nr/fi/Trapzd.java | 0 .../java}/com/nr/interp/BaryRat_interp.java | 0 .../main/java}/com/nr/interp/Base_interp.java | 0 .../java}/com/nr/interp/Bilin_interp.java | 0 .../java}/com/nr/interp/Curve_interp.java | 0 .../main/java}/com/nr/interp/Krig.java | 0 .../java}/com/nr/interp/Laplace_interp.java | 0 .../java}/com/nr/interp/Linear_interp.java | 0 .../main/java}/com/nr/interp/PolCoef.java | 0 .../java}/com/nr/interp/Poly2D_interp.java | 0 .../main/java}/com/nr/interp/Poly_interp.java | 0 .../main/java}/com/nr/interp/Powvargram.java | 0 .../main/java}/com/nr/interp/RBF_fn.java | 0 .../main/java}/com/nr/interp/RBF_gauss.java | 0 .../main/java}/com/nr/interp/RBF_interp.java | 0 .../nr/interp/RBF_inversemultiquadric.java | 0 .../java}/com/nr/interp/RBF_multiquadric.java | 0 .../java}/com/nr/interp/RBF_thinplate.java | 0 .../java}/com/nr/interp/Rational_interp.java | 0 .../main/java}/com/nr/interp/Shep_interp.java | 0 .../java}/com/nr/interp/Spline2D_interp.java | 0 .../java}/com/nr/interp/Spline_interp.java | 0 .../main/java}/com/nr/inv/Fred2.java | 0 .../main/java}/com/nr/inv/Quad_matrix.java | 0 .../main/java}/com/nr/inv/Volterra.java | 0 .../main/java}/com/nr/inv/Wwghts.java | 0 .../src => src/main/java}/com/nr/la/ADAT.java | 0 .../main/java}/com/nr/la/Bandec.java | 0 .../main/java}/com/nr/la/Cholesky.java | 0 .../main/java}/com/nr/la/GaussJordan.java | 0 .../main/java}/com/nr/la/LUdcmp.java | 0 .../main/java}/com/nr/la/Linbcg.java | 0 .../main/java}/com/nr/la/NRsparseCol.java | 0 .../main/java}/com/nr/la/NRsparseLinbcg.java | 0 .../main/java}/com/nr/la/NRsparseMat.java | 0 .../main/java}/com/nr/la/QRdcmp.java | 0 .../src => src/main/java}/com/nr/la/SVD.java | 0 .../main/java}/com/nr/la/Toepltz.java | 0 .../main/java}/com/nr/la/Tridag.java | 0 .../main/java}/com/nr/la/Vander.java | 0 .../main/java}/com/nr/lna/Arithcode.java | 0 .../main/java}/com/nr/lna/Gray.java | 0 .../main/java}/com/nr/lna/Huffcode.java | 0 .../main/java}/com/nr/lna/Icrc.java | 0 .../main/java}/com/nr/lna/MParith.java | 0 .../main/java}/com/nr/lna/Machar.java | 0 .../main/java}/com/nr/lna/PSpage.java | 0 .../main/java}/com/nr/lna/PSplot.java | 0 .../main/java}/com/nr/min/Amebsa.java | 0 .../main/java}/com/nr/min/Amoeba.java | 0 .../main/java}/com/nr/min/Anneal.java | 0 .../main/java}/com/nr/min/Bracketmethod.java | 0 .../main/java}/com/nr/min/Brent.java | 0 .../main/java}/com/nr/min/Dbrent.java | 0 .../main/java}/com/nr/min/Df1dim.java | 0 .../main/java}/com/nr/min/Dlinemethod.java | 0 .../main/java}/com/nr/min/Dynpro.java | 0 .../main/java}/com/nr/min/F1dim.java | 0 .../main/java}/com/nr/min/Frprmn.java | 0 .../main/java}/com/nr/min/Funcd.java | 0 .../main/java}/com/nr/min/Golden.java | 0 .../main/java}/com/nr/min/Linemethod.java | 0 .../main/java}/com/nr/min/Powell.java | 0 .../main/java}/com/nr/min/QuasiNewton.java | 0 .../main/java}/com/nr/min/StringAlign.java | 0 .../main/java}/com/nr/model/FGauss.java | 0 .../main/java}/com/nr/model/Fitab.java | 0 .../main/java}/com/nr/model/Fitexy.java | 0 .../main/java}/com/nr/model/Fitlin.java | 0 .../main/java}/com/nr/model/Fitmed.java | 0 .../main/java}/com/nr/model/Fitmrq.java | 0 .../main/java}/com/nr/model/Fitsvd.java | 0 .../main/java}/com/nr/model/MultiFuncd.java | 0 .../main/java}/com/nr/model/Plog.java | 0 .../main/java}/com/nr/model/Proposal.java | 0 .../main/java}/com/nr/model/State.java | 0 .../main/java}/com/nr/ode/DerivativeInf.java | 0 .../main/java}/com/nr/ode/Hypderiv.java | 0 .../main/java}/com/nr/ode/Odeint.java | 0 .../main/java}/com/nr/ode/Output.java | 0 .../main/java}/com/nr/ode/StepperBS.java | 0 .../main/java}/com/nr/ode/StepperBase.java | 0 .../main/java}/com/nr/ode/StepperDopr5.java | 0 .../main/java}/com/nr/ode/StepperDopr853.java | 0 .../main/java}/com/nr/ode/StepperRoss.java | 0 .../main/java}/com/nr/ode/StepperSie.java | 0 .../main/java}/com/nr/ode/StepperStoerm.java | 0 .../main/java}/com/nr/ode/Stochsim.java | 0 .../main/java}/com/nr/pde/Mgfas.java | 0 .../main/java}/com/nr/pde/Mglin.java | 0 .../main/java}/com/nr/pde/Relaxation.java | 0 .../main/java}/com/nr/pde/Weights.java | 0 .../main/java}/com/nr/ran/Binomialdev.java | 0 .../main/java}/com/nr/ran/Cauchydev.java | 0 .../main/java}/com/nr/ran/Expondev.java | 0 .../main/java}/com/nr/ran/Gammadev.java | 0 .../main/java}/com/nr/ran/Hash.java | 0 .../main/java}/com/nr/ran/HashAll.java | 0 .../main/java}/com/nr/ran/Hashfn1.java | 0 .../main/java}/com/nr/ran/Hashfn2.java | 0 .../main/java}/com/nr/ran/Hashtable.java | 0 .../main/java}/com/nr/ran/Logisticdev.java | 0 .../main/java}/com/nr/ran/MCintegrate.java | 0 .../main/java}/com/nr/ran/Mhash.java | 0 .../main/java}/com/nr/ran/Miser.java | 0 .../main/java}/com/nr/ran/Multinormaldev.java | 0 .../main/java}/com/nr/ran/Normaldev.java | 0 .../main/java}/com/nr/ran/Normaldev_BM.java | 0 .../main/java}/com/nr/ran/Poissondev.java | 0 .../main/java}/com/nr/ran/Primpolytest.java | 0 .../src => src/main/java}/com/nr/ran/Ran.java | 0 .../main/java}/com/nr/ran/Ranbyte.java | 0 .../main/java}/com/nr/ran/Ranfib.java | 0 .../main/java}/com/nr/ran/Ranhash.java | 0 .../main/java}/com/nr/ran/Ranlim32.java | 0 .../main/java}/com/nr/ran/Ranq1.java | 0 .../main/java}/com/nr/ran/Ranq2.java | 0 .../main/java}/com/nr/ran/Sobol.java | 0 .../main/java}/com/nr/ran/VEGAS.java | 0 .../main/java}/com/nr/root/MNEWT.java | 0 .../main/java}/com/nr/root/NRfdjac.java | 0 .../main/java}/com/nr/root/NRfmin.java | 0 .../main/java}/com/nr/root/Roots.java | 0 .../main/java}/com/nr/sf/Bessel.java | 0 .../main/java}/com/nr/sf/Bessik.java | 0 .../main/java}/com/nr/sf/Bessjy.java | 0 .../src => src/main/java}/com/nr/sf/Beta.java | 0 .../main/java}/com/nr/sf/Betadist.java | 0 .../main/java}/com/nr/sf/Binomialdist.java | 0 .../main/java}/com/nr/sf/Cauchydist.java | 0 .../main/java}/com/nr/sf/Chisqdist.java | 0 .../main/java}/com/nr/sf/Elliptic.java | 0 .../src => src/main/java}/com/nr/sf/Erf.java | 0 .../main/java}/com/nr/sf/Expondist.java | 0 .../main/java}/com/nr/sf/Fdist.java | 0 .../main/java}/com/nr/sf/Fermi.java | 0 .../main/java}/com/nr/sf/Gamma.java | 0 .../main/java}/com/nr/sf/Gammadist.java | 0 .../main/java}/com/nr/sf/Gauleg18.java | 0 .../main/java}/com/nr/sf/Hypergeo.java | 0 .../main/java}/com/nr/sf/Integrals.java | 0 .../main/java}/com/nr/sf/KSdist.java | 0 .../main/java}/com/nr/sf/Legendre.java | 0 .../main/java}/com/nr/sf/Logisticdist.java | 0 .../main/java}/com/nr/sf/Lognormaldist.java | 0 .../main/java}/com/nr/sf/Normaldist.java | 0 .../main/java}/com/nr/sf/Poissondist.java | 0 .../main/java}/com/nr/sf/Studenttdist.java | 0 .../main/java}/com/nr/sort/EClass.java | 0 .../java}/com/nr/sort/EquivalenceInf.java | 0 .../main/java}/com/nr/sort/Heapselect.java | 0 .../main/java}/com/nr/sort/IQagent.java | 0 .../main/java}/com/nr/sort/Indexx.java | 0 .../main/java}/com/nr/sort/Sorter.java | 0 .../main/java}/com/nr/sp/BartlettWin.java | 0 .../main/java}/com/nr/sp/Daub4.java | 0 .../main/java}/com/nr/sp/Daub4i.java | 0 .../main/java}/com/nr/sp/Daubs.java | 0 .../main/java}/com/nr/sp/DftInt.java | 0 .../main/java}/com/nr/sp/Fourier.java | 0 .../src => src/main/java}/com/nr/sp/Hann.java | 0 .../main/java}/com/nr/sp/Slepian.java | 0 .../main/java}/com/nr/sp/Slepwindow.java | 0 .../main/java}/com/nr/sp/Spectolap.java | 0 .../main/java}/com/nr/sp/Spectreg.java | 0 .../main/java}/com/nr/sp/SquareWin.java | 0 .../main/java}/com/nr/sp/Wavelet.java | 0 .../main/java}/com/nr/sp/WelchWin.java | 0 .../main/java}/com/nr/sp/WindowFun.java | 0 .../main/java}/com/nr/stat/Moment.java | 0 .../main/java}/com/nr/stat/Quadvl.java | 0 .../main/java}/com/nr/stat/QuadvlInf.java | 0 .../com/nr/stat/SavitzkyGolayFilter.java | 0 .../main/java}/com/nr/stat/Stattests.java | 0 .../main/java}/com/nr/util/Calendar.java | 0 .../main/java/eu/mihosoft/vrl/v3d/Bounds.java | 0 .../main/java/eu/mihosoft/vrl/v3d/CSG.java | 0 .../main/java/eu/mihosoft/vrl/v3d/Cube.java | 0 .../java/eu/mihosoft/vrl/v3d/Cylinder.java | 0 .../main/java/eu/mihosoft/vrl/v3d/Edge.java | 0 .../java/eu/mihosoft/vrl/v3d/Extrude.java | 0 .../java/eu/mihosoft/vrl/v3d/FileUtil.java | 0 .../eu/mihosoft/vrl/v3d/Intersection.java | 0 .../main/java/eu/mihosoft/vrl/v3d/Main.java | 0 .../java/eu/mihosoft/vrl/v3d/Matrix3d.java | 0 .../eu/mihosoft/vrl/v3d/MeshContainer.java | 0 .../java/eu/mihosoft/vrl/v3d/Modifier.java | 0 .../main/java/eu/mihosoft/vrl/v3d/Node.java | 0 .../java/eu/mihosoft/vrl/v3d/ObjFile.java | 0 .../main/java/eu/mihosoft/vrl/v3d/Plane.java | 0 .../java/eu/mihosoft/vrl/v3d/Polygon.java | 0 .../java/eu/mihosoft/vrl/v3d/Polyhedron.java | 0 .../java/eu/mihosoft/vrl/v3d/Primitive.java | 0 .../eu/mihosoft/vrl/v3d/PropertyStorage.java | 0 .../java/eu/mihosoft/vrl/v3d/RoundedCube.java | 0 .../main/java/eu/mihosoft/vrl/v3d/STL.java | 0 .../main/java/eu/mihosoft/vrl/v3d/Sphere.java | 0 .../java/eu/mihosoft/vrl/v3d/Transform.java | 0 .../eu/mihosoft/vrl/v3d/UnityModifier.java | 0 .../java/eu/mihosoft/vrl/v3d/VFX3DUtil.java | 0 .../java/eu/mihosoft/vrl/v3d/Vector3d.java | 0 .../main/java/eu/mihosoft/vrl/v3d/Vertex.java | 0 .../eu/mihosoft/vrl/v3d/WeightFunction.java | 0 .../java/eu/mihosoft/vrl/v3d/XModifier.java | 0 .../java/eu/mihosoft/vrl/v3d/YModifier.java | 0 .../java/eu/mihosoft/vrl/v3d/ZModifier.java | 0 .../vrl/v3d/ext/imagej/STLLoader.java | 0 .../v3d/ext/openjfx/importers/Importer.java | 0 .../v3d/ext/openjfx/importers/Importer3D.java | 0 .../ext/openjfx/importers/ImporterFinder.java | 0 .../v3d/ext/openjfx/importers/Optimizer.java | 0 .../openjfx/importers/SmoothingGroups.java | 0 .../v3d/ext/openjfx/importers/Validator.java | 0 .../openjfx/importers/obj/FloatArrayList.java | 0 .../importers/obj/IntegerArrayList.java | 0 .../ext/openjfx/importers/obj/MtlReader.java | 0 .../openjfx/importers/obj/ObjImporter.java | 0 .../importers/obj/ObjOrPolyObjImporter.java | 0 .../importers/obj/PolyObjImporter.java | 0 .../v3d/ext/openjfx/shape3d/PolygonMesh.java | 0 .../ext/openjfx/shape3d/PolygonMeshView.java | 0 .../ext/openjfx/shape3d/SubdivisionMesh.java | 0 .../shape3d/symbolic/OriginalPointArray.java | 0 .../symbolic/SubdividedPointArray.java | 0 .../shape3d/symbolic/SymbolicPointArray.java | 0 .../shape3d/symbolic/SymbolicPolygonMesh.java | 0 .../symbolic/SymbolicSubdivisionBuilder.java | 0 .../v3d/ext/openjfx/utils3d/DragSupport.java | 0 .../v3d/ext/org/poly2tri/AdvancingFront.java | 0 .../ext/org/poly2tri/AdvancingFrontIndex.java | 0 .../ext/org/poly2tri/AdvancingFrontNode.java | 0 .../ext/org/poly2tri/AnyToXYTransform.java | 0 .../ext/org/poly2tri/ConstrainedPointSet.java | 0 .../ext/org/poly2tri/CoordinateTransform.java | 0 .../vrl/v3d/ext/org/poly2tri/DTSweep.java | 0 .../ext/org/poly2tri/DTSweepConstraint.java | 0 .../v3d/ext/org/poly2tri/DTSweepContext.java | 0 .../ext/org/poly2tri/DTSweepDebugContext.java | 0 .../org/poly2tri/DTSweepPointComparator.java | 0 .../ext/org/poly2tri/DelaunayTriangle.java | 0 .../vrl/v3d/ext/org/poly2tri/Edge.java | 0 .../ext/org/poly2tri/FloatBufferPoint.java | 0 .../ext/org/poly2tri/Matrix3Transform.java | 0 .../vrl/v3d/ext/org/poly2tri/NoTransform.java | 0 .../vrl/v3d/ext/org/poly2tri/Point.java | 0 .../v3d/ext/org/poly2tri/PointGenerator.java | 0 .../org/poly2tri/PointOnEdgeException.java | 0 .../vrl/v3d/ext/org/poly2tri/PointSet.java | 0 .../vrl/v3d/ext/org/poly2tri/Poly2Tri.java | 0 .../vrl/v3d/ext/org/poly2tri/Polygon.java | 0 .../ext/org/poly2tri/PolygonGenerator.java | 0 .../v3d/ext/org/poly2tri/PolygonPoint.java | 0 .../vrl/v3d/ext/org/poly2tri/PolygonSet.java | 0 .../vrl/v3d/ext/org/poly2tri/PolygonUtil.java | 0 .../vrl/v3d/ext/org/poly2tri/TPoint.java | 0 .../v3d/ext/org/poly2tri/Triangulatable.java | 0 .../org/poly2tri/TriangulationAlgorithm.java | 0 .../org/poly2tri/TriangulationConstraint.java | 0 .../org/poly2tri/TriangulationContext.java | 0 .../poly2tri/TriangulationDebugContext.java | 0 .../ext/org/poly2tri/TriangulationMode.java | 0 .../ext/org/poly2tri/TriangulationPoint.java | 0 .../org/poly2tri/TriangulationProcess.java | 0 .../poly2tri/TriangulationProcessEvent.java | 0 .../TriangulationProcessListener.java | 0 .../ext/org/poly2tri/TriangulationUtil.java | 0 .../vrl/v3d/ext/org/poly2tri/Tuple2.java | 0 .../vrl/v3d/ext/org/poly2tri/Tuple3.java | 0 .../ext/org/poly2tri/XYToAnyTransform.java | 0 .../org/jlab/analysis/efficiency/Truth.java | 0 .../analysis/eventmerger/ADCTDCMerger.java | 0 .../analysis/eventmerger/EventMerger.java | 0 .../eventmerger/EventMergerConstants.java | 0 .../analysis/eventmerger/EventMergerEnum.java | 0 .../analysis/eventmerger/FilterBankSize.java | 0 .../jlab/analysis/eventmerger/FilterFcup.java | 0 .../analysis/eventmerger/FilterTrigger.java | 0 .../eventmerger/RandomTriggerFilter.java | 0 .../eventmerger/RandomTriggerSplit.java | 0 .../eventmerger/SortedWriterUtils.java | 0 .../java/org/jlab/analysis/math/ClasMath.java | 0 .../org/jlab/analysis/physics/TestEvent.java | 0 .../jlab/analysis/postprocess/Processor.java | 0 .../analysis/postprocess/RebuildScalers.java | 0 .../analysis/postprocess/Tag1ToEvent.java | 0 .../org/jlab/analysis/postprocess/Util.java | 0 .../org/jlab/analysis/roads/Dictionary.java | 0 .../analysis/roads/DictionaryCreator.java | 0 .../analysis/roads/DictionaryGenerator.java | 0 .../jlab/analysis/roads/DictionaryMerger.java | 0 .../analysis/roads/DictionaryValidator.java | 0 .../java/org/jlab/analysis/roads/README.md | 0 .../java/org/jlab/analysis/roads/Road.java | 0 .../detectors/CTOFBankBuilder.java | 0 .../detectors/CalibBankBuilder.java | 0 .../calibration/detectors/DCBankBuilder.java | 0 .../detectors/FTOFBankBuilder.java | 0 .../detectors/RICHBankBuilder.java | 0 .../calibration/service/CalibBanksEngine.java | 0 .../org/jlab/clas/clas/math/FastMath.java | 0 .../java/org/jlab/clas/clas/math/Icecore.java | 0 .../org/jlab/clas/clas/math/Icecore2.java | 0 .../java/org/jlab/clas/clas/math/Kappa.java | 0 .../java/org/jlab/clas/clas/math/Riven.java | 0 .../java/org/jlab/clas/clas/math/Test.java | 0 .../jlab/clas/decay/analysis/Analysis.java | 0 .../clas/decay/analysis/AnalysisEngine.java | 0 .../jlab/clas/decay/analysis/Constants.java | 0 .../org/jlab/clas/decay/analysis/Decay.java | 0 .../jlab/clas/decay/analysis/Particle.java | 0 .../jlab/clas/decay/analysis/Reaction.java | 0 .../org/jlab/clas/decay/banks/Reader.java | 0 .../org/jlab/clas/decay/banks/Writer.java | 0 .../clas/detector/CalorimeterResponse.java | 0 .../jlab/clas/detector/CherenkovResponse.java | 0 .../org/jlab/clas/detector/DetectorData.java | 0 .../org/jlab/clas/detector/DetectorEvent.java | 0 .../jlab/clas/detector/DetectorHeader.java | 0 .../jlab/clas/detector/DetectorParticle.java | 0 .../clas/detector/DetectorParticlePOCA.java | 0 .../clas/detector/DetectorParticleStatus.java | 0 .../clas/detector/DetectorParticleTraj.java | 0 .../jlab/clas/detector/DetectorResponse.java | 0 .../detector/DetectorResponseComparators.java | 0 .../detector/DetectorResponseFactory.java | 0 .../org/jlab/clas/detector/DetectorTrack.java | 0 .../clas/detector/RingCherenkovResponse.java | 0 .../clas/detector/ScintillatorResponse.java | 0 .../jlab/clas/detector/TaggerResponse.java | 0 .../jlab/clas/detector/matching/AMatch.java | 0 .../jlab/clas/detector/matching/IMatch.java | 0 .../jlab/clas/detector/matching/MatchCND.java | 0 .../clas/detector/matching/MatchDOCA.java | 0 .../clas/detector/matching/MatchPOCA.java | 0 .../clas/detector/matching/MatchThetaPhi.java | 0 .../detector/matching/MatchTrajDistance.java | 0 .../org/jlab/clas/fastmc/Clas12FastMC.java | 0 .../jlab/clas/fastmc/IParticleResolution.java | 0 .../fastmc/ParticleResolutionCentralIn.java | 0 .../fastmc/ParticleResolutionCentralOut.java | 0 .../org/jlab/clas/fastmc/ParticleSwimmer.java | 0 .../java/org/jlab/clas/pdg/PDGDatabase.java | 0 .../java/org/jlab/clas/pdg/PDGParticle.java | 0 .../org/jlab/clas/pdg/PhysicsConstants.java | 0 .../org/jlab/clas/physics/EventFilter.java | 0 .../org/jlab/clas/physics/LorentzVector.java | 0 .../java/org/jlab/clas/physics/Particle.java | 0 .../org/jlab/clas/physics/ParticleFinder.java | 0 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.../org/jlab/clas/tracking/objects/Strip.java | 0 .../jlab/clas/tracking/objects/TObject.java | 0 .../tracking/patternrec/CircleHoughTrans.java | 0 .../tracking/patternrec/LineHoughTrans.java | 0 .../jlab/clas/tracking/trackrep/Helix.java | 0 .../org/jlab/clas/tracking/trackrep/Seed.java | 0 .../clas/tracking/trackrep/Trajectory.java | 0 .../clas/tracking/utilities/MatrixOps.java | 0 .../tracking/utilities/OverlapRemover.java | 0 .../tracking/utilities/RungeKuttaDoca.java | 0 .../utilities/SelectEventsToFile.java | 0 .../main/java/org/jlab/coat/package-info.java | 0 .../org/jlab/detector/banks/FilteredBank.java | 0 .../java/org/jlab/detector/banks/RawBank.java | 0 .../org/jlab/detector/banks/RawDataBank.java | 0 .../detector/base/DetectorCollection.java | 0 .../detector/base/DetectorDescriptor.java | 0 .../org/jlab/detector/base/DetectorLayer.java | 0 .../org/jlab/detector/base/DetectorType.java | 0 .../jlab/detector/base/GeometryFactory.java | 0 .../calib/tasks/CalibrationEngine.java | 0 .../calib/tasks/CalibrationEngineTask.java | 0 .../calib/tasks/CalibrationEngineView.java | 0 .../calib/utils/CalibrationConstants.java | 0 .../utils/CalibrationConstantsListener.java | 0 .../calib/utils/CalibrationConstantsView.java | 0 .../calib/utils/ConstantsManager.java | 0 .../calib/utils/DatabaseConstantProvider.java | 0 .../detector/calib/utils/RCDBConstants.java | 0 .../detector/calib/utils/RCDBProvider.java | 0 .../org/jlab/detector/decode/CLASDecoder.java | 0 .../jlab/detector/decode/CLASDecoder4.java | 0 .../jlab/detector/decode/CLASDecoder4U.java | 0 .../jlab/detector/decode/CodaDecoders.java | 0 .../detector/decode/CodaEventDecoder.java | 0 .../detector/decode/DetectorBankDgtz.java | 0 .../detector/decode/DetectorDataDgtz.java | 0 .../detector/decode/DetectorDataFilter.java | 0 .../detector/decode/DetectorDecoderDebug.java | 0 .../detector/decode/DetectorDecoderView.java | 0 .../detector/decode/DetectorEventDecoder.java | 0 .../detector/decode/ExtendedFADCFitter.java | 0 .../org/jlab/detector/decode/FADCData.java | 0 .../org/jlab/detector/decode/IFADCFitter.java | 0 .../org/jlab/detector/decode/MVTFitter.java | 0 .../detector/decode/TranslationTable.java | 0 .../java/org/jlab/detector/epics/Epics.java | 0 .../jlab/detector/epics/EpicsSequence.java | 0 .../detector/examples/DaqPulsePlotter.java | 0 .../detector/examples/DetectorTiming.java | 0 .../detector/examples/RawEventViewer.java | 0 .../detector/geant4/BSTGeant4Factory.java | 0 .../jlab/detector/geant4/DCGeant4Factory.java | 0 .../jlab/detector/geant4/ECGeant4Factory.java | 0 .../detector/geant4/FTOFGeant4Factory.java | 0 .../detector/geant4/v2/CTOFGeant4Factory.java | 0 .../detector/geant4/v2/DCGeant4Factory.java | 0 .../detector/geant4/v2/ECGeant4Factory.java | 0 .../detector/geant4/v2/FTOFGeant4Factory.java | 0 .../detector/geant4/v2/Geant4Factory.java | 0 .../geant4/v2/MPGD/MUVT/MUVTConstants.java | 0 .../v2/MPGD/MUVT/MUVTGeant4Factory.java | 0 .../geant4/v2/MPGD/MUVT/MUVTStripFactory.java | 0 .../geant4/v2/MPGD/URWT/URWTConstants.java | 0 .../v2/MPGD/URWT/URWTGeant4Factory.java | 0 .../geant4/v2/MPGD/URWT/URWTStripFactory.java | 0 .../trapezoid/MPGDTrapezoidConstants.java | 0 .../trapezoid/MPGDTrapezoidGeant4Factory.java | 0 .../trapezoid/MPGDTrapezoidStripFactory.java | 0 .../detector/geant4/v2/PCALGeant4Factory.java | 0 .../detector/geant4/v2/RICHGeant4Factory.java | 0 .../geant4/v2/SVT/AlignmentFactory.java | 0 .../jlab/detector/geant4/v2/SVT/Matrix.java | 0 .../geant4/v2/SVT/SVTAlignmentFactory.java | 0 .../detector/geant4/v2/SVT/SVTConstants.java | 0 .../geant4/v2/SVT/SVTStripFactory.java | 0 .../geant4/v2/SVT/SVTVolumeFactory.java | 0 .../org/jlab/detector/geant4/v2/SVT/Util.java | 0 .../detector/geant4/v2/SVTGeant4Factory.java | 0 .../geant4/v2/recoil/RecoilConstants.java | 0 .../geant4/v2/recoil/RecoilGeant4Factory.java | 0 .../geant4/v2/recoil/RecoilStripFactory.java | 0 .../detector/geom/RICH/RICHComponent.java | 0 .../jlab/detector/geom/RICH/RICHFrame.java | 0 .../geom/RICH/RICHGeoCalibration.java | 0 .../detector/geom/RICH/RICHGeoConstants.java | 0 .../detector/geom/RICH/RICHGeoFactory.java | 0 .../detector/geom/RICH/RICHGeoParameters.java | 0 .../detector/geom/RICH/RICHIntersection.java | 0 .../jlab/detector/geom/RICH/RICHLayer.java | 0 .../detector/geom/RICH/RICHLayerType.java | 0 .../jlab/detector/geom/RICH/RICHPixel.java | 0 .../jlab/detector/geom/RICH/RICHPixelMap.java | 0 .../org/jlab/detector/geom/RICH/RICHRay.java | 0 .../jlab/detector/geom/dc/DCGeantFactory.java | 0 .../jlab/detector/geom/dc/GeantFactory.java | 0 .../detector/helicity/DecoderBoardTest.java | 0 .../detector/helicity/DecoderBoardUtil.java | 0 .../helicity/HelicityAnalysisSimple.java | 0 .../jlab/detector/helicity/HelicityBit.java | 0 .../detector/helicity/HelicityGenerator.java | 0 .../detector/helicity/HelicityInterval.java | 0 .../detector/helicity/HelicityPattern.java | 0 .../detector/helicity/HelicitySequence.java | 0 .../helicity/HelicitySequenceDelayed.java | 0 .../helicity/HelicitySequenceManager.java | 0 .../jlab/detector/helicity/HelicityState.java | 0 .../jlab/detector/helicity/SequenceUtil.java | 0 .../org/jlab/detector/hits/CTOFDetHit.java | 0 .../java/org/jlab/detector/hits/DetHit.java | 0 .../java/org/jlab/detector/hits/DetId.java | 0 .../org/jlab/detector/hits/FTOFDetHit.java | 0 .../org/jlab/detector/hits/PCALDetHit.java | 0 .../jlab/detector/pulse/HipoExtractor.java | 0 .../org/jlab/detector/pulse/IExtractor.java | 0 .../java/org/jlab/detector/pulse/Mode3.java | 0 .../java/org/jlab/detector/pulse/Mode7.java | 0 .../org/jlab/detector/pulse/ModeAHDC.java | 0 .../java/org/jlab/detector/pulse/Pulse.java | 0 .../java/org/jlab/detector/qadb/QadbBin.java | 0 .../jlab/detector/qadb/QadbBinSequence.java | 0 .../org/jlab/detector/scalers/DaqScaler.java | 0 .../org/jlab/detector/scalers/DaqScalers.java | 0 .../detector/scalers/DaqScalersSequence.java | 0 .../org/jlab/detector/scalers/Dsc2Scaler.java | 0 .../jlab/detector/scalers/StruckScaler.java | 0 .../jlab/detector/scalers/StruckScalers.java | 0 .../org/jlab/detector/swaps/SwapManager.java | 0 .../org/jlab/detector/swaps/SwapTable.java | 0 .../org/jlab/detector/units/Measurement.java | 0 .../jlab/detector/units/SystemOfUnits.java | 0 .../jlab/detector/view/DetectorListener.java | 0 .../jlab/detector/view/DetectorPane2D.java | 0 .../jlab/detector/view/DetectorShape2D.java | 0 .../jlab/detector/view/DetectorView2D.java | 0 .../org/jlab/detector/view/ViewWorld.java | 0 .../org/jlab/detector/view/ViewerTests.java | 0 .../java/org/jlab/detector/volume/G4Box.java | 0 .../org/jlab/detector/volume/G4Operation.java | 0 .../java/org/jlab/detector/volume/G4Pgon.java | 0 .../java/org/jlab/detector/volume/G4Stl.java | 0 .../java/org/jlab/detector/volume/G4Trap.java | 0 .../java/org/jlab/detector/volume/G4Trd.java | 0 .../java/org/jlab/detector/volume/G4Tubs.java | 0 .../org/jlab/detector/volume/G4World.java | 0 .../org/jlab/detector/volume/Geant4Basic.java | 0 .../java/org/jlab/display/ec/ECDisplay.java | 0 .../java/org/jlab/display/ec/ECMonitor.java | 0 .../org/jlab/display/ec/ECPion.java-DISABLED | 0 .../org/jlab/display/ec/ECPionFinder.java | 0 .../org/jlab/display/ec/ECRECMonitor.java | 0 .../java/org/jlab/display/ec/Renderer.java | 0 .../java/org/jlab/geom/CoordinateSystem.java | 0 .../main/java/org/jlab/geom/DetectorHit.java | 0 .../main/java/org/jlab/geom/DetectorId.java | 0 .../main/java/org/jlab/geom/G4Volume.java | 0 .../main/java/org/jlab/geom/G4VolumeMap.java | 0 .../main/java/org/jlab/geom/Showable.java | 0 .../org/jlab/geom/abs/AbstractComponent.java | 0 .../org/jlab/geom/abs/AbstractDetector.java | 0 .../java/org/jlab/geom/abs/AbstractLayer.java | 0 .../org/jlab/geom/abs/AbstractSector.java | 0 .../org/jlab/geom/abs/AbstractSuperlayer.java | 0 .../java/org/jlab/geom/abs/MeshComponent.java | 0 .../java/org/jlab/geom/base/Component.java | 0 .../org/jlab/geom/base/ConstantProvider.java | 0 .../java/org/jlab/geom/base/Detector.java | 0 .../geom/base/DetectorTransformation.java | 0 .../main/java/org/jlab/geom/base/Factory.java | 0 .../main/java/org/jlab/geom/base/Layer.java | 0 .../main/java/org/jlab/geom/base/Sector.java | 0 .../java/org/jlab/geom/base/Superlayer.java | 0 .../jlab/geom/component/DriftChamberWire.java | 0 .../geom/component/PrismaticComponent.java | 0 .../geom/component/RectangularComponent.java | 0 .../jlab/geom/component/ScintillatorMesh.java | 0 .../geom/component/ScintillatorPaddle.java | 0 .../java/org/jlab/geom/component/SiStrip.java | 0 .../org/jlab/geom/component/TrackerStrip.java | 0 .../detector/alert/AHDC/AlertDCDetector.java | 0 .../detector/alert/AHDC/AlertDCFactory.java | 0 .../detector/alert/AHDC/AlertDCLayer.java | 0 .../detector/alert/AHDC/AlertDCSector.java | 0 .../alert/AHDC/AlertDCSuperlayer.java | 0 .../geom/detector/alert/AHDC/AlertDCWire.java | 0 .../detector/alert/AHDC/ConcaveComponent.java | 0 .../detector/alert/ATOF/AlertTOFDetector.java | 0 .../detector/alert/ATOF/AlertTOFFactory.java | 0 .../detector/alert/ATOF/AlertTOFLayer.java | 0 .../detector/alert/ATOF/AlertTOFSector.java | 0 .../alert/ATOF/AlertTOFSuperlayer.java | 0 .../jlab/geom/detector/bst/BSTDetector.java | 0 .../jlab/geom/detector/bst/BSTFactory.java | 0 .../org/jlab/geom/detector/bst/BSTLayer.java | 0 .../org/jlab/geom/detector/bst/BSTRing.java | 0 .../org/jlab/geom/detector/bst/BSTSector.java | 0 .../jlab/geom/detector/bst/BSTSuperlayer.java | 0 .../jlab/geom/detector/cnd/CNDDetector.java | 0 .../jlab/geom/detector/cnd/CNDFactory.java | 0 .../org/jlab/geom/detector/cnd/CNDLayer.java | 0 .../org/jlab/geom/detector/cnd/CNDSector.java | 0 .../jlab/geom/detector/cnd/CNDSuperlayer.java | 0 .../org/jlab/geom/detector/dc/DCDetector.java | 0 .../org/jlab/geom/detector/dc/DCFactory.java | 0 .../geom/detector/dc/DCFactoryUpdated.java | 0 .../org/jlab/geom/detector/dc/DCLayer.java | 0 .../org/jlab/geom/detector/dc/DCSector.java | 0 .../jlab/geom/detector/dc/DCSuperlayer.java | 0 .../jlab/geom/detector/dc/DriftChamber.java | 0 .../java/org/jlab/geom/detector/dc/Layer.java | 0 .../org/jlab/geom/detector/dc/Region.java | 0 .../org/jlab/geom/detector/dc/Sector.java | 0 .../org/jlab/geom/detector/dc/Superlayer.java | 0 .../org/jlab/geom/detector/ec/ECDetector.java | 0 .../jlab/geom/detector/ec/ECDetectorDraw.java | 0 .../org/jlab/geom/detector/ec/ECFactory.java | 0 .../org/jlab/geom/detector/ec/ECLayer.java | 0 .../org/jlab/geom/detector/ec/ECSector.java | 0 .../jlab/geom/detector/ec/ECSuperlayer.java | 0 .../jlab/geom/detector/fmt/FMTDetector.java | 0 .../jlab/geom/detector/fmt/FMTFactory.java | 0 .../org/jlab/geom/detector/fmt/FMTLayer.java | 0 .../org/jlab/geom/detector/fmt/FMTSector.java | 0 .../jlab/geom/detector/fmt/FMTSuperlayer.java | 0 .../jlab/geom/detector/ft/FTCALDetector.java | 0 .../jlab/geom/detector/ft/FTCALFactory.java | 0 .../org/jlab/geom/detector/ft/FTCALLayer.java | 0 .../jlab/geom/detector/ft/FTCALSector.java | 0 .../geom/detector/ft/FTCALSuperlayer.java | 0 .../jlab/geom/detector/ftof/FTOFDetector.java | 0 .../geom/detector/ftof/FTOFDetectorMesh.java | 0 .../jlab/geom/detector/ftof/FTOFFactory.java | 0 .../jlab/geom/detector/ftof/FTOFLayer.java | 0 .../geom/detector/ftof/FTOFLayerMesh.java | 0 .../jlab/geom/detector/ftof/FTOFSector.java | 0 .../geom/detector/ftof/FTOFSectorMesh.java | 0 .../geom/detector/ftof/FTOFSuperlayer.java | 0 .../detector/ftof/FTOFSuperlayerMesh.java | 0 .../jlab/geom/detector/ftof/ForwardTOF.java | 0 .../org/jlab/geom/detector/ftof/Paddle.java | 0 .../org/jlab/geom/detector/ftof/Panel.java | 0 .../org/jlab/geom/detector/ftof/Sector.java | 0 .../geom/fx/DetectoMesh2DViewApp.java-BAK | 0 .../geom/fx/DetectorEventHandler.java-BAK | 0 .../org/jlab/geom/fx/DetectorMesh2D.java-BAK | 0 .../geom/fx/DetectorMesh2DCanvas.java-BAK | 0 .../jlab/geom/fx/DetectorMesh2DLayer.java-BAK | 0 .../org/jlab/geom/fx/DetectorTabView.java-BAK | 0 .../java/org/jlab/geom/fx/Mesh3D.java-BAK | 0 .../java/org/jlab/geom/fx/PopupText.java-BAK | 0 .../org/jlab/geom/geant/G4BaseVolume.java | 0 .../java/org/jlab/geom/geant/G4Material.java | 0 .../main/java/org/jlab/geom/geant/G4Trd.java | 0 .../java/org/jlab/geom/geant/Geant4Basic.java | 0 .../java/org/jlab/geom/geant/Geant4Box.java | 0 .../java/org/jlab/geom/geant/Geant4Mesh.java | 0 .../org/jlab/geom/geant/GemcTestProgram.java | 0 .../java/org/jlab/geom/geant/IG4Volume.java | 0 .../org/jlab/geom/geant/IGeant4Volume.java | 0 .../java/org/jlab/geom/gemc/GemcBank.java | 0 .../java/org/jlab/geom/gemc/GemcDetector.java | 0 .../main/java/org/jlab/geom/gemc/GemcHit.java | 0 .../java/org/jlab/geom/gemc/GemcMaterial.java | 0 .../org/jlab/geom/gemc/GemcPropertyMap.java | 0 .../org/jlab/geom/gemc/GemcPropertyMaps.java | 0 .../jlab/geom/gui/DetectorComponentUI.java | 0 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.../org/jlab/io/stream/EvioStreamObject.java | 0 .../org/jlab/io/task/DataSourceProcessor.java | 0 .../jlab/io/task/DataSourceProcessorPane.java | 0 .../org/jlab/io/task/IDataEventListener.java | 0 .../main/java/org/jlab/io/ui/BasicDialog.java | 0 .../java/org/jlab/io/ui/ConnectionDialog.java | 0 .../org/jlab/io/ui/ConnectionDialogHipo.java | 0 .../java/org/jlab/io/ui/DialogUtilities.java | 0 .../jlab/io/utils/CompositeFormatReader.java | 0 .../org/jlab/io/utils/DictionaryLoader.java | 0 .../main/java/org/jlab/io/utils/DstMaker.java | 0 .../main/java/org/jlab/io/utils/EvioCure.java | 0 .../org/jlab/io/utils/EvioFileRecover.java | 0 .../org/jlab/logging/SplitLogManager.java | 0 .../jlab/logging/SplitLogManagerConfig.java | 0 .../java/org/jlab/logging/TestLogManager.java | 0 .../jlab/physics/analysis/EventOperator.java | 0 .../analysis/GenericEventOperator.java | 0 .../physics/analysis/PhysicsAnalysis.java | 0 .../physics/analysis/PhysicsDataObject.java | 0 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| 0 .../org/jlab/rec/ahdc/AI/PreClustering.java | 0 .../rec/ahdc/AI/TrackCandidatesGenerator.java | 0 .../org/jlab/rec/ahdc/AI/TrackPrediction.java | 0 .../jlab/rec/ahdc/Banks/RecoBankWriter.java | 0 .../org/jlab/rec/ahdc/Cluster/Cluster.java | 0 .../jlab/rec/ahdc/Cluster/ClusterFinder.java | 0 .../jlab/rec/ahdc/Distance/CircleFitPars.java | 0 .../jlab/rec/ahdc/Distance/CircleFitter.java | 0 .../org/jlab/rec/ahdc/Distance/Distance.java | 0 .../rec/ahdc/DocaCluster/DocaCluster.java | 0 .../ahdc/DocaCluster/DocaClusterRefiner.java | 0 .../jlab/rec/ahdc/HelixFit/HelixFitJava.java | 0 .../rec/ahdc/HelixFit/HelixFitObject.java | 0 .../main/java/org/jlab/rec/ahdc/Hit/Hit.java | 0 .../java/org/jlab/rec/ahdc/Hit/HitReader.java | 0 .../java/org/jlab/rec/ahdc/Hit/TrueHit.java | 0 .../ahdc/HoughTransform/HoughTransform.java | 0 .../jlab/rec/ahdc/KalmanFilter/Hit_beam.java | 0 .../jlab/rec/ahdc/KalmanFilter/KFitter.java | 0 .../rec/ahdc/KalmanFilter/KalmanFilter.java | 0 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0 .../java/org/jlab/rec/ctof/Constants.java | 0 .../java/org/jlab/rec/ctof/package-info.java | 0 .../main/java/org/jlab/rec/cvt/Constants.java | 0 .../main/java/org/jlab/rec/cvt/Geometry.java | 0 .../org/jlab/rec/cvt/banks/HitReader.java | 0 .../jlab/rec/cvt/banks/RecoBankReader.java | 0 .../jlab/rec/cvt/banks/RecoBankWriter.java | 0 .../org/jlab/rec/cvt/bmt/BMTConstants.java | 0 .../org/jlab/rec/cvt/bmt/BMTGeometry.java | 0 .../java/org/jlab/rec/cvt/bmt/BMTType.java | 0 .../jlab/rec/cvt/bmt/CCDBConstantsLoader.java | 0 .../java/org/jlab/rec/cvt/bmt/Lorentz.java | 0 .../org/jlab/rec/cvt/cluster/Cluster.java | 0 .../jlab/rec/cvt/cluster/ClusterFinder.java | 0 .../java/org/jlab/rec/cvt/cross/Cross.java | 0 .../org/jlab/rec/cvt/cross/CrossList.java | 0 .../org/jlab/rec/cvt/cross/CrossMaker.java | 0 .../rec/cvt/cross/HelixCrossListFinder.java | 0 .../cross/StraightTrackCrossListFinder.java | 0 .../org/jlab/rec/cvt/fit/CircleCalcPars.java | 0 .../jlab/rec/cvt/fit/CircleCalculator.java | 0 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.../org/jlab/rec/cvt/svt/SVTGeometry.java | 0 .../org/jlab/rec/cvt/svt/SVTParameters.java | 0 .../java/org/jlab/rec/cvt/track/Cell.java | 0 .../java/org/jlab/rec/cvt/track/MakerCA.java | 0 .../java/org/jlab/rec/cvt/track/Seed.java | 0 .../org/jlab/rec/cvt/track/StraightTrack.java | 0 .../track/StraightTrackCandListFinder.java | 0 .../rec/cvt/track/StraightTrackSeeder.java | 0 .../java/org/jlab/rec/cvt/track/Track.java | 0 .../org/jlab/rec/cvt/track/TrackSeeder.java | 0 .../org/jlab/rec/cvt/track/TrackSeederCA.java | 0 .../org/jlab/rec/cvt/track/TrackSeederRZ.java | 0 .../rec/cvt/track/TrackSeederSVTLinker.java | 0 .../org/jlab/rec/cvt/track/TrackSeederXY.java | 0 .../org/jlab/rec/cvt/trajectory/Helix.java | 0 .../java/org/jlab/rec/cvt/trajectory/Ray.java | 0 .../org/jlab/rec/cvt/trajectory/StateVec.java | 0 .../jlab/rec/cvt/trajectory/Trajectory.java | 0 .../rec/cvt/trajectory/TrajectoryFinder.java | 0 .../main/java/org/jlab/rec/dc/Constants.java | 0 .../org/jlab/rec/dc/DCTranslationTable.java | 0 .../java/org/jlab/rec/dc/banks/Banks.java | 0 .../java/org/jlab/rec/dc/banks/HitReader.java | 0 .../org/jlab/rec/dc/banks/RecoBankWriter.java | 0 .../java/org/jlab/rec/dc/cluster/Cluster.java | 0 .../dc/cluster/ClusterCleanerUtilities.java | 0 .../jlab/rec/dc/cluster/ClusterFinder.java | 0 .../jlab/rec/dc/cluster/ClusterFitter.java | 0 .../jlab/rec/dc/cluster/FittedCluster.java | 0 .../java/org/jlab/rec/dc/cross/Cross.java | 0 .../java/org/jlab/rec/dc/cross/CrossList.java | 0 .../jlab/rec/dc/cross/CrossListFinder.java | 0 .../org/jlab/rec/dc/cross/CrossMaker.java | 0 .../java/org/jlab/rec/dc/hit/FittedHit.java | 0 .../main/java/org/jlab/rec/dc/hit/Hit.java | 0 .../java/org/jlab/rec/dc/nn/PatternRec.java | 0 .../java/org/jlab/rec/dc/segment/Segment.java | 0 .../jlab/rec/dc/segment/SegmentFinder.java | 0 .../rec/dc/timetodistance/T2DFunctions.java | 0 .../rec/dc/timetodistance/TableLoader.java | 0 .../TimeToDistanceEstimator.java | 0 .../java/org/jlab/rec/dc/track/Track.java | 0 .../rec/dc/track/TrackCandListFinder.java | 0 .../jlab/rec/dc/track/TrackListFinder.java | 0 .../jlab/rec/dc/track/fit/KFitterDoca.java | 0 .../jlab/rec/dc/track/fit/MeasVecsDoca.java | 0 .../jlab/rec/dc/track/fit/RungeKuttaDoca.java | 0 .../jlab/rec/dc/track/fit/StateVecsDoca.java | 0 .../rec/dc/track/fit/basefit/LineFitPars.java | 0 .../rec/dc/track/fit/basefit/LineFitter.java | 0 .../java/org/jlab/rec/dc/trajectory/Road.java | 0 .../jlab/rec/dc/trajectory/RoadFinder.java | 0 .../rec/dc/trajectory/SegmentTrajectory.java | 0 .../org/jlab/rec/dc/trajectory/StateVec.java | 0 .../org/jlab/rec/dc/trajectory/Surface.java | 0 .../org/jlab/rec/dc/trajectory/TrackVec.java | 0 .../jlab/rec/dc/trajectory/Trajectory.java | 0 .../rec/dc/trajectory/TrajectoryFinder.java | 0 .../rec/dc/trajectory/TrajectorySurfaces.java | 0 .../org/jlab/rec/dc/trajectory/Vertex.java | 0 .../java/org/jlab/rec/eb/EBCCDBConstants.java | 0 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{common-tools/cnuphys/numRec/src => src/main/java}/com/nr/eig/Jacobi.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/eig/Symmeig.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/eig/Unsymmeig.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/Bandec_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/Chebyshev_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/Cholesky_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/Cyclic_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/FFT_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/GaussJordan_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/LUdcmp_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/Levin_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/QRdcmp_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/SVD_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/Solvde_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/Toepltz_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/Trigag_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/Vander_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/Zrhqr_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/example/Zroots_Ex.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/fe/Chebyshev.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/fe/Dfridr.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/fe/Epsalg.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/fe/Eulsum.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/fe/Levin.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/fe/Poly.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/fe/Ratfn.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/fft/FFT.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/fft/WrapVecDoub.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/fi/Adapt.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/fi/DErule.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/fi/GaussianWeights.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/fi/Midexp.java (100%) rename {common-tools/cnuphys/numRec/src => 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src/main/java}/com/nr/interp/Base_interp.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/interp/Bilin_interp.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/interp/Curve_interp.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/interp/Krig.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/interp/Laplace_interp.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/interp/Linear_interp.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/interp/PolCoef.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/interp/Poly2D_interp.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/interp/Poly_interp.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/interp/Powvargram.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/interp/RBF_fn.java 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{common-tools/cnuphys/numRec/src => src/main/java}/com/nr/la/NRsparseMat.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/la/QRdcmp.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/la/SVD.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/la/Toepltz.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/la/Tridag.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/la/Vander.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/lna/Arithcode.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/lna/Gray.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/lna/Huffcode.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/lna/Icrc.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/lna/MParith.java (100%) rename {common-tools/cnuphys/numRec/src 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{common-tools/cnuphys/numRec/src => src/main/java}/com/nr/pde/Mglin.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/pde/Relaxation.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/pde/Weights.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Binomialdev.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Cauchydev.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Expondev.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Gammadev.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Hash.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/HashAll.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Hashfn1.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Hashfn2.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Hashtable.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Logisticdev.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/MCintegrate.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Mhash.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Miser.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Multinormaldev.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Normaldev.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Normaldev_BM.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Poissondev.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Primpolytest.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/ran/Ran.java (100%) 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{common-tools/cnuphys/numRec/src => src/main/java}/com/nr/root/Roots.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/sf/Bessel.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/sf/Bessik.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/sf/Bessjy.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/sf/Beta.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/sf/Betadist.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/sf/Binomialdist.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/sf/Cauchydist.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/sf/Chisqdist.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/sf/Elliptic.java (100%) rename {common-tools/cnuphys/numRec/src => src/main/java}/com/nr/sf/Erf.java (100%) rename 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{reconstruction/alert/src => src}/test/java/org/jlab/service/alert/ATOFTest.java (100%) rename {reconstruction/dc/src => src}/test/java/org/jlab/service/dc/DCReconstructionTest.java (100%) rename {reconstruction/eb/src => src}/test/java/org/jlab/service/eb/EBReconstructionTest.java (100%) rename {reconstruction/ec/src => src}/test/java/org/jlab/service/ec/ECReconstructionTest.java (100%) rename {reconstruction/ft/src => src}/test/java/org/jlab/service/ft/FTEBEngineTest.java (100%) rename {reconstruction/ft/src => src}/test/java/org/jlab/service/ft/FTTRKEngineTest.java (100%) diff --git a/build-coatjava.sh b/build-coatjava.sh index 3bf00d346b..8c1bb14e88 100755 --- a/build-coatjava.sh +++ b/build-coatjava.sh @@ -333,31 +333,37 @@ fi # install ################################################################################ -# NOTE: a maven plugin, such as `maven-assembly-plugin`, would be better, but it seems that they: -# - require significantly more repetition of the module names and/or generation of additional XML file(s) -# - seem to break thread safety of `mvn install`, i.e., we'd need to run `mvn package` first, then `mvn install` -# - we just want copy the produced JAR files to a final installation directory, so the following bash code gets the job done without drama -install_jars() { - src=$(dirname $1) - dest=$2 - [ $# -ge 3 ] && filter="$3" || filter='*.jar' - if [ -d $src/target ]; then - for f in $(find $src/target -name $filter); do - mkdir -p $dest - cp $f $dest/ - done - fi -} -for pom in $(find reconstruction -name pom.xml); do - install_jars $pom $prefix_dir/lib/services +# Post-merge: the single root pom.xml produces two artifacts in target/ +# - target/coatjava-.jar (thin jar, intra-project classes) +# - target/coatjava--coat-libs.jar (shaded uber-jar, attached with +# classifier "coat-libs"; see +# maven-shade-plugin in pom.xml) +# Install layout (libexec/env.sh puts lib/clas first on classpath; the shaded +# uber-jar wins on duplicates): +# - lib/clas/coat-libs-.jar <- renamed from coatjava--coat-libs.jar +# (preserves downstream consumer file +# names: iguana, mon12, etc.) +# - lib/services/coatjava-.jar <- the thin jar +mkdir -p $prefix_dir/lib/clas $prefix_dir/lib/services +for f in $(find $src_dir/target -maxdepth 1 -name 'coatjava-*-coat-libs.jar'); do + fname=$(basename $f) + # strip the "coatjava-" prefix and "-coat-libs" classifier infix so the + # final filename is coat-libs-.jar (matches pre-merge convention) + ver=${fname#coatjava-} + ver=${ver%-coat-libs.jar} + cp $f $prefix_dir/lib/clas/coat-libs-${ver}.jar done -for pom in $(find common-tools -name pom.xml); do - if [[ "$pom" =~ coat-libs ]]; then - install_jars $pom $prefix_dir/lib/clas 'coat-libs-*.jar' - # else # FIXME, consumers may be need these after https://github.com/JeffersonLab/coatjava/pull/632 ; alternatively add needed deps to `coat-libs` - # install_jars $pom $prefix_dir/lib/services - fi +for f in $(find $src_dir/target -maxdepth 1 -name 'coatjava-*.jar' ! -name '*-coat-libs.jar' ! -name '*-sources.jar' ! -name '*-javadoc.jar'); do + cp $f $prefix_dir/lib/services/ done +# ai.djl runtime jars are deposited in target/lib/services/ by the +# maven-dependency-plugin copy-djl-runtime-jars execution (pom.xml). +# They must reach coatjava/lib/services/ so AHDCEngine etc. can resolve +# ai/djl/translate/Translator at runtime (pre-merge: copied from +# reconstruction/alert/target/lib/services/). +if [ -d $src_dir/target/lib/services ]; then + cp $src_dir/target/lib/services/*.jar $prefix_dir/lib/services/ +fi echo "installed coatjava to: $prefix_dir" diff --git a/common-tools/clara-io/pom.xml b/common-tools/clara-io/pom.xml deleted file mode 100644 index e75018765d..0000000000 --- a/common-tools/clara-io/pom.xml +++ /dev/null @@ -1,76 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - clara-io - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - - org.jlab.coda - jclara - - - - org.jlab.coda - jevio - jar-with-dependencies - - - - org.json - json - - - - org.jlab.jnp - jnp-hipo - - - - org.jlab.jnp - jnp-hipo4 - - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-analysis - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - - org.apache.commons - commons-text - 1.15.0 - - - - - diff --git a/common-tools/clas-analysis/pom.xml b/common-tools/clas-analysis/pom.xml deleted file mode 100644 index 1260cfe315..0000000000 --- a/common-tools/clas-analysis/pom.xml +++ /dev/null @@ -1,88 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - clas-analysis - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - - org.apache.commons - commons-math3 - - - - org.jlab - groot - - - - org.jlab.jnp - jnp-hipo - - - - org.jlab.jnp - jnp-hipo4 - - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-jcsg - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - - org.jlab.clas - swim-tools - 13.8.4-SNAPSHOT - - - - - diff --git a/common-tools/clas-decay-tools/pom.xml b/common-tools/clas-decay-tools/pom.xml deleted file mode 100644 index 384a4bcfa9..0000000000 --- a/common-tools/clas-decay-tools/pom.xml +++ /dev/null @@ -1,74 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - clas-decay-tools - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - org.jlab.jnp - jnp-hipo4 - - - org.jlab.clas - swim-tools - 13.8.4-SNAPSHOT - jar - - - cnuphys - swimmer - 13.8.4-SNAPSHOT - - - cnuphys - magfield - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-vtx - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - diff --git a/common-tools/clas-detector/pom.xml b/common-tools/clas-detector/pom.xml deleted file mode 100644 index 63f7f53bb4..0000000000 --- a/common-tools/clas-detector/pom.xml +++ /dev/null @@ -1,68 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - - org.jlab - groot - - - - org.jlab.jnp - jnp-hipo - - - - org.jlab.jnp - jnp-hipo4 - - - - org.jlab.ccdbrcdb - ccdbrcdb - - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-logging - 13.8.4-SNAPSHOT - - - - junit - junit - - - - - diff --git a/common-tools/clas-geometry/pom.xml b/common-tools/clas-geometry/pom.xml deleted file mode 100644 index c22d685037..0000000000 --- a/common-tools/clas-geometry/pom.xml +++ /dev/null @@ -1,33 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - org.openjfx - javafx-base - linux - - - org.openjfx - javafx-graphics - linux - - - org.jlab.ccdbrcdb - ccdbrcdb - - - - diff --git a/common-tools/clas-io/pom.xml b/common-tools/clas-io/pom.xml deleted file mode 100644 index 06daa9b4b1..0000000000 --- a/common-tools/clas-io/pom.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - - org.jlab.coda - xmsg - 2.3 - - - - org.json - json - - - - org.yaml - snakeyaml - - - - org.jlab.jnp - jnp-hipo - - - - org.jlab.jnp - jnp-hipo4 - - - - org.jlab.coda - et - 14.0 - - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - - - diff --git a/common-tools/clas-jcsg/pom.xml b/common-tools/clas-jcsg/pom.xml deleted file mode 100644 index 1e33cf8332..0000000000 --- a/common-tools/clas-jcsg/pom.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - clas-jcsg - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - org.openjfx - javafx-fxml - linux - - - org.openjfx - javafx-graphics - linux - - - org.openjfx - javafx-base - linux - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - java3d - vecmath - 1.3.1 - - - org.slf4j - slf4j-api - - - - diff --git a/common-tools/clas-logging/pom.xml b/common-tools/clas-logging/pom.xml deleted file mode 100644 index 1a57384ab0..0000000000 --- a/common-tools/clas-logging/pom.xml +++ /dev/null @@ -1,16 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - clas-logging - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - diff --git a/common-tools/clas-math/pom.xml b/common-tools/clas-math/pom.xml deleted file mode 100644 index a849951d91..0000000000 --- a/common-tools/clas-math/pom.xml +++ /dev/null @@ -1,23 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - clas-math - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - org.apache.commons - commons-math3 - - - - diff --git a/common-tools/clas-physics/pom.xml b/common-tools/clas-physics/pom.xml deleted file mode 100644 index 3d819ebf25..0000000000 --- a/common-tools/clas-physics/pom.xml +++ /dev/null @@ -1,23 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - junit - junit - - - - diff --git a/common-tools/clas-reco/pom.xml b/common-tools/clas-reco/pom.xml deleted file mode 100644 index b839caa297..0000000000 --- a/common-tools/clas-reco/pom.xml +++ /dev/null @@ -1,94 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - - org.json - json - - - - org.openjfx - javafx-base - linux - - - - org.jlab.coda - jclara - - - - org.jlab.jnp - jnp-hipo - - - - org.jlab.jnp - jnp-hipo4 - - - - org.jlab.coda - jtools - 2.2 - - - - cnuphys - magfield - 13.8.4-SNAPSHOT - - - - cnuphys - swimmer - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - - - diff --git a/common-tools/clas-tracking/pom.xml b/common-tools/clas-tracking/pom.xml deleted file mode 100644 index adb391695f..0000000000 --- a/common-tools/clas-tracking/pom.xml +++ /dev/null @@ -1,56 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - clas-tracking - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - org.apache.commons - commons-math3 - - - org.jlab.jnp - jnp-hipo - - - org.ejml - ejml-simple - - - gov.nist.math - jama - - - org.jlab.clas - swim-tools - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - - diff --git a/common-tools/clas-utils/pom.xml b/common-tools/clas-utils/pom.xml deleted file mode 100644 index 460ad95fe7..0000000000 --- a/common-tools/clas-utils/pom.xml +++ /dev/null @@ -1,29 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - org.apache.commons - commons-text - 1.15.0 - - - org.jlab.clas - clas-logging - 13.8.4-SNAPSHOT - - - - diff --git a/common-tools/cnuphys/apache/.gitignore b/common-tools/cnuphys/apache/.gitignore deleted file mode 100644 index ae3c172604..0000000000 --- a/common-tools/cnuphys/apache/.gitignore +++ /dev/null @@ -1 +0,0 @@ -/bin/ diff --git a/common-tools/cnuphys/coatjava/etc/bankdefs/hipo/FMT.json b/common-tools/cnuphys/coatjava/etc/bankdefs/hipo/FMT.json deleted file mode 100644 index a532c3f7c9..0000000000 --- a/common-tools/cnuphys/coatjava/etc/bankdefs/hipo/FMT.json +++ /dev/null @@ -1,63 +0,0 @@ - [ - { - "bank": "FMTRec::Hits", - "group": 20821, - "info": "reconstructed FMT hits", - "items": [ - {"name":"ID", "id":1, "type":"int16" , "info":"hit ID"}, - {"name":"sector", "id":2, "type":"int8" , "info":"hit sector"}, - {"name":"layer", "id":3, "type":"int8" , "info":"hit layer"}, - {"name":"strip", "id":4, "type":"int32" , "info":"hit strip"}, - {"name":"fitResidual", "id":5, "type":"float" , "info":"fitted hit residual"}, - {"name":"trkingStat", "id":6, "type":"int32" , "info":"tracking status"}, - {"name":"clusterID", "id":7, "type":"int16" , "info":"associated cluster ID"}, - {"name":"trkID", "id":8, "type":"int16" , "info":"associated track ID"} - ] - }, - { - "bank": "FMTRec::Clusters", - "group": 20822, - "info": "reconstructed FMT clusters", - "items": [ - {"name":"ID", "id":1, "type":"int16" , "info":"ID"}, - {"name":"sector", "id":2, "type":"int8" , "info":"sector"}, - {"name":"layer", "id":3, "type":"int8" , "info":"layer"}, - {"name":"size", "id":4, "type":"int16" , "info":"cluster size"}, - {"name":"ETot", "id":5, "type":"float" , "info":"cluster total energy"}, - {"name":"seedE", "id":6, "type":"float" , "info":"energy of the seed "}, - {"name":"seedStrip", "id":7, "type":"int32" , "info":"seed strip"}, - {"name":"centroid", "id":8, "type":"float" , "info":"centroid strip number"}, - {"name":"centroidResidual","id":9, "type":"float" , "info":"centroid residual"}, - {"name":"seedResidual", "id":10, "type":"float" , "info":"seed residual"}, - {"name":"Hit1_ID", "id":11, "type":"int16" , "info":"Index of hit 1 in cluster"}, - {"name":"Hit2_ID", "id":12, "type":"int16" , "info":"Index of hit 2 in cluster"}, - {"name":"Hit3_ID", "id":13, "type":"int16" , "info":"Index of hit 3 in cluster"}, - {"name":"Hit4_ID", "id":14, "type":"int16" , "info":"Index of hit 4 in cluster"}, - {"name":"Hit5_ID", "id":15, "type":"int16" , "info":"Index of hit 5 in cluster"}, - {"name":"trkID", "id":16, "type":"int16", "info":"associated track ID"}, - {"name":"Tmin", "id":17, "type":"float", "info":"min T between strips"} - ] - }, - { - "bank": "FMTRec::Crosses", - "group": 20825, - "info": "reconstructed FMT crosses", - "items": [ - {"name":"ID", "id":1, "type":"int16" , "info":"ID"}, - {"name":"sector", "id":2, "type":"int8" , "info":"sector"}, - {"name":"region", "id":3, "type":"int8" , "info":"region"}, - {"name":"x", "id":4, "type":"float" , "info":"BMT cross x-coordinate"}, - {"name":"y", "id":5, "type":"float" , "info":"BMT cross y-coordinate"}, - {"name":"z", "id":6, "type":"float" , "info":"BMT cross z-coordinate"}, - {"name":"err_x", "id":7, "type":"float" , "info":"BMT cross x-coordinate error"}, - {"name":"err_y", "id":8, "type":"float" , "info":"BMT cross y-coordinate error"}, - {"name":"err_z", "id":9, "type":"float" , "info":"BMT cross z-coordinate error"}, - {"name":"ux", "id":10, "type":"float" , "info":"BMT cross x-direction (track unit tangent vector at the cross)"}, - {"name":"uy", "id":11, "type":"float" , "info":"BMT cross y-direction (track unit tangent vector at the cross)"}, - {"name":"uz", "id":12, "type":"float" , "info":"BMT cross z-direction (track unit tangent vector at the cross)"}, - {"name":"Cluster1_ID", "id":13, "type":"int16" , "info":"ID of the cluster in the Cross"}, - {"name":"Cluster2_ID", "id":14, "type":"int16" , "info":"ID of the top layer cluster in the Cross"}, - {"name":"trkID", "id":15, "type":"int16" , "info":"associated track ID"} - ] - } - ] diff --git a/common-tools/cnuphys/magfield/pom.xml b/common-tools/cnuphys/magfield/pom.xml deleted file mode 100644 index bcd4854fea..0000000000 --- a/common-tools/cnuphys/magfield/pom.xml +++ /dev/null @@ -1,23 +0,0 @@ - - - 4.0.0 - - cnuphys - magfield - 13.8.4-SNAPSHOT - jar - - - cnuphys - clas12 - 13.8.4-SNAPSHOT - - - - - org.apache.commons - commons-math3 - - - - diff --git a/common-tools/cnuphys/magfield/src/main/java/build.xml b/common-tools/cnuphys/magfield/src/main/java/build.xml deleted file mode 100644 index 308166a4e4..0000000000 --- a/common-tools/cnuphys/magfield/src/main/java/build.xml +++ /dev/null @@ -1,69 +0,0 @@ - - - - - - ${user.dir} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Building the mag field jar - - - - Building magfield jar - - - - - - diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/bin/build.xml b/common-tools/cnuphys/magfield/src/main/java/cnuphys/bin/build.xml deleted file mode 100644 index 308166a4e4..0000000000 --- a/common-tools/cnuphys/magfield/src/main/java/cnuphys/bin/build.xml +++ /dev/null @@ -1,69 +0,0 @@ - - - - - - ${user.dir} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Building the mag field jar - - - - Building magfield jar - - - - - - diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/.gitignore b/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/.gitignore deleted file mode 100644 index ea92ed18a9..0000000000 --- a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/.gitignore +++ /dev/null @@ -1,33 +0,0 @@ -/AngularUnit.class -/ColorScaleModel.class -/CompositeField.class -/ConstantField.class -/CoordinateSystem.class -/FieldUnit.class -/GridCoordinate.class -/IField.class -/LengthUnit.class -/MacTestField.class -/MagneticField.class -/MagneticFieldCanvas$1.class -/MagneticFieldCanvas$2.class -/MagneticFieldCanvas$3.class -/MagneticFieldCanvas$CSType.class -/MagneticFieldCanvas$Trajectory.class -/MagneticFieldCanvas.class -/MagneticFieldChangeListener.class -/MagneticFields$1.class -/MagneticFields$2.class -/MagneticFields$3.class -/MagneticFields$4.class -/MagneticFields$5.class -/MagneticFields$FieldType.class -/MagneticFields.class -/PerfectSolenoid.class -/RotatedCompositeField.class -/ScaleFieldPanel$1.class -/ScaleFieldPanel$2.class -/ScaleFieldPanel.class -/Solenoid.class -/Test.class -/Torus.class diff --git a/common-tools/cnuphys/numRec/ExpectedAllTests.xml b/common-tools/cnuphys/numRec/ExpectedAllTests.xml deleted file mode 100644 index 84d18c750c..0000000000 --- a/common-tools/cnuphys/numRec/ExpectedAllTests.xml +++ /dev/null @@ -1,1306 +0,0 @@ - - - - - diff --git a/common-tools/cnuphys/numRec/INSTALL.txt b/common-tools/cnuphys/numRec/INSTALL.txt deleted file mode 100644 index 1ff92a59d6..0000000000 --- a/common-tools/cnuphys/numRec/INSTALL.txt +++ /dev/null @@ -1,104 +0,0 @@ -INSTALLATION - -Java Source Code Translations of Numerical Recipes C++ Source Code ------------------------------------------------------------------- -ver. 3.04 ---------- - -This directory tree contains translations to Java source code by Huang -Wen Hui of copyrighted Numerical Recipes Third Edition C++ source -code. Please see the file LICENSE.txt for copyright and license -information. Your use of these files is subject to the terms given -there, including the Disclaimer of Warranty. - -Note that these Java translations are not a supported product of -Numerical Recipes Software, but are provided only as a convenience to -our users. - -The file NAMES.txt gives the correspondence between C++ routines as -printed in the Numerical Recipes Third Edition book or ebook and the -Java packages and classes in this distribution. For information about -the book or ebook, see http://www.nr.com . - -All the translations are in the directory src/ . If you want to -discover on your own how to use them, just dig in! However, for the -rest of us, this distribution is packaged as a self-contained full -test suite. By running this test suite, you can verify that all the -translations run correctly in your environment. Then, you can examine -any specific test routines in the test/ directory to learn how the -translation's packages and classes may be invoked. - -PREREQUISITES - -To run the test suite you need: - -1. Java SE (Java Platform Standard Edition) ver. 6 or later. If -already installed, then the command "java -version" should produce -output something like this: - java version "1.6.0_32" - Java(TM) SE Runtime Environment (build 1.6.0_32-b05) - Java HotSpot(TM) Client VM (build 20.7-b02, mixed mode, sharing) - -We downloaded Java SE from http://java.com/en/download/index.jsp - -2. JDK (Java SE Development Kit) ver. 6 or later. If already -installed, then the command "javac -version" should produce -output something like this: - javac 1.6.0_32 -(Note, however, that you might need to add the jdk bin/ directory -to your path for this check to work. It is not necessary to do -this to run the test suite.) - -We downloaded JDK from -http://www.oracle.com/technetwork/java/javase/downloads/index.html - -3. Apache Ant, a test suite driver written in Java. If already -installed, then the command "ant -version" should produce output -something like this: - Apache Ant(TM) version 1.8.3 compiled on February 26 2012 -You may need to add the ant bin/ directory to your path, and you may -need to set the environment variables ANT_HOME to the top-level ant -directory; and JAVA_HOME to the top-level JDK directory. For -example, on our Windows machine, the set command indicates: -ANT_HOME=C:\ant -JAVA_HOME=c:\Program Files\Java\jdk1.6.0_32 - -We downloaded Ant from http://ant.apache.org/ - -RUNNING THE TEST SUITE - -1. From the Java_304 directory, which contains the file build.xml, -first try the command "ant clean". You should get output like: - Buildfile: [your directory]/build.xml - clean: - BUILD SUCCESSFUL - Total time: 0 seconds - -2. Next try the command "ant build". The output should resemble: - -Buildfile: [your directory]/build.xml -init: - [mkdir] Created dir: [whatever]/Java_304/build/classes - [mkdir] Created dir: [whatever]/Java_304/build/test -build: - [echo] NR3: [whatever]/Java_304/build.xml - [javac] Compiling 257 source files to [whatever]/Java_304/build/classes - [javac] Compiling 308 source files to [whatever]/Java_304/build/test -BUILD SUCCESSFUL -Total time: 3 seconds - -3. Now for the big test. Try the command "ant AllTests". You will -get a lot of output, hopefully interspersed with many lines that say: - [junit] Passed -These lines indicate that the individual test routines gave the -expected results. To see if *all* the test routines give expected -results, locate the file junit/TEST-com.nr.test.AllTests.xml that was -produced by AllTests. Compare this to the provided file -ExpectedAllTests.xml. Your AllTests.xml file will have many extra -irrelevant lines that have been deleted from ExpectedAllTests.xml, but -all lines in common should agree. (Note that end-of-line conventions -may be different on different machines and are not significant.) - -If all of the above went well, then you are now ready to use the Java -translations of the Numerical Recipes Third Edition routines in your -own programming. diff --git a/common-tools/cnuphys/numRec/build.xml b/common-tools/cnuphys/numRec/build.xml deleted file mode 100644 index 9b290b2bcc..0000000000 --- a/common-tools/cnuphys/numRec/build.xml +++ /dev/null @@ -1,86 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Building the jar for clasJlib - - - - Building numRec jar - - - - - diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/AllTests.java b/common-tools/cnuphys/numRec/test/com/nr/test/AllTests.java deleted file mode 100644 index 8cef90dcb6..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/AllTests.java +++ /dev/null @@ -1,342 +0,0 @@ -package com.nr.test; - -import org.junit.runner.RunWith; -import org.junit.runners.Suite; -import org.junit.runners.Suite.SuiteClasses; - -import com.nr.test.test_chapter1.*; -import com.nr.test.test_chapter2.*; -import com.nr.test.test_chapter3.*; -import com.nr.test.test_chapter4.*; -import com.nr.test.test_chapter5.*; -import com.nr.test.test_chapter6.*; -import com.nr.test.test_chapter7.*; -import com.nr.test.test_chapter8.*; -import com.nr.test.test_chapter9.*; -import com.nr.test.test_chapter10.*; -import com.nr.test.test_chapter11.*; -import com.nr.test.test_chapter12.*; -import com.nr.test.test_chapter13.*; -import com.nr.test.test_chapter14.*; -import com.nr.test.test_chapter15.*; -import com.nr.test.test_chapter16.*; -import com.nr.test.test_chapter17.*; -import com.nr.test.test_chapter18.*; -import com.nr.test.test_chapter19.*; -import com.nr.test.test_chapter20.*; -import com.nr.test.test_chapter21.*; -import com.nr.test.test_chapter22.*; - - -@RunWith(Suite.class) -@SuiteClasses({ - Test_caldat.class, - Test_flmoon.class, - Test_julday.class, - Test_Amebsa.class, - Test_Amoeba.class, - Test_Anneal.class, - Test_Bracketmethod.class, - Test_Brent.class, - Test_Dbrent.class, - Test_Frprmn.class, - Test_Golden.class, - Test_Linemethod.class, - Test_Powell.class, - Test_dfpmin.class, - Test_dynpro.class, - Test_fdfunc.class, - Test_stringalign.class, - Test_Jacobi.class, - Test_Symmeig.class, - Test_Unsymmeig.class, - Test_WrapVecDoub.class, - Test_cosft1.class, - Test_cosft2.class, - Test_four1.class, - Test_fourfs.class, - Test_fourn.class, - Test_realft.class, - Test_rlft3.class, - Test_sinft.class, - Test_Daub4.class, - Test_Daub4i.class, - Test_Daubs.class, - Test_Hann.class, - Test_Slepian.class, - Test_Spectolap.class, - Test_Spectreg.class, - Test_Square.class, - Test_bartlett.class, - Test_convlv.class, - Test_correl.class, - Test_dftint.class, - Test_evlmem.class, - Test_fasper.class, - Test_fixrts.class, - Test_memcof.class, - Test_period.class, - Test_predic.class, - Test_spread.class, - Test_welch.class, - Test_wt0.class, - Test_wtn.class, - Test_avevar.class, - Test_chsone.class, - Test_chstwo.class, - Test_cntab.class, - Test_crank.class, - Test_ftest.class, - Test_kendl1.class, - Test_kendl2.class, - Test_ks2d1s.class, - Test_ks2d2s.class, - Test_ksone.class, - Test_kstwo.class, - Test_moment.class, - Test_pearsn.class, - Test_quadct.class, - Test_quadvl.class, - Test_savgol.class, - Test_spear.class, - Test_tptest.class, - Test_ttest.class, - Test_tutest.class, - Test_Fitab.class, - Test_Fitexy.class, - Test_Fitlin.class, - Test_Fitmed.class, - Test_Fitmrq.class, - Test_Fitsvd.class, - Test_fleg.class, - Test_fpoly.class, - com.nr.test.test_chapter15.Test_mcmc.class, - Test_Gaumixmod.class, - Test_HMM.class, - Test_Kmeans.class, - Test_Phylo_clc.class, - Test_Phylo_nj.class, - Test_Phylo_slc.class, - Test_Phylo_upgma.class, - Test_Phylo_wpgma.class, - Test_Svm.class, - Test_markovgen.class, - Test_newick.class, - Test_StepperBS.class, - Test_StepperDopr5.class, - Test_StepperDopr853.class, - Test_StepperRoss.class, - Test_StepperSie.class, - Test_StepperStoerm.class, - Test_Stochsim.class, - Test_rk4.class, - Test_Shoot.class, - Test_Shootf.class, - Test_Solvde.class, - Test_sfroid.class, - Test_Fred2.class, - Test_Fredex.class, - Test_Wwghts.class, - Test_voltra.class, - Test_ADAT.class, - Test_Bandec.class, - Test_Cholesky.class, - Test_LUdcmp.class, - Test_Linbcg.class, - Test_NRsparseCol.class, - Test_NRsparseMat.class, - Test_QRdcmp.class, - Test_SVD.class, - Test_cyclic.class, - Test_gaussj.class, - Test_mprove.class, - Test_toeplz.class, - Test_tridag.class, - Test_vander.class, - Test_Mgfas.class, - Test_Mglin.class, - Test_sor.class, - Test_weights.class, - Test_Box.class, - Test_Boxnode.class, - Test_Circle.class, - Test_Convexhull.class, - Test_Delaunay.class, - Test_KDtree.class, - Test_Minspantree.class, - Test_Nearpoints.class, - Test_Point.class, - Test_Qotree.class, - Test_Sphcirc.class, - Test_Triel.class, - Test_Voredge.class, - Test_Voronoi.class, - Test_circumcircle.class, - Test_dist.class, - Test_incircle.class, - Test_ispolysimple.class, - Test_polywind.class, - Test_Arithcode.class, - Test_Gray.class, - Test_Huffcode.class, - Test_Icrc.class, - Test_MParith.class, - Test_Machar.class, - Test_PSpage.class, - Test_PSplot.class, - Test_decchk.class, - Test_BaryRat_interp.class, - Test_Bilin_interp.class, - Test_Curve_interp.class, - Test_Krig.class, - Test_Laplace_interp.class, - Test_Linear_interp.class, - Test_Poly2D_interp.class, - Test_Poly_interp.class, - Test_RBF_interp.class, - Test_Rat_interp.class, - Test_Shep_interp.class, - Test_Spline2D_interp.class, - Test_Spline_interp.class, - Test_bcuint.class, - Test_polcoe.class, - Test_polcof.class, - Test_Adapt.class, - Test_Stiel.class, - Test_derule.class, - Test_gaucof.class, - Test_gauher.class, - Test_gaujac.class, - Test_gaulag.class, - Test_gauleg.class, - Test_lobatto.class, - Test_midexp.class, - Test_midinf.class, - Test_midpnt.class, - Test_midsql.class, - Test_midsqu.class, - Test_qgaus.class, - Test_qromb.class, - Test_qromo.class, - Test_qsimp.class, - Test_qtrap.class, - Test_quad3d.class, - Test_radau.class, - Test_trapzd.class, - Test_Chebyshev.class, - Test_Epsalg.class, - Test_Eulsum.class, - Test_Levin.class, - Test_Poly.class, - Test_Ratfn.class, - Test_ddpoly.class, - Test_dfridr.class, - Test_ipcshft.class, - Test_levex.class, - Test_pade.class, - Test_pcshft.class, - Test_poldiv.class, - Test_ratlsq.class, - Test_Bessel.class, - Test_Bessik.class, - Test_Bessjy.class, - Test_Betadist.class, - Test_Binomialdist.class, - Test_Cauchydist.class, - Test_Chisqdist.class, - Test_Erf.class, - Test_Expondist.class, - Test_Fdist.class, - Test_Fermi.class, - Test_Gamma.class, - Test_Gammadist.class, - Test_KSdist.class, - Test_Logisticdist.class, - Test_Lognormaldist.class, - Test_Normaldist.class, - Test_Poissondist.class, - Test_Studenttdist.class, - Test_beta.class, - Test_betai.class, - Test_bico.class, - Test_cisi.class, - Test_dawson.class, - Test_ei.class, - Test_elle.class, - Test_ellf.class, - Test_ellpi.class, - Test_erfcc.class, - Test_expint.class, - Test_factln.class, - Test_factrl.class, - Test_frenel.class, - Test_gammln.class, - Test_hypgeo.class, - Test_invxlogx.class, - Test_plegendre.class, - Test_rc.class, - Test_rd.class, - Test_rf.class, - Test_rj.class, - Test_sncndn.class, - Test_Binomialdev.class, - Test_Cauchydev.class, - Test_Expondev.class, - Test_Gammadev.class, - Test_Hash.class, - Test_Hashtable.class, - Test_Logisticdev.class, - Test_MCintegrate.class, - Test_Mhash.class, - Test_Multinormaldev.class, - Test_Normaldev.class, - Test_Normaldev_BM.class, - Test_Poissondev.class, - Test_Primpolytest.class, - Test_Ran.class, - Test_Ranbyte.class, - Test_Ranfib.class, - Test_Ranhash.class, - Test_Ranlim32.class, - Test_Ranq1.class, - Test_Ranq2.class, - Test_hashall.class, - com.nr.test.test_chapter7.Test_mcmc.class, - Test_miser.class, - Test_psdes.class, - Test_sobseq.class, - Test_vegas.class, - Test_Heapselect.class, - Test_IQagent.class, - Test_Indexx.class, - Test_eclass.class, - Test_eclazz.class, - Test_hpsort.class, - Test_piksr2.class, - Test_piksrt.class, - Test_select.class, - Test_selip.class, - Test_shell.class, - Test_sort.class, - Test_sort2.class, - Test_broydn.class, - Test_laguer.class, - Test_lnsrch.class, - Test_mnewt.class, - Test_newt.class, - Test_qroot.class, - Test_rtbis.class, - Test_rtflsp.class, - Test_rtnewt.class, - Test_rtsafe.class, - Test_rtsec.class, - Test_zbrac.class, - Test_zbrak.class, - Test_zbrent.class, - Test_zrhqr.class, - Test_zriddr.class, - Test_zroots.class - }) -public class AllTests { - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/NRTestUtil.java b/common-tools/cnuphys/numRec/test/com/nr/test/NRTestUtil.java deleted file mode 100644 index 443879c88e..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/NRTestUtil.java +++ /dev/null @@ -1,219 +0,0 @@ -package com.nr.test; - -import com.nr.ran.Ran; -import static java.lang.Math.*; - -public class NRTestUtil { - public static Ran ran = new Ran(10101); // global ranno generator - - private NRTestUtil(){} - - public static void ranmat(double[][] a) { // fill matrix with ran - ranmat(a, 0.); - } - - public static void ranmat(double[][] a, double dadd) { // fill matrix with ran - int m = a.length, n=a[0].length; - for (int i=0;i max) max = abs(a[i][j]); - } - return max; - } - - - public static double maxel(final double[] a) { - int i,m=a.length; - double max = 0.; - for (i=0;i max) max = abs(a[i]); - } - return max; - } - - - public static double[][] ident(int n, double dum) { - double[][] c; - //c.assign(n,n,(T)0); - c = new double[n][n]; - for (int i=0;i max) max = abs(a[i][j]); - } - return max; - } - - - public static int maxel(final int[] a) { - int i,m=a.length; - int max = 0; - for (i=0;i max) max = abs(a[i]); - } - return max; - } - - - public static int[][] ident(int n, int dum) { - int[][] c; - //c.assign(n,n,(T)0); - c = new int[n][n]; - for (int i=0;i= j2.val ? 0.5 : -0.5)); - for (i=0;i < 12;i++) { - n++; - flmoon(n,nph,j2,frac); - frac.val=24.0*frac.val; - if (frac.val < 0.0) { - j2.val--; - frac.val += 24.0; - } - if (frac.val > 12.0) { - j2.val++; - frac.val -= 12.0; - } else - frac.val += 12.0; - i1=(int)(frac.val); // hours - i2=(int)(60.0*(frac.val-i1)); // minutes - caldat(j2.val,im,id,iy); - - localflag = (im.val != i+1); - globalflag = globalflag || localflag; - if (localflag) { - System.out.println("*** flmoon: There should be a full moon in each month"); - - } - - localflag = (id.val != nday[i]); - globalflag = globalflag || localflag; - if (localflag) { - System.out.println("*** flmoon: Day of full moon disagrees with U.S. Naval Observatory"); - - } - -// System.out.printf(frac-(nhour[i]+nmin[i]/60.0) << endl; - localflag = abs(frac.val-(nhour[i]+nmin[i]/60.0)) > 1.0; - globalflag = globalflag || localflag; - if (localflag) { - System.out.println("*** flmoon: Time of full moon disagrees with U.S. Naval Observatory by > 2 hrs"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter1/Test_julday.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter1/Test_julday.java deleted file mode 100644 index ba50495952..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter1/Test_julday.java +++ /dev/null @@ -1,69 +0,0 @@ -package com.nr.test.test_chapter1; - - -import static com.nr.util.Calendar.*; -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -public class Test_julday { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,id,im,iy,nrjday,N=16; - /* - char *event[]={"End of millenium","One day later", - "Day before Gregorian calendar","Gregorian calendar adopted", - "Benjamin Franklin born","Abraham Lincoln shot", - "San Francisco earthquake","Sinking of the Lusitania", - "Pancho Villa assassinated","Bonnie and Clyde subdued", - "John Dillinger shot","Bruno Hauptman electrocuted", - "Hindenburg disaster","Sinking of the Andrea Doria", - "Teton dam collapse","Julian Day 2440000"};*/ - int nmonth[]={12,1,10,10,1,4,4,5,7,5,7,4,5,7,6,5}; - int nday[]={31,01,04,15,17,14,18,7,20,23,22,3,6,26,5,23}; - int nyear[]={-1,1,1582,1582,1706,1865,1906,1915,1923,1934, - 1934,1936,1937,1956,1976,1968}; - // Corresponding Julian days from U.S. Naval Observatory - int expect[]={1721423,1721424,2299160,2299161,2344180, - 2402341,2417319,2420625,2423621,2427581,2427641, - 2428262,2428660,2435681,2442935,2440000}; - boolean localflag, globalflag=false; - - - // Test julday - System.out.println("Testing julday"); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Amebsa, interface 1: Incorrect minimum function value"); - - } - - sbeps=1.e-4; - localflag = false; - for (i=0;i<4;i++) - localflag = localflag || abs(amb1.pb[i]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Amebsa, interface 1: Did not converge to the global minumum at the origin"); - - } - - // Test interface #2 - Amebsa amb2 = new Amebsa(point,dels,func_amebsa,FTOL); - - iter.val=1000; - temperature=100.0; - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Amebsa, interface 2: Incorrect minimum function value"); - - } - - sbeps=1.e-4; - localflag = false; - for (i=0;i<4;i++) - localflag = localflag || abs(amb2.pb[i]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Amebsa, interface 2: Did not converge to the global minumum at the origin"); - - } - - // Test interface #3 - - Amebsa amb3 =new Amebsa(p,func_amebsa,FTOL); - - iter.val=1000; - temperature=100.0; - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Amebsa, interface 3: Incorrect minimum function value"); - - } - - sbeps=1.e-4; - localflag = false; - for (i=0;i<4;i++) - localflag = localflag || abs(amb3.pb[i]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Amebsa, interface 3: Did not converge to the global minumum at the origin"); - - } - - localflag = false; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Amebsa: **********************"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class func_amebsa implements RealValueFun { - public double funk(double[] p){ - int j,N=4; - double q,r,sumd=0.0,sumr=0.0,RAD=0.3,AUG=2.0; - double wwid[]={1.0,3.0,10.0,30.0}; - double[] wid=buildVector(wwid); - - for (j=0;j= 0 ? (int)(q+0.5) : -(int)(0.5-q)); - sumr += q*q; - sumd += (q-r)*(q-r); - } - return 1.0+sumr*(1.0+(sumd > RAD*RAD ? AUG : AUG*sumd/(RAD*RAD))); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Amoeba.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Amoeba.java deleted file mode 100644 index 6431691fe5..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Amoeba.java +++ /dev/null @@ -1,106 +0,0 @@ -package com.nr.test.test_chapter10; - -import static java.lang.Math.abs; -import static java.lang.Math.pow; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.RealValueFun; -import com.nr.UniVarRealValueFun; -import com.nr.min.Amoeba; -import com.nr.sf.Bessjy; - -public class Test_Amoeba { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=20,M=2; - double tol=1.e-12,del=1.0,sbeps=0.; - double[] point=new double[M],min=new double[M]; - boolean localflag=false, globalflag=false; - - Func_Amoeba Func_Amoeba= new Func_Amoeba(); - Bessj1_Amoeba Bessj1_Amoeba = new Bessj1_Amoeba(); - - // Test Amoeba - System.out.println("Testing Amoeba, interface1"); - Amoeba amb1=new Amoeba(tol); - for (i=0;i sbeps) - || (abs(2*min[1]) > sbeps); - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Amoeba, interface1: Gradient not zero at one of the identified minima"); - - } - - System.out.println("Testing Amoeba, interface2"); - Amoeba amb2 = new Amoeba(tol); - double[] dels=new double[M]; - dels[0]=del; - dels[1]=0.5*del; - for (i=0;i sbeps) - || (abs(2*min[1]) > sbeps); - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Amoeba, interface2: Gradient not zero at one of the identified minima"); - - } - - System.out.println("Testing Amoeba, interface3"); - Amoeba amb3 = new Amoeba(tol); - double[][] pp = new double[3][2]; - for (i=0;i sbeps) - || (abs(2*min[1]) > sbeps); - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Amoeba, interface3: Gradient not zero at one of the identified minima"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class Func_Amoeba implements RealValueFun { - public double funk(final double[] x) { - Bessjy b = new Bessjy(); - return(b.j0(x[0])+pow(x[1],2.0)); - } - } - class Bessj1_Amoeba implements UniVarRealValueFun { - public double funk(final double x) { - Bessjy b = new Bessjy(); - return(b.j1(x)); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Anneal.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Anneal.java deleted file mode 100644 index 89ba3437c2..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Anneal.java +++ /dev/null @@ -1,90 +0,0 @@ -package com.nr.test.test_chapter10; - -import static com.nr.NRUtil.SQR; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.min.Anneal; -import com.nr.ran.Ran; - -public class Test_Anneal { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,k,N=100,M=10; - double length,linit,rms,ave; - int[] iorder= new int[N]; - double[] x= new double[N],y= new double[N],l=new double[M]; - boolean localflag, globalflag=false; - - - - // Test Anneal - System.out.println("Testing Anneal"); - - Ran myran=new Ran(17); - for (i=0;i 0.10); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Anneal: Successive runs did not result is substantially same path length"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Bracketmethod.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Bracketmethod.java deleted file mode 100644 index f9c7848fa6..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Bracketmethod.java +++ /dev/null @@ -1,76 +0,0 @@ -package com.nr.test.test_chapter10; - -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.min.Bracketmethod; -import com.nr.ran.Ran; -import com.nr.sf.Bessjy; - -public class Test_Bracketmethod implements UniVarRealValueFun{ - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=100; - double a,b,span=1.0; - boolean localflag=false, globalflag=false; - - - - // Test Bracketmethod - System.out.println("Testing Bracketmethod"); - - Ran myran=new Ran(17); - Bracketmethod br = new Bracketmethod(); - for (i=0;isbeps - || abs(br.fb - funk(br.bx))>sbeps - || abs(br.fc - funk(br.cx))>sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bracketmethod: Function values don't agree with coordinates"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - public double funk(final double x) { - Bessjy b = new Bessjy(); - return(b.j0(x)); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Brent.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Brent.java deleted file mode 100644 index ad07b70e61..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Brent.java +++ /dev/null @@ -1,65 +0,0 @@ -package com.nr.test.test_chapter10; - -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.min.Brent; -import com.nr.sf.Bessjy; - -public class Test_Brent implements UniVarRealValueFun{ - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=50; - double a,b,min,span=1.0,sbeps=1.0e-7; - boolean localflag=false, globalflag=false; - - - - // Test Brent - System.out.println("Testing Brent"); - - Brent br = new Brent(); - for (i=0;i sbeps); - } - - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Brent: Identified minimum is not a zero of the function derivative"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - public double funk(final double x) { - return Bessj0_Brent(x); - } - double Bessj0_Brent(final double x) { - Bessjy b = new Bessjy(); - return(b.j0(x)); - } - - double Bessj1_Brent(final double x) { - Bessjy b = new Bessjy(); - return(b.j1(x)); - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Dbrent.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Dbrent.java deleted file mode 100644 index 3920f24fb4..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Dbrent.java +++ /dev/null @@ -1,63 +0,0 @@ -package com.nr.test.test_chapter10; - -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniValRealValueFunWithDiff; -import com.nr.min.Dbrent; -import com.nr.sf.Bessjy; - -public class Test_Dbrent { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=50; - double a,b,min,span=1.0,sbeps=1.0e-7; - boolean localflag=false, globalflag=false; - - - - // Test Dbrent - System.out.println("Testing Dbrent"); - - Funcd_Dbrent funcd = new Funcd_Dbrent(); - Dbrent dbr = new Dbrent(); - for (i=0;i sbeps); - } - - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Dbrent: Identified minimum is not a zero of the function derivative"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class Funcd_Dbrent implements UniValRealValueFunWithDiff{ - Bessjy b = new Bessjy(); - public double funk (final double x) { - return b.j0(x); - } - public double df(final double x) { - return -b.j1(x); - } - }; -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Frprmn.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Frprmn.java deleted file mode 100644 index 57d5c9e444..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Frprmn.java +++ /dev/null @@ -1,88 +0,0 @@ -package com.nr.test.test_chapter10; - -import static com.nr.NRUtil.*; -import static java.lang.Math.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.RealValueFunWithDiff; -import com.nr.min.Frprmn; -import com.nr.sf.Bessjy; - -public class Test_Frprmn { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=20; - double theta,phi,f0,f,d0,d,pi=acos(-1.0); - double sbeps1=1.0e-7,sbeps2=5.0e-16; - double[] p = new double[3]; - boolean localflag=false, globalflag=false; - - - - // Test Frprmn - System.out.println("Testing Frprmn"); - - Funcd_Frprmn fd = new Funcd_Frprmn(); - Frprmn frprmn = new Frprmn(fd); - p[0]=p[1]=p[2]=0.1; - p=frprmn.minimize(p); - f0=frprmn.fret; - d0=sqrt(SQR(p[0])+SQR(p[1])+SQR(p[2])); - - for (i=0;i sbeps1; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Frprmn: First minimum of radial function reported at different radius for different starting points"); - - } - - localflag = localflag || abs(f-f0) > sbeps2; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Frprmn: Reported function value at first minimum is different for different starting points"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Funcd_Frprmn implements RealValueFunWithDiff{ - Bessjy b = new Bessjy(); - double u; - public double funk (double[] x) { - return(b.j0(sqrt(SQR(x[0])+SQR(x[1])+SQR(x[2])))); - } - public void df(double[] x, double[] deriv) { - u=sqrt(SQR(x[0])+SQR(x[1])+SQR(x[2])); - deriv[0]= -x[0]*b.j1(u)/u; - deriv[1]= -x[1]*b.j1(u)/u; - deriv[2]= -x[2]*b.j1(u)/u; - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Golden.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Golden.java deleted file mode 100644 index 419888750a..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Golden.java +++ /dev/null @@ -1,65 +0,0 @@ -package com.nr.test.test_chapter10; - -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.min.Golden; -import com.nr.sf.Bessjy; - -public class Test_Golden implements UniVarRealValueFun{ - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=50; - double a,b,min,span=1.0,sbeps=1.0e-7; - boolean localflag=false, globalflag=false; - - - - // Test Golden - System.out.println("Testing Golden"); - - Golden gold = new Golden(); - for (i=0;i sbeps); - } - - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Golden: Identified minimum is not a zero of the function derivative"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - public double funk(final double x) { - return Bessj0_Golden(x); - } - double Bessj0_Golden(final double x) { - Bessjy b = new Bessjy();; - return(b.j0(x)); - } - - double Bessj1_Golden(final double x) { - Bessjy b = new Bessjy(); - return(b.j1(x)); - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Linemethod.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Linemethod.java deleted file mode 100644 index 936a4f4ab8..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Linemethod.java +++ /dev/null @@ -1,90 +0,0 @@ -package com.nr.test.test_chapter10; - -import static com.nr.NRUtil.SQR; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.cos; -import static java.lang.Math.sin; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.RealValueFun; -import com.nr.min.Linemethod; -import com.nr.sf.Bessjy; - -public class Test_Linemethod implements RealValueFun{ - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=20; - double theta,phi,f0,f,d0,d,pi=acos(-1.0); - double sbeps1=5.0e-8,sbeps2=1.0e-15; - double[] p=new double[3],xi=new double[3]; - boolean localflag=false, globalflag=false; - - - - // Test Linemethod - System.out.println("Testing Linemethod"); - Linemethod line=new Linemethod(this); - - p[0]=p[1]=p[2]=0.0; - xi[0]=1.0; - xi[1]=xi[2]=0.0; - line.p=p; - line.xi=xi; - f0=line.linmin(); - d0=sqrt(SQR(line.p[0])+SQR(line.p[1])+SQR(line.p[2])); - - for (i=0;i sbeps1; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Linemethod: First minimum of radial function reported at different radius for different xi[]"); - - } - - localflag = localflag || abs(f-f0) > sbeps2; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Linemethod: Reported function value at first minimum is different for different xi[i]"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - public double funk(final double[] x) { - Bessjy b = new Bessjy(); - return(b.j0(sqrt(SQR(x[0])+SQR(x[1])+SQR(x[2])))); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Powell.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Powell.java deleted file mode 100644 index cec929c8b0..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_Powell.java +++ /dev/null @@ -1,123 +0,0 @@ -package com.nr.test.test_chapter10; - -import static com.nr.NRUtil.SQR; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.cos; -import static java.lang.Math.sin; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.RealValueFun; -import com.nr.min.Powell; -import com.nr.sf.Bessjy; - -public class Test_Powell implements RealValueFun { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=20; - double theta,phi,f0,f,d0,d,pi=acos(-1.0); - double sbeps1=5.0e-8,sbeps2=1.0e-15; - double[] p=new double[3]; - double[][] ximat = new double[3][3]; - boolean localflag=false, globalflag=false; - - - - // Test Powell - System.out.println("Testing Powell, interface1"); - - Powell pow1 = new Powell(this); - p[0]=p[1]=p[2]=0.0; - p=pow1.minimize(p); - f0=pow1.fret; - d0=sqrt(SQR(p[0])+SQR(p[1])+SQR(p[2])); - - for (i=0;i sbeps1; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Powell, interface1: First minimum of radial function reported at different radius for different starting points"); - - } - - localflag = localflag || abs(f-f0) > sbeps2; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Powell, interface1: Reported function value at first minimum is different for different starting points"); - - } - } - - System.out.println("Testing Powell, interface2"); - Powell pow2 = new Powell(this); - for (i=0;i sbeps1; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Powell, interface2: First minimum of radial function reported at different radius for different xi[]"); - - } - - localflag = localflag || abs(f-f0) > sbeps2; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Powell, interface2: Reported function value at first minimum is different for different xi[i]"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - public double funk(double[] x) { - return Bessj0_Powell(x); - } - - double Bessj0_Powell(double[] x) { - Bessjy b = new Bessjy(); - return(b.j0(sqrt(SQR(x[0])+SQR(x[1])+SQR(x[2])))); - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_dfpmin.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_dfpmin.java deleted file mode 100644 index 3df0a435a9..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_dfpmin.java +++ /dev/null @@ -1,91 +0,0 @@ -package com.nr.test.test_chapter10; -import static com.nr.NRUtil.SQR; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.cos; -import static java.lang.Math.sin; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; -import org.netlib.util.intW; - -import com.nr.RealValueFunWithDiff; -import com.nr.min.QuasiNewton; -import com.nr.sf.Bessjy; - -public class Test_dfpmin { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=20; - intW iter = new intW(0); - doubleW f0=new doubleW(0),f=new doubleW(0); - double theta,phi,d0,d,pi=acos(-1.0); - double sbeps1=5.0e-8,sbeps2=5.0e-16,gtol=5.0e-8; - double[] p = new double[3]; - boolean localflag=false, globalflag=false; - - - - // Test dfpmin - System.out.println("Testing dfpmin"); - - Funcd_dfpmin fd = new Funcd_dfpmin(); - p[0]=p[1]=p[2]=0.5; - QuasiNewton.dfpmin(p,gtol,iter,f0,fd); - d0=sqrt(SQR(p[0])+SQR(p[1])+SQR(p[2])); - - for (i=0;i sbeps1; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** dfpmin: First minimum of radial function reported at different radius for different starting points"); - - } - - localflag = localflag || abs(f.val-f0.val) > sbeps2; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** dfpmin: Reported function value at first minimum is different for different starting points"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class Funcd_dfpmin implements RealValueFunWithDiff{ - Bessjy b = new Bessjy(); - double u; - public double funk (double[] x) { - return(b.j0(sqrt(SQR(x[0])+SQR(x[1])+SQR(x[2])))); - } - public void df(double[] x, double[] deriv) { - u=sqrt(SQR(x[0])+SQR(x[1])+SQR(x[2])); - deriv[0]= -x[0]*b.j1(u)/u; - deriv[1]= -x[1]*b.j1(u)/u; - deriv[2]= -x[2]*b.j1(u)/u; - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_dynpro.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_dynpro.java deleted file mode 100644 index 46825e2b3f..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_dynpro.java +++ /dev/null @@ -1,129 +0,0 @@ -package com.nr.test.test_chapter10; - -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.min.Dynpro; -import com.nr.ran.Ran; - -public class Test_dynpro { - Ran myran=new Ran(17); - Penalty pen = new Penalty(); - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,m,n,NSTAGE=6,NTRIAL=10; - double test0,test1,testmin,sbeps; - int[] nstate=new int[NSTAGE],path=new int[NSTAGE]; - boolean localflag, globalflag=false; - - - - // Test dynpro - System.out.println("Testing dynpro"); - - int[] v; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** dynpro: Calculated cost in exhaustive search was lower"); - - } - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - public double cost(int j, int k, int i){ - return pen.c[j][k][i]; - } - - class Penalty { - double[][][] c = new double[10][10][6]; - - Penalty() { - fillmatrix(); - } - - void fillmatrix() { - int i,j,k; - for (i=0;i<10;i++) - for (j=0;j<10;j++) - for (k=0;k<6;k++) - c[i][j][k]=myran.doub(); - } - - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_fdfunc.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_fdfunc.java deleted file mode 100644 index a2eedf73a0..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_fdfunc.java +++ /dev/null @@ -1,85 +0,0 @@ -package com.nr.test.test_chapter10; - -import static com.nr.NRUtil.SQR; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.cos; -import static java.lang.Math.sin; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; -import org.netlib.util.intW; - -import com.nr.RealValueFun; -import com.nr.min.Funcd; -import com.nr.min.QuasiNewton; -import com.nr.sf.Bessjy; - -public class Test_fdfunc implements RealValueFun{ - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=20; - intW iter = new intW(0); - doubleW f0=new doubleW(0),f=new doubleW(0); - double theta,phi,d0,d,pi=acos(-1.0); - double sbeps1=5.0e-8,sbeps2=5.0e-16,gtol=1.0e-8; - double[] p=new double[3]; - boolean localflag=false, globalflag=false; - - - - // Test fdfunc - System.out.println("Testing fdfunc"); - - Funcd fd = new Funcd(this); - p[0]=p[1]=p[2]=0.5; - QuasiNewton.dfpmin(p,gtol,iter,f0,fd); - d0=sqrt(SQR(p[0])+SQR(p[1])+SQR(p[2])); - - for (i=0;i sbeps1; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** fdfunc: First minimum of radial function reported at different radius for different starting points"); - - } - - localflag = localflag || abs(f.val-f0.val) > sbeps2; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** fdfunc: Reported function value at first minimum is different for different starting points"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - public double funk(final double[] x) { - Bessjy b=new Bessjy(); - return(b.j0(sqrt(SQR(x[0])+SQR(x[1])+SQR(x[2])))); - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_stringalign.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_stringalign.java deleted file mode 100644 index 7740b7c1d6..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter10/Test_stringalign.java +++ /dev/null @@ -1,108 +0,0 @@ -package com.nr.test.test_chapter10; - -import static com.nr.min.StringAlign.stringalign; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; - -public class Test_stringalign { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,N1=100,N2=64; - char protein[]={'A','C','T','G'}; - char[] string1,string2,string3,aout,bout,summary; - boolean localflag, globalflag=false; - - - - // Test stringalign - System.out.println("Testing stringalign"); - - string1=new char[N1+1]; - string2=new char[N2+1]; - string3=new char[N2+1]; - string1[N1]='\0'; - string2[N2]='\0'; - string3[N2]='\0'; - - Ran myran = new Ran(17); - for (i=0;i sbeps); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** pearsn: Probability modified when arrays swapped"); - - } - - localflag = (abs(z2.val-z1.val) > sbeps); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** pearsn: Fisher's z modified when arrays swapped"); - - } - - localflag = (abs(z2.val-0.5*log((1+r2.val)/(1-r2.val)))) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** pearsn: Fisher's z not compatible with correlation coefficient"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_quadct.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_quadct.java deleted file mode 100644 index 98acdb5129..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_quadct.java +++ /dev/null @@ -1,75 +0,0 @@ -package com.nr.test.test_chapter14; - -import static com.nr.stat.Stattests.quadct; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.ran.Ran; - -public class Test_quadct { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=8192; - doubleW fa=new doubleW(0),fb = new doubleW(0); - doubleW fc = new doubleW(0),fd = new doubleW(0); - double x=0.5,y=0.5; - double ffa=0.25/4.0,ffb=0.25*3.0/4.0,ffc=0.25*9.0/4.0,ffd=0.25*3.0/4.0; - double[] xx=new double[N],yy=new double[N]; - boolean localflag=false,globalflag=false; - - - - // Test quadct - System.out.println("Testing quadct"); - - Ran myran=new Ran(17); - j=0; - for (i=0;i 0.02) || (abs(fb.val-ffb) > 0.02) || (abs(fc.val-ffc) > 0.02) || (abs(fd.val-ffd) > 0.02); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** quadct: Fractions do not agree adequately with uniform distribution"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_quadvl.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_quadvl.java deleted file mode 100644 index 6d37f886b8..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_quadvl.java +++ /dev/null @@ -1,86 +0,0 @@ -package com.nr.test.test_chapter14; - -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.ran.Ran; -import com.nr.stat.Quadvl; - -public class Test_quadvl { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,NTRIES=100; - doubleW faW=new doubleW(0),fbW = new doubleW(0); - doubleW fcW = new doubleW(0),fdW = new doubleW(0); - double x,y,fa,fb,fc,fd,sbeps; - boolean localflag,globalflag=false; - - - - // Test quadvl - System.out.println("Testing quadvl"); - - Ran myran = new Ran(16); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** quadvl: Sum of reported fractions is not 1.0"); - - } - - localflag = abs(fa-0.25*(1.0-x)*(1.0-y)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** quadvl: Quadrant 1 reporting wrong fraction"); - - } - - localflag = abs(fb-0.25*(x+1.0)*(1.0-y)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** quadvl: Quadrant 2 reporting wrong fraction"); - - } - - localflag = abs(fc-0.25*(x+1.0)*(y+1.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** quadvl: Sum of reported fractions is not 1.0"); - - } - - localflag = abs(fd-0.25*(1.0-x)*(y+1.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** quadvl: Sum of reported fractions is not 1.0"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_savgol.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_savgol.java deleted file mode 100644 index f3db6dc8bb..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_savgol.java +++ /dev/null @@ -1,91 +0,0 @@ -package com.nr.test.test_chapter14; - -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import java.util.Scanner; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.stat.SavitzkyGolayFilter; - -public class Test_savgol { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int NMAX=1000,NTEST=6; - int mtest[]={2,2,2,2,4,4}; - int nltest[]={2,3,4,5,4,5}; - int nrtest[]={2,1,0,5,4,5}; - String ans[]={ - " -0.086 0.343 0.486 0.343 -0.086", - " -0.143 0.171 0.343 0.371 0.257", - " 0.086 -0.143 -0.086 0.257 0.886", - " -0.084 0.021 0.103 0.161 0.196 0.207 0.196 0.161 0.103 0.021 -0.084", - " 0.035 -0.128 0.070 0.315 0.417 0.315 0.070 -0.128 0.035", - " 0.042 -0.105 -0.023 0.140 0.280 0.333 0.280 0.140 -0.023 -0.105 0.042"}; - int i,j,m,nl,np,nr; - double sum,sbeps; - double[] c=new double[NMAX]; - boolean localflag,globalflag=false; - - - - // Test savgol - System.out.println("Testing savgol"); - - // Test against table from the book - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** savgol: Sum of coefficients was not 1.0 for case "+ i); - - } - - Scanner sc = new Scanner(ans[i]); - localflag=false; - sbeps=1.e-3; - double r; - for (j=nl;j>=0;j--) { - r = sc.nextDouble(); -// System.out.printf(c[j] << " %f\n", w << " %f\n", abs(c[j]-atof(w.c_str()))); - localflag = localflag || abs(c[j]-r) > sbeps; - } - for (j=0;j sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** savgol: Computed coefficients do not agree with book for case "+ i); - - } - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_spear.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_spear.java deleted file mode 100644 index 1d14c92a39..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_spear.java +++ /dev/null @@ -1,239 +0,0 @@ -package com.nr.test.test_chapter14; - -import static com.nr.NRUtil.buildVector; -import static com.nr.stat.Stattests.spear; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -public class Test_spear { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - doubleW d1=new doubleW(0),zd1 = new doubleW(0),probd1 = new doubleW(0); - doubleW rs1=new doubleW(0),probrs1 = new doubleW(0); - doubleW d2=new doubleW(0),zd2 = new doubleW(0),probd2 = new doubleW(0); - doubleW rs2=new doubleW(0),probrs2 = new doubleW(0); - - double sbeps=1.e-6; - double adata[]={0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0}; - double bdata[]={9.0,8.0,7.0,6.0,5.0,4.0,3.0,2.0,1.0,0.0}; - double cdata[]={1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,0.0}; // Note 0.0 at end - double edata[]={1.0,2.0,1.0,2.0,1.0,2.0,1.0,2.0,1.0,2.0}; - double fdata[]={2.0,1.0,2.0,1.0,2.0,1.0,2.0,1.0,2.0,1.0}; - // Expected results for each test case - double ae[]={0.0,-3.0,0.0026998,1.0,0.0}; - double be[]={330.0,3.0,0.0026998,-1.0,0.0}; - double ce[]={90.0,-1.363636,0.172682,0.454545,0.186905}; - double ee[]={250.0,3.0,0.0026998,-1.0,0.0}; - double[] a=buildVector(adata),b=buildVector(bdata),c=buildVector(cdata); - double[] e=buildVector(edata),f=buildVector(fdata); - boolean localflag=false,globalflag=false; - - - - // Test spear - System.out.println("Testing spear"); - - // Test 1 - spear(a,a,d1,zd1,probd1,rs1,probrs1); -// System.out.printf(d1 << " %f\n", zd1 << " %f\n", probd1 << " %f\n", rs1 << " %f\n", probrs1); - localflag = localflag || (d1.val != ae[0]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Squared difference of ranks not zero for identical distributions"); - - } - - localflag = localflag || (zd1.val != ae[1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Unexpected standard deviation (should be -3) for special case"); - - } - - localflag = localflag || abs(probd1.val-ae[2]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Unexpected probability for d, given the standard deviation"); - - } - - localflag = localflag || (rs1.val != ae[3]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Spearman's rank correlation should be 1 for identical distributions"); - - } - - localflag = localflag || (probrs1.val != ae[4]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Probrs should be zero for identical distributions"); - - } - - // Test 2 - spear(a,b,d1,zd1,probd1,rs1,probrs1); -// System.out.printf(d1 << " %f\n", zd1 << " %f\n", probd1 << " %f\n", rs1 << " %f\n", probrs1); - localflag = localflag || (d1.val != be[0]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Sum squared difference of ranks should be 2*(81+49+25+9+1)=330"); - - } - - localflag = localflag || (zd1.val != be[1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Standard deviation should be (330/55)-3=3"); - - } - - localflag = localflag || abs(probd1.val-be[2]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Unexpected probability for d, given the standard deviation"); - - } - - localflag = localflag || (rs1.val != be[3]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Spearman's rank correlation should be -1 for perfect anticorrelation"); - - } - - localflag = localflag || abs(probrs1.val - be[4])>1.e-16; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Probrs should be zero for perfect anticorrelation"); - - } - - // Test 3 - spear(b,a,d2,zd2,probd2,rs2,probrs2); -// System.out.printf(d2 << " %f\n", zd2 << " %f\n", probd2 << " %f\n", rs2 << " %f\n", probrs2); - localflag = localflag || (d1.val != d2.val) || (zd1.val != zd2.val) || - (probd1.val != probd2.val) || (rs1.val != rs2.val) || (probrs1.val != probrs2.val); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Results changed when two arrays were swapped (case 1)"); - - } - - // Test 4 - spear(a,c,d1,zd1,probd1,rs1,probrs1); -// System.out.printf(d1 << " %f\n", zd1 << " %f\n", probd1 << " %f\n", rs1 << " %f\n", probrs1); - localflag = localflag || (d1.val != ce[0]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Sum squared difference of ranks should be 9*(1^2)+1*(9^2)=90"); - - } - - localflag = localflag || abs(zd1.val-ce[1]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Standard deviation should be (90/55)-3=-1.363636"); - - } - - localflag = localflag || abs(probd1.val-ce[2]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Unexpected probability for d, given the standard deviation"); - - } - - localflag = localflag || abs(rs1.val-ce[3]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Spearman's rank correlation should be 1-6*90/990=0.454545"); - - } - - localflag = localflag || abs(probrs1.val-ce[4]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Unexpected probability for rs, given the rank correlation"); - - } - - // Test 5 - spear(c,a,d2,zd2,probd2,rs2,probrs2); -// System.out.printf(d2 << " %f\n", zd2 << " %f\n", probd2 << " %f\n", rs2 << " %f\n", probrs2); - localflag = localflag || (d1.val != d2.val) || (zd1.val != zd2.val) || - (probd1.val != probd2.val) || (rs1.val != rs2.val) || (probrs1.val != probrs2.val); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Results changed when two arrays were swapped (case 2)"); - - } - - // Test 6 - spear(e,f,d1,zd1,probd1,rs1,probrs1); -// System.out.printf(d1 << " %f\n", zd1 << " %f\n", probd1 << " %f\n", rs1 << " %f\n", probrs1); - localflag = localflag || (d1.val != ee[0]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Sum squared difference of ranks should be 10*(8-3)^2=250"); - - } - - localflag = localflag || (zd1.val != ee[1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Standard deviation should be (250-125)/55/(1-240/990)=3"); - - } - - localflag = localflag || abs(probd1.val-ee[2]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Unexpected probability for d, given the standard deviation"); - - } - - localflag = localflag || (rs1.val != ee[3]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Spearman's rank correlation should be -1 for perfect anticorrelation (case 2)"); - - } - - localflag = localflag || (probrs1.val != ee[4]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Probrs should be zero for perfect anticorrelation (case 2)"); - - } - - // Test 7 - spear(f,e,d2,zd2,probd2,rs2,probrs2); -// System.out.printf(d2 << " %f\n", zd2 << " %f\n", probd2 << " %f\n", rs2 << " %f\n", probrs2); - localflag = localflag || (d1.val != d2.val) || (zd1.val != zd2.val) || - (probd1.val != probd2.val) || (rs1.val != rs2.val) || (probrs1.val != probrs2.val); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** spear: Results changed when two arrays were swapped (case 3)"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_tptest.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_tptest.java deleted file mode 100644 index 6e55294ae9..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_tptest.java +++ /dev/null @@ -1,105 +0,0 @@ -package com.nr.test.test_chapter14; - -import static com.nr.NRUtil.buildVector; -import static com.nr.stat.Moment.avevar; -import static com.nr.stat.Stattests.tptest; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.ran.Normaldev; - -public class Test_tptest { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,NPTS=10000,NSHFT=10; - doubleW ave1=new doubleW(0),ave2 = new doubleW(0); - doubleW var1 = new doubleW(0), var2 = new doubleW(0); - double cov,sd,EPS=0.01,sbeps; - double fingerprint[]={0.012206481763442537,0.044962205835956524, - 0.13262719786074151,0.31606378510286803,0.61616056459021917, - 1.0,0.61616056459021917,0.31606378510286803,0.13262719786074151, - 0.044962205835956524,0.012206481763442537}; - double[] data1=new double[NPTS],data2=new double[NPTS]; - double[] t=new double[NSHFT+1],prob=new double[NSHFT+1],texpect= new double[NSHFT+1]; - double[] fp=buildVector(fingerprint); - boolean localflag=false,globalflag=false; - - - - // Test tptest - System.out.println("Testing tptest"); - - Normaldev ndev = new Normaldev(0.0,1.0,17); - // Generate identical data but with a shift - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** tptest: Incorrect returned values for Student's t"); - - } - - sbeps=1.e-15; - localflag=false; - for (i=1;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** tptest: Probabilities unsymmetrical for symmetrical shifts"); - - } - - //Fingerprint test - sbeps=3.e-12; - localflag = maxel(vecsub(prob,fp)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** tptest: Probabilities do not match fingerprint"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_ttest.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_ttest.java deleted file mode 100644 index d920acf636..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_ttest.java +++ /dev/null @@ -1,92 +0,0 @@ -package com.nr.test.test_chapter14; - -import static com.nr.stat.Moment.avevar; -import static com.nr.stat.Stattests.ttest; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.ran.Normaldev; - -public class Test_ttest { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j; - int NPTS=10000,NSHFT=10; - doubleW ave1=new doubleW(0),ave2 = new doubleW(0); - doubleW var1 = new doubleW(0), var2 = new doubleW(0); - double sd,EPS=0.005,sbeps; - double fingerprint[]={0.076341,0.156226,0.287591,0.478354,0.722981, - 1.0,0.722981,0.478354,0.287591,0.156226,0.076341}; - double[] data1=new double[NPTS],data2=new double[NPTS]; - double[] t=new double[NSHFT+1],prob=new double[NSHFT+1],tt= new double[NSHFT+1]; - boolean localflag=false, globalflag=false; - - - - // Test ttest - System.out.println("Testing ttest"); - - // Generate gaussian distributed data - Normaldev ndev=new Normaldev(0.0,1.0,17); - // Special case: identical distributions - for (i=0;i sbeps); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ttest: Returned t statistic incorrect for special case of identical distributions"); - - } - - for (i=0;i<=NSHFT/2;i++) - localflag = localflag || abs(t[i]+t[NSHFT-i]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ttest: Returned t statistic has incorrect symmetry"); - - } - - sbeps=1.e-6; - for (i=0;isbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ttest: Return probabilities don't match fingerprint"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_tutest.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_tutest.java deleted file mode 100644 index aeb8fec4a7..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter14/Test_tutest.java +++ /dev/null @@ -1,93 +0,0 @@ -package com.nr.test.test_chapter14; - -import static com.nr.stat.Moment.avevar; -import static com.nr.stat.Stattests.tutest; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.ran.Normaldev; - -public class Test_tutest { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,NPTS=10000,NSHFT=10; - doubleW ave1=new doubleW(0),ave2 = new doubleW(0); - doubleW var1 = new doubleW(0), var2 = new doubleW(0); - double EPS=0.01,sd,sbeps; - double fingerprint[]={0.024980,0.072904,0.178591,0.369851,0.653879, - 1.0,0.653879,0.369851,0.178591,0.072904,0.024980}; - double[] data1=new double[NPTS],data2=new double[NPTS]; - double[] t=new double[NSHFT+1],prob=new double[NSHFT+1],tt= new double[NSHFT+1]; - boolean localflag=false,globalflag=false; - - - - // Test tutest - System.out.println("Testing tutest"); - - // Generate two gaussian distributions of different variance - Normaldev ndev = new Normaldev(0.0,1.0,17); - for (i=0;i sbeps); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** tutest: Returned t statistic incorrect for special case of scaled distributions"); - - } - - for (i=0;i<=NSHFT/2;i++) - localflag = localflag || abs(t[i]+t[NSHFT-i]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** tutest: Returned t statistic has incorrect symmetry"); - - } - - sbeps=1.e-6; - for (i=0;isbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** tutest: Return probabilities don't match fingerprint"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_Fitab.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_Fitab.java deleted file mode 100644 index 7d956158ed..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_Fitab.java +++ /dev/null @@ -1,183 +0,0 @@ -package com.nr.test.test_chapter15; - -import static com.nr.NRUtil.*; -import static java.lang.Math.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.model.Fitab; -import com.nr.ran.Normaldev; -import com.nr.ran.Ran; -public class Test_Fitab { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=100,M=10; - double pi=acos(-1.0),sumx2,sa=0,sb=0,sbeps; - double[] x= new double[N],y= new double[N],yy= new double[N],sig= new double[N]; - boolean localflag, globalflag=false; - - - - // Test Fitab - System.out.println("Testing Fitab"); - - Ran myran =new Ran(17); - sumx2=0; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab: Fitted constant term a has incorrect value"); - - } - - localflag = abs(fit1.b-pi) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab: Fitted slope b has incorrect value"); - - } - - localflag = fit1.chi2 > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab: Chi^2 not zero for perfect linear data"); - - } - - localflag = abs(fit1.q-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab: Probability not 1.0 for perfect linear data"); - - } - - localflag = abs(fit1.siga/fit1.sigb - sqrt(sumx2/N)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab: Ratio of siga/sigb incorrect for special case"); - - } - - // Test 2 - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab,Test2: Fitted constant term a has incorrect value"); - - } - - localflag = abs(fit.b-pi) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab,Test2: Fitted slope b has incorrect value"); - - } - - localflag = fit.chi2 > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab,Test2: Chi^2 not zero for perfect linear data"); - - } - - localflag = abs(fit.q-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab,Test2: Probability not 1.0 for perfect linear data"); - - } - - if (j == 0) { - sa=fit.siga; - sb=fit.sigb; - } else { - localflag = (fit.siga/sa - (j+1)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab,Test2: siga did not scale properly with data errors"); - - } - - localflag = (fit.sigb/sb - (j+1)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab,Test2: sigb did not scale properly with data errors"); - - } - } - } - - // Test 3 - Normaldev ndev=new Normaldev(0.0,1.0,17); - for (j=0;j 3.0*fit3.siga; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab,Test3: Fitted constant term a, or error siga, may be incorrect"); - - } - - localflag = abs(fit3.b-pi) > 3.0*fit3.sigb; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab,Test3: Fitted slope b, or error sigb, may be incorrect"); - - } - - localflag = fit3.chi2 > 1.3*N; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab,Test3: Chi^2 is unexpectedly high"); - - } - - localflag = abs(fit3.q) < 0.1; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitab,Test3: Probability q suggests a possibly bad fit"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_Fitexy.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_Fitexy.java deleted file mode 100644 index 9d28014955..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_Fitexy.java +++ /dev/null @@ -1,242 +0,0 @@ -package com.nr.test.test_chapter15; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.NRUtil.*; -import static java.lang.Math.*; -import com.nr.ran.*; -import com.nr.model.*; - -public class Test_Fitexy { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=100,M=10; - double pi=acos(-1.0),sumx2,sa=0,sb=0,sbeps; - double[] x= new double[N],y= new double[N],yy= new double[N],sigx= new double[N],sigy= new double[N]; - boolean localflag, globalflag=false; - - - - // Test Fitexy - System.out.println("Testing Fitexy"); - - Ran myran=new Ran(17); - sumx2=0; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy: Fitted constant term a has incorrect value"); - - } - - localflag = abs(fit1.b-pi) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy: Fitted slope b has incorrect value"); - - } - - localflag = fit1.chi2 > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy: Chi^2 not zero for perfect linear data"); - - } - - localflag = abs(fit1.q-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy: Probability not 1.0 for perfect linear data"); - - } - -// System.out.printf(fit1.siga/fit1.sigb << " %f\n", sqrt(sumx2/N)); - localflag = abs(fit1.siga/fit1.sigb - sqrt(sumx2/N)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy: Ratio of siga/sigb incorrect for special case"); - - } - - // Test 2 - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test2: Fitted constant term a has incorrect value"); - - } - - localflag = abs(fit.b-pi) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test2: Fitted slope b has incorrect value"); - - } - - localflag = fit.chi2 > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test2: Chi^2 not zero for perfect linear data"); - - } - - localflag = abs(fit.q-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test2: Probability not 1.0 for perfect linear data"); - - } - - if (j == 0) { - sa=fit.siga; - sb=fit.sigb; - } else { - localflag = (fit.siga/sa - (j+1)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test2: siga did not scale properly with data errors"); - - } - - // System.out.printf(fit.sigb/sb << " %f\n", j+1); - localflag = (fit.sigb/sb - (j+1)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test2: sigb did not scale properly with data errors"); - - } - } - } - - // Test 3 - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test3: Fitted constant term a has incorrect value"); - - } - - localflag = abs(fit.b-pi) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test3: Fitted slope b has incorrect value"); - - } - - localflag = fit.chi2 > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test3: Chi^2 not zero for perfect linear data"); - - } - - localflag = abs(fit.q-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test3: Probability not 1.0 for perfect linear data"); - - } - - if (j == 0) { - sa=fit.siga; - sb=fit.sigb; - } else { - localflag = (fit.siga/sa - (j+1)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test3: siga did not scale properly with data errors"); - - } - - // System.out.printf(fit.sigb/sb << " %f\n", j+1); - localflag = (fit.sigb/sb - (j+1)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test3: sigb did not scale properly with data errors"); - - } - } - } - - // Test 4 - Normaldev ndev=new Normaldev(0.0,1.0,17); - for (j=0;j 3.0*fit4.siga; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test4: Fitted constant term a, or error siga, may be incorrect"); - - } - - localflag = abs(fit4.b-pi) > 3.0*fit4.sigb; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test4: Fitted slope b, or error sigb, may be incorrect"); - - } - - localflag = fit4.chi2 > 1.3*N; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test4: Chi^2 is unexpectedly high"); - - } - - localflag = abs(fit4.q) < 0.1; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitexy,Test4: Probability q suggests a possibly bad fit"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_Fitlin.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_Fitlin.java deleted file mode 100644 index b2a28c06c5..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_Fitlin.java +++ /dev/null @@ -1,232 +0,0 @@ -package com.nr.test.test_chapter15; - -import static java.lang.Math.abs; -import static java.lang.Math.sin; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealMultiValueFun; -import com.nr.model.Fitlin; -import com.nr.ran.Normaldev; -public class Test_Fitlin implements UniVarRealMultiValueFun{ - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,ma,N=100; - double stdev,amp[]={1.0,0.1,1.0,0.3,0.1}; - double[] x=new double[N],y= new double[N],sig= new double[N]; - boolean localflag, globalflag=false; - - - - // Test Fitlin - System.out.println("Testing Fitlin"); - - double[] f=Fitlin_funcs(x[0]); - ma=f.length; - stdev=0.02; - Normaldev ndev=new Normaldev(0.0,stdev,17); - - for (i=0;i 2.0*sqrt(myfit.covar[j][j]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitlin: Fitted parameters not within estimated uncertainty"); - - } - } - -// System.out.printf(fixed << setprecision(6); -// for (i=0;i 2.0*sqrt(myfit.covar[j][j]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitlin: Fitted parameters (with 2 parameters held) not within estimated uncertainty"); - - } - } - - localflag=false; - for (i=0;i 2.0*sqrt(myfit.covar[j][j]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitlin: Fitted parameter (with 1 parameters held) not within estimated uncertainty"); - - } - } - - localflag=false; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitmed: Fitted constant term a has incorrect value"); - - } - - localflag = abs(fit1.b-pi) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitmed: Fitted slope b has incorrect value"); - - } - - localflag = fit1.abdev > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitmed: abdev not zero for perfect linear data"); - - } - - // Test 2 - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitmed,Test2: Fitted constant term a is incorrect"); - - } - - sbeps=5.e-5; - localflag = abs(fit2.b-(pi+0.1*j/M/x[N-1])) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitmed,Test2: Fitted slope b is incorrect"); - - } - - localflag = fit2.abdev > 0.05; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitmed,Test2: Calculated abdev is too high"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_Fitmrq.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_Fitmrq.java deleted file mode 100644 index 6fd566482a..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_Fitmrq.java +++ /dev/null @@ -1,214 +0,0 @@ -package com.nr.test.test_chapter15; - -import static com.nr.NRUtil.SQR; -import static com.nr.NRUtil.buildVector; -import static java.lang.Math.abs; -import static java.lang.Math.exp; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.model.FGauss; -import com.nr.model.Fitmrq; -import com.nr.ran.Normaldev; - -public class Test_Fitmrq { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=100,MA=6; - double aa[]={5.0,2.0,3.0,2.0,5.0,3.0}; - double gguess[]={4.5,2.2,2.8,2.5,4.9,2.8}; - double SPREAD=0.01; - double[] x= new double[N],y= new double[N],sig= new double[N]; - double[] a=buildVector(aa),guess=buildVector(gguess); - boolean localflag, globalflag=false; - - - - // Test Fitmrq - System.out.println("Testing Fitmrq"); - - Normaldev ndev=new Normaldev(0.0,1.0,17); - // First try a sum of two Gaussians - for (i=0;i 2.0*sqrt(myfit.covar[j][j]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitmrq: Fitted parameters not within estimated uncertainty"); - - } - } - - // Test the hold() method on parameters 1 and 4 - myfit.hold(1,2.0); - myfit.hold(4,5.0); - myfit.fit(); - -// System.out.printf(setw(18) << "chi-squared:%f\n", setw(13) << myfit.chisq); -// for (i=0;i 2.0*sqrt(myfit.covar[j][j]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitmrq: Fitted parameters (with 2 parameters held) not within estimated uncertainty"); - - } - } - - localflag=false; - for (i=0;i 2.0*sqrt(myfit.covar[j][j]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitlin: Fitted parameter (with 1 parameters held) not within estimated uncertainty"); - - } - } - - localflag=false; - for (i=0;i 2.0*sqrt(mysvdfit.covar[j][j]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitsvd: Fitted parameters not within estimated uncertainty"); - - } - } - - Fitlin mylinfit = new Fitlin(x,y,sig,this); - mylinfit.fit(); - sbeps=TOL; - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitsvd: SVD fit does not agree with Fitlin on parameters"); - - } - - localflag = abs(sqrt(mysvdfit.covar[j][j])-sqrt(mylinfit.covar[j][j])) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fitsvd: SVD fit does not agree with Fitlin on uncertainties"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - public double[] funk(final double x) { - return Fitsvd_funcs(x); - } - - double[] Fitsvd_funcs(final double x) { - int i; - double[] ans=new double[5]; - - ans[0]=1.0; - ans[1]=x; - for (i=2;i<5;i++) ans[i]=sin((i-1)*x); - return ans; - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_fleg.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_fleg.java deleted file mode 100644 index e6e32e460d..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter15/Test_fleg.java +++ /dev/null @@ -1,94 +0,0 @@ -package com.nr.test.test_chapter15; - -import static java.lang.Math.abs; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealMultiValueFun; -import com.nr.model.Fitsvd; -import com.nr.ran.Normaldev; -public class Test_fleg implements UniVarRealMultiValueFun{ - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=100; - double stdev,TOL=1.e-12; - double amp[]={1.0,2.0,3.0,2.0,1.0,0.0,0.0,0.0,0.0,0.0}; - double[] x= new double[N],y= new double[N],sig= new double[N]; - boolean localflag, globalflag=false; - - - - // Test fleg - System.out.println("Testing fleg"); - - stdev=1.e-3; - double[] f=fleg(x[0]); - int NP=f.length; - Normaldev ndev = new Normaldev(0.0,stdev,17); - - for (i=0;i 2.0*sqrt(myfit.covar[j][j]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** fleg: Fitted parameters not within estimated uncertainty"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - public double[] funk(final double x) { - return fleg(x); - } - - double[] fleg(final double x) { - final int fleg_nl = 10; - - int j; - double twox,f2,f1,d; - double[] pl =new double[fleg_nl]; - pl[0]=1.; - pl[1]=x; - if (fleg_nl > 2) { - twox=2.*x; - f2=x; - d=1.; - for (j=2;j 2.0*sqrt(myfit.covar[j][j]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** fpoly: Fitted parameters not within estimated uncertainty"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - public double[] funk(final double x) { - return fpoly(x); - } - - double[] fpoly(final double x) { - final int fpoly_np=10; - int j; - double[] p=new double[fpoly_np]; - p[0]=1.0; - for (j=1;j 0.05; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** mcmc: Model parameter lambda1 was not correctly determined"); - - } - - localflag = abs(lam2ave-lambda2)/lambda2 > 0.05; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** mcmc: Model parameter lambda2 was not correctly determined"); - - } - - localflag = kk1 != k1; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** mcmc: Model parameter k1 was not correctly determined"); - - } - - localflag = kk2 != k2; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** mcmc: Model parameter k2 was not correctly determined"); - - } - - localflag = abs(tcave-tc)/tc > 0.01; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** mcmc: Critical time tc was not accurately determined"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Gaumixmod.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Gaumixmod.java deleted file mode 100644 index 457b0127e9..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Gaumixmod.java +++ /dev/null @@ -1,109 +0,0 @@ -package com.nr.test.test_chapter16; - -import static com.nr.NRUtil.SQR; -import static com.nr.NRUtil.*; -import static com.nr.test.NRTestUtil.*; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ci.Gaumixmod; -import com.nr.ran.Normaldev; - -public class Test_Gaumixmod { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,NDIM=2,NMEANS=4,NPT=1000; - double flag=0,sqrt2=sqrt(2.0),d0,d1,sbeps; - double ffrac[]={0.25,0.25,0.25,0.25}; - double mmeans[]={0.0,0.0,0.75,0.0,-0.25,-0.25,0.33,0.66}; - double gguess[]={0.1,0.1,0.7,0.1,-0.2,-0.3,0.3,0.5}; - double ssigma[]={0.1,0.1,0.02,0.2,0.01,0.1,0.1,0.05}; - double vvec1[]={1.0,0.0,1.0,0.0,sqrt2,sqrt2,sqrt2,sqrt2}; - double vvec2[]={0.0,1.0,0.0,1.0,-sqrt2,sqrt2,-sqrt2,sqrt2}; - double[] frac=buildVector(ffrac),offset = new double[NMEANS]; - double[][] guess=buildMatrix(NMEANS,NDIM,gguess); - double[][] means=buildMatrix(NMEANS,NDIM,mmeans),sigma=buildMatrix(NMEANS,NDIM,ssigma); - double[][] vec1=buildMatrix(NMEANS,NDIM,vvec1),vec2=buildMatrix(NMEANS,NDIM,vvec2),x=new double[NPT][NDIM]; - boolean localflag, globalflag=false; - - - - // Test Gaumixmod - System.out.println("Testing Gaumixmod"); - - Normaldev ndev=new Normaldev(0.0,1.0,17); - - // Generate four groups of data - k=0; - for (i=0;i<4;i++) { - for (j=0;j<(int)(NPT*frac[i]);j++) { - d0=sigma[i][0]*ndev.dev(); - d1=sigma[i][1]*ndev.dev(); - x[k][0]=means[i][0]+d0*vec1[i][0]+d1*vec2[i][0]; - x[k][1]=means[i][1]+d0*vec1[i][1]+d1*vec2[i][1]; - k++; - } - } - - Gaumixmod gmix = new Gaumixmod(x,guess); - - for (i=0;i<100;i++) { - flag=gmix.estep(); - if (flag < 1.e-6) break; - gmix.mstep(); - } - - // check for convergence - // System.out.println(" flag: %f\n", flag); - localflag = flag > 1.e-6; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gaumixmod: No solution with 100 iterations"); - - } - - // Check for correct determination of population fractions - // System.out.printf(maxel(vecsub(gmix.frac,frac))); - sbeps=0.005; - localflag = maxel(vecsub(gmix.frac,frac)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gaumixmod: Population fractions not accurately determined"); - - } - - // Check for correct determination of means - for (i=0;i 0.01; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gaumixmod: Means are incorrectly identified"); - - } - - // Check for correct determination of covariance matrices - for (i=0;i test) { - test=hmm.pstate[i][j]; - jmax=j; - } - } -// System.out.printf(state[i] << " %f\n", jmax); - if (jmax == state[i]) ncorrect++; - } - System.out.printf("Fraction correct: %f\n", (double)(ncorrect)/N); - localflag = (double)(ncorrect)/N < 0.75; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** HMM: Actual state was not the top probability more than 25% of the time"); - - } - - // Inspect reconstructed transition matrix - int jpen=0; - ncorrect=0; - for (i=0;i test) { - test=hmm.pstate[i][j]; - jmax=j; - } - } - - // Find second largest - test=0.0; - for (j=0;j test) { - test=hmm.pstate[i][j]; - jpen=j; - } - } - } - -// System.out.printf(state[i] << " %f\n", jmax); - if (jmax == state[i] || jpen == state[i]) ncorrect++; - } - System.out.printf("Fraction correct: %f\n", (double)(ncorrect)/N); - double beforeBW=(double)(ncorrect)/N; - localflag = (double)(ncorrect)/N < 0.95; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** HMM: Actual state was not in top 2 probabilities more than 5% of the time"); - - } - -// System.out.println("Log-likelihood: %f\n", hmm.loglikelihood()); - - // Test Baum-Welch reestimation - for (i=0;i<100;i++) { - hmm.baumwelch(); - hmm.forwardbackward(); -// System.out.println("Log-likelihood: %f\n", hmm.loglikelihood()); - } - - // Inspect reconstructed transition matrix - ncorrect=0; - for (i=0;i test) { - test=hmm.pstate[i][j]; - jmax=j; - } - } - - // Find second largest - test=0.0; - for (j=0;j test) { - test=hmm.pstate[i][j]; - jpen=j; - } - } - } - -// System.out.printf(state[i] << " %f\n", jmax); - if (jmax == state[i] || jpen == state[i]) ncorrect++; - } - System.out.printf("Fraction correct after Baum-Welch: %f\n", (double)(ncorrect)/N); - double afterBW=(double)(ncorrect)/N; - localflag = afterBW <= beforeBW; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** HMM: Baum-Welch reestimation did not improve model"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Kmeans.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Kmeans.java deleted file mode 100644 index 33c87a127d..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Kmeans.java +++ /dev/null @@ -1,122 +0,0 @@ -package com.nr.test.test_chapter16; - -import static com.nr.NRUtil.SQR; -import static com.nr.NRUtil.buildMatrix; -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ci.Kmeans; -import com.nr.ran.Normaldev; - -public class Test_Kmeans { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,flag=0,NDIM=2,NMEANS=4,NPT=1000; - double sqrt2=sqrt(2.0),d0,d1,sbeps; - double ffrac[]={0.25,0.25,0.25,0.25}; - double mmeans[]={0.0,0.0,0.75,0.0,-0.25,-0.25,0.33,0.66}; - double gguess[]={0.1,0.1,0.7,0.1,-0.2,-0.3,0.3,0.5}; - double ssigma[]={0.1,0.1,0.02,0.2,0.01,0.1,0.1,0.05}; - double vvec1[]={1.0,0.0,1.0,0.0,sqrt2,sqrt2,sqrt2,sqrt2}; - double vvec2[]={0.0,1.0,0.0,1.0,-sqrt2,sqrt2,-sqrt2,sqrt2}; - int[] count=new int[NMEANS],error=new int[NMEANS]; - double[] frac=buildVector(ffrac),offset=new double[NMEANS]; - double[][] guess=buildMatrix(NMEANS,NDIM,gguess); - double[][] means=buildMatrix(NMEANS,NDIM,mmeans),sigma=buildMatrix(NMEANS,NDIM,ssigma); - double[][] vec1=buildMatrix(NMEANS,NDIM,vvec1),vec2=buildMatrix(NMEANS,NDIM,vvec2),x=new double[NPT][NDIM]; - boolean localflag, globalflag=false; - - - - // Test Kmeans - System.out.println("Testing Kmeans"); - - Normaldev ndev = new Normaldev(0.0,1.0,17); - - // Generate four groups of data - k=0; - for (i=0;i<4;i++) { - count[i]=(int)(NPT*frac[i]); - for (j=0;j 0; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Kmeans: No solution with 100 iterations"); - - } - - // Check for correct populations -// for (i=0;i 0 ? error[i] : -error[i]) > 15; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Kmeans: Populations are not the correct approximate size"); - - } - } - - // Check group assignments - k=0; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Kmeans: Means are incorrectly identified"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_clc.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_clc.java deleted file mode 100644 index eee1e013fe..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_clc.java +++ /dev/null @@ -1,194 +0,0 @@ -package com.nr.test.test_chapter16; - -import static com.nr.NRUtil.buildMatrix; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ci.Phylo_clc; - -public class Test_Phylo_clc { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,hamming,mother,ndif,NSEQ=16,NCHAR=16; - double sbeps=1.e-15; - // char base[]={'C','G','T','A'}; - int ssequence[]={ - 3,1,1,1,1,1,1,1,0,1,1,1,1,1,2,2, - 3,1,1,1,1,1,1,1,0,1,1,1,1,1,2,3, - 3,0,1,1,1,1,1,1,0,1,1,1,1,1,3,1, - 3,3,1,1,1,1,1,1,0,1,1,1,1,1,3,1, - 3,1,1,1,2,1,1,1,2,1,1,3,1,1,1,1, - 3,1,1,1,0,1,1,1,2,1,1,3,1,1,1,1, - 3,1,1,1,1,1,1,1,2,2,1,0,1,1,1,1, - 3,1,1,1,1,1,1,1,2,0,1,0,1,1,1,1, - 2,1,1,0,1,1,3,1,1,1,1,1,3,1,1,1, - 2,1,1,0,1,1,3,1,1,1,1,1,2,1,1,1, - 2,1,1,0,1,1,0,1,1,1,0,1,1,1,1,1, - 2,1,1,0,1,1,0,1,1,1,3,1,1,1,1,1, - 2,1,3,2,1,1,1,0,1,1,1,1,1,1,1,1, - 2,1,0,2,1,1,1,0,1,1,1,1,1,1,1,1, - 2,1,1,2,1,3,1,3,1,1,1,1,1,1,1,1, - 2,1,1,2,1,0,1,3,1,1,1,1,1,1,1,1 - }; - int[][] sequence = buildMatrix(NSEQ,NCHAR,ssequence); - double[][] dist=new double[NSEQ][NSEQ]; - boolean localflag, globalflag=false; - - - - // Test Phylo_clc - System.out.println("Testing Phylo_clc"); - - // Printout sequences for testing -// for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_clc: Hamming distance between two daughters is not twice the mother distance"); - - } - } - -// System.out.println("Tree:"); -// print_tree(tree,tree.root); - -// System.out.println("Check expected order of leafs on tree:"); - Check_tree ct = new Check_tree(tree); - ct.test(tree.root); - - localflag = ct.flag; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_clc: Leaves of the tree were not encountered in the expected order"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - - } - class Check_tree { - int i; - boolean flag; - Phylo_clc tree; - - Check_tree(Phylo_clc ttree) { - tree = ttree; - i=0; - flag = false; - } - void test(int node) { - if (tree.t[node].ldau != -1) { - test(tree.t[node].ldau); - } else { - flag = flag || (node != i++); -// System.out.printf(node << " %f\n", flag); - return; - } - - if (tree.t[node].rdau != -1) { - test(tree.t[node].rdau); - } else { - flag = flag || (node != i++); -// System.out.printf(node << " %f\n", flag); - return; - } - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_nj.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_nj.java deleted file mode 100644 index 56887b0563..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_nj.java +++ /dev/null @@ -1,294 +0,0 @@ -package com.nr.test.test_chapter16; - -import static com.nr.NRUtil.buildMatrix; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import java.io.IOException; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ci.Phylagglom; -import com.nr.ci.Phylo_nj; -public class Test_Phylo_nj { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() throws IOException { - int i,j,k,hamming,mother,ndif,NSEQ=16,NCHAR=16; - double sbeps=1.e-15; - char base[]={'C','G','T','A'}; - int ssequence[]={ - 3,1,1,1,1,1,1,1,0,1,1,1,1,1,2,2, - 3,1,1,1,1,1,1,1,0,1,1,1,1,1,2,3, - 3,0,1,1,1,1,1,1,0,1,1,1,1,1,3,1, - 3,3,1,1,1,1,1,1,0,1,1,1,1,1,3,1, - 3,1,1,1,2,1,1,1,2,1,1,3,1,1,1,1, - 3,1,1,1,0,1,1,1,2,1,1,3,1,1,1,1, - 3,1,1,1,1,1,1,1,2,2,1,0,1,1,1,1, - 3,1,1,1,1,1,1,1,2,0,1,0,1,1,1,1, - 2,1,1,0,1,1,3,1,1,1,1,1,3,1,1,1, - 2,1,1,0,1,1,3,1,1,1,1,1,2,1,1,1, - 2,1,1,0,1,1,0,1,1,1,0,1,1,1,1,1, - 2,1,1,0,1,1,0,1,1,1,3,1,1,1,1,1, - 2,1,3,2,1,1,1,0,1,1,1,1,1,1,1,1, - 2,1,0,2,1,1,1,0,1,1,1,1,1,1,1,1, - 2,1,1,2,1,3,1,3,1,1,1,1,1,1,1,1, - 2,1,1,2,1,0,1,3,1,1,1,1,1,1,1,1 - }; - char[][] str=new char[NSEQ][NCHAR+1]; - int[][] sequence=buildMatrix(NSEQ,NCHAR,ssequence); - double[][] dist=new double[NSEQ][NSEQ]; - boolean localflag, globalflag=false; - - - - // Test Phylo_nj - System.out.println("Testing Phylo_nj"); - - // Printout sequences used for the test -// for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_nj: Mother distances should be 0.5 for all leaves"); - - } - } - - localflag = abs(tree.t[29].modist) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_nj: Mother distances of node 29 should be zero"); - - } - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_nj: Distance of two daughters is not the sum of the mother distances"); - - } - } - -// System.out.println("Tree:"); -// print_tree(tree,tree.root); - -// System.out.println("Check expected order of leaves on tree:"); - Check_tree ct=new Check_tree(tree); - ct.test(tree.root); - - localflag = ct.flag; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_nj: Leaves of the tree were not encountered in the expected order"); - - } - - i=tree.comancestor(0,7); -// System.out.println("Common ancestor of 0,7: %f\n", i); - Phylo_nj rerootedtree=new Phylo_nj(dist,i); - -// System.out.println("Rerooted Tree:"); -// print_tree(rerootedtree,rerootedtree.root); - - // System.out.println("parents"); -// for (i=0;i<30;i++) { -// System.out.printf(i << " %f\n", rerootedtree.t[i].mo); -// } - - // Inspect the tree - localflag = (rerootedtree.t[rerootedtree.root].nel != NSEQ); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_nj: Root node does not contain all the elements"); - - } - -// System.out.printf(rerootedtree.t[rerootedtree.t[rerootedtree.root].ldau].nel); - localflag = (rerootedtree.t[rerootedtree.t[rerootedtree.root].ldau].nel != NSEQ/2); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_nj: Left side of rerooted tree does not report half the elements"); - - } - -// System.out.printf(rerootedtree.t[rerootedtree.t[rerootedtree.root].rdau].nel); - localflag = (rerootedtree.t[rerootedtree.t[rerootedtree.root].rdau].nel != NSEQ/2); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_nj: Right side of rerooted tree does not report half the elements"); - - } - - localflag = (rerootedtree.t[rerootedtree.root].modist != 0.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_nj: Mother distance of root is not zero"); - - } - - // Tree is now symmetric - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_nj: Left and right daughter of a node reported different mother distances"); - - } - - localflag = abs(rerootedtree.t[i].modist-0.5) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_nj: Mother distance should be 0.5 for all leaves"); - - } - - ndif=0; - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_nj: Distance of two daughters is not twice the mother distance"); - - } - } - - for (i=0;i<2*NSEQ-2;i++) { - localflag = abs(rerootedtree.t[rerootedtree.t[rerootedtree.t[i].mo].ldau].modist- - rerootedtree.t[rerootedtree.t[rerootedtree.t[i].mo].rdau].modist) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_nj: Left and right daughter of a node reported different mother distances"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class Check_tree { - int i; - boolean flag; - Phylo_nj tree; - - Check_tree(Phylo_nj ttree) { - tree = ttree; - i=0; - flag=false; - } - - void test(int node) { - if (tree.t[node].ldau != -1) { - test(tree.t[node].ldau); - } else { - flag = flag || (node != i++); -// System.out.printf(node << " %f\n", flag); - return; - } - - if (tree.t[node].rdau != -1) { - test(tree.t[node].rdau); - } else { - flag = flag || (node != i++); -// System.out.printf(node << " %f\n", flag); - return; - } - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_slc.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_slc.java deleted file mode 100644 index ca9f21443f..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_slc.java +++ /dev/null @@ -1,193 +0,0 @@ -package com.nr.test.test_chapter16; - -import static com.nr.NRUtil.buildMatrix; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ci.Phylo_slc; - -public class Test_Phylo_slc { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,hamming,mother,ndif,NSEQ=16,NCHAR=16; - double sbeps=1.e-15; - // char base[]={'C','G','T','A'}; - int ssequence[]={ - 3,1,1,1,1,1,1,1,0,1,1,1,1,1,2,2, - 3,1,1,1,1,1,1,1,0,1,1,1,1,1,2,3, - 3,0,1,1,1,1,1,1,0,1,1,1,1,1,3,1, - 3,3,1,1,1,1,1,1,0,1,1,1,1,1,3,1, - 3,1,1,1,2,1,1,1,2,1,1,3,1,1,1,1, - 3,1,1,1,0,1,1,1,2,1,1,3,1,1,1,1, - 3,1,1,1,1,1,1,1,2,2,1,0,1,1,1,1, - 3,1,1,1,1,1,1,1,2,0,1,0,1,1,1,1, - 2,1,1,0,1,1,3,1,1,1,1,1,3,1,1,1, - 2,1,1,0,1,1,3,1,1,1,1,1,2,1,1,1, - 2,1,1,0,1,1,0,1,1,1,0,1,1,1,1,1, - 2,1,1,0,1,1,0,1,1,1,3,1,1,1,1,1, - 2,1,3,2,1,1,1,0,1,1,1,1,1,1,1,1, - 2,1,0,2,1,1,1,0,1,1,1,1,1,1,1,1, - 2,1,1,2,1,3,1,3,1,1,1,1,1,1,1,1, - 2,1,1,2,1,0,1,3,1,1,1,1,1,1,1,1 - }; - int[][] sequence=buildMatrix(NSEQ,NCHAR,ssequence); - double[][] dist=new double[NSEQ][NSEQ]; - boolean localflag, globalflag=false; - - - - // Test Phylo_slc - System.out.println("Testing Phylo_slc"); - - // Printout sequences for testing -// for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_slc: Hamming distance between two daughters is not twice the mother distance"); - - } - } - -// System.out.println("Tree:"); -// print_tree(tree,tree.root); - -// System.out.println("Check expected order of leafs on tree:"); - Check_tree ct=new Check_tree(tree); - ct.test(tree.root); - - localflag = ct.flag; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_slc: Leaves of the tree were not encountered in the expected order"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class Check_tree { - int i; - boolean flag; - Phylo_slc tree; - - Check_tree(Phylo_slc ttree) { - tree=ttree; - i=0; - flag=false; - } - void test(int node) { - if (tree.t[node].ldau != -1) { - test(tree.t[node].ldau); - } else { - flag = flag || (node != i++); -// System.out.printf(node << " %f\n", flag); - return; - } - - if (tree.t[node].rdau != -1) { - test(tree.t[node].rdau); - } else { - flag = flag || (node != i++); -// System.out.printf(node << " %f\n", flag); - return; - } - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_upgma.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_upgma.java deleted file mode 100644 index 18525d4dd2..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_upgma.java +++ /dev/null @@ -1,193 +0,0 @@ -package com.nr.test.test_chapter16; - -import static com.nr.NRUtil.buildMatrix; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ci.Phylo_upgma; - -public class Test_Phylo_upgma { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,hamming,mother,ndif,NSEQ=16,NCHAR=16; - double sbeps=1.e-15; - // char base[]={'C','G','T','A'}; - int ssequence[]={ - 3,1,1,1,1,1,1,1,0,1,1,1,1,1,2,2, - 3,1,1,1,1,1,1,1,0,1,1,1,1,1,2,3, - 3,0,1,1,1,1,1,1,0,1,1,1,1,1,3,1, - 3,3,1,1,1,1,1,1,0,1,1,1,1,1,3,1, - 3,1,1,1,2,1,1,1,2,1,1,3,1,1,1,1, - 3,1,1,1,0,1,1,1,2,1,1,3,1,1,1,1, - 3,1,1,1,1,1,1,1,2,2,1,0,1,1,1,1, - 3,1,1,1,1,1,1,1,2,0,1,0,1,1,1,1, - 2,1,1,0,1,1,3,1,1,1,1,1,3,1,1,1, - 2,1,1,0,1,1,3,1,1,1,1,1,2,1,1,1, - 2,1,1,0,1,1,0,1,1,1,0,1,1,1,1,1, - 2,1,1,0,1,1,0,1,1,1,3,1,1,1,1,1, - 2,1,3,2,1,1,1,0,1,1,1,1,1,1,1,1, - 2,1,0,2,1,1,1,0,1,1,1,1,1,1,1,1, - 2,1,1,2,1,3,1,3,1,1,1,1,1,1,1,1, - 2,1,1,2,1,0,1,3,1,1,1,1,1,1,1,1 - }; - int[][] sequence=buildMatrix(NSEQ,NCHAR,ssequence); - double[][] dist=new double[NSEQ][NSEQ]; - boolean localflag, globalflag=false; - - - - // Test Phylo_upgma - System.out.println("Testing Phylo_upgma"); - - // Printout sequences for testing -// for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_upgma: Hamming distance between two daughters is not twice the mother distance"); - - } - } - -// System.out.println("Tree:"); -// print_tree(tree,tree.root); - -// System.out.println("Check expected order of leaves on tree:"); - Check_tree ct=new Check_tree(tree); - ct.test(tree.root); - - localflag = ct.flag; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_upgma: Leaves of the tree were not encountered in the expected order"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class Check_tree { - int i; - boolean flag; - Phylo_upgma tree; - - Check_tree(Phylo_upgma ttree) { - tree=ttree; - i=0; - flag=false; - } - void test(int node) { - if (tree.t[node].ldau != -1) { - test(tree.t[node].ldau); - } else { - flag = flag || (node != i++); -// System.out.printf(node << " %f\n", flag); - return; - } - - if (tree.t[node].rdau != -1) { - test(tree.t[node].rdau); - } else { - flag = flag || (node != i++); -// System.out.printf(node << " %f\n", flag); - return; - } - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_wpgma.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_wpgma.java deleted file mode 100644 index 159e489129..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Phylo_wpgma.java +++ /dev/null @@ -1,194 +0,0 @@ -package com.nr.test.test_chapter16; - -import static com.nr.NRUtil.buildMatrix; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ci.Phylo_wpgma; - -public class Test_Phylo_wpgma { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,hamming,mother,ndif,NSEQ=16,NCHAR=16; - double sbeps=1.e-15; - // char base[]={'C','G','T','A'}; - int ssequence[]={ - 3,1,1,1,1,1,1,1,0,1,1,1,1,1,2,2, - 3,1,1,1,1,1,1,1,0,1,1,1,1,1,2,3, - 3,0,1,1,1,1,1,1,0,1,1,1,1,1,3,1, - 3,3,1,1,1,1,1,1,0,1,1,1,1,1,3,1, - 3,1,1,1,2,1,1,1,2,1,1,3,1,1,1,1, - 3,1,1,1,0,1,1,1,2,1,1,3,1,1,1,1, - 3,1,1,1,1,1,1,1,2,2,1,0,1,1,1,1, - 3,1,1,1,1,1,1,1,2,0,1,0,1,1,1,1, - 2,1,1,0,1,1,3,1,1,1,1,1,3,1,1,1, - 2,1,1,0,1,1,3,1,1,1,1,1,2,1,1,1, - 2,1,1,0,1,1,0,1,1,1,0,1,1,1,1,1, - 2,1,1,0,1,1,0,1,1,1,3,1,1,1,1,1, - 2,1,3,2,1,1,1,0,1,1,1,1,1,1,1,1, - 2,1,0,2,1,1,1,0,1,1,1,1,1,1,1,1, - 2,1,1,2,1,3,1,3,1,1,1,1,1,1,1,1, - 2,1,1,2,1,0,1,3,1,1,1,1,1,1,1,1 - }; - int[][] sequence=buildMatrix(NSEQ,NCHAR,ssequence); - double[][] dist=new double[NSEQ][NSEQ]; - boolean localflag, globalflag=false; - - - - // Test Phylo_wpgma - System.out.println("Testing Phylo_wpgma"); - - // Printout sequences for testing -// for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_wpgma: Hamming distance between two daughters is not twice the mother distance"); - - } - } - -// System.out.println("Tree:"); -// print_tree(tree,tree.root); - -// System.out.println("Check expected order of leafs on tree:"); - Check_tree ct=new Check_tree(tree); - ct.test(tree.root); - - localflag = ct.flag; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Phylo_wpgma: Leaves of the tree were not encountered in the expected order"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Check_tree { - int i; - boolean flag; - Phylo_wpgma tree; - - Check_tree(Phylo_wpgma ttree){ - tree=ttree; - i=0; - flag=false; - } - void test(int node) { - if (tree.t[node].ldau != -1) { - test(tree.t[node].ldau); - } else { - flag = flag || (node != i++); -// System.out.printf(node << " %f\n", flag); - return; - } - - if (tree.t[node].rdau != -1) { - test(tree.t[node].rdau); - } else { - flag = flag || (node != i++); -// System.out.printf(node << " %f\n", flag); - return; - } - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Svm.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Svm.java deleted file mode 100644 index aff409be82..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_Svm.java +++ /dev/null @@ -1,285 +0,0 @@ -package com.nr.test.test_chapter16; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ci.Svm; -import com.nr.ci.Svmgausskernel; -import com.nr.ci.Svmlinkernel; -import com.nr.ci.Svmpolykernel; -import com.nr.ran.Normaldev; -import com.nr.ran.Ran; - -public class Test_Svm { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,M=1000,N=2; - double a,b,lambda,omega=1.3,test,yy; - double[]x=new double[2]; - double[] y=new double[M]; - double[][] data=new double[M][N]; - boolean localflag, globalflag=false; - - - - // Test Svm - System.out.println("Testing Svm"); - - // Create two disjoint sets of points - Ran myran=new Ran(17); - for (i=0;i 1.e-3 && k < 100); - int nerror=0; - for (i=0;i= 1.0)); -// if ((y[i] == 1.0) != (linsvm.predict(i) >= 1.0)) -// System.out.printf(data[i][0] << " %f\n", data[i][1] << " %f\n", y[i] << " %f\n", linsvm.predict(i)); - nerror += ((y[i]==1.0) != (linsvm.predict(i) >= 0.0) ? 1 : 0); - } - System.out.printf("Errors: %d\n", nerror); - - // Polynomial kernel - Svmpolykernel polykernel=new Svmpolykernel(data,y,1.0,1.0,2.0); - Svm polysvm=new Svm(polykernel); - lambda=10; - k=0; - do { - test=polysvm.relax(lambda,omega); -// System.out.printf(test); - k++; - } while (test > 1.e-3 && k < 100); - nerror=0; - for (i=0;i= 0.0) ? 1 : 0); - } - System.out.printf("Errors: %d\n", nerror); - - // Gaussian kernel - Svmgausskernel gausskernel=new Svmgausskernel(data,y,1.0); - Svm gausssvm=new Svm(gausskernel); - lambda=10; - k=0; - do { - test=gausssvm.relax(lambda,omega); -// System.out.printf(test); - k++; - } while (test > 1.e-3 && k < 100); - nerror=0; - for (i=0;i= 0.0) ? 1 : 0); - } - System.out.printf("Errors: %d\n", nerror); - - - // Need to add tests for harder test case and resolve issue that the two - // support vectors give an erroneous indication for two of the kernels above - - // Example similar to the book - Normaldev ndev=new Normaldev(0.0,0.5,17); - for (j=0;j<4;j++) { // Four quadrants - for (i=0;i 1.e-3 && k < 100); - nerror=0; - for (i=0;i= 0.0) ? 1 : 0); - } - System.out.printf("%d ",nerror); - // Test new data - nerror=0; - for (j=0;j<4;j++) { // Four quadrants - for (i=0;i= 0.0) ? 1 : 0); - } - } - System.out.printf("%d ",nerror); - } - System.out.println(); - - // Polynomial kernel - Svmpolykernel polykernel2 = new Svmpolykernel(data,y,1.0,1.0,4.0); - Svm polysvm2=new Svm(polykernel2); - System.out.printf("Errors: "); - for (lambda=0.001;lambda<10000;lambda *= 10) { - k=0; - do { - test=polysvm2.relax(lambda,omega); -// System.out.printf(test); - k++; - } while (test > 1.e-3 && k < 100); - // Test training set - nerror=0; - for (i=0;i= 0.0) ? 1 : 0); - } - System.out.printf("%d ",nerror); - // Test new data - nerror=0; - for (j=0;j<4;j++) { // Four quadrants - for (i=0;i= 0.0) ? 1 : 0); - } - } - System.out.printf("%d ",nerror); - } - System.out.println(); - - // Gaussian kernel - Svmgausskernel gausskernel2=new Svmgausskernel(data,y,1.0); - Svm gausssvm2=new Svm(gausskernel2); - System.out.printf("Errors: "); - for (lambda=0.001;lambda<10000;lambda *= 10) { - k=0; - do { - test=gausssvm2.relax(lambda,omega); -// System.out.printf(test); - k++; - } while (test > 1.e-3 && k < 100); - nerror=0; - for (i=0;i= 0.0) ? 1 : 0); - } - System.out.printf("%d ",nerror); - // Test new data - nerror=0; - for (j=0;j<4;j++) { // Four quadrants - for (i=0;i= 0.0) ? 1 : 0); - } - } - System.out.printf("%d ",nerror); - } - System.out.println(); - - // Test the algorithm on test data after learning - // Do a scan over lambda to find best value - - localflag = false; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Svm: *************************"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_markovgen.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_markovgen.java deleted file mode 100644 index 98dfd9707c..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter16/Test_markovgen.java +++ /dev/null @@ -1,96 +0,0 @@ -package com.nr.test.test_chapter16; - -import static com.nr.NRUtil.buildMatrix; -import static com.nr.test.NRTestUtil.matsub; -import static com.nr.test.NRTestUtil.maxel; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ci.HMM; - -public class Test_markovgen { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=10000,M=5; - double sbeps,aatrans[]={ - 0.0,0.7,0.1,0.0,0.2, - 0.2,0.4,0.0,0.2,0.2, - 0.0,1.0,0.0,0.0,0.0, - 0.0,0.3,0.0,0.7,0.0, - 0.1,0.1,0.0,0.0,0.8 - }; - int[] state=new int[N]; - double[][] atrans=buildMatrix(M,M,aatrans); - boolean localflag, globalflag=false; - - - - // Test markovgen - System.out.println("Testing markovgen"); - - HMM.markovgen(atrans,state,0,17); - -// for (i=0;i<10;i++) { -// for (j=0;j<10;j++) -// System.out.printf(state[10*i+j] << " "; -// System.out.printf(endl; -// } -// System.out.printf(endl; - - // Measure the transition probabilities in the result - int[][] measure=new int[M][M]; - int[] ntimes=new int[M]; - for (i=1;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** markovgen: Transistion probabilities don't agree with specification"); - - } - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** StepperBS: Inaccurate integration"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class rhs_StepperBS implements DerivativeInf { - public void derivs(final double x,double[] y,double[] dydx) { - dydx[0]= -y[1]; - dydx[1]=y[0]-(1.0/x)*y[1]; - dydx[2]=y[1]-(2.0/x)*y[2]; - dydx[3]=y[2]-(3.0/x)*y[3]; - } - public void jacobian(final double x, double[] y, double[] dfdx, double[][] dfdy){} - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter17/Test_StepperDopr5.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter17/Test_StepperDopr5.java deleted file mode 100644 index 141591a3de..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter17/Test_StepperDopr5.java +++ /dev/null @@ -1,80 +0,0 @@ -package com.nr.test.test_chapter17; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ode.DerivativeInf; -import com.nr.ode.Odeint; -import com.nr.ode.Output; -import com.nr.ode.StepperDopr5; -import com.nr.sf.Bessjy; - -public class Test_StepperDopr5 { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,nvar=4; - final double atol=1.0e-6,rtol=atol,h1=0.01,hmin=0.0,x1=1.0,x2=2.0; - double sbeps; - //dydx= new double[nvar] - double[] y= new double[nvar],yout= new double[nvar],yexp= new double[nvar]; - boolean localflag, globalflag=false; - - - - // Test StepperDopr5 - System.out.println("Testing StepperDopr5"); - - Bessjy bess = new Bessjy(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** StepperDopr5: Inaccurate integration"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class rhs_StepperDopr5 implements DerivativeInf { - public void derivs (final double x, final double[] y, final double[]dydx) { - dydx[0]= -y[1]; - dydx[1]=y[0]-(1.0/x)*y[1]; - dydx[2]=y[1]-(2.0/x)*y[2]; - dydx[3]=y[2]-(3.0/x)*y[3]; - } - public void jacobian(final double x, double[] y, double[] dfdx, double[][] dfdy){} - - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter17/Test_StepperDopr853.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter17/Test_StepperDopr853.java deleted file mode 100644 index 0b2ad78ca2..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter17/Test_StepperDopr853.java +++ /dev/null @@ -1,79 +0,0 @@ -package com.nr.test.test_chapter17; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ode.DerivativeInf; -import com.nr.ode.Odeint; -import com.nr.ode.Output; -import com.nr.ode.StepperDopr853; -import com.nr.sf.Bessjy; - -public class Test_StepperDopr853 { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,nvar=4; - final double atol=1.0e-6,rtol=atol,h1=0.01,hmin=0.0,x1=1.0,x2=2.0; - double sbeps; - // dydx= new double[nvar], - double[] y= new double[nvar],yout= new double[nvar],yexp= new double[nvar]; - boolean localflag, globalflag=false; - - - - // Test StepperDopr853 - System.out.println("Testing StepperDopr853"); - - Bessjy bess = new Bessjy(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** StepperDopr853: Inaccurate integration"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class rhs_StepperDopr853 implements DerivativeInf{ - public void derivs(final double x,double[] y,double[] dydx) { - dydx[0]= -y[1]; - dydx[1]=y[0]-(1.0/x)*y[1]; - dydx[2]=y[1]-(2.0/x)*y[2]; - dydx[3]=y[2]-(3.0/x)*y[3]; - } - public void jacobian(final double x, double[] y, double[] dfdx, double[][] dfdy){} - - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter17/Test_StepperRoss.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter17/Test_StepperRoss.java deleted file mode 100644 index e456c7801e..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter17/Test_StepperRoss.java +++ /dev/null @@ -1,95 +0,0 @@ -package com.nr.test.test_chapter17; - -import static java.lang.Math.abs; -import static java.lang.Math.exp; -import static java.lang.Math.pow; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ode.DerivativeInf; -import com.nr.ode.Odeint; -import com.nr.ode.Output; -import com.nr.ode.StepperRoss; - -public class Test_StepperRoss { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,nvar=3; - final double atol=1.0e-6,rtol=atol,h1=2.9e-4,hmin=0.0,x1=0.0,x2=50.0; - double sbeps; - //dydx= new double[nvar] - double[] y= new double[nvar],yout= new double[nvar]; - boolean localflag, globalflag=false; - - - - // Test StepperRoss - System.out.println("Testing StepperRoss"); - - y[0]=1.0; y[1]=1.0; y[2]=0.0; - Output out=new Output(20); - rhs_StepperRoss d = new rhs_StepperRoss(); - StepperRoss s = new StepperRoss(); - Odeint ode = new Odeint(y,x1,x2,atol,rtol,h1,hmin,out,d,s); - ode.integrate(); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** StepperRoss: Inaccurate relationship #1 among y[i] components"); - - } - - System.out.println(abs(yout[1]-pow(yout[0]*exp(0.013*x2),2.5))); - localflag = abs(yout[1]-pow(yout[0]*exp(0.013*x2),2.5)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** StepperRoss: Inaccurate relationship #2 among y[i] components"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class rhs_StepperRoss implements DerivativeInf{ - public void derivs(final double x,double[] y,double[] dydx) { - dydx[0]= -0.013*y[0]-1000.0*y[0]*y[2]; - dydx[1]= -2500.0*y[1]*y[2]; - dydx[2]= -0.013*y[0]-1000.0*y[0]*y[2]-2500.0*y[1]*y[2]; - } - - public void jacobian(final double x,double[] y,double[] dfdx,double[][] dfdy) { - int n=y.length; - for (int i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** StepperSie: Inaccurate relationship #1 among yout[i] components"); - - } - - System.out.println(abs(yout[1]-pow(yout[0]*exp(0.013*x2),2.5))); - localflag = abs(yout[1]-pow(yout[0]*exp(0.013*x2),2.5)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** StepperSie: Inaccurate relationship #2 among y[i] components"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class rhs_StepperSie implements DerivativeInf{ - public void derivs(final double x,double[] y,double[] dydx) { - dydx[0]= -0.013*y[0]-1000.0*y[0]*y[2]; - dydx[1]= -2500.0*y[1]*y[2]; - dydx[2]= -0.013*y[0]-1000.0*y[0]*y[2]-2500.0*y[1]*y[2]; - } - - public void jacobian(final double x,double[] y,double[] dfdx,double[][] dfdy) { - int n=y.length; - for (int i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** StepperStoerm: Inaccurate integration #1"); - - } - - y[0]=1.0/pow(3.0,2.0/3.0)/exp(gammln(2.0/3.0)); // Ai(x) - y[nvar]=-1.0/pow(3.0,1.0/3.0)/exp(gammln(1.0/3.0)); - dydx[0]=0.0; - y[1]=1.0/pow(3.0,1.0/6.0)/exp(gammln(2.0/3.0)); // Bi(x) - y[nvar+1]=pow(3.0,1.0/6.0)/exp(gammln(1.0/3.0)); - dydx[1]=0.0; - - x1=0.0;x2=-1.0; - StepperStoerm s2 = new StepperStoerm(); - Odeint ode2 = new Odeint(y,x1,x2,atol,rtol,h1,hmin,out,d,s2); - ode2.integrate(); - yexp[0]=bess.airy_ai(-1.0); - yexp[1]=bess.airy_bi(-1.0); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** StepperStoerm: Inaccurate integration #2"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class rhs_StepperStoerm implements DerivativeInf{ - public void derivs(final double x,double[] y,double[] dydx) { - dydx[0]=x*y[0]; - dydx[1]=x*y[1]; - } - public void jacobian(final double x,double[] y,double[] dfdx,double[][] dfdy) {} - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter17/Test_Stochsim.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter17/Test_Stochsim.java deleted file mode 100644 index d9ff2f9965..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter17/Test_Stochsim.java +++ /dev/null @@ -1,118 +0,0 @@ -package com.nr.test.test_chapter17; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ode.Stochsim; -public class Test_Stochsim { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,NVAR=4,M=420; - double t; - double[] sinit=new double[NVAR],tsav=new double[M/10],smax=new double[NVAR]; - double[][] ssav=new double[M/10][NVAR]; - boolean localflag, globalflag=false; - - - - // Test Stochsim - System.out.println("Testing Stochsim"); - - sinit[0]=150.0; - sinit[1]=10.0; - sinit[2]=10.0; - sinit[3]=0.0; - Stochsim stoch = new Stochsim(sinit); - - for (k=0;k smax[k]) smax[k]=stoch.s[k]; - if (i % 10 == 0) { - j=i/10; - tsav[j]=t; -// System.out.printf(tsav[j]; - for (k=0;k sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rk4: Inaccurate Runge-Kutta step"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - void rk4_derivs(final double x,final double[] y,final double[] dydx) { - dydx[0]= -y[1]; - dydx[1]=y[0]-(1.0/x)*y[1]; - dydx[2]=y[1]-(2.0/x)*y[2]; - dydx[3]=y[2]-(3.0/x)*y[3]; - } - - class RK4_derivs implements DerivativeInf { - public void derivs(final double x, double[] y, double[] dydx){ - rk4_derivs(x,y,dydx); - } - public void jacobian(final double x, double[] y, double[] dfdx, double[][] dfdy){} - } - - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter18/Test_Shoot.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter18/Test_Shoot.java deleted file mode 100644 index 7f93bd2b2a..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter18/Test_Shoot.java +++ /dev/null @@ -1,152 +0,0 @@ -package com.nr.test.test_chapter18; - -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.booleanW; - -import com.nr.bvp.Shoot; -import com.nr.ode.DerivativeInf; -import com.nr.root.Roots; - -public class Test_Shoot { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - booleanW check=new booleanW(false); - int i,j,nvar=3,N2=1; - int n[]={2,2,2,5,5,11,8,10,12}; - int m[]={2,2,2,2,2,4,7,9,11}; - double result=0,dx=1.0e-8; - double c2[]={0.1,1.0,4.0,1.0,16.0,-1.0,0.0,1.0,-1.0}; - double expect[]={6.01426631394,6.14094899057,6.54249527439, - 30.43614538636,36.9962674974,131.560080919, - 72.0000000000,110.130237996,155.888762517}; - double[] v=new double[N2]; - double gmma,q1,x1,x2,sbeps=1.e-10; - boolean localflag, globalflag=false; - - - - // Test Shoot - System.out.println("Testing Shoot"); - - for (j=0;j<9;j++) { - gmma=1.0; - q1=n[j]; - for (i=1;i<=m[j];i++) gmma *= -0.5*(n[j]+i)*(q1--/i); - v[0]=n[j]*(n[j]+1)-m[j]*(m[j]+1)+c2[j]/2.0; - x1= -1.0+dx; - x2=0.0; - final Load load = new Load(n[j],m[j],gmma,c2[j],dx); - Rhs d = new Rhs(m[j],c2[j]); - final Score score = new Score(n[j],m[j]); - Shoot shoot =new Shoot(nvar,x1,x2, d) { - - @Override - public double[] load(double x, double[] v) { - return load.load(x, v); - } - - @Override - public double[] score(double x, double[] v) { - return score.score(x, v); - } - - }; - - //Shoot shoot(nvar,x1,x2,load,d,score); - Roots.newt(v,check,shoot); - if (check.val) { - System.out.println("shoot failed; bad initial guess"); - } else { -// System.out.println(" %f\n", "mu(m,n)"); - result=v[0]+m[j]*(m[j]+1); - System.out.println( result); - } - -// System.out.printf(abs(result/expect[j]-1.0)); - localflag = abs(result/expect[j]-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Shoot: Did not achieve expected accuracy in the eigenvalue"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Rhs implements DerivativeInf{ - int m; - double c2; - - Rhs(final int mm, final double cc2) { - m =mm; - c2 =cc2; - } - public void derivs (final double x, final double[] y, final double[] dydx) - { - dydx[0]=y[1]; - dydx[1]=(2.0*x*(m+1.0)*y[1]-(y[2]-c2*x*x)*y[0])/(1.0-x*x); - dydx[2]=0.0; - } - public void jacobian(final double x, final double[] y, final double[] dfdx, final double[][] dfdy) { - // TODO Auto-generated method stub - - } - } - - class Load { - int n,m; - double gmma,c2,dx; - double[] y; - - Load(final int nn, final int mm, final double gmmaa, double cc2, final double dxx) { - n=nn; - m=mm; - gmma=gmmaa; - c2=cc2; - dx=dxx; - y =new double[3]; - } - - double[] load(final double x1, final double[] v) - { - double y1 = ((n-m & 1) != 0 ? -gmma : gmma); - y[2]=v[0]; - y[1] = -(y[2]-c2)*y1/(2*(m+1)); - y[0]=y1+y[1]*dx; - return y; - } - } - - class Score { - int n,m; - double[] f; - - Score(final int nn,final int mm) { - n=nn; - m=mm; - f=new double[1]; - } - - double[] score(final double xf, final double[] y) - { - f[0]=((n-m & 1) != 0 ? y[0] : y[1]); - return f; - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter18/Test_Shootf.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter18/Test_Shootf.java deleted file mode 100644 index fe1619c11c..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter18/Test_Shootf.java +++ /dev/null @@ -1,176 +0,0 @@ -package com.nr.test.test_chapter18; - -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.booleanW; - -import com.nr.bvp.Shootf; -import com.nr.ode.DerivativeInf; -import com.nr.root.Roots; - -public class Test_Shootf { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - booleanW check=new booleanW(false); - int i,j,N1=2,N2=1,NTOT=N1+N2,nvar=NTOT,n2=N2; - int n[]= {2,2,2,5,5,11,8,10,12}; - int m[]= {2,2,2,2,2,4,7,9,11}; - double c2[]={0.1,1.0,4.0,1.0,16.0,-1.0,0.0,1.0,-1.0}; - double expect[]={6.01426631394,6.14094899057,6.54249527439, - 30.43614538636,36.9962674974,131.560080919, - 72.0000000000,110.130237996,155.888762517}; - double gmma,q1,result=0,dx=1.0e-7,sbeps=1.e-10; - double[] v=new double[NTOT]; - boolean localflag, globalflag=false; - - - - // Test Shootf - System.out.println("Testing Shootf"); - - for (j=0;j<9;j++) { - gmma=1.0; - q1=n[j]; - for (i=1;i<=m[j];i++) gmma *= -0.5*(n[j]+i)*(q1--/i); - v[0]=n[j]*(n[j]+1)-m[j]*(m[j]+1)+c2[j]/2.0; - v[2]=v[0]; - v[1]=gmma*(1.0-(v[2]-c2[j])*dx/(2*(m[j]+1))); - double x1=-1.0+dx; - double x2=1.0-dx; - double xf=0.0; - final Load1 load1 = new Load1(n[j],m[j],gmma,c2[j],dx); - final Load2 load2 =new Load2(m[j],c2[j]); - Rhs d = new Rhs(m[j],c2[j]); - final Score score = new Score(); - Shootf shootf = new Shootf(nvar,n2,x1,x2,xf,d){ - - @Override - public double[] load1(double x, double[] v) { - return load1.load(x,v); - } - - @Override - public double[] load2(double x, double[] v) { - return load2.load(x, v); - } - - @Override - public double[] score(double x, double[] v) { - return score.score(x,v); - } - - }; - Roots.newt(v,check,shootf); - if (check.val) { - System.out.println("shootf failed; bad initial guess"); - } else { -// System.out.println(" %f\n", "mu(m,n)"); - result=v[0]+m[j]*(m[j]+1); - System.out.println( result); - } - -// System.out.printf(abs(result/expect[j]-1.0)); - localflag = abs(result/expect[j]-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Shootf: Did not achieve expected accuracy in the eigenvalue"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Rhs implements DerivativeInf{ - int m; - double c2; - - Rhs(int mm, double cc2) { - m=mm; - c2=cc2; - } - - public void derivs (final double x, double[] y, double[] dydx) - { - dydx[0]=y[1]; - dydx[1]=(2.0*x*(m+1.0)*y[1]-(y[2]-c2*x*x)*y[0])/(1.0-x*x); - dydx[2]=0.0; - } - - public void jacobian(double x, double[] y, double[] dfdx, double[][] dfdy) { - // TODO Auto-generated method stub - - } - } - - class Load1 { - int n,m; - double gmma,c2,dx; - double[] y; - - Load1(int nn, int mm, double gmmaa, double cc2, double dxx){ - n=nn; - m=mm; - gmma=gmmaa; - c2=cc2; - dx=dxx; - y = new double[3]; - } - - public double[] load (final double xx1, double[] v1) - { - double y1 = ((n-m & 1) != 0 ? -gmma : gmma); - y[2]=v1[0]; - y[1] = -(y[2]-c2)*y1/(2*(m+1)); - y[0]=y1+y[1]*dx; - return y; - } - } - - class Load2 { - int m; - double c2; - double[] y; - - Load2(int mm, double cc2) { - m=mm; - c2=cc2; - y=new double[3]; - } - - double[] load (final double x2, double[] v2) - { - y[2]=v2[1]; - y[0]=v2[0]; - y[1]=(y[2]-c2)*y[0]/(2*(m+1)); - return y; - } - } - - class Score { - double[] f; - - Score() { - f=new double[3]; - } - double[] score (final double xf, double[] y) - { - for (int i=0;i<3;i++) f[i]=y[i]; - return f; - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter18/Test_Solvde.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter18/Test_Solvde.java deleted file mode 100644 index 7cba536ef7..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter18/Test_Solvde.java +++ /dev/null @@ -1,99 +0,0 @@ -package com.nr.test.test_chapter18; - -import static com.nr.sf.Legendre.plgndr; -import static java.lang.Math.abs; -import static java.lang.Math.exp; -import static java.lang.Math.log; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.bvp.Difeq; -import com.nr.bvp.Solvde; - -public class Test_Solvde { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int M=100,NE=3,NB=1,NYJ=NE,NYK=M+1; - int i,mpt=M+1,itmax=100; - int n[]={2,2,2,5,5,11,8,10,12}; - int mm[]={2,2,2,2,2,4,7,9,11}; - double anorm,q1,fac1,fac2,deriv,conv=1.0e-15,slowc=1.0; - double h=1.0/M,result,sbeps=1.e-4; - double c2[]={0.1,1.0,4.0,1.0,16.0,-1.0,0.0,1.0,-1.0}; - double expect[]={6.01426631394,6.14094899057,6.54249527439, - 30.43614538636,36.9962674974,131.560080919, - 72.0000000000,110.130237996,155.888762517}; - int[] indexv=new int[NE]; - double[] x=new double[M+1],scalv=new double[NE]; - double[][] y=new double[NYJ][NYK]; - boolean localflag, globalflag=false; - - - - // Test Solvde - System.out.println("Testing Solvde"); - - for (i=0;i<9;i++) { - if ((n[i]+mm[i] & 1) != 0) { - indexv[0]=0; - indexv[1]=1; - indexv[2]=2; - } else { - indexv[0]=1; - indexv[1]=0; - indexv[2]=2; - } - anorm=1.0; - if (mm[i] != 0) { - q1=n[i]; - for (int k=1;k<=mm[i];k++) anorm = -0.5*anorm*(n[i]+k)*(q1--/k); - } - for (int k=0;k scalv[0] ? y[1][M] : scalv[0]); - scalv[2]=(y[2][M] > 1.0 ? y[2][M] : 1.0); - Difeq difeq = new Difeq(mm[i],n[i],mpt,h,c2[i],anorm,x); - new Solvde(itmax,conv,slowc,scalv,indexv,NB,y,difeq); - result=y[2][0]+mm[i]*(mm[i]+1); - System.out.printf(" m = %d n = %d c**2 = %f lamda = %f\n", - mm[i], n[i], c2[i],result); - -// System.out.printf(abs(result/expect[i]-1.0)); - localflag = abs(result/expect[i]-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Solvde: Did not achieve expected accuracy in eigenvalue"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter18/Test_sfroid.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter18/Test_sfroid.java deleted file mode 100644 index 2cadbf170a..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter18/Test_sfroid.java +++ /dev/null @@ -1,93 +0,0 @@ -package com.nr.test.test_chapter18; - -import static java.lang.Math.abs; -import static java.lang.Math.exp; -import static java.lang.Math.log; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.bvp.Difeq; -import com.nr.bvp.Solvde; -import static com.nr.sf.Legendre.*; - -public class Test_sfroid { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - boolean localflag,globalflag=false; - - // Test sfroid - System.out.println("Testing sfroid"); - - localflag = main_sfroid() != 0; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** sfroid : Program did not indicate successful completion"); - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - int main_sfroid() - { - final int M=40,MM=4; - final int NE=3,NB=1,NYJ=NE,NYK=M+1; - int mm=3,n=5,mpt=M+1; - int[] indexv=new int[NE]; - double[] x=new double[M+1],scalv=new double[NE]; - double[][] y=new double[NYJ][NYK]; - int itmax=100; - double c2[]={16.0,20.0,-16.0,-20.0}; - double conv=1.0e-14,slowc=1.0,h=1.0/M; - if ((n+mm & 1) != 0) { - indexv[0]=0; - indexv[1]=1; - indexv[2]=2; - } else { - indexv[0]=1; - indexv[1]=0; - indexv[2]=2; - } - double anorm=1.0; - if (mm != 0) { - double q1=n; - for (int i=1;i<=mm;i++) anorm = -0.5*anorm*(n+i)*(q1--/i); - } - for (int k=0;k scalv[0] ? y[1][M] : scalv[0]); - scalv[2]=(y[2][M] > 1.0 ? y[2][M] : 1.0); - for (int j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fred2: Unexpected or imprecise abscissas"); - - } - - sbeps = 5.0e-6; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fred2: Unexpected or imprecise weights"); - - } - - sbeps = 2.0e-6; - System.out.println(maxel(vecsub(f,fexp))); - localflag = maxel(vecsub(f,fexp)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fred2: Imprecise result from integral equation at Gaussian quadrature abscissas "); - - } - - // Test method fredin() - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fred2 (fredin): Imprecise interpolation of Fredholm result"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class Gfunc { - public double funk (double t) { - return sqrt(t)-pow(PI/2.0,2.25)*pow(t,0.75)/2.25; - } - }; - - class Kernel { - public double funk (final double t, final double s) { - return pow(t*s,0.75); - } - }; -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter19/Test_Fredex.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter19/Test_Fredex.java deleted file mode 100644 index 09b9354c12..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter19/Test_Fredex.java +++ /dev/null @@ -1,60 +0,0 @@ -package com.nr.test.test_chapter19; - -import static java.lang.Math.PI; -import static java.lang.Math.sin; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.inv.Quad_matrix; -import com.nr.la.LUdcmp; - -public class Test_Fredex { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - boolean localflag, globalflag=false; - - - - // Test Fredex - System.out.println("Testing Fredex"); - - localflag = main_fredex() != 0; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fredex : Program did not indicate successful completion"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - int main_fredex() - { - final int N=40; - double[] g=new double[N]; - double[][] a=new double[N][N]; - new Quad_matrix(a); - LUdcmp alu = new LUdcmp(a); - for (int j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Wwghts: 2-point weights do not add to 1.0"); - - } - - // Check integral of 1+x => x + x^2/2 - expect=1.0+0.5; - sum=w2[0]*1.0+w2[1]*2.0; -// System.out.printf(expect << " %f\n", sum); - localflag = abs(sum/expect-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Wwghts: 2-point weights fail on linear function"); - - } - - Wwghts weight3 = new Wwghts(1.0/2.0,3,quad); - w3=weight3.weights(); -// for (i=0;i<3;i++) System.out.printf(w3[i] << " "; -// System.out.printf(endl; - - sum=0.0; - for (i=0;i<3;i++) sum += w3[i]; -// System.out.printf(abs(sum-1.0)); - localflag = abs(sum-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Wwghts: 3-point weights do not add to 1.0"); - - } - - // Check integral of 1+x+x^2 => x + x^2/2 + x^3/3 - expect=1.0+0.5+1.0/3.0; - sum=w3[0]*1.0+w3[1]*(1.0+0.5*(1.0+0.5))+w3[2]*3.0; -// System.out.printf(expect << " %f\n", sum); - localflag = abs(sum/expect-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Wwghts: 3-point weights fail on quadratic function"); - - } - - Wwghts weight4 = new Wwghts(1.0/3.0,4,quad); - w4=weight4.weights(); -// for (i=0;i<4;i++) System.out.printf(w4[i] << " "; -// System.out.printf(endl; - - sum=0.0; - for (i=0;i<4;i++) sum += w4[i]; -// System.out.printf(abs(sum-1.0)); - localflag = abs(sum-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Wwghts: 4-point weights do not add to 1.0"); - - } - - // Check integral of 1+x+x^2+x^3 => x + x^2/2 + x^3/3 + x^4/4 - expect=1.0+0.5+1.0/3.0+0.25; - sum=w4[0]*1.0 - +w4[1]*(1.0+(1.0/3.0)*(1.0+(1.0/3.0)*(1.0+(1.0/3.0)))) - +w4[2]*(1.0+(2.0/3.0)*(1.0+(2.0/3.0)*(1.0+(2.0/3.0)))) - +w4[3]*4.0; -// System.out.printf(expect << " %f\n", sum); - localflag = abs(sum/expect-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Wwghts: 4-point weights fail on cubic polynomial"); - - } - - Wwghts weight5=new Wwghts(1.0/4.0,5,quad); - w5=weight5.weights(); -// for (i=0;i<5;i++) System.out.printf(w5[i] << " "; -// System.out.printf(endl; - - sum=0.0; - for (i=0;i<5;i++) sum += w5[i]; -// System.out.printf(abs(sum-1.0)); - localflag = abs(sum-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Wwghts: 5-point weights do not add to 1.0"); - - } - - // Check integral of 1+x+x^2+x^3 => x + x^2/2 + x^3/3 + x^4/4 - expect=1.0+0.5+1.0/3.0+0.25; - sum=w5[0]*1.0 - +w5[1]*(1.0+0.25*(1.0+0.25*1.25)) - +w5[2]*(1.0+0.50*(1.0+0.50*1.50)) - +w5[3]*(1.0+0.75*(1.0+0.75*1.75)) - +w5[4]*4.0; -// System.out.printf(expect << " %f\n", sum); - localflag = abs(sum/expect-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Wwghts: 5-point weights fail on cubic polynomial"); - - } - - Wwghts weight6=new Wwghts(1.0/5.0,6,quad); - w6=weight6.weights(); -// for (i=0;i<6;i++) System.out.printf(w6[i] << " "; -// System.out.printf(endl; - - sum=0.0; - for (i=0;i<6;i++) sum += w6[i]; -// System.out.printf(abs(sum-1.0)); - localflag = abs(sum-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Wwghts: 6-point weights do not add to 1.0"); - - } - - // Check integral of 1+x+x^2+x^3 => x + x^2/2 + x^3/3 + x^4/4 - expect=1.0+0.5+1.0/3.0+0.25; - sum=w6[0]*1.0 - +w6[1]*(1.0+0.2*(1.0+0.2*1.2)) - +w6[2]*(1.0+0.4*(1.0+0.4*1.4)) - +w6[3]*(1.0+0.6*(1.0+0.6*1.6)) - +w6[4]*(1.0+0.8*(1.0+0.8*1.8)) - +w6[5]*4.0; -// System.out.printf(expect << " %f\n", sum); - localflag = abs(sum/expect-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Wwghts: 6-point weights fail on fifth-order polynomial"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Quad implements UniVarRealMultiValueFun{ - public double[] funk(final double y) { - int i; - double[] w=new double[4]; - for (i=0;i<4;i++) - w[i]=pow(y,1.0*(i+1))/(i+1.0); - return w; - } - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter19/Test_voltra.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter19/Test_voltra.java deleted file mode 100644 index 33a674a122..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter19/Test_voltra.java +++ /dev/null @@ -1,97 +0,0 @@ -package com.nr.test.test_chapter19; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.test.NRTestUtil.*; -import static com.nr.NRUtil.*; -import static java.lang.Math.*; -import com.nr.inv.*; - -public class Test_voltra { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=20,M=2; - double h=0.05,t0=0.0,sbeps; - double[] t=new double[N],fac1= new double[N],fac2= new double[N]; - double[][] f=new double[M][N]; - boolean localflag, globalflag=false; - - - - // Test voltra - System.out.println("Testing voltra"); - - final Gfunc gfun = new Gfunc(); - final Kernel ker =new Kernel(); - - Volterra voltra = new Volterra(){ - - @Override - public double g(int k, double t) { - return gfun.funk(k, t); - } - - @Override - public double ak(int k, int l, double t, double s) { - return ker.funk(k, l, t, s); - } - - }; - voltra.voltra(t0, h, t, f); - - // exact soln is f[1]=exp(-t), f[2]=2sin(t) - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** voltra: Imprecise result for function exp(-t)"); - - } - - sbeps = 2.0e-3; - System.out.println(maxel(fac2)); - localflag = maxel(fac2) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** voltra: Imprecise result for function 2.0*sin(t)"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class Gfunc - { - public double funk (final int k, final double t) { - return (k == 0 ? cosh(t)+t*sin(t) : - 2.0*sin(t)+t*(SQR(sin(t))+exp(t))); - } - }; - - class Kernel - { - public double funk (final int k, final int l, final double t, final double s) { - return ((k == 0) ? (l == 0 ? -exp(t-s) : -cos(t-s)) : - (l == 0 ? -exp(t+s) : -t*cos(s))); - } - }; - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_ADAT.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_ADAT.java deleted file mode 100644 index 373bdadf31..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_ADAT.java +++ /dev/null @@ -1,140 +0,0 @@ -package com.nr.test.test_chapter2; - -import static com.nr.test.NRTestUtil.*; -import static org.junit.Assert.fail; -import static java.lang.Math.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.la.ADAT; -import com.nr.la.NRsparseMat; -import com.nr.ran.Ran; - -public class Test_ADAT { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps=1.e-12; - int i,j,k,nvals,N=30,M=50; - double[][] a =new double[N][M]; - boolean localflag, globalflag=false; - - - - // Test ADAT - System.out.println("Testing ADAT (and NRsparseMat)"); - Ran myran = new Ran(17); - nvals=N+M; // Create a sparse matrix with random non-zero entries - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ADAT: Matrix entries differ between sparse matrix and brute force result."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_Bandec.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_Bandec.java deleted file mode 100644 index 49a879834e..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_Bandec.java +++ /dev/null @@ -1,49 +0,0 @@ -package com.nr.test.test_chapter2; - -import com.nr.la.Bandec; -import static com.nr.test.NRTestUtil.*; -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -public class Test_Bandec { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps; - double[] r =new double[50],y =new double[50],rr =new double[50]; - boolean localflag, globalflag=false; - - - - // Test banmul and bandec - System.out.println("Testing bandec and banmul"); - double[][] c = new double[50][17]; - ranmat(c); - Bandec clu = new Bandec(c,9,7); - ranvec(r); - clu.solve(r,y); - Bandec.banmul(c,9,7,y,rr); - sbeps = 5.e15; - localflag = maxel(vecsub(r,rr)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** bandec,banmul: Inconsistent solution vector"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_Cholesky.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_Cholesky.java deleted file mode 100644 index 36a2f622a8..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_Cholesky.java +++ /dev/null @@ -1,73 +0,0 @@ -package com.nr.test.test_chapter2; - -import static com.nr.NRUtil.*; -import static com.nr.test.NRTestUtil.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.la.Cholesky; - -public class Test_Cholesky { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps, diag=10.0; - double[][] a = new double[50][50]; - double[] r=new double[50],y=new double[50]; - boolean localflag, globalflag=false; - ranmat(a,diag); - ranvec(r); - - - - // Test cholesky - System.out.println("Testing cholesky"); - double[][] aposdef = matmul(a,transpose(a)); - Cholesky ach = new Cholesky(aposdef); - ach.solve(r,y); - sbeps = 5.e-15; - localflag = maxel(vecsub(matmul(aposdef,y),r)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** cholesky: Error in solve() method"); - - } - - ranvec(y); - double[] yy = new double[y.length]; - ach.elmult(y,r); - ach.elsolve(r,yy); - sbeps = 5.e-15; - localflag = maxel(vecsub(y,yy)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** cholesky: Error in method elmult() or elsolve()"); - - } - - double[][] ainv = buildMatrix(a); - ach.inverse(ainv); - sbeps = 5.e-15; - localflag = maxel(matsub(matmul(ainv,aposdef),ident(aposdef.length,1.))) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** cholesky: Error in method inverse()"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_LUdcmp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_LUdcmp.java deleted file mode 100644 index 57b714e979..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_LUdcmp.java +++ /dev/null @@ -1,71 +0,0 @@ -package com.nr.test.test_chapter2; - -import static com.nr.test.NRTestUtil.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.la.LUdcmp; - -public class Test_LUdcmp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps, diag=10.0; - double[][] a = new double[50][50],b = new double[50][30]; - boolean localflag, globalflag=false; - ranmat(a,diag); - ranmat(b); - - - - // Test ludcmp - System.out.println("Testing ludcmp"); - LUdcmp alu = new LUdcmp(a); - double[][] x = new double[b.length][b[0].length]; - alu.solve(b,x); - sbeps=5.e-15; - double maxel = maxel(matsub(matmul(a,x),b)); - localflag = maxel > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ludcmp: test of solution vector failed: "+ maxel); - - } - - // Test inverse - double[][] ainv; // = buildMatrix(a); not need it - ainv = alu.inverse(); - sbeps = 5.e-15; - localflag = maxel(matsub(matmul(ainv,a),ident(a.length,1.))) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ludcmp: Test of inverse failed"); - - } - - // Test determinant - LUdcmp ainvlu = new LUdcmp(ainv); - sbeps = 5.e-15; - localflag = (alu.det()*ainvlu.det()-1.) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ludcmp: Test of determinant failed"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_Linbcg.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_Linbcg.java deleted file mode 100644 index b02e9e245c..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_Linbcg.java +++ /dev/null @@ -1,114 +0,0 @@ -package com.nr.test.test_chapter2; - -import static com.nr.NRUtil.*; -import static com.nr.test.NRTestUtil.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; -import org.netlib.util.intW; - -import com.nr.la.Linbcg; -import com.nr.la.NRsparseMat; - -public class Test_Linbcg { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps; - int i,j; - boolean localflag, globalflag=false; - - - - // Test Linbcg (and NRsparseMat) - System.out.println("Testing Linbcg (and NRsparseMat)"); - final int NP=20; - final int NSIZE=58; - NRsparseMat sa = new NRsparseMat(NP,NP,NSIZE); - sa.col_ptr[1]=2; - for (i=1;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Linbcg: Derived class gives inconsistent solution vector"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - - class TestLinbcg extends Linbcg { - NRsparseMat a; - - TestLinbcg(NRsparseMat sa) { - a = sa; - } - - public void asolve(final double[] b, final double[] x, final int itrnsp) { - for (int i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** NRsparseCol: Reconstructed matrix is not correct"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_NRsparseMat.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_NRsparseMat.java deleted file mode 100644 index 8bdc26c1e5..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_NRsparseMat.java +++ /dev/null @@ -1,116 +0,0 @@ -package com.nr.test.test_chapter2; - -import static com.nr.test.NRTestUtil.matsub; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.ranvec; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.la.NRsparseMat; -import com.nr.ran.Ran; - -public class Test_NRsparseMat { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double val,sbeps; - int i,j,k,N=50,M=30,nvals; - boolean localflag, globalflag=false; - - - - // Test NRsparseMat - System.out.println("Testing NRsparseMat"); - Ran myran = new Ran(17); - double[][] a = new double[N][M]; - nvals=N+M; - - // XXX java not support unsigned int. - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** NRsparseMat: Reconstructed matrix is incorrect"); - - } - - // Test multiplication of sparse matrix by vector - double[] c = new double[as.ncols]; - ranvec(c); - double[] d=as.ax(c); // Sparse multiplication by vector - // Find same result by brute force - double[] e = new double[as.nrows]; - for (i=0;i sbeps); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** NRsparseMat: Multiplication of sparse matrix by vector failed."); - - } - - // Test multiplication of sparse transpose by vector - double[] f = new double[as.nrows]; - ranvec(f); - double[] g=as.atx(f); // Sparse transpose multiplied by vector - // Find same result by brute force - double[] h= new double[as.ncols]; - for (i=0;i sbeps); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** NRsparseMat: Multiplication of sparse transpose by vector failed."); - - } - - // Note: Member function transpose() is tested in routine test_ADAT - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_QRdcmp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_QRdcmp.java deleted file mode 100644 index 6ff57af62c..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_QRdcmp.java +++ /dev/null @@ -1,80 +0,0 @@ -package com.nr.test.test_chapter2; - -import static com.nr.NRUtil.*; -import static com.nr.test.NRTestUtil.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.la.QRdcmp; - -public class Test_QRdcmp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps, diag=10.0; - int i,j; - double[][] a = new double[50][50]; - double[] r = new double[50], y = new double[50]; - boolean localflag, globalflag=false; - ranmat(a,diag); - - - - // Test QRdcmp - System.out.println("Testing QRdcmp"); - QRdcmp aqr = new QRdcmp(a); - sbeps = 5.e-14; - localflag = maxel(matsub(matmul(transpose(aqr.qt),aqr.r),a)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** QRdcmp: QR decomposition was unsuccessful"); - - } - - localflag = maxel(matsub(matmul(transpose(aqr.qt),aqr.qt),ident(a.length,1.))) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** QRdcmp: Matrix aqr.qt is not orthogonal"); - - } - - ranvec(r); - aqr.solve(r,y); - localflag = maxel(vecsub(matmul(a,y),r)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** QRdcmp: Error in solve() method"); - - } - - // test update - double[][] aa = buildMatrix(a); - double[] s = new double[aa.length],t = new double[aa.length]; - ranvec(s); ranvec(t); - double[] u = new double[aa.length],v = buildVector(t); - aqr.qtmult(s,u); - aqr.update(u,v); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** QRdcmp: Error in method qtmult() or update()"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_SVD.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_SVD.java deleted file mode 100644 index 8e6975463d..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_SVD.java +++ /dev/null @@ -1,74 +0,0 @@ -package com.nr.test.test_chapter2; - -import static com.nr.test.NRTestUtil.matmul; -import static com.nr.test.NRTestUtil.matsub; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.ranmat; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.la.SVD; - -public class Test_SVD { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps, diag=10.0; - int N=50,i; // M=30 not use it. - double[][] a = new double[N][N],b = new double[N][N]; - boolean localflag, globalflag=false; - ranmat(a,diag); - ranmat(b); - - - - // Test SVD (not very deeply, however) - System.out.println("Testing SVD"); - SVD svd = new SVD(a); - double[][] x = new double[b.length][b[0].length]; - svd.solve(b,x); - sbeps = 1.e-14; - localflag = maxel(matsub(matmul(a,x),b)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** SVD: Inconsistent solution vector"); - - } - -// System.out.println("svd: rank = " << svd.rank() << " nullity = " << svd.nullity() << endl; - localflag = (svd.rank() != 50 || svd.nullity() != 0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** SVD: Unexpected rank or nullity in original matrix"); - - } - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** cyclic: Inconsistant solution vector.\n"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_gaussj.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_gaussj.java deleted file mode 100644 index 4f8bb72b7a..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_gaussj.java +++ /dev/null @@ -1,74 +0,0 @@ -package com.nr.test.test_chapter2; - -import static com.nr.la.GaussJordan.gaussj; -import static com.nr.test.NRTestUtil.*; -import static com.nr.NRUtil.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -public class Test_gaussj { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps, diag=10.0; - double[][] a = new double[50][50],b =new double[50][30]; - boolean localflag, globalflag=false; - ranmat(a,diag); - ranmat(b); - double[][] aa = buildMatrix(a),bb = buildMatrix(b); // saved original values - -// System.out.println("Matrices a,b initialized with maxels " << maxel(a) << maxel(b) << endl; - - - - // Test gaussj - System.out.println("Testing gaussj"); - - gaussj(a,b); - // test inverse matrix - sbeps = 5.e-15; - localflag = maxel(matsub(matmul(a,aa),ident(a.length,1.))) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** gaussj: Test of inverse failed"); - - } - - // Test rhs's - sbeps = 5.e-15; - localflag = maxel(matsub(matmul(aa,b),bb)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** gaussj: Test of RHS failed"); - - } - - // restore original a - a = buildMatrix(aa); - - // Test inverse with no rhs's - gaussj(a); - sbeps = 5.e-15; - localflag = maxel(matsub(matmul(a,aa),ident(a.length,1.))) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** gaussj: test of inverse with no RHS failed"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_mprove.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_mprove.java deleted file mode 100644 index f31f147073..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_mprove.java +++ /dev/null @@ -1,60 +0,0 @@ -package com.nr.test.test_chapter2; - -import static com.nr.test.NRTestUtil.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.la.LUdcmp; - -public class Test_mprove { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps, diag=10.0; - int i; - double[][] a = new double[50][50]; - double[] r = new double[50],y = new double[50]; - boolean localflag, globalflag=false; - ranmat(a,diag); - - - - // Test mprove - System.out.println("Testing mprove"); - - ranvec(r); - LUdcmp alu = new LUdcmp(a); - alu.solve(r,y); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** mprove: Attempt to recover accurate solution failed"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_toeplz.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_toeplz.java deleted file mode 100644 index 18f690a530..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_toeplz.java +++ /dev/null @@ -1,53 +0,0 @@ -package com.nr.test.test_chapter2; - -import static com.nr.la.Toepltz.*; -import static com.nr.test.NRTestUtil.*; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -public class Test_toeplz { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps; - int i,j,N=10; - double[] r =new double[2*N-1],x = new double[N],y= new double[N],yy= new double[N]; - boolean localflag, globalflag=false; - ranvec(r); - ranvec(y); - - - - // Test toeplz - System.out.println("Testing toeplz"); - toeplz(r,x,y); - // test solution w[] - sbeps = 5.e-14; - for(i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** toeplz: Inconsistant solution vector.\n"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_tridag.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_tridag.java deleted file mode 100644 index 240a475f76..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_tridag.java +++ /dev/null @@ -1,54 +0,0 @@ -package com.nr.test.test_chapter2; - -import static com.nr.test.NRTestUtil.*; -import static com.nr.la.Tridag.*; -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -public class Test_tridag { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps,diag=10.0; - int i; - double[] a=new double[50],b=new double[50],c=new double[50],r=new double[50],u=new double[50],rr=new double[50]; - boolean localflag, globalflag=false; - ranvec(a); - ranvec(b); - ranvec(c); - ranvec(r); - for(i=0;i<50;i++) b[i] += diag; - - - - // Test tridag - System.out.println("Testing tridag"); - tridag(a,b,c,r,u); - // test solution u[] - sbeps = 5.e-15; - rr[0]=b[0]*u[0]+c[0]*u[1]; - rr[49]=a[49]*u[48]+b[49]*u[49]; - for(i=1;i<49;i++) rr[i]=a[i]*u[i-1]+b[i]*u[i]+c[i]*u[i+1]; - localflag = maxel(vecsub(rr,r)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** tridag: Inconsistant solution vector.\n"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_vander.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_vander.java deleted file mode 100644 index e94cee16a9..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter2/Test_vander.java +++ /dev/null @@ -1,54 +0,0 @@ -package com.nr.test.test_chapter2; - -import static com.nr.la.Vander.*; -import static com.nr.test.NRTestUtil.*; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -public class Test_vander { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps; - int i,j,N=5; - double[] x = new double[N],q = new double[N],w = new double[N],qq = new double[N]; - boolean localflag, globalflag=false; - ranvec(x); - ranvec(q); - - // Test vander - System.out.println("Testing vander"); - vander(x,w,q); - // test solution w[] - sbeps = 1.e-6; - for(i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** vander: Inconsistant solution vector.\n"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter20/Test_Mgfas.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter20/Test_Mgfas.java deleted file mode 100644 index cf869a37d9..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter20/Test_Mgfas.java +++ /dev/null @@ -1,82 +0,0 @@ -package com.nr.test.test_chapter20; - -import static com.nr.NRUtil.SQR; -import static java.lang.Math.abs; -import static java.lang.Math.pow; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.pde.Mgfas; - -public class Test_Mgfas { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int JMAX=33; - int i,j; - double diff,maxdiff,sumsq,rms,sbeps; - double[][] f=new double[JMAX][JMAX], u=new double[JMAX][JMAX],expect=new double[JMAX][JMAX]; - boolean localflag, globalflag=false; - - - // Test Mgfas - System.out.println("Testing Mgfas"); - - for (i=0;i maxdiff) maxdiff=abs(diff); - sumsq += pow(diff,2.0); - } - } - rms=sqrt(sumsq/(JMAX-2)/(JMAX-2)); - System.out.printf("max difference = %f\n", maxdiff); - System.out.printf("rms error = %f\n", rms); - - sbeps=1.e-3; - localflag = rms > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Mgfas: RMS error is unexpectedly large"); - - } - - sbeps=1.e-2; - localflag = maxdiff > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Mgfas: Maximum deviation is unexpectedly large"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter20/Test_Mglin.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter20/Test_Mglin.java deleted file mode 100644 index 7a0285c5e4..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter20/Test_Mglin.java +++ /dev/null @@ -1,75 +0,0 @@ -package com.nr.test.test_chapter20; - -import static com.nr.NRUtil.SQR; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.pde.Mglin; - -public class Test_Mglin { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int JMAX=33; - int i,j,midl=JMAX/2; - double sbeps; - double[][] f=new double[JMAX][JMAX], u=new double[JMAX][JMAX]; - boolean localflag, globalflag=false; - - - - // Test Mglin - System.out.println("Testing Mglin"); - - u[midl][midl]=2.0; - Mglin mglin = new Mglin(u,20);u=mglin.u; - -// System.out.printf(endl << " Test that solution satisfies difference equations:"; -// System.out.printf(endl; -// System.out.printf(setprecision(2); -// for (i=NSTEP;i sbeps; - else - localflag = localflag || abs(f[i][j]-2.0) > sbeps; - } - } - - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Mglin: Solution u[i][j] does not satisfy the original difference equations"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter20/Test_sor.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter20/Test_sor.java deleted file mode 100644 index c735994c98..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter20/Test_sor.java +++ /dev/null @@ -1,79 +0,0 @@ -package com.nr.test.test_chapter20; - -import static com.nr.NRUtil.SQR; -import static com.nr.NRUtil.buildMatrix; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.cos; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.pde.Relaxation; - -public class Test_sor { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,midl,JMAX=33; - double rjac,sbeps,PI=acos(-1.0); - double[][] a=buildMatrix(JMAX,JMAX,1.0),b=buildMatrix(JMAX,JMAX,1.0),c=buildMatrix(JMAX,JMAX,1.0); - double[][] d=buildMatrix(JMAX,JMAX,1.0),e=buildMatrix(JMAX,JMAX,-4.0),f=buildMatrix(JMAX,JMAX,0.0); - double[][] u=buildMatrix(JMAX,JMAX,0.0); - boolean localflag, globalflag=false; - - - - // Test sor - System.out.println("Testing sor"); - - midl=JMAX/2; - f[midl][midl]=2000.0/SQR(JMAX-1.0); - rjac=cos(PI/JMAX); - Relaxation.sor(a,b,c,d,e,f,u,rjac); - -// System.out.printf(endl << " Test that solution satisfies difference equations:"; -// System.out.printf(endl; -// System.out.printf(setprecision(2); -// for (i=NSTEP;i sbeps; - else - localflag = localflag || abs(f[i][j]-2000.0/SQR(JMAX-1.0)) > sbeps; - } - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** sor: Solution u[i][j] does not satisfy the original difference equations"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter20/Test_weights.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter20/Test_weights.java deleted file mode 100644 index 1756a11727..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter20/Test_weights.java +++ /dev/null @@ -1,94 +0,0 @@ -package com.nr.test.test_chapter20; - -import static java.lang.Math.abs; -import static java.lang.Math.atan; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.pde.Weights; -import com.nr.ran.Ran; -import com.nr.sf.Bessjy; - -public class Test_weights { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=17,M=3; - double scale,y,f,f1,f2,sbeps; - double[] x=new double[N]; - double[][] c=new double[N][M]; // ,d1=new double[N][N],d2=new double[N][N]; - boolean localflag, globalflag=false; - - - - // Test weights - System.out.println("Testing weights"); - - // Choose some collocation points - scale=3.0/N; - for (i=0;i<=N/2;i++) { - x[i]=10.0*atan((N/2-i)*scale); - x[N-1-i]= -x[i]; - } -// for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** weights: Evaluation of function was inaccurate"); - - } - - sbeps=1.e-3; - localflag = abs(0.5*(bess.jn(4,y)-bess.jn(6,y))-f1) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** weights: Evaluation of first derivative was inaccurate"); - - } - - sbeps=1.e-3; - localflag = abs(0.25*(bess.jn(3,y)-2.0*bess.jn(5,y)+bess.jn(7,y))-f2) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** weights: Evaluation of second derivative was inaccurate"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Box.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Box.java deleted file mode 100644 index 776b1bf072..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Box.java +++ /dev/null @@ -1,118 +0,0 @@ -package com.nr.test.test_chapter21; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.cg.Box; -import com.nr.cg.Point; - -public class Test_Box { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - Point zero2=new Point(0.0,0.0),one2=new Point(1.0,1.0); - Point zero3=new Point(0.0,0.0,0.0),one3=new Point(1.0,1.0,1.0); - boolean localflag, globalflag=false; - - - - // Test Box - System.out.println("Testing Box"); - - // Test constructor defaults for 1,2,3 dimensions - Box b2 = new Box(2); - Box b3 = new Box(3); - - localflag = false; - localflag = !(b2.lo.equals(zero2)) || !(b2.hi.equals(zero2)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Box: Faulty default constructor for 2D"); - - } - - localflag = false; - localflag = !(b3.lo.equals(zero3)) || !(b3.hi.equals(zero3)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Box: Faulty default constructor for 3D"); - - } - - // Test constructor with arguments - Box c2=new Box(zero2,one2); - Box c3=new Box(zero3,one3); - - localflag = false; - localflag = !(c2.lo.equals(zero2)) || !(c2.hi.equals(one2)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Box: Faulty assignment of lo or hi for 2D constructor"); - - } - - localflag = false; - localflag = !(c3.lo.equals(zero3)) || !(c3.hi.equals(one3)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Box: Faulty assignment of lo or hi for 3D constructor"); - - } - - // Test assignment operator - b2= b2.copyAssign(c2); - b3=b3.copyAssign(c3); - - localflag = false; - localflag = !(b2.lo.equals(zero2)) || !(b2.hi.equals(one2)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Box: Failure of assignment operator for 2D"); - - } - - localflag = false; - localflag = !(b3.lo.equals(zero3)) || !(b3.hi.equals(one3)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Box: Failure of assignment operator for 3D"); - - } - - // Test copy constructor - - Box d2 = new Box(c2); - Box d3 = new Box(c3); - - localflag = false; - localflag = !(d2.lo.equals(c2.lo)) || !(d2.hi.equals(c2.hi)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Box: Failure of copy constructor for 2D"); - - } - - localflag = false; - localflag = !(d3.lo.equals(c3.lo)) || !(d3.hi.equals(c3.hi)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Box: Failure of copy constructor for 3D"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Boxnode.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Boxnode.java deleted file mode 100644 index dc07fb0a9c..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Boxnode.java +++ /dev/null @@ -1,131 +0,0 @@ -package com.nr.test.test_chapter21; - -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.cg.Boxnode; -import com.nr.cg.Point; -import com.nr.ran.Ran; - -public class Test_Boxnode { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,NBOX=7; - double d1,d2,a,b,c,d,expect1,expect2,sbeps=1.e-15; - boolean localflag, globalflag=false; - - - - // Test Boxnode - System.out.println("Testing Boxnode"); - - // Create a tree of Boxnodes: 0 -> 1,2 ; 1 -> 3,4 ; 2 -> 5,6 - // With 2 points in each box - - Boxnode boxes2[]=new Boxnode[NBOX]; - Point[] points2=new Point[2*NBOX]; - - Ran myran=new Ran(17); - for (i=0;i sbeps) || (abs(d-expect2) > sbeps); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Boxnode: Coordinate 0 of daughter-daughter path failed"); - - } - - a=boxes2[boxes2[boxes2[0].dau1].dau2].lo.x[1]; - b=boxes2[boxes2[boxes2[0].dau1].dau2].hi.x[1]; -// System.out.printf(a << " %f\n", a+0.3*(b-a) << " %f\n", a+0.6*(b-a) << " %f\n", b); - c=points2[boxes2[4].ptlo].x[1]; - d=points2[boxes2[4].pthi].x[1]; -// System.out.printf(c << " %f\n", d); - - expect1=a+0.3*(b-a); - expect2=a+0.6*(b-a); - localflag = (abs(c-expect1) > sbeps) || (abs(d-expect2) > sbeps); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Boxnode: Coordinate 1 of daughter-daughter path failed"); - - } - - // Track through mothers and daughters - a=boxes2[boxes2[boxes2[boxes2[NBOX-1].mom].mom].dau1].lo.x[0]; - b=boxes2[boxes2[boxes2[boxes2[NBOX-1].mom].mom].dau1].hi.x[0]; -// System.out.printf(a << " %f\n", a+0.3*(b-a) << " %f\n", a+0.6*(b-a) << " %f\n", b); - c=points2[boxes2[1].ptlo].x[0]; - d=points2[boxes2[1].pthi].x[0]; -// System.out.printf(c << " %f\n", d); - - expect1=a+0.3*(b-a); - expect2=a+0.6*(b-a); - localflag = (abs(c-expect1) > sbeps) || (abs(d-expect2) > sbeps); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Boxnode: Coordinate 0 of mother-mother-daughter path failed"); - - } - - a=boxes2[boxes2[boxes2[boxes2[NBOX-1].mom].mom].dau1].lo.x[1]; - b=boxes2[boxes2[boxes2[boxes2[NBOX-1].mom].mom].dau1].hi.x[1]; -// System.out.printf(a << " %f\n", a+0.3*(b-a) << " %f\n", a+0.6*(b-a) << " %f\n", b); - c=points2[boxes2[1].ptlo].x[1]; - d=points2[boxes2[1].pthi].x[1]; -// System.out.printf(c << " %f\n", d); - - expect1=a+0.3*(b-a); - expect2=a+0.6*(b-a); - localflag = (abs(c-expect1) > sbeps) || (abs(d-expect2) > sbeps); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Boxnode: Coordinate 1 of mother-mother-daughter path failed"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Circle.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Circle.java deleted file mode 100644 index 40d164b128..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Circle.java +++ /dev/null @@ -1,58 +0,0 @@ -package com.nr.test.test_chapter21; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.cg.Circle; -import com.nr.cg.Point; - -public class Test_Circle { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - Point center=new Point(2); - double radius,sbeps=1.e-16; - boolean localflag, globalflag=false; - - - - // Test Circle - System.out.println("Testing Circle"); - - center.x[0]=1.5; - center.x[1]=2.5; - radius=3.5; - - Circle cir = new Circle(center,radius); - - localflag = Point.dist(center,cir.center) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Circle: Circle does not have correct center"); - - } - - sbeps=1.0e-15; - localflag = abs(radius-cir.radius) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Circle: Circle does not have correct radius"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Convexhull.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Convexhull.java deleted file mode 100644 index 246be30c2e..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Convexhull.java +++ /dev/null @@ -1,94 +0,0 @@ -package com.nr.test.test_chapter21; - -import static com.nr.test.NRTestUtil.maxel; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.cg.Convexhull; -import com.nr.cg.Point; -import com.nr.cg.Polygon; -import com.nr.ran.Ran; - - -public class Test_Convexhull { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,nwind,N=10000; - Point p=new Point(2); - Point[] pvec = new Point[N]; - for(i=0;i 0.02; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Convexhull: Convex hull unexpectedly far from unit square"); - - } - - Point[] hull = new Point[cvx.nhull]; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Delaunay, interpolate(): Unexpectedly inaccurate interpolated value "); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_KDtree.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_KDtree.java deleted file mode 100644 index 72e84dadcc..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_KDtree.java +++ /dev/null @@ -1,387 +0,0 @@ -package com.nr.test.test_chapter21; - -import static com.nr.NRUtil.SQR; -import static com.nr.NRUtil.buildVector; -import static com.nr.cg.Point.dist; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import java.util.Arrays; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.cg.KDtree; -import com.nr.cg.Point; -import com.nr.ran.Ran; - - - -public class Test_KDtree { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @SuppressWarnings("unused") - @Test - public void test() { - boolean debug=false; - int i,N=1000,M=100; - double sbeps; - Point[] kd2=new Point[N]; // vector of 2D Points - Point[] kd3=new Point[N]; // vector of 3D Points - boolean localflag=false, globalflag=false; - - - - // Test KDtree - System.out.println("Testing KDtree"); - - Ran myran=new Ran(17); - - // Test KDtree in 2D - for (i=0;i tree2.boxes[nb].hi.x[0]); - localflag = localflag || (y.x[1] < tree2.boxes[nb].lo.x[1]); - localflag = localflag || (y.x[1] > tree2.boxes[nb].hi.x[1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KDtree<2>,locate(Point): The located box does not contain selected point"); - - } - } - - // Test locate(int) method - int n0; - localflag=false; - for (i=0;i tree2.boxes[nb].hi.x[0]); - localflag = localflag || (kd2[n0].x[1] < tree2.boxes[nb].lo.x[1]); - localflag = localflag || (kd2[n0].x[1] > tree2.boxes[nb].hi.x[1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KDtree<2>,locate(int): The located box does not contain selected point"); - - } - } - - // Test disti() method - int n1,n2; - sbeps=1.e-15; - localflag=false; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KDtree<2>,disti(): The disti() method gave an incorrect result"); - - } - } - - // Test nearest() method - int j,n3; - double dis2sq; - localflag=false; - for (i=0;i,nearest(): Exhaustive search found closer point"); - - } - } - - // Test nnearest() method - int n4,n,nfar,K=5; - boolean test; - double far; - int[]nn=new int[K]; - double[] dn=new double[K]; - localflag=false; - for (i=0;i far) { - far=dn[j]; - nfar=nn[j]; - } - test=false; - for (j=0;j,nnearest(): Found a nearer point than the supposed n nearest"); - - } - } - } - - // Test locatenear() method - int nmax=N/10; - int[] list=new int[nmax]; - double r=0.1; - y.x[0]=0.5; - y.x[1]=0.5; - int nret=tree2.locatenear(y,r,list,nmax); - // Check the result by brute force - int[] list2=new int[nmax]; - int nret2=0; - for (i=0;i,locatenear(): Found different number of points closer than radius r"); - - } - - // Make sure list[] and list2[] are the same - int[] llist=buildVector(list),llist2=buildVector(list2); - Arrays.sort(llist); - Arrays.sort(llist2); - localflag=false; - for (i=0;i,locatenear(): The list of nearby points is not correct"); - - } - - // Repeat all the tests in 3D - // Test KDtree in 3D - for (i=0;i tree3.boxes[nb].hi.x[0]); - localflag = localflag || (yy.x[1] < tree3.boxes[nb].lo.x[1]); - localflag = localflag || (yy.x[1] > tree3.boxes[nb].hi.x[1]); - localflag = localflag || (yy.x[2] < tree3.boxes[nb].lo.x[2]); - localflag = localflag || (yy.x[2] > tree3.boxes[nb].hi.x[2]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KDtree<3>,locate(Point): The located box does not contain selected point"); - - } - } - - // Test locate(int) method in 3D - localflag=false; - for (i=0;i tree3.boxes[nb].hi.x[0]); - localflag = localflag || (kd3[n0].x[1] < tree3.boxes[nb].lo.x[1]); - localflag = localflag || (kd3[n0].x[1] > tree3.boxes[nb].hi.x[1]); - localflag = localflag || (kd3[n0].x[2] < tree3.boxes[nb].lo.x[2]); - localflag = localflag || (kd3[n0].x[2] > tree3.boxes[nb].hi.x[2]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KDtree<3>,locate(int): The located box does not contain selected point"); - - } - } - - // Test disti() method in 3D - sbeps=1.e-15; - localflag=false; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KDtree<3>,disti(): The disti() method gave an incorrect result"); - - } - } - - // Test nearest() method in 3D - double dis3sq; - localflag=false; - for (i=0;i,nearest(): Exhaustive search found closer point"); - - } - } - - // Test nnearest() method in 3D - localflag=false; - for (i=0;i far) { - far=dn[j]; - nfar=nn[j]; - } - test=false; - for (j=0;j,nnearest(): Found a nearer point than the supposed n nearest"); - - } - } - } - - // Test locatenear() method in 3D - r=0.2; - yy.x[0]=0.5; - yy.x[1]=0.5; - yy.x[2]=0.5; - nret=tree3.locatenear(yy,r,list,nmax); - // Check the result by brute force - nret2=0; - for (i=0;i,locatenear(): Found different number of points closer than radius r"); - - } - - // Make sure list[] and list2[] are the same - int[] llist3=buildVector(list),llist4=buildVector(list2); - Arrays.sort(llist3); - Arrays.sort(llist4); - localflag=false; - for (i=0;i,locatenear(): The list of nearby points is not correct"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Minspantree.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Minspantree.java deleted file mode 100644 index 7d09a7ff22..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Minspantree.java +++ /dev/null @@ -1,146 +0,0 @@ -package com.nr.test.test_chapter21; - -import static com.nr.cg.Point.dist; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.cg.Minspantree; -import com.nr.cg.Point; -import com.nr.ran.Ran; - - -public class Test_Minspantree { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,min,N=1000; - Point[] pvec=new Point[N],qvec=new Point[N]; - for(i=0;i dist(pvec[minspan.minsega[i+1]],pvec[minspan.minsegb[i+1]]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Minspantree: Segments of tree are not in order of length"); - - } - } - - // Check whether every point is actually in the tree - // (i.e. whether the combination of all minsega and minsegb - // include all numbers from 1 to N - int[] flags=new int[N]; - for (i=0;i dist(qvec[minspan2.minsega[i+1]],qvec[minspan2.minsegb[i+1]]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Minspantree: Segments of second tree are not in order of length"); - - } - } - - // Check whether every point is actually in the tree - // (i.e. whether the combination of all minsega and minsegb - // include all numbers from 1 to N - int[] flags2=new int[N]; - for (i=0;i N-i for the two trees (meaning that the two trees are - // really the same). Note: minsega and minsegb also get swapped. - for (i=0;i in 2D - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Nearpoints,2D: A point identified by KDtree was not found by Nearpoints"); - - } - } - } - - // Create KDtree and Qotree of same Points<3> in 3D - Point test3pt=new Point(3); - Point[] p3vec=new Point[N]; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Nearpoints: A point identified by KDtree was not found by Nearpoints"); - - } - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Point.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Point.java deleted file mode 100644 index d51c37987f..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Point.java +++ /dev/null @@ -1,174 +0,0 @@ -package com.nr.test.test_chapter21; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.cg.Point; - -public class Test_Point { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - boolean localflag, globalflag=false; - - - - // Test Point - System.out.println("Testing Point"); - - // Test constructor defaults for 1,2,3 dimensions - Point x1= new Point(1); - Point x2= new Point(2); - Point x3= new Point(3); - - localflag = false; - localflag = (x1.x[0] != 0.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Faulty default constructor for 1D"); - - } - - localflag = false; - localflag = (x2.x[0] != 0.0) || (x2.x[1] != 0.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Faulty default constructor for 2D"); - - } - - localflag = false; - localflag = (x3.x[0] != 0.0) || (x3.x[1] != 0.0) || (x3.x[2] != 0.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Faulty default constructor for 3D"); - - } - - Point x11=new Point(1,1.0); - Point x21=new Point(1.0,1.0); - Point x31=new Point(1.0,1.0,1.0); - - localflag = false; - localflag = (x11.x[0] != 1.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Faulty element assignments for 1D constructor"); - - } - - localflag = false; - localflag = (x21.x[0] != 1.0) || (x21.x[1] != 1.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Faulty element assignments for 2D constructor"); - - } - - localflag = false; - localflag = (x31.x[0] != 1.0) || (x31.x[1] != 1.0) || (x31.x[2] != 1.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Faulty element assignments for 3D constructor"); - - } - - // Test assignment operator - x1.copyAssign(x11); - x2.copyAssign(x21); - x3.copyAssign(x31); - - localflag = false; - localflag = (x1.x[0] != 1.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Failure of assignment operator for 1D"); - - } - - localflag = false; - localflag = (x2.x[0] != 1.0) || (x2.x[1] != 1.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Failure of assignment operator for 2D"); - - } - - localflag = false; - localflag = (x3.x[0] != 1.0) || (x3.x[1] != 1.0) || (x3.x[2] != 1.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Failure of assignment operator for 3D"); - - } - - // Test boolean equality operator - localflag = false; - localflag = !(x11.equals(x1)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Failure of boolean equality operator for 1D"); - - } - - localflag = false; - localflag = !(x21.equals(x2)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Failure of boolean equality operator for 2D"); - - } - - localflag = false; - localflag = !(x31.equals(x3)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Failure of boolean equality operator for 3D"); - - } - - // Test copy constructor - Point y1=new Point(x1); - Point y2=new Point(x2); - Point y3=new Point(x3); - - localflag = false; - localflag = !(y1.equals(x1)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Failure of copy constructor for 1D"); - - } - - localflag = false; - localflag = !(y2.equals(x2)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Failure of copy constructor for 2D"); - - } - - localflag = false; - localflag = !(y3.equals(x3)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Point: Failure of copy constructor for 3D"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Qotree.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Qotree.java deleted file mode 100644 index 4b000fc272..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Qotree.java +++ /dev/null @@ -1,455 +0,0 @@ -package com.nr.test.test_chapter21; - -import static com.nr.cg.Point.dist; -import static java.lang.Math.pow; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.cg.Box; -import com.nr.cg.Point; -import com.nr.cg.Qotree; -import com.nr.cg.Sphcirc; - - -public class Test_Qotree { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,nbox,nlist,N=100; - double sbeps=1.e-15; - boolean localflag, globalflag=false; - - - - // Test Qotree - System.out.println("Testing Qotree"); - - // Ran myran=new Ran(17); - - // Test Qotree in 2D - Qotree qotree2 = new Qotree(2,N,N,5); - - // Test setouterbox in 2D - Point lo2=new Point(0.0,0.0),hi2=new Point(1.0,1.0); - qotree2.setouterbox(lo2,hi2); - - // Test qobox in 2D - Box b2=new Box(2); - b2=qotree2.qobox(1); -// System.out.printf(dist(b2.lo,lo2)); - localflag = dist(b2.lo,lo2) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,2D: Outer box lower corner improperly set"); - - } - -// System.out.printf(dist(b2.hi,hi2)); - localflag = dist(b2.hi,hi2) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,2D: Outer box upper corner improperly set"); - - } - - Point half=new Point(hi2.x[0]/2.0,hi2.x[1]/2.0); - - b2=qotree2.qobox(2); -// System.out.printf(dist(b2.hi,half)); - localflag = dist(b2.hi,half) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,2D: Box 2 upper corner should be in center of outer box"); - - } - - b2=qotree2.qobox(5); -// System.out.printf(dist(b2.lo,half)); - localflag = dist(b2.lo,half) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,2D: Box 5 lower corner should be in center of outer box"); - - } - - // Test qowhichbox in 2D - Sphcirc s2 = new Sphcirc(2); - s2.center=new Point(5.5/16.0,10.5/16.0); - int ans[]={1,4,15,239}; - for (i=0;i<4;i++) { - s2.radius=0.25/pow(2.0,i); - nbox=qotree2.qowhichbox(s2); -// System.out.printf(s2.radius << " %f\n", nbox); - - localflag = (nbox != ans[i]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,2D: Method qowhichbox() identified wrong box for specified circle"); - - } - } - - // Test qostore in 2D - s2.center=new Point(5.5/16.0,10.5/16.0); - for (i=0;i<4;i++) { - s2.radius=0.25/pow(2.0,i); - nbox=qotree2.qostore(s2); -// System.out.println("box: %f\n", nbox); - - localflag = (nbox != ans[i]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,2D: Method qostore() stored specified circle in wrong box"); - - } - } - - // Test qoerase in 2D - s2.center=new Point(5.5/16.0,10.5/16.0); - for (i=0;i<4;i++) { - s2.radius=0.25/pow(2.0,i); - nbox=qotree2.qoerase(s2); -// System.out.printf(nbox); - - localflag = (nbox != ans[i]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,2D: Method qoerase() removed circle from wrong box"); - - } - } - - // Store 16 circles in the tree - s2.center=new Point(5.5/16.0,10.5/16.0); - for (i=0;i<4;i++) { - s2.radius=0.25/pow(2.0,i); - qotree2.qostore(s2); - } - s2.center=new Point(10.5/16.0,10.5/16.0); - for (i=0;i<4;i++) { - s2.radius=0.25/pow(2.0,i); - qotree2.qostore(s2); - } - s2.center=new Point(10.5/16.0,5.5/16.0); - for (i=0;i<4;i++) { - s2.radius=0.25/pow(2.0,i); - qotree2.qostore(s2); - } - s2.center=new Point(5.5/16.0,5.5/16.0); - for (i=0;i<4;i++) { - s2.radius=0.25/pow(2.0,i); - qotree2.qostore(s2); - } - - // Test qoget in 2D - Sphcirc[]list2=new Sphcirc[N]; - nlist=qotree2.qoget(1,list2,N); - System.out.println(nlist); - for (i=0;i list2[i].radius; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,2D: Method qodump() returned a circle that does not contain the given point"); - - } - } - - // Test qocollides in 2D - s2.center=new Point(0.75,0.75); - s2.radius=0.10; - nlist=qotree2.qocollides(s2,list2,N); -// System.out.printf(nlist); - - localflag = (nlist != 3); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,2D: Method qocollides() did not find 3 circles that collide with target"); - - } - - for (i=0;i list2[i].radius+s2.radius); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,2D: Incorrect collision detection by method qocollides()"); - - } - } - - // Test Qotree in 3D - Qotree qotree3=new Qotree(3,N,N,5); - - // Test setouterbox in 3D - Point lo3=new Point(0.0,0.0,0.0),hi3=new Point(1.0,1.0,1.0); - qotree3.setouterbox(lo3,hi3); - - // Test qobox in 3D - Box b3=new Box(3); - b3=qotree3.qobox(1); -// System.out.printf(dist(b3.lo,lo3)); - localflag = dist(b3.lo,lo3) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,3D: Outer box lower corner improperly set"); - - } - -// System.out.printf(dist(b3.hi,hi3)); - localflag = dist(b3.hi,hi3) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,3D: Outer box upper corner improperly set"); - - } - - Point half3=new Point(hi3.x[0]/2.0,hi3.x[1]/2.0,hi3.x[2]/2.0); - - b3=qotree3.qobox(2); -// System.out.printf(dist(b3.hi,half3)); - localflag = dist(b3.hi,half3) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,3D: Box 2 upper corner should be in center of outer box"); - - } - - b3=qotree3.qobox(9); -// System.out.printf(dist(b3.lo,half3)); - localflag = dist(b3.lo,half3) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,3D: Box 9 lower corner should be in center of outer box"); - - } - - // Test qowhichbox in 3D - Sphcirc s3=new Sphcirc(3); - int ans3[]={1,8,59,3771}; - s3.center=new Point(5.5/16.0,10.5/16.0,10.5/16.0); - for (i=0;i<4;i++) { - s3.radius=0.25/pow(2.0,i); - nbox=qotree3.qowhichbox(s3); -// System.out.printf(s3.radius << " %f\n", nbox); - - localflag = (nbox != ans3[i]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,3D: Method qowhichbox() identified wrong box for specified sphere"); - - } - } - - // Test qostore in 3D - s3.center=new Point(5.5/16.0,10.5/16.0,10.5/16.0); - for (i=0;i<4;i++) { - s3.radius=0.25/pow(2.0,i); - nbox=qotree3.qostore(s3); -// System.out.println("box: %f\n", nbox); - - localflag = (nbox != ans3[i]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,3D: Method qostore() stored specified sphere in wrong box"); - - } - } - - // Test qoerase in 3D - s3.center=new Point(5.5/16.0,10.5/16.0,10.5/16.0); - for (i=0;i<4;i++) { - s3.radius=0.25/pow(2.0,i); - nbox=qotree3.qoerase(s3); -// System.out.printf(nbox); - - localflag = (nbox != ans3[i]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,3D: Method qoerase() removed sphere from wrong box"); - - } - } - - // Store 32 circles in the tree - s3.center=new Point(5.5/16.0,5.5/16.0,5.5/16.0); - for (i=0;i<4;i++) { - s3.radius=0.25/pow(2.0,i); - qotree3.qostore(s3); - } - s3.center=new Point(5.5/16.0,5.5/16.0,10.5/16.0); - for (i=0;i<4;i++) { - s3.radius=0.25/pow(2.0,i); - qotree3.qostore(s3); - } - s3.center=new Point(5.5/16.0,10.5/16.0,5.5/16.0); - for (i=0;i<4;i++) { - s3.radius=0.25/pow(2.0,i); - qotree3.qostore(s3); - } - s3.center=new Point(5.5/16.0,10.5/16.0,10.5/16.0); - for (i=0;i<4;i++) { - s3.radius=0.25/pow(2.0,i); - qotree3.qostore(s3); - } - s3.center=new Point(10.5/16.0,5.5/16.0,5.5/16.0); - for (i=0;i<4;i++) { - s3.radius=0.25/pow(2.0,i); - qotree3.qostore(s3); - } - s3.center=new Point(10.5/16.0,5.5/16.0,10.5/16.0); - for (i=0;i<4;i++) { - s3.radius=0.25/pow(2.0,i); - qotree3.qostore(s3); - } - s3.center=new Point(10.5/16.0,10.5/16.0,5.5/16.0); - for (i=0;i<4;i++) { - s3.radius=0.25/pow(2.0,i); - qotree3.qostore(s3); - } - s3.center=new Point(10.5/16.0,10.5/16.0,10.5/16.0); - for (i=0;i<4;i++) { - s3.radius=0.25/pow(2.0,i); - qotree3.qostore(s3); - } - - // Test qoget in 3D - Sphcirc[] list3=new Sphcirc[N]; - nlist=qotree3.qoget(1,list3,N); -// System.out.printf(nlist); -// for (i=0;i list3[i].radius; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,3D: Method qodump() returned a sphere that does not contain the given point"); - - } - } - - // Test qocollides in 3D - s3.center=new Point(0.75,0.75,0.75); - s3.radius=0.10; - nlist=qotree3.qocollides(s3,list3,N); -// System.out.printf(nlist); - - localflag = (nlist != 3); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,3D: Method qocollides() did not find 3 spheres that collide with target"); - - } - - for (i=0;i list3[i].radius+s3.radius); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Qotree,3D: Incorrect collision detection by method qocollides()"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Sphcirc.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Sphcirc.java deleted file mode 100644 index 6ae0120cf8..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Sphcirc.java +++ /dev/null @@ -1,249 +0,0 @@ -package com.nr.test.test_chapter21; - -import static com.nr.cg.Point.dist; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.cg.Box; -import com.nr.cg.Point; -import com.nr.cg.Sphcirc; -import com.nr.ran.Ran; - - -public class Test_Sphcirc { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - boolean test; - int i,j,N=1000; - double radius1,radius2; - Point p21=new Point(2),p22=new Point(2); - Point p31=new Point(3),p32=new Point(3); - boolean localflag, globalflag=false; - - - - // Test Sphcirc - System.out.println("Testing Sphcirc"); - - Ran myran=new Ran(17); - - // Test method operator== in 2D - Sphcirc[] circ=new Sphcirc[N]; - - for (i=0;i 1,2,3 ; 1 -> 4,5,6 ; 2 -> 7,8,9 ; 3 -> 10,11,12 - - Point []points=new Point[NPTS]; - for (i=0;i ptest; -// for (i=0;i 0.0); -// System.out.printf(z.x[0] << " %f\n", test); - - localflag = (test != (z.x[0] < 1.0)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Triel: A point that should be inside a tringle was identified as outside all of them"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Voredge.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Voredge.java deleted file mode 100644 index c647d70b46..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Voredge.java +++ /dev/null @@ -1,69 +0,0 @@ -package com.nr.test.test_chapter21; - -import static com.nr.cg.Point.dist; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.cg.Point; -import com.nr.cg.Voronoi; -import com.nr.ran.Ran; - - - -public class Test_Voredge { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,NPTS=3; - double sbeps=1.e-15; - boolean localflag, globalflag=false; - - - - // Test Voredge - System.out.println("Testing Voredge"); - - Ran myran=new Ran(17); - Point[] points=new Point[NPTS]; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Voredge: First endpoint of edge improperly initialized"); - - } - - localflag = dist(v.p[1],points[1]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Voredge: Second endpoint of edge improperly initialized"); - - } - - localflag = v.nearpt != 2; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Voredge: integer pointer to nearby point is improperly initialized"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Voronoi.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Voronoi.java deleted file mode 100644 index e5a76071a1..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_Voronoi.java +++ /dev/null @@ -1,101 +0,0 @@ -package com.nr.test.test_chapter21; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.cg.Point; -import com.nr.cg.Triel; -import com.nr.cg.Voronoi; -import com.nr.ran.Ran; - - -public class Test_Voronoi { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @SuppressWarnings("unused") - @Test - public void test() { - int i,j,k,mm,N=1000,M=100; - long key; - double sbeps=1.e-15; - Point[] pvec=new Point[N]; - for(i=0;i sbeps) && (dotprodj > sbeps); - key=vor.hashfn.int64(i)-vor.hashfn.int64(nsite); - Integer[] k_w = new Integer[1]; - vor.linehash.get(key,k_w,0);k=k_w[0]; - if (k == jfirst) break; - j=i; - i=k; - } - - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Voronoi: Chosen Voronoi edge is not perpendicular to any local Delaunay edge"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_circumcircle.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_circumcircle.java deleted file mode 100644 index f2004d86fd..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_circumcircle.java +++ /dev/null @@ -1,68 +0,0 @@ -package com.nr.test.test_chapter21; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.test.NRTestUtil.*; -import com.nr.ran.*; - -import com.nr.cg.*; -import static com.nr.cg.Circle.*; - - -public class Test_circumcircle { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=10; - double sbeps=1.e-15; - Point a =new Point(2),b =new Point(2),c =new Point(2); - Circle cir=new Circle(a,0.0); // placeholder - double[] d=new double[3]; - boolean localflag, globalflag=false; - - - - // Test circumcircle - System.out.println("Testing circumcircle"); - - Ran myran=new Ran(17); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** circumcircle: At least one point is not on supposed circumcircle"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_dist.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_dist.java deleted file mode 100644 index de10969ee0..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_dist.java +++ /dev/null @@ -1,143 +0,0 @@ -package com.nr.test.test_chapter21; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.test.NRTestUtil.*; -import static com.nr.NRUtil.*; -import static java.lang.Math.*; - -import com.nr.ran.*; - -import com.nr.cg.*; -import static com.nr.cg.Point.*; - - -public class Test_dist { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=100; - double sbeps; - double[] d=new double[100],dexp=new double[100]; - boolean localflag, globalflag=false; - - - - // Test dist - System.out.println("Testing dist"); - - // Distance between two points in 2D - Ran myran=new Ran(17); - Point x=new Point(2),y=new Point(2); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** dist: Error in distance between two Points in 2D"); - - } - - // Distance between two points in 3D - Point xx=new Point(3),yy=new Point(3); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** dist: Error in distance between two Points in 3D"); - - } - - // Distance between a Point and a Box in 2D - x.x[0]=0.25; - x.x[1]=0.25; - y.x[0]=0.75; - y.x[1]=0.75; - Box box=new Box(x,y); - for (i=0;i box.hi.x[j]) - dexp[i] += SQR(box.hi.x[j]-x.x[j]); - } - dexp[i]=sqrt(dexp[i]); - d[i]=Box.dist(box,x); - } - sbeps=1.0e-15; - localflag = maxel(vecsub(d,dexp)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** dist: Error in distance between a Point and Box in 2D"); - - } - - // Distance between a Point and a Box in 3D - xx.x[0]=0.25; - xx.x[1]=0.25; - xx.x[2]=0.25; - yy.x[0]=0.75; - yy.x[1]=0.75; - yy.x[2]=0.75; - Box bbox=new Box(xx,yy); - for (i=0;i bbox.hi.x[j]) - dexp[i] += SQR(bbox.hi.x[j]-xx.x[j]); - } - dexp[i]=sqrt(dexp[i]); - d[i]=Box.dist(bbox,xx); - } - sbeps=1.0e-15; - localflag = maxel(vecsub(d,dexp)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** dist: Error in distance between a Point and Box in 3D"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_incircle.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_incircle.java deleted file mode 100644 index 0930533a0a..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_incircle.java +++ /dev/null @@ -1,81 +0,0 @@ -package com.nr.test.test_chapter21; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.NRUtil.*; -import static java.lang.Math.*; - -import com.nr.ran.*; - -import com.nr.cg.*; - - -public class Test_incircle { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=1000; - double cx,cy,radius,pio2,result,d,sbeps=4.e-13; - Point a=new Point(2),b=new Point(2),c=new Point(2),test=new Point(2); - double[] theta=new double[3]; - boolean localflag, globalflag=false; - - - - // Test incircle - System.out.println("Testing incircle"); - - // Points on circle at center=(0.5,0.5), radius=0.4 - Ran myran=new Ran(17); - pio2=acos(-1.0); - cx=0.5; - cy=0.5; - radius=0.4; - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** incircle: Incorrect returned value"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_ispolysimple.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_ispolysimple.java deleted file mode 100644 index fcc1d518d1..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter21/Test_ispolysimple.java +++ /dev/null @@ -1,171 +0,0 @@ -package com.nr.test.test_chapter21; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.cg.Point; -import com.nr.cg.Polygon; - -public class Test_ispolysimple { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,ntest,N1=14,N2=6,N3=8,N4=8; - // Polygon 1, complex - double x0[]={-1.0,-1.0,1.0,1.0,-0.75,-0.75,0.75,0.75,-0.5,-0.5,0.5,0.5,0.0,0.0}; - double x1[]={0.0,1.0,1.0,-1.0,-1.0,0.75,0.75,-0.75,-0.75,0.5,0.5,-0.5,-0.5,0.0}; - // Polygon 2, simple and convex - double x2[]={-1.0,0.0,1.0,1.0,1.0,0.0}; - double x3[]={0.0,1.0,1.0,0.0,-1.0,-1.0}; - // Polygon 3, simple and concave - double x4[]={-1.0,-0.5,0.0,0.5,1.0,0.5,0.0,-0.5}; - double x5[]={0.0,1.0,0.5,1.0,0.0,-1.0,-0.5,-1.0}; - // Polygon 4, complex - double x6[]={-1.0,-0.5,0.0,0.5,1.0,0.5,0.0,-0.5}; - double x7[]={0.0,1.0,-0.1,1.0,0.0,-1.0,0.1,-1.0}; - Point[] poly1=new Point[N1],poly2=new Point[N2],poly3=new Point[N3],poly4=new Point[N4]; - for(i=0;i6 we get inaccuracy errors below - String s1,s2,s3,s4; - double x1=0,x2=0,x3=0,x4,sbeps; - char[] w =new char[N],u=new char[N],v=new char[N]; - boolean localflag, globalflag=false; - - - - // Test MParith - System.out.println("Testing MParith"); - - Ran myran=new Ran(17); - - // Test mpadd() - System.out.println(" Test mpadd()"); - localflag=false; - sbeps=1.e-15; - char[] w2=new char[N+1]; - for (j=0;j=0;i--) { - x1=x1/256+(int)(u[i]); - x2=x2/256+(int)(v[i]); - } - for (i=N;i>0;i--) - x3=x3/256+(int)(w2[i]); - x3 += 256*(int)(w2[0]); // Note!! w2 is right-shifted by the algorithm -// System.out.printf(x1 << " %f\n", x2 << " %f\n", x3 << " %f\n", abs(1.0-(x1+x2)/x3)); - localflag=localflag || abs(1.0-(x1+x2)/x3) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MParith: Multiple precision addition was inaccurate."); - - } - - // Test mpsub() - System.out.println(" Test mpsub()"); - localflag=false; - sbeps=1.e-14; - for (j=0;j=0;i--) { - x1=x1/256+(int)(u[i]); - x2=x2/256+(int)(v[i]); - x3=x3/256+(int)(w[i]); - } -// System.out.printf(abs(x3-abs(x1-x2))); - localflag=localflag || abs(x3-abs(x1-x2)) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MParith: Multiple precision subtraction was inaccurate."); - - } - - // Test mpsad() - System.out.println(" Test mpsad()"); - localflag=false; - sbeps=1.e-15; - for (j=0;j<=M;j++) { - for (i=0;i=0;i--) { - x1=x1/256+(int)(u[i]); - x2=x2/256+(i==(N-1) ? iv : 0); - } - for (i=N;i>0;i--) { - x3=x3/256+(int)(w2[i]); - } - x3 += 256*(int)(w2[0]); // Note!! w2 is right-shifted by the algorithm -// System.out.printf(abs(1.0-(x2+x1)/x3)); - localflag=localflag || abs(1.0-(x2+x1)/x3) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MParith: Multiple precision short addition was inaccurate."); - - } - - // Test mpsmu() - System.out.println(" Test mpsmu()"); - localflag=false; - sbeps=1.e-15; - for (j=0;j=0;i--) - x1=x1/256+(int)(u[i]); - x2=(int)(iv); - for (i=N;i>0;i--) - x3=x3/256+(int)(w2[i]); - x3 += 256*(int)(w2[0]); // Note!! w2 is right-shifted by the algorithm -// System.out.printf(abs(1.0-x2*x1/x3)); - localflag=localflag || abs(1.0-x2*x1/x3) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MParith: Multiple precision short multiplication was inaccurate."); - - } - - // Test mpsdv() - System.out.println(" Test mpsdv()"); - localflag=false; - sbeps=1.e-14; - for (j=0;j=0;i--) { - x1=x1/256+(int)(u[i]); - x3=x3/256+(int)(w[i]); - x4=x4/256+(i==(N-1) ? (int)(ir) : 0.0); - } - x2=(int)(iv); -// System.out.printf(1.0-(x3*x2+x4)/x1 << " %f\n", x4); - localflag=localflag || abs(1.0-(x3*x2+x4)/x1) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MParith: Multiple precision short division was inaccurate."); - - } - - // Test mpneg() - System.out.println(" Test mpneg()"); - localflag=false; - sbeps=1.e-15; - for (j=0;j=0;i--) { - x1=x1/256+(int)(u[i]); - x2=x2/256+(int)(v[i]); - } -// System.out.printf(x1 << " %f\n", x2 << " %f\n", abs(1.0-(x1+x2)/256.0)); - localflag=localflag || abs(1.0-(x1+x2)/256.0) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MParith: Multiple precision twos-complement negation is inaccurate."); - - } - - // Test mpmov() - System.out.println(" Test mpmov()"); - localflag=false; - for (j=0;j=0;i--) { - x1=x1/256+(int)(u[i]); - x2=x2/256+(int)(v[i]); - } - for (i=2*N-2;i>0;i--) - x3=x3/256+(int)(w3[i]); - x3 += 256*(int)(w3[0]); // w3[] was effectively right shifted to include all digits of result -// System.out.printf(x1 << " %f\n", x2 << " %f\n", x3 << " %f\n", abs(1.0-x1*x2/x3)); - localflag = localflag || abs(1.0-x1*x2/x3) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MParith: Multiple precision long multiplication in inaccurate."); - - } - - // Test mpinv() - System.out.println(" Test mpinv()"); - localflag=false; - sbeps=1.e-14; - for (j=0;j=0;i--) { - x1=x1/256+(int)(v[i]); - x2=x2/256+(int)(u[i]); - } -// System.out.printf(x1 << " %f\n", x2 << " %f\n", abs(x1*x2-1.0)); - localflag = localflag || abs(x1*x2-1.0) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MParith: Multiple precision inverse in inaccurate."); - } - - // Test mpdiv() - System.out.println(" Test mpdiv()"); - localflag=false; - sbeps=1.e-14; - char[] v2=new char[N-2]; - char[] q=new char[3],r=new char[N-2]; - for (j=0;j=0;i--) - x1=x1/256+(int)(u[i]); - for (i=N-3;i>=0;i--) - x2=x2/256+(int)(v2[i]); - for (i=2;i>=0;i--) - x3=x3/256+(int)(q[i]); - for (i=N-3;i>=0;i--) - x4=x4/256+(int)(r[i]); -// System.out.printf(x1 << " %f\n", x2 << " %f\n", x3 << " %f\n", x4 << " %f\n", abs(1.0-x2*x3/x1-(x4/x1/256/256))); - localflag=localflag || abs(1.0-x2*x3/x1-(x4/x1/256/256)) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MParith: Multiple precision long division is inaccurate."); - } - - // Test mpsqrt() - System.out.println(" Test mpsqrt()"); - localflag=false; - sbeps=1.e-14; - for (j=0;j=0;i--) { - x1=x1/256+(int)(v[i]); - x2=x2/256+(int)(w[i]); - x3=x3/256+(int)(u[i]); - } -// System.out.printf(x1 << " %f\n", x2 << " %f\n", x3 << " %f\n", abs(1.0-x2*x2/x1) << " %f\n", abs(1.0-x2*x3)); - localflag = localflag || abs(1.0-x2*x2/x1) > sbeps || abs(1.0-x2*x3) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MParith: Multiple precision square root is inaccurate."); - - } - - // Test mp2dfr() - System.out.println(" Test mp2dfr()"); - x1=0.0; - for (i=0;i=0;i--) - x1=x1/256+(int)(v[i]); - s1=mp2dfr(v); - s1=s1.substring(0, 17); //.erase(17,s1.length()); - String s6 = String.format("%20.18f",x1); - s6=s6.substring(0, 17); - // System.out.println(s1); - // System.out.println(s6); - localflag = (!s1.equals(s6)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MParith: Method mp2dfr() did not produce the correct string"); - - } - - // Test mppi() - System.out.println(" Test mppi()"); - String pi1="3.1415926535897932384626433832795028"; - String pi2="841971693993751058209749445923078164"; - String pi3=pi1+pi2; - s1=mppi(30); -// System.out.printf(s1 << " %f\n", pi3); - localflag = (!s1.equals(pi3)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MParith: method mppi() gives inaccurate value for PI"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter22/Test_Machar.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter22/Test_Machar.java deleted file mode 100644 index 90462ebf26..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter22/Test_Machar.java +++ /dev/null @@ -1,97 +0,0 @@ -package com.nr.test.test_chapter22; - -import static com.nr.NRUtil.DBL_EPSILON; -import static com.nr.NRUtil.DBL_MANT_DIG; -import static com.nr.NRUtil.FLT_RADIX; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.lna.Machar; - -public class Test_Machar { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - boolean localflag=false, globalflag=false; - - - - // Test Machar - System.out.println("Testing Machar"); - - Machar mch=new Machar(); -// mch.report(); - - localflag = mch.ibeta != FLT_RADIX; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Machar: Calculated radix does not agree with numeric_limits"); - - } - - localflag = mch.it != DBL_MANT_DIG; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Machar: Calculated number of mantissa digits does not agree with numeric_limits"); - - } - - /* - localflag = (mch.irnd==5); // && (numeric_limits::round_style != 1); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Machar: Calculated rounding method does not agree with numeric_limits"); - } - */ - - localflag = mch.eps != DBL_EPSILON; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Machar: Calculated smallest step around 1.0 does not agree with numeric_limits"); - - } - - localflag = mch.minexp != Double.MIN_EXPONENT; //numeric_limits::min_exponent; // WHP added +1 - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Machar: Calculated minimum exponent does not agree with numeric_limits"); - - } - - localflag = mch.maxexp != Double.MAX_EXPONENT+1; //numeric_limits::max_exponent; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Machar: Calculated maximum exponent does not agree with numeric_limits"); - - } - - localflag = mch.xmin != Double.MIN_NORMAL; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Machar: Calculated minimum normalized value does not agree with numeric_limits"); - - } - - localflag = mch.xmax != Double.MAX_VALUE; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Machar: Calculated maximum finite value does not agree with numeric_limits"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter22/Test_PSpage.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter22/Test_PSpage.java deleted file mode 100644 index 6cf06dd05c..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter22/Test_PSpage.java +++ /dev/null @@ -1,97 +0,0 @@ -package com.nr.test.test_chapter22; - -import static com.nr.NRUtil.buildVector; - -import java.io.IOException; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.lna.PSpage; - -public class Test_PSpage { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() throws IOException { - boolean globalflag=false; - - - - // Test PSpage - System.out.println("Testing PSpage"); - - PSpage pg=new PSpage(new java.io.File("PSpage_output.ps")); - pg.puttext("Hello",100,100,0.0); -// pg.addtext(" World"); - pg.putctext("Hello World",200,100,0.0); - pg.putrtext("Hello World",300,100,0.0); - pg.lineseg(400,100,500,100); - pg.pointsymbol(550,100,72,16.0); - - pg.setlinewidth(3.0); - pg.setdash("4 4"); - pg.puttext("Hello",100,200,90.0); -// pg.addtext(" World"); - pg.putctext("Hello World",200,200,90.0); - pg.putrtext("Hello World",300,200,90.0); - pg.lineseg(400,200,500,200); - pg.pointsymbol(550,200,108,20.0); - - pg.setdash(""); - pg.puttext("Hello",100,300,45.0); -// pg.addtext(" World"); - pg.putctext("Hello World",200,300,45.0); - pg.putrtext("Hello World",300,300,45.0); - pg.lineseg(400,300,500,300); - pg.pointsymbol(550,300,115,20.0); - - pg.gsave(); - pg.setgray(0.7); - pg.puttext("Hello",100,400,45.0); -// pg.addtext(" World"); - pg.putctext("Hello World",200,400,45.0); - pg.putrtext("Hello World",300,400,45.0); - pg.lineseg(400,400,500,400); - pg.pointsymbol(550,400,110,20.0); - - pg.grestore(); - pg.puttext("Hello",100,500,45.0); -// pg.addtext(" World"); - pg.putctext("Hello World",200,500,45.0); - pg.putrtext("Hello World",300,500,45.0); - pg.lineseg(400,500,500,500); - pg.pointsymbol(550,500,112,12.0); - - pg.puttext("Hello",100,600,45.0); - pg.rawps("gsave 200.0 600.0 translate 90.0 rotate 0 0 mt "); - pg.addtext(" World"); - pg.rawps("grestore\n"); - - double xx[]={300.0,350.0,400.0,350.0,300.0}; - double yy[]={650.0,650.0,600.0,550.0,550.0}; - double[] x=buildVector(xx),y=buildVector(yy); - pg.polyline(x,y,true,false,false); - - pg.setcolor(255,0,0); - double xx2[]={450.0,500.0,550.0,500.0,450.0}; - double yy2[]={650.0,650.0,600.0,550.0,550.0}; - double[] x2=buildVector(xx2),y2=buildVector(yy2); - pg.polyline(x2,y2,true,true,false); - - pg.close(); - // pg.display(); - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter22/Test_PSplot.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter22/Test_PSplot.java deleted file mode 100644 index 79571fdc4b..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter22/Test_PSplot.java +++ /dev/null @@ -1,83 +0,0 @@ -package com.nr.test.test_chapter22; - -import static com.nr.NRUtil.SQR; -import static java.lang.Math.cos; -import static java.lang.Math.exp; -import static java.lang.Math.sin; -import static java.lang.Math.sqrt; - -import java.io.IOException; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.lna.PSpage; -import com.nr.lna.PSplot; - -public class Test_PSplot { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() throws IOException{ - double[] x1=new double[500],x2=new double[500],y1=new double[500],y2=new double[500],y3=new double[500],y4=new double[500]; - boolean globalflag=false; - - - - // Test PSplot - System.out.println("Testing PSplot"); - - for (int i=0;i<500;i++) { - x1[i] = 5.*i/499.; - y1[i] = exp(-0.5*x1[i]); - y2[i] = exp(-0.5*SQR(x1[i])); - y3[i] = exp(-0.5*sqrt(5.-x1[i])); - x2[i] = cos(0.062957*i); - y4[i] = sin(0.088141*i); - } - - PSpage pg=new PSpage(new java.io.File("PSplot_output.ps")); - PSplot plot1=new PSplot(pg,100.,500.,100.,500.); - - plot1.setlimits(0.,5.,0.,1.); - plot1.frame(); - plot1.autoscales(); - plot1.xlabel("abscissa"); - plot1.ylabel("ordinate"); - plot1.lineplot(x1,y1); - plot1.setdash("2 4"); - plot1.lineplot(x1,y2); - plot1.setdash("6 2 4 2"); - plot1.lineplot(x1,y3); - plot1.setdash(""); - - plot1.pointsymbol(1.,exp(-0.5),72,16.); - plot1.pointsymbol(2.,exp(-1.),108,12.); - plot1.pointsymbol(2.,exp(-2.),115,12.); - plot1.label("dingbat 72",1.1,exp(-0.5)); - plot1.label("dingbat 108",2.1,exp(-1.)); - plot1.label("dingbat 115",2.1,exp(-2.)); - - PSplot plot2=new PSplot(pg,325.,475.,325.,475.); - plot2.clear(); - plot2.setlimits(-1.2,1.2,-1.2,1.2); - plot2.frame(); - plot2.scales(1.,0.5,1.,0.5); - plot2.lineplot(x2,y4); - - pg.close(); - // pg.display(); - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter22/Test_decchk.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter22/Test_decchk.java deleted file mode 100644 index 56626b6427..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter22/Test_decchk.java +++ /dev/null @@ -1,201 +0,0 @@ -package com.nr.test.test_chapter22; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.lna.Icrc.*; -public class Test_decchk { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,nbad,ntot,N=7; - byte[] ch = new byte[1]; - boolean localflag=false, globalflag=false; - - - - // Test decchk - System.out.println("Testing decchk"); - - byte[] s1="8635741".getBytes(); - byte[] s2="0".getBytes(); - byte[] s3; - - // Test for functionality of the check digit - ntot=nbad=0; - for (i=0;i 86jki41 where i != j - ntot=nbad=0; - for (i='0';i<='9';i++) { - for (j='0';j<='9';j++) { - for (k='0';k<='9';k++) { - s3=new String(s1).getBytes(); - s3[3]=(byte)k; - if (i != j) { - ntot++; - s3[2]=(byte)i; - s3[4]=(byte)j; - decchk(s3,s2,0); - s3=(new String(s3)+new String(s2)).getBytes(); - s3[2]=(byte)j; // Transpose digits - s3[4]=(byte)i; - if (!decchk(s3,ch,0)) nbad++; // See if it works with transposition - } - } - } - } -// System.out.println("Jump Transitions:"); -// System.out.println(" Total tries:%f\n", " %f\n", ntot); -// System.out.println(" Bad tries:%f\n", " %f\n", nbad); - localflag = localflag || (nbad != 848); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** decchk: Failure to identify 848 of the possible 900 Jump Transition errors"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_BaryRat_interp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_BaryRat_interp.java deleted file mode 100644 index 457479e841..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_BaryRat_interp.java +++ /dev/null @@ -1,68 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.test.NRTestUtil.*; -import static java.lang.Math.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.interp.BaryRat_interp; -import com.nr.ran.Ran; - -public class Test_BaryRat_interp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - double func_BaryRat(double x) - { - return (1.0-x*(0.5-0.1*x))/(1.0+(x-2.0)*(x-2.0)); - } - - @Test - public void test() { - int i,j,N=20,M=6; - double ymax,dy,sbeps; - double[] x=new double[N],y=new double[N],xx=new double[N],yy=new double[N],zz=new double[N]; - boolean localflag, globalflag=false; - - - - // Test BaryRat_interp - System.out.println("Testing BaryRat_interp"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** BaryRat_interp: Inaccurate interpolation of rational function."); - - } - } - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Bilin_interp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Bilin_interp.java deleted file mode 100644 index eb5f1eb3dd..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Bilin_interp.java +++ /dev/null @@ -1,63 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.test.NRTestUtil.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.interp.Bilin_interp; -import com.nr.ran.Ran; - -public class Test_Bilin_interp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps,xx1,xx2; - int i,j,N=20; - double[] x1=new double[N],x2=new double[N],yy=new double[N],zz=new double[N]; - double[][] y = new double[N][N]; - boolean localflag, globalflag=false; - - - - // Test Bilin_interp - System.out.println("Testing Bilin_interp"); - for(i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bilin_interp: Inaccurate interpolation of 2D linear function."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Curve_interp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Curve_interp.java deleted file mode 100644 index 1a8612b5a9..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Curve_interp.java +++ /dev/null @@ -1,96 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.NRUtil.*; -import static com.nr.test.NRTestUtil.*; -import static java.lang.Math.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.interp.Curve_interp; - -public class Test_Curve_interp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps; - int i,NDIM=3,NPTS=20; - boolean close; - double vec[]={2.0/sqrt(29.0),3.0/sqrt(29.0),4.0/sqrt(29.0)}; - double[] target = new double[NDIM]; - double[][] ptsin = new double[NPTS][NDIM]; - boolean localflag, globalflag=false; - - - - // Test Curve_interp - System.out.println("Testing Curve_interp"); - - // Test straight line - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Curve_interp: Does not work for data on a 3D straight line."); - - } - - // Test closed circle - double a[]={0.0,vec[2],-vec[1]}; // vec x (1,0,0) - double norm=sqrt(SQR(vec[2])+SQR(vec[1])); // normalize a[] - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Curve_interp: Does not work for data on a 3D circle."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Krig.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Krig.java deleted file mode 100644 index 8444ccefa6..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Krig.java +++ /dev/null @@ -1,72 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.cos; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.interp.Krig; -import com.nr.interp.Powvargram; -import com.nr.ran.Ran; - -public class Test_Krig { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,NPTS=100,NDIM=2,N=10,M=10; - double sbeps=0.01; // p=5.0, - double[][] pts = new double[NPTS][NDIM]; - double[] y = new double[NPTS],actual = new double[M],estim = new double[M],ppt = new double[2]; - boolean localflag, globalflag=false; - - - - // Test Krig (and Powvargram) - System.out.println("Testing Krig (and Powvargram)"); - Ran myran = new Ran(17); - double[][] pt = new double[M][2]; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Krig, Powvargram: Inaccurate Krig interpolation."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Laplace_interp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Laplace_interp.java deleted file mode 100644 index 797343cef9..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Laplace_interp.java +++ /dev/null @@ -1,60 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.NRUtil.*; -import static com.nr.test.NRTestUtil.*; -import static java.lang.Math.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.interp.Laplace_interp; -import com.nr.ran.Ran; - -public class Test_Laplace_interp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,p,q,N=100,M=100,NBAD=1000; - double sbeps=0.01; - double[][] actual = new double[N][M]; - boolean localflag, globalflag=false; - - - - // Test Laplace_interp - System.out.println("Laplace_interp"); - Ran myran = new Ran(17); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Laplace_interp: Inaccurate Laplace interpolation of missing matrix data."); - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Linear_interp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Linear_interp.java deleted file mode 100644 index caf3f1c153..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Linear_interp.java +++ /dev/null @@ -1,57 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.interp.Linear_interp; -import com.nr.ran.Ran; - -public class Test_Linear_interp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps=5.e-15; - int i,N=10; - double[] x=new double[N],y=new double[N],xx=new double[N],yy=new double[N],zz=new double[N]; - boolean localflag, globalflag=false; - - - - // Test Linear_interp - System.out.println("Testing Linear_interp"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Linear_interp: interpolation of linear function unsuccessful."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Poly2D_interp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Poly2D_interp.java deleted file mode 100644 index 5820d43dfc..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Poly2D_interp.java +++ /dev/null @@ -1,49 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.NRUtil.buildVector; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.interp.Poly2D_interp; - -public class Test_Poly2D_interp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps=5.e-15; - int i,j; - double xx1[]={1.0,2.0,3.0,4.0},xx2[]={1.0,2.0,3.0,4.0}; - double[] x1 = buildVector(xx1),x2 = buildVector(xx2); - double[][] y = new double[4][4]; - for(i=0;i<4;i++) for(j=0;j<4;j++) y[i][j]=xx1[i]+xx2[j]; - boolean localflag, globalflag=false; - - - - // Test Poly2D_interp - System.out.println("Testing Poly2D_interp"); - Poly2D_interp z = new Poly2D_interp(x1,x2,y,3,3); - localflag = abs(z.interp(2.5,2.5)-5.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poly2D_interp: Inaccurate 2D polynomial interpolation."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Poly_interp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Poly_interp.java deleted file mode 100644 index ae2063fad4..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Poly_interp.java +++ /dev/null @@ -1,60 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.test.NRTestUtil.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.interp.Poly_interp; -import com.nr.ran.Ran; - -public class Test_Poly_interp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps; - int i,N=20; - double[] x= new double[N],y= new double[N],xx= new double[N],yy= new double[N],zz= new double[N],dyy= new double[N]; - boolean localflag, globalflag=false; - - - - // Test Poly_interp - System.out.println("Testing Poly_interp"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poly_interp: interpolation of 4th-order polynomial unsuccessful."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_RBF_interp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_RBF_interp.java deleted file mode 100644 index 1f805216f0..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_RBF_interp.java +++ /dev/null @@ -1,193 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.cos; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.interp.RBF_gauss; -import com.nr.interp.RBF_interp; -import com.nr.interp.RBF_inversemultiquadric; -import com.nr.interp.RBF_multiquadric; -import com.nr.interp.RBF_thinplate; -import com.nr.ran.Ran; - -public class Test_RBF_interp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,NPTS=100,NDIM=2,N=10,M=10; - double scale,sbeps=0.05; - double[][] pts =new double[NPTS][NDIM]; - double[] y = new double[NPTS],actual = new double[M],estim = new double[M],ppt = new double[2]; - boolean localflag, globalflag=false; - - - - // Test RBF_interp - Ran myran = new Ran(17); - double[][] pt = new double[M][2]; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** RBF_interp,multiquadric: Inaccurate multquadric interpolation with no normalization."); - - } - - System.out.println("Testing RBF_interp with thinplate function"); - scale=2.0; - RBF_thinplate thinplate = new RBF_thinplate(scale); - RBF_interp myRBFtpf = new RBF_interp(pts,y,thinplate,false); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** RBF_interp,thinplate: Inaccurate thinplate interpolation with no normalization."); - - } - - System.out.println("Testing RBF_interp with gauss function"); - scale=5.0; - RBF_gauss gauss = new RBF_gauss(scale); - RBF_interp myRBFgf = new RBF_interp (pts,y,gauss,false); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** RBF_interp,gauss: Inaccurate gauss interpolation with no normalization."); - - } - - System.out.println("Testing RBF_interp with inversemultiquadric function"); - scale=3.0; - RBF_inversemultiquadric inversemultiquadric = new RBF_inversemultiquadric(scale); - RBF_interp myRBFimqf =new RBF_interp(pts,y,inversemultiquadric,false); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** RBF_interp,inversemultiquadric: Inaccurate inversemultiquadric interpolation with no normalization."); - - } - - // Test same interpolators with normalization turned on - scale=3.0; - System.out.println("Testing RBF_interp with multiquadric function"); - RBF_interp myRBFmqt = new RBF_interp(pts,y,multiquadric,true); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** RBF_interp,multiquadric: Inaccurate multiquadric interpolation with normalization."); - - } - - System.out.println("Testing RBF_interp with thinplate function"); - scale=2.0; - RBF_interp myRBFtpt =new RBF_interp(pts,y,thinplate,true); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** RBF_interp,thinplate: Inaccurate thinplate interpolation with normalization."); - - } - - System.out.println("Testing RBF_interp with gauss function"); - scale=5.0; - RBF_interp myRBFgt = new RBF_interp(pts,y,gauss,true); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** RBF_interp,gauss: Inaccurate gauss interpolation with normalization."); - - } - - System.out.println("Testing RBF_interp with inversemultiquadric function"); - scale=2.0; - RBF_interp myRBFimqt = new RBF_interp(pts,y,inversemultiquadric,true); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** RBF_interp,inversemultiquadric: Inaccurate inversemultiquadric interpolation with normalization."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Rat_interp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Rat_interp.java deleted file mode 100644 index c531b0fec8..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Rat_interp.java +++ /dev/null @@ -1,61 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.interp.Rational_interp; -import com.nr.ran.Ran; - -public class Test_Rat_interp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps; - int i,N=20; - double[] x= new double[N],y= new double[N],xx= new double[N],yy= new double[N],zz= new double[N],dyy= new double[N]; - boolean localflag, globalflag=false; - - - - // Test Rat_interp - System.out.println("Testing Rat_interp"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Rat_interp: Inaccurate interpolation of rational function."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Shep_interp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Shep_interp.java deleted file mode 100644 index f0741ecce5..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Shep_interp.java +++ /dev/null @@ -1,70 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.cos; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.interp.Shep_interp; -import com.nr.ran.Ran; - -public class Test_Shep_interp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,NPTS=100,NDIM=2,N=10,M=10; - double p=5.0,sbeps=0.05; - double[][] pts = new double[NPTS][NDIM]; - double[] y = new double[NPTS],actual = new double[M],estim = new double[M],ppt = new double[2]; - boolean localflag, globalflag=false; - - - - // Test Shep_interp - System.out.println("Testing Shep_interp"); - Ran myran = new Ran(17); - double[][] pt = new double[M][2]; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Shepard: Inaccurate Shepard interpolation."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Spline2D_interp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Spline2D_interp.java deleted file mode 100644 index fec8a4d14b..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Spline2D_interp.java +++ /dev/null @@ -1,50 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.NRUtil.buildVector; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.interp.Spline2D_interp; - -public class Test_Spline2D_interp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps=5.e-15; - int i,j; - double xx1[]={1.0,2.0,3.0,4.0},xx2[]={1.0,2.0,3.0,4.0}; - double[] x1 = buildVector(xx1),x2 = buildVector(xx2); - double[][] y =new double[4][4]; - boolean localflag, globalflag=false; - - - - // Test Spline2D_interp - System.out.println("Testing Spline2D_interp"); - for(i=0;i<4;i++) - for(j=0;j<4;j++) - y[i][j]=xx1[i]+xx2[j]; - Spline2D_interp z = new Spline2D_interp(x1,x2,y); - localflag = abs(z.interp(2.5,2.5)-5.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Spline2D_interp: ."); - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Spline_interp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Spline_interp.java deleted file mode 100644 index 522b930477..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_Spline_interp.java +++ /dev/null @@ -1,65 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.acos; -import static java.lang.Math.sin; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.interp.Spline_interp; -import com.nr.ran.Ran; - -public class Test_Spline_interp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps; - int i,N=20; - double yp1,ypn,pi; - double[] x= new double[N],y= new double[N],xx= new double[N],yy= new double[N],zz= new double[N]; - boolean localflag, globalflag=false; - - - - // Test Spline_interp - System.out.println("Testing Spline_interp"); - pi=acos(-1.0); - for(i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Spline_interp: Inaccurate interpolation of sin() function."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_bcuint.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_bcuint.java deleted file mode 100644 index a67e717567..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_bcuint.java +++ /dev/null @@ -1,75 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.NRUtil.*; -import static com.nr.interp.Spline2D_interp.bcuint; -import static com.nr.test.NRTestUtil.*; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -public class Test_bcuint { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i; // N=10; - double x1l,x1u,x2l,x2u,uv,sbeps=1.e-16; - double u[]={0.0,0.5,0.5,0.0}; - double v[]={0.0,0.0,0.5,0.5}; - double[] yy=new double[4],yy1=new double[4],yy2=new double[4],yy12=new double[4]; - boolean localflag, globalflag=false; - - - - // Test bcucof and bcuint - System.out.println("Testing bcucof and bcuint"); - x1l=u[0]; - x1u=u[1]; - x2l=v[0]; - x2u=v[3]; - for (i=0;i<4;i++) { - uv=u[i]*v[i]; - yy[i]=uv*uv; - yy1[i]=2.0*v[i]*uv; - yy2[i]=2.0*u[i]*uv; - yy12[i]=4.0*uv; - } - double[] y = buildVector(yy),y1 = buildVector(yy1),y2 = buildVector(yy2),y12 = buildVector(yy12); - double x1[]={0.1,0.2,0.3,0.4,0.5}; - double x2[]={0.2,0.4,0.1,0.3,0.3}; - double act[]={0.0004,0.0064,0.0009,0.0144,0.0225}; - double[] ansy=new double[5],ansy1=new double[5],ansy2=new double[5]; - for (i=0;i<5;i++) { - doubleW ansyW = new doubleW(ansy[i]); - doubleW ansy1W = new doubleW(ansy1[i]); - doubleW ansy2W = new doubleW(ansy2[i]); - - bcuint(y,y1,y2,y12,x1l,x1u,x2l,x2u,x1[i],x2[i],ansyW,ansy1W,ansy2W); - ansy[i] = ansyW.val; - ansy1[i] = ansy1W.val; - ansy2[i] = ansy2W.val; - } - - double[] actual = buildVector(act),answer=buildVector(ansy); - localflag = maxel(vecsub(actual,answer)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** bcucof,bcuint: Inaccurate bicubic interpolation."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_polcoe.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_polcoe.java deleted file mode 100644 index e7753bcbe9..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_polcoe.java +++ /dev/null @@ -1,58 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.test.NRTestUtil.*; -import static com.nr.interp.PolCoef.*; -import static java.lang.Math.*; -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -public class Test_polcoe { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double pi,sbeps; - int i,j,N=10; - double[] x= new double[N],y= new double[N],z= new double[N]; - double[] cof= new double[N]; - boolean localflag, globalflag=false; - - - - // Test Linear_interp - System.out.println("Testing polcoe"); - pi=acos(-1.0); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** polcoe: Inaccurate polynomial approximation of sin() function."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_polcof.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_polcof.java deleted file mode 100644 index 1221e90a9f..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter3/Test_polcof.java +++ /dev/null @@ -1,57 +0,0 @@ -package com.nr.test.test_chapter3; - -import static com.nr.test.NRTestUtil.*; -import static com.nr.interp.PolCoef.*; -import static java.lang.Math.*; -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -public class Test_polcof { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double pi,sbeps; - int i,j,N=10; - double[] x= new double[N],y= new double[N],cof= new double[N],z= new double[N]; - boolean localflag, globalflag=false; - - - - // Test Linear_interp - System.out.println("Testing polcof"); - pi=acos(-1.0); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** polcof: ."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_Adapt.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_Adapt.java deleted file mode 100644 index 53755f64e9..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_Adapt.java +++ /dev/null @@ -1,68 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Adapt; -import com.nr.sf.Bessjy; - -public class Test_Adapt { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=10; - double x1,x2,sbeps=1.e-14; - double[] y= new double[N],yy= new double[N]; - boolean localflag, globalflag=false; - - // Test Adapt - System.out.println("Testing Adapt"); - Bessj0_Adapt bj0 = new Bessj0_Adapt(); - Bessj1_Adapt bj1 = new Bessj1_Adapt(); - Adapt adp = new Adapt(0.0); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Adapt: Failure to achieve advertised accuracy in integral"); - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Bessj0_Adapt implements UniVarRealValueFun{ - public double funk (double x) { - Bessjy b = new Bessjy(); - return(b.j0(x)); - } - }; - - class Bessj1_Adapt implements UniVarRealValueFun{ - public double funk (double x) { - Bessjy b = new Bessjy(); - return(b.j1(x)); - } - }; - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_Stiel.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_Stiel.java deleted file mode 100644 index 60f1c4cae9..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_Stiel.java +++ /dev/null @@ -1,124 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.GaussianWeights.gaulag; -import static com.nr.fi.GaussianWeights.gauleg; -import static com.nr.sort.Sorter.sort2; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.exp; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.fi.Stiel; - -public class Test_Stiel { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int N=10; - double sbeps; - double[] x1= new double[N],w1= new double[N],x2= new double[N],w2= new double[N]; - boolean localflag, globalflag=false; - - - - // Test Stiel - System.out.println("Testing Stiel"); - - MyStiel ss1 = new MyStiel(N,-1.0,1.0,3.7); - ss1.get_weights(x1,w1); // Largest abscissas are first - sort2(x1,w1); - - gauleg(-1.0,1.0,x2,w2); - - sbeps=1.e-15; -// System.out.printf(maxel(vecsub(x1,x2)) << endl; - localflag = maxel(vecsub(x1,x2)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Stiel: Incorrect abscissas for Gauss-Legendre"); - - } - - sbeps=1.e-14; -// System.out.printf(maxel(vecsub(w1,w2)) << endl; - localflag = maxel(vecsub(w1,w2)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Stiel: Incorrect weights for Gauss-Legendre"); - - } - - MyStiel ss2 = new MyStiel(N,-5.0,5.0); - ss2.get_weights(x1,w1); - sort2(x1,w1); - - gaulag(x2,w2,1.0); - - sbeps=5.e-14; -// System.out.printf(maxel(vecsub(x1,x2)) << endl; - localflag = maxel(vecsub(x1,x2)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Stiel: Incorrect abscissas for Gauss-Laguerre"); - - } - - sbeps=1.e-14; -// System.out.printf(maxel(vecsub(w1,w2)) << endl; - localflag = maxel(vecsub(w1,w2)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Stiel: Incorrect weights for Gauss-Laguerre"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class MyStiel extends Stiel { - - public MyStiel(int nn, double aaa, double bbb) { - super(nn, aaa, bbb); - } - - public MyStiel(final int nn, final double aaa, final double bbb, - final double hmaxx) { - super(nn, aaa, bbb, hmaxx); - } - - @Override - public double wt1(final double x, final double del) { - return 1.0; // Gauss-Legendre - } - - @Override - public double wt2(final double x) { - return x * exp(-x); - } - - @Override - public double fx(final double t) { - return exp(t - exp(-t)); - } - - @Override - public double fdxdt(final double t) { - double s = exp(-t); - return exp(t - s) * (1.0 + s); - } - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_derule.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_derule.java deleted file mode 100644 index 2c8b899648..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_derule.java +++ /dev/null @@ -1,102 +0,0 @@ -package com.nr.test.test_chapter4; - -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.log; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.RealValueFun; -import com.nr.fi.DErule; - -public class Test_derule { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,M=10; - double PI=acos(-1.0); // ,INFTY=1.0e99; - double a,b,s=0,sold,expect,sbeps; - boolean localflag, globalflag=false; - - // Test DErule - System.out.println("Testing DErule"); - - a=0.0; - b=1.0; - func_DErule func_DErule = new func_DErule(); - DErule derule = new DErule(func_DErule,a,b); - expect=2.0-PI*PI/6.0; - - sold=derule.next(); - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** DErule,case 2: Failure to achieve expected accuracy in improper integral"); - - } - - a=0.0; - b=1.0; - - func_DErule2 func_DErule2 = new func_DErule2(); - DErule derule2 = new DErule(func_DErule2,a,b,4.5); - expect=PI; - - sold=derule2.next(); - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** DErule,case 2: Failure to achieve expected accuracy in improper integral"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - //Test functions - class func_DErule implements RealValueFun { - public double funk(double[] x) {//final double x, final double delta) - return log(x[0])*log(1.0-x[0]); - } - } - - class func_DErule2 implements RealValueFun { - public double funk(final double[] xx) { //final double x, final double delta) - double x = xx[0], delta = xx[1]; - if (x < 0.1) return (1.0/sqrt(delta)/sqrt(1.0-x)); - else if (x > 0.9) return (1.0/sqrt(x)/sqrt(delta)); - else return (1.0/sqrt(x)/sqrt(1.0-x)); - } - } - - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gaucof.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gaucof.java deleted file mode 100644 index 9fedbfc557..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gaucof.java +++ /dev/null @@ -1,63 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.GaussianWeights.gaucof; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -public class Test_gaucof { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=10; - double amu0,check,PI=acos(-1.0),sbeps; - double[] a= new double[N],b= new double[N],x= new double[N],w= new double[N]; - boolean localflag, globalflag=false; - - // Test gaucof - System.out.println("Testing gaucof"); - - // Test with Gauss-Hermite - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** gaucof: Gaussian weights do not sum to correct value"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gauher.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gauher.java deleted file mode 100644 index e86942318f..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gauher.java +++ /dev/null @@ -1,76 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.NRUtil.SQR; -import static com.nr.fi.GaussianWeights.gauher; -import static com.nr.fi.Trapzd.qsimp; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.exp; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.sf.Bessjy; - -public class Test_gauher { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,N=8,M=20; - double val,sbeps=1.e-14; - double[] y= new double[N],yy= new double[N],x = new double[M],w = new double[M]; - boolean localflag, globalflag=false; - - // Test gauher - System.out.println("Testing gauher"); - Bessjn_gauher bjn = new Bessjn_gauher(); - gauher(x,w); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** gauher: Failure to achieve accurate integral"); - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Bessjn_gauher { - double get(int n,double x) { - Bessjy b = new Bessjy(); - return(b.jn(n,x)); - } - }; - - class Func_gauher implements UniVarRealValueFun { - int n; - - Func_gauher(int nn) {n = nn;} - - public double funk (double x) { - Bessjn_gauher bjn = new Bessjn_gauher() ; - return(exp(-SQR(x))*bjn.get(n,x)); - } - }; - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gaujac.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gaujac.java deleted file mode 100644 index 71cd339061..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gaujac.java +++ /dev/null @@ -1,76 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.GaussianWeights.gaujac; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.sf.Bessjy; - -public class Test_gaujac { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=8,M=20; - double alfa,beta,val,sbeps=1.e-11; - double[] y= new double[N],yy= new double[N],x= new double[M],w= new double[M]; - boolean localflag, globalflag=false; - - // Test gaujac - System.out.println("Testing gaujac"); - Bessj0_gaujac bj0 = new Bessj0_gaujac(); - Bessj1_gaujac bj1 = new Bessj1_gaujac(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** gaujac: Failure to achieve accurate integral"); - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Bessj0_gaujac implements UniVarRealValueFun{ - public double funk (double x) { - Bessjy b = new Bessjy(); - return(b.j0(x)); - } - }; - - class Bessj1_gaujac implements UniVarRealValueFun{ - public double funk (double x) { - Bessjy b = new Bessjy(); - return(b.j1(x)); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gaulag.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gaulag.java deleted file mode 100644 index 060f95ad3f..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gaulag.java +++ /dev/null @@ -1,81 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.GaussianWeights.gaulag; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.sf.Bessjy; - -public class Test_gaulag { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=8,M=20; - double alf,val,sbeps=1.e-8; - double[] y= new double[N],yy= new double[N],x= new double[M],w= new double[M]; - boolean localflag, globalflag=false; - - - - // Test gaulag - System.out.println("Testing gaulag"); - Bessj0_gaulag bj0 = new Bessj0_gaulag(); - Bess_sum bs = new Bess_sum(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** gaulag: Failure to achieve accurate integral"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class Bessj0_gaulag implements UniVarRealValueFun{ - public double funk(double x) { - Bessjy b = new Bessjy(); - return(b.j0(x)); - } - }; - - class Bessj1_gaulag implements UniVarRealValueFun{ - public double funk (double x) { - Bessjy b= new Bessjy(); - return(b.j1(x)); - } - }; - - class Bess_sum implements UniVarRealValueFun{ - public double funk(double x) { - Bessj0_gaulag b0 = new Bessj0_gaulag(); - Bessj1_gaulag b1 = new Bessj1_gaulag(); - return(b0.funk(x)+b1.funk(x)); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gauleg.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gauleg.java deleted file mode 100644 index 4b813d4729..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_gauleg.java +++ /dev/null @@ -1,71 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.GaussianWeights.gauleg; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.sf.Bessjy; - -public class Test_gauleg { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=10,M=10; - double x1,x2,val,sbeps=51.e-14; - double[] y= new double[N],yy= new double[N],x= new double[M],w= new double[M]; - boolean localflag, globalflag=false; - - - - // Test gauleg - System.out.println("Testing gauleg"); - Bessj0_gauleg bj0 = new Bessj0_gauleg(); - Bessj1_gauleg bj1 = new Bessj1_gauleg(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** gauleg: Failure to achieve accurate integral"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class Bessj0_gauleg implements UniVarRealValueFun{ - public double funk (double x) { - Bessjy b=new Bessjy(); - return(b.j0(x)); - } - }; - - class Bessj1_gauleg implements UniVarRealValueFun{ - public double funk (double x) { - Bessjy b =new Bessjy(); - return(b.j1(x)); - } - }; -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_lobatto.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_lobatto.java deleted file mode 100644 index 946ecba52d..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_lobatto.java +++ /dev/null @@ -1,81 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.GaussianWeights.lobatto; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -public class Test_lobatto { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=10; - double amu0,check,sbeps,PI=acos(-1.0); - double[] a= new double[N],b= new double[N],x= new double[N],w= new double[N]; - boolean localflag, globalflag=false; - - - - // Test lobatto - System.out.println("Testing lobatto"); - // Test with Gauss-Chebyshev - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** lobatto: Gaussian quadrature weights to not add to the correct value"); - - } - - sbeps=1.e-15; -// System.out.printf(abs(x[0]-1.0) << endl; - localflag = abs(x[0]-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** lobatto: First element of x[] is not the requested value of 1.0"); - - } - - sbeps=1.e-15; -// System.out.printf(abs(x[N-1]+1.0) << endl; - localflag = abs(x[N-1]+1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** lobatto: Last element of x[] is not the requested value of -1.0"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midexp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midexp.java deleted file mode 100644 index 75f89f1a7e..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midexp.java +++ /dev/null @@ -1,61 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.Midpnt.qromo; -import static java.lang.Math.abs; -import static java.lang.Math.exp; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Midexp; - -public class Test_midexp implements UniVarRealValueFun{ - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - // int i,j,M=14; - double INFTY=1.e99; - double a,b,s,expect,eps=3.0e-10,sbeps=1.e-6; - boolean localflag, globalflag=false; - - - - // Test midexp - System.out.println("Testing midexp"); - - a=1.0; - b=INFTY; - Midexp midexp = new Midexp(this,a,b); - s=qromo(midexp,eps); - - expect=2.0/exp(1.0); - -// System.out.printf(s << " %f\n", expect << endl; - - System.out.printf("midexp: Maximum discrepancy = %f\n", abs(s-expect)); - localflag = abs(s-expect) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** midexp: Failure to achieve expected accuracy in improper integral"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - //Test function - public double funk(final double x) { - return x*exp(-x); - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midinf.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midinf.java deleted file mode 100644 index ec0a83972c..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midinf.java +++ /dev/null @@ -1,85 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.Midpnt.qromo; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.exp; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Midinf; - -public class Test_midinf { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - // int i,j,M=14; - double INFTY=1.e20,PI=acos(-1.0); - double a,b,s1,s2,expect,sbeps=1.e-6; - boolean localflag, globalflag=false; - - - - // Test midinf - System.out.println("Testing midinf"); - - expect=sqrt(PI)/2.0/exp(1.0); - - a=-INFTY; - b=-1.0; - func_midinf1 func_midinf1 =new func_midinf1(); - Midinf midinf1 = new Midinf(func_midinf1,a,b); - s1=qromo(midinf1); - - System.out.printf("midinf,case 1: Maximum discrepancy = %f\n", abs(s1-expect)); - localflag = abs(s1-expect) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** midinf,case 1: Failure to achieve expected accuracy in improper integral"); - - } - - a=1.0; - b=INFTY; - func_midinf2 func_midinf2 = new func_midinf2(); - Midinf midinf2 = new Midinf(func_midinf2,a,b); - s2=qromo(midinf2); - - System.out.printf("midinf,case 2: Maximum discrepancy = %f\n", abs(s2-expect)); - localflag = abs(s2-expect) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** midinf,case 2: Failure to achieve expected accuracy in improper integral"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - // Test function - class func_midinf1 implements UniVarRealValueFun { - public double funk(final double x) { - return sqrt(-x - 1) * exp(x); - } - } - - class func_midinf2 implements UniVarRealValueFun { - public double funk(final double x) { - return sqrt(x - 1) * exp(-x); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midpnt.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midpnt.java deleted file mode 100644 index ea564514cb..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midpnt.java +++ /dev/null @@ -1,76 +0,0 @@ -package com.nr.test.test_chapter4; - -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.cos; -import static java.lang.Math.sin; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Midpnt; - -public class Test_midpnt { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int j,M=14; - double a,b,s=0,expect,PI=acos(-1.0),sbeps=1.e-10; - boolean localflag, globalflag=false; - - - - // Test midpnt - System.out.println("Testing midpnt"); - -// a=0.0; -// b=1.0; - a=0.0; - b=PI; - func_midpnt func_midpnt = new func_midpnt(); - Midpnt mpt = new Midpnt(func_midpnt,a,b); - - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** midpnt: Failure to achieve expected accuracy in improper integral"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class func_midpnt implements UniVarRealValueFun { - public double funk(final double x) { - return sin(x); - } - } - - //integral of test function - double fint_midpnt(final double x) - { - return -cos(x); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midsql.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midsql.java deleted file mode 100644 index 0b1674f89d..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midsql.java +++ /dev/null @@ -1,61 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.Midpnt.qromo; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Midsql; - -public class Test_midsql implements UniVarRealValueFun{ - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - // int i,j,M=14; - double PI=acos(-1.0); - double a,b,s,sbeps=1.e-10; // expect - boolean localflag, globalflag=false; - - - - // Test Nidsql - System.out.println("Testing Midsql"); - - a=0.0; - b=0.5; - Midsql msql = new Midsql(this,a,b); - s=qromo(msql); - -// System.out.printf(s << endl; - - System.out.printf("Midsql: Maximum discrepancy = %f\n", abs(s-PI/2.0)); - localflag = abs(s-PI/2.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Midsql: Failure to achieve expected accuracy in improper integral"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - // Test function - public double funk(final double x) { - return 1.0 / sqrt(x) / sqrt(1.0 - x); - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midsqu.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midsqu.java deleted file mode 100644 index 0b9d72d091..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_midsqu.java +++ /dev/null @@ -1,61 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.Midpnt.qromo; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Midsqu; - -public class Test_midsqu implements UniVarRealValueFun{ - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - // int i,j,M=14; - double PI=acos(-1.0); - double a,b,s,sbeps=1.e-10; //expect - boolean localflag, globalflag=false; - - - - // Test midsqu - System.out.println("Testing midsqu"); - - a=0.5; - b=1.0; - Midsqu midsqu = new Midsqu(this,a,b); - s=qromo(midsqu); - -// System.out.printf(s << endl; - - System.out.printf("midsqu: Maximum discrepancy = %f\n", abs(s-PI/2.0)); - localflag = abs(s-PI/2.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** midsqu: Failure to achieve expected accuracy in improper integral"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - // Test function - public double funk(final double x) { - return 1.0 / sqrt(x) / sqrt(1.0 - x); - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qgaus.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qgaus.java deleted file mode 100644 index ad1f56fe4b..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qgaus.java +++ /dev/null @@ -1,68 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.GaussianWeights.qgaus; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.sf.Bessjy; - -public class Test_qgaus { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=10; - double x1,x2,sbeps=5.e-15; - double[] y= new double[N],yy= new double[N]; - boolean localflag, globalflag=false; - - - - // Test qgaus - System.out.println("Testing qgaus"); - Bessj0_qgaus bj0 = new Bessj0_qgaus(); - Bessj1_qgaus bj1 = new Bessj1_qgaus(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** qgaus: Failure to achieve accurate integral"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class Bessj0_qgaus implements UniVarRealValueFun{ - public double funk(double x) { - Bessjy b = new Bessjy(); - return(b.j0(x)); - } - }; - - class Bessj1_qgaus implements UniVarRealValueFun{ - public double funk(double x) { - Bessjy b = new Bessjy(); - return(b.j1(x)); - } - }; -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qromb.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qromb.java deleted file mode 100644 index 3b94a9ac65..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qromb.java +++ /dev/null @@ -1,69 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.Trapzd.qromb; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.sf.Bessjy; - -public class Test_qromb { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=10; - double x1,x2,sbeps=1.e-10; - double[] y= new double[N],yy= new double[N]; - boolean localflag, globalflag=false; - - - - // Test qromb - System.out.println("Testing qromb"); - Bessj0_qromb bj0 = new Bessj0_qromb(); - Bessj1_qromb bj1 = new Bessj1_qromb(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** qromb: Failure to achieve advertised accuracy in integral"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Bessj0_qromb implements UniVarRealValueFun{ - public double funk(double x) { - Bessjy b = new Bessjy(); - return(b.j0(x)); - } - }; - - class Bessj1_qromb implements UniVarRealValueFun{ - public double funk (double x) { - Bessjy b = new Bessjy(); - return(b.j1(x)); - } - }; -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qromo.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qromo.java deleted file mode 100644 index d15bf99eef..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qromo.java +++ /dev/null @@ -1,69 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.Midpnt.qromo; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.cos; -import static java.lang.Math.sin; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Midpnt; - -public class Test_qromo implements UniVarRealValueFun{ - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - // int i,j,M=14; - double a,b,s,expect,PI=acos(-1.0),sbeps=1.e-11; - boolean localflag, globalflag=false; - - - - // Test qromo - System.out.println("Testing qromo"); - - a=0.0; - b=PI; - Midpnt mpt = new Midpnt(this,a,b); - s=qromo(mpt); - - expect=fint_qromo(b)-fint_qromo(a); -// System.out.printf(setw(9) << expect << endl; - - System.out.printf("qromo: Maximum discrepancy = %f\n", abs(s-expect)); - localflag = abs(s-expect) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** qromo: Failure to achieve expected accuracy in improper integral"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } -//Test function -public double funk(final double x) -{ - return sin(x); -} - -//integral of test function -double fint_qromo(final double x) -{ - return -cos(x); -} - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qsimp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qsimp.java deleted file mode 100644 index 737a231de7..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qsimp.java +++ /dev/null @@ -1,67 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.Trapzd.qsimp; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.sf.Bessjy; - -public class Test_qsimp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=10; - double x1,x2,sbeps=1.e-10; - double[] y= new double[N],yy= new double[N]; - boolean localflag, globalflag=false; - - // Test qsimp - System.out.println("Testing qsimp"); - Bessj0_qsimp bj0 = new Bessj0_qsimp(); - Bessj1_qsimp bj1 = new Bessj1_qsimp(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** qsimp: Failure to achieve advertised accuracy in integral"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Bessj0_qsimp implements UniVarRealValueFun { - public double funk(double x) { - Bessjy b = new Bessjy(); - return(b.j0(x)); - } - }; - - class Bessj1_qsimp implements UniVarRealValueFun{ - public double funk (double x) { - Bessjy b = new Bessjy(); - return(b.j1(x)); - } - }; -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qtrap.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qtrap.java deleted file mode 100644 index 5f26ebbe56..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_qtrap.java +++ /dev/null @@ -1,70 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.Trapzd.qtrap; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.sf.Bessjy; - -public class Test_qtrap { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=10; - double x1,x2,sbeps=1.e-10; - double[] y= new double[N],yy= new double[N]; - boolean localflag, globalflag=false; - - - - // Test qtrap - System.out.println("Testing qtrap"); - Bessj0_qtrap bj0 = new Bessj0_qtrap(); - Bessj1_qtrap bj1 = new Bessj1_qtrap(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** qtrap: Failure to achieve advertised accuracy in integral"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Bessj0_qtrap implements UniVarRealValueFun{ - public double funk (double x) { - Bessjy b = new Bessjy(); - return(b.j0(x)); - } - }; - - class Bessj1_qtrap implements UniVarRealValueFun{ - public double funk(double x) { - Bessjy b= new Bessjy(); - return(b.j1(x)); - } - }; - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_quad3d.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_quad3d.java deleted file mode 100644 index 33aad889e7..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_quad3d.java +++ /dev/null @@ -1,120 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.NRUtil.SQR; -import static com.nr.fi.NRf3.quad3d; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.exp; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.RealValueFun; - -public class Test_quad3d { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double s,expect,sbeps,PI=acos(-1.0); - boolean localflag, globalflag=false; - - - - // Test quad3d - System.out.println("Testing quad3d"); - func func = new func(); - func2 func2 = new func2(); - y1 y1 = new y1(); - y2 y2 = new y2(); - z1 z1 = new z1(); - z2 z2 = new z2(); - - s=quad3d(func,-1.0,1.0,y1,y2,z1,z2); - expect=2.0*PI/3.0; - -// System.out.printf(s << " %f\n", expect << endl; - - sbeps=1.e-3; -// System.out.printf(fabs(s-expect)/expect << endl; - localflag = abs(s-expect)/expect > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** quad3d: integral of hemispherical volume was inaccurate"); - - } - - s=quad3d(func2,-1.0,1.0,y1,y2,z1,z2); - expect=2.0*PI*(2.0-5.0/exp(1.0)); - -// System.out.printf(s << " %f\n", expect << endl; - - sbeps=1.e-3; -// System.out.printf(abs(s-expect)/expect << endl; - localflag = abs(s-expect)/expect > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** quad3d: Weighted integral over hemispherical volume was inaccurate"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class y1 implements RealValueFun { - public double funk(final double[] xx) { - double x = xx[0]; - return -sqrt(1.0 - SQR(x)); - } - } - - class y2 implements RealValueFun { - public double funk(final double[] xx) { - double x = xx[0]; - return sqrt(1.0 - SQR(x)); - } - } - - class z1 implements RealValueFun { - public double funk(final double[] x) { - return 0.0; - } - } - - class z2 implements RealValueFun { - public double funk(final double[] xx) { - double x = xx[0], y = xx[1]; - - return sqrt(1.0 - SQR(x) - SQR(y)); - } - } - - class func implements RealValueFun { - public double funk(final double[] x) { - return 1.0; - } - } - - class func2 implements RealValueFun { - public double funk(final double[] xx) { - double x = xx[0], y = xx[1], z = xx[2]; - - double r; - - r = sqrt(SQR(x) + SQR(y) + SQR(z)); - return exp(-r); - } - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_radau.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_radau.java deleted file mode 100644 index eb6471564e..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_radau.java +++ /dev/null @@ -1,106 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.fi.GaussianWeights.radau; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -public class Test_radau { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=10; - double amu0,check,sbeps,PI=acos(-1.0); - double[] a= new double[N],b= new double[N],x= new double[N],w= new double[N]; - boolean localflag, globalflag=false; - - - - // Test radau - System.out.println("Testing radau"); - - // Test with Gauss-Chebyshev - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** radau: Gaussian weights do not sum to correct value"); - - } - - sbeps=1.e-15; - localflag = abs(x[0]-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** radau: First element of x[] is not the requested value of 1.0"); - - } - - // Since arrays a[],b[] are modified, we recompute them - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** radau: Gaussian weights do not sum to correct value"); - - } - - sbeps=1.e-15; - localflag = abs(x[N-1]+1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** radau: Last element of x[] is not the requested value of -1.0"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_trapzd.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_trapzd.java deleted file mode 100644 index 4b680f52b9..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter4/Test_trapzd.java +++ /dev/null @@ -1,72 +0,0 @@ -package com.nr.test.test_chapter4; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Trapzd; -import com.nr.sf.Bessjy; - -public class Test_trapzd { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=10,M=16; - double x1,x2,val=0,sbeps=1.e-9; - double[] y=new double[N],yy=new double[N]; - boolean localflag, globalflag=false; - - - - // Test trapzd - System.out.println("Testing trapzd"); - Bessj0_trapzd bj0 = new Bessj0_trapzd(); - Bessj1_trapzd bj1 = new Bessj1_trapzd(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** trapzd: Incorrect integral value"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Bessj0_trapzd implements UniVarRealValueFun { - public double funk(double x) { - Bessjy b = new Bessjy(); - return(b.j0(x)); - } - }; - - class Bessj1_trapzd implements UniVarRealValueFun{ - public double funk (double x) { - Bessjy b = new Bessjy(); - return(b.j1(x)); - } - }; - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Chebyshev.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Chebyshev.java deleted file mode 100644 index 1d1d2f270b..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Chebyshev.java +++ /dev/null @@ -1,149 +0,0 @@ -package com.nr.test.test_chapter5; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fe.Chebyshev; -import com.nr.sf.Bessjy; - -public class Test_Chebyshev { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=5,NN=50,m,MM=11; - double x,xx,aa=-5.0,bb=5.0,val,thresh=1.e-6,sbeps=1.e-6; - double[] y = new double[MM],yy = new double[MM]; - Bessjy b = new Bessjy(); - boolean localflag, globalflag=false; - - - - // Test Chebyshev (eval) - System.out.println("Testing Chebyshev (eval)"); - bjn bjn = new bjn(); - Chebyshev cheb = new Chebyshev(bjn,aa,bb,NN); - m=cheb.setm(thresh); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Chebyshev (eval): Chebyshev approximation does not evaluate to accurate function values"); - - } - - // Test Chebyshev (polycofs) - System.out.println("Testing Chebyshev (polycofs)"); - double[] d=cheb.polycofs(m); - for (i=0;i=0;j--) val=val*xx+d[j]; - yy[i]=val; -// System.out.printf(y[i] << " %f\n", yy[i] << endl; - } - System.out.printf("Chebyshev (polycofs): Maximum discrepancy = %f\n", maxel(vecsub(y,yy))); - localflag = maxel(vecsub(y,yy)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Chebyshev (polycofs): Polynomial coefficients do not yield correct function values"); - - } - - // Test Chebyshev (derivative) - System.out.println("Testing Chebyshev (derivative)"); - Chebyshev cder=cheb.derivative(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Chebyshev (derivative): Chebyshev derivative has incorrect values"); - - } - - // Test Chebyshev (integral) - System.out.println("Testing Chebyshev (integral)"); - bj1 bj1 = new bj1(); - Chebyshev cheb1 = new Chebyshev(bj1,aa,bb,NN); - Chebyshev cint=cheb1.integral(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Chebyshev (integral): Chebyshev integral has incorrect values"); - - } - - // Test Chebyshev (construct from polynomial) - System.out.println("Testing Chebyshev (construct from polynomial)"); - Chebyshev chebnew = new Chebyshev(d); - double[] z = new double[m],zz = new double[m]; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Chebyshev (integral): Chebyshev (construct from polynomial): Reconstructed Chebyshev coeffiecients not the same as originals"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class bjn implements UniVarRealValueFun{ - public double funk(final double x) { - int N=5; - - Bessjy b = new Bessjy(); - return(b.jn(N,x)); - } - } - - class bj1 implements UniVarRealValueFun{ - public double funk(final double x) { - int N=1; - - Bessjy b = new Bessjy(); - return(b.jn(N,x)); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Epsalg.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Epsalg.java deleted file mode 100644 index 43a0472660..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Epsalg.java +++ /dev/null @@ -1,59 +0,0 @@ -package com.nr.test.test_chapter5; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.pow; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.fe.Epsalg; - -public class Test_Epsalg { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,k,N=9,M=100; - double x,partialsum,val=0,eps=1.e-15,sbeps=5.e-15; - double[] y=new double[N],yy=new double[N]; - boolean localflag, globalflag=false; - - - - // Test Epsalg - System.out.println("Testing Epsalg"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Epsalg: Inaccurate estimate of series value"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Eulsum.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Eulsum.java deleted file mode 100644 index a950d7a87f..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Eulsum.java +++ /dev/null @@ -1,57 +0,0 @@ -package com.nr.test.test_chapter5; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.fe.Eulsum; - -public class Test_Eulsum { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=9,M=100; - double x,term,val=0,eps=1.e-15,sbeps=5.e-15; - double[] y=new double[N],yy=new double[N]; - boolean localflag, globalflag=false; - - - - // Test Eulsum - System.out.println("Testing Eulsum"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Eulsum: Inaccurate estimate of series value"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Levin.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Levin.java deleted file mode 100644 index 345d4ffe59..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Levin.java +++ /dev/null @@ -1,60 +0,0 @@ -package com.nr.test.test_chapter5; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.fe.Levin; - -public class Test_Levin { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,k,N=9,M=100; - double x,partialsum,omega,beta=1.0,val=0,eps=1.e-14,sbeps=5.e-14; - double[] y=new double[N],yy=new double[N]; - boolean localflag, globalflag=false; - - - - // Test Levin - System.out.println("Testing Levin"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Levin: Inaccurate estimate of series value"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Poly.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Poly.java deleted file mode 100644 index 8deff84f20..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Poly.java +++ /dev/null @@ -1,55 +0,0 @@ -package com.nr.test.test_chapter5; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.pow; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.fe.Poly; - -public class Test_Poly { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,M=11; - double x,sbeps=1.e-15; - double c[]={-1.0,5.0,-10.0,10.0,-5.0,1.0}; // Coefficients of (x-1.0)^5; - double[] cc = buildVector(c),y= new double[M],yy= new double[M]; - boolean localflag, globalflag=false; - - - - // Test Poly - System.out.println("Testing Poly"); - Poly p = new Poly(cc); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poly: Polynomial returns incorrect values"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Ratfn.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Ratfn.java deleted file mode 100644 index 97f3d190da..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_Ratfn.java +++ /dev/null @@ -1,72 +0,0 @@ -package com.nr.test.test_chapter5; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.pow; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.fe.Ratfn; - -public class Test_Ratfn { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,M=10; - double x,sbeps=1.e-15; - double b[]={-3.0,15.0,-30.0,30.0,-15.0,3.0}; // Coefficients of 3.0*(x-1.0)^5; - double c[]={-2.0,6.0,-6.0,2.0}; // Coefficients of 2.0*(x-1.0)^3 - double d[]={1.5,-7.5,15.0,-15.0,7.5,-1.5,-3.0,3.0,-1.0}; - double[] bb = buildVector(b),cc = buildVector(c),dd = buildVector(d),y= new double[M],yy= new double[M]; - boolean localflag, globalflag=false; - - - - // Test Ratfn - System.out.println("Testing Ratfn: constructor #1"); - Ratfn rp1 = new Ratfn(bb,cc); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Ratfn: Rational function returns incorrect values"); - - } - - System.out.println("Testing Ratfn: constructor #2"); - Ratfn rp2= new Ratfn(dd,6,4); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Ratfn: Rational function returns incorrect values"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_ddpoly.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_ddpoly.java deleted file mode 100644 index 49343a597a..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_ddpoly.java +++ /dev/null @@ -1,57 +0,0 @@ -package com.nr.test.test_chapter5; - -import static com.nr.test.NRTestUtil.*; -import static com.nr.NRUtil.*; -import static java.lang.Math.*; -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import com.nr.fe.Poly; -public class Test_ddpoly { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,M=11; - double x,sbeps=1.e-15; - double c[]={-1.0,5.0,-10.0,10.0,-5.0,1.0}; // Coefficients of (x-1.0)^5; - double[] cc = buildVector(c),pd = new double[6],p = new double[6],y = new double[M]; - boolean localflag, globalflag=false; - - - - // Test ddpoly - System.out.println("Testing ddpoly"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ddpoly: Incorrect values for function or derivatives"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_dfridr.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_dfridr.java deleted file mode 100644 index 265b12b8f6..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_dfridr.java +++ /dev/null @@ -1,101 +0,0 @@ -package com.nr.test.test_chapter5; - -import static com.nr.fe.Dfridr.dfridr; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.UniVarRealValueFun; -import com.nr.sf.Bessjy; - -public class Test_dfridr { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,M=10; - double x,h=0.2,sbeps=5.e-14; - doubleW err = new doubleW(0); - double[] y= new double[M],yy= new double[M]; - boolean localflag, globalflag=false; - - - - // Test dfridr - System.out.println("Testing dfridr"); - - // Test with function - bj0_dfridr bj0_dfridr = new bj0_dfridr(); - bj1_dfridr bj1_dfridr = new bj1_dfridr(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** dfridr: Derivative returns incorrect values with function"); - - } - - // Test with functor - Bessj0_dfridr bj0 = new Bessj0_dfridr(); - Bessj1_dfridr bj1 = new Bessj1_dfridr(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** dfridr: Derivative returns incorrect values with functor"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Bessj0_dfridr implements UniVarRealValueFun{ - Bessjy b = new Bessjy(); - public double funk (final double x) { - return(b.j0(x)); - } - }; - - class Bessj1_dfridr implements UniVarRealValueFun{ - Bessjy b = new Bessjy(); - public double funk (final double x) { - return(b.j1(x)); - } - }; - - class bj0_dfridr implements UniVarRealValueFun{ - public double funk(final double x) { - Bessjy b = new Bessjy(); - return(b.j0(x)); - } - } - class bj1_dfridr implements UniVarRealValueFun{ - public double funk(final double x) { - Bessjy b = new Bessjy(); - return(b.j1(x)); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_ipcshft.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_ipcshft.java deleted file mode 100644 index c3b23e56a6..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_ipcshft.java +++ /dev/null @@ -1,67 +0,0 @@ -package com.nr.test.test_chapter5; - -import static com.nr.NRUtil.buildVector; -import static com.nr.fe.Chebyshev.ipcshft; -import static com.nr.fe.Chebyshev.pcshft; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -public class Test_ipcshft { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - // int M=6; - double a=1.0,b=3.0,sbeps=1.e-13; - double d[]={-1,6.0,-10.0,10.0,-6.0,1.0}; - double[] dd = buildVector(d); - boolean localflag, globalflag=false; - - - - // Test ipcshft - System.out.println("Testing ipcshft"); - double[] g = buildVector(dd); - pcshft(a,b,g); - double[] h = buildVector(g); - ipcshft(a,b,h); - - localflag = maxel(vecsub(g,dd)) < 1.0; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ipcshft: Polynomial was not shifted"); - - } - - localflag = maxel(vecsub(h,g)) < 1.0; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ipcshft: Polynomial was not inverse shifted"); - - } - - System.out.printf("ipcshft: Maximum discrepancy = %f\n", maxel(vecsub(h,dd))); - localflag = maxel(vecsub(h,dd)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ipcshft: Inverse shift did not undo the shift properly"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_levex.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_levex.java deleted file mode 100644 index 768a6b5894..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_levex.java +++ /dev/null @@ -1,76 +0,0 @@ -package com.nr.test.test_chapter5; - -import static java.lang.Math.*; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fe.Levin; -import com.nr.sf.Bessel; -import static com.nr.fi.Trapzd.qromb; - -public class Test_levex implements UniVarRealValueFun{ - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - boolean localflag, globalflag=false; - - - - // Test levex - System.out.println("Testing levex"); - - localflag = main_levex() != 0; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Levex : Program did not indicate successful completion"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - - public double funk(final double x) - { - if (x == 0.0) - return 0.0; - else { - Bessel bess = new Bessel(); - return x*bess.jnu(0.0,x)/(1.0+x*x); - } - } - - int main_levex(){ - int nterm=12; - double beta=1.0,a=0.0,b=0.0,sum=0.0; - Levin series = new Levin(100,0.0); - //cout << setw(5) << "N" << setw(19) << "Sum (direct)" << setw(21) - // << "Sum (Levin)" << endl; - for (int n=0; n<=nterm; n++) { - b+=PI; - double s=qromb(this,a,b,1.e-8); - a=b; - sum+=s; - double omega=(beta+n)*s; - double ans=series.next(sum,omega,beta); - //cout << setw(5) << n << fixed << setprecision(14) << setw(21) - // << sum << setw(21) << ans << endl; - System.out.printf("%f %f\n", sum, ans); - } - return 0; - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_pade.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_pade.java deleted file mode 100644 index 91470d8e76..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_pade.java +++ /dev/null @@ -1,76 +0,0 @@ -package com.nr.test.test_chapter5; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.log; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.fe.Ratfn; - -public class Test_pade { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=10,M=12; - double val,fac,d1,d2,x,sbeps=1.e-6; - double[] c= new double[M],y=new double[N],yy=new double[N],yyy=new double[N]; - boolean localflag, globalflag=false; - - - - // Test pade - System.out.println("Testing pade"); - fac=1.0; - for (i=0;i=0;j--) { - val=val*x+c[j]; - } - yyy[i]=val; - } - System.out.printf("pade: Maximum error of Pade approximant = %f\n", (d1=maxel(vecsub(y,yy)))); - localflag = maxel(vecsub(y,yy)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** pade: Pade approximant is inaccurate"); - - } - System.out.printf("pade: Maximum discrepancy of power series = %f\n", (d2=maxel(vecsub(y,yyy)))); - localflag = d1 > d2; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** pade: Pade approximant is less accurate than power series"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - double Func_pade(double x) { - return(x==0.0 ? 1.0 : log(1.0+x)/x); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_pcshft.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_pcshft.java deleted file mode 100644 index 10ef2e3f5b..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_pcshft.java +++ /dev/null @@ -1,67 +0,0 @@ -package com.nr.test.test_chapter5; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.fe.Chebyshev; - -public class Test_pcshft { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=11,M=6; - double x,xx,a=1.0,b=3.0,val,sbeps=1.e-13; - double d[]={-1,6.0,-10.0,10.0,-6.0,1.0}; - double[] dd = buildVector(d),y=new double[N],yy=new double[N]; - boolean localflag, globalflag=false; - - - - // Test pcshft - System.out.println("Testing pcshft"); - double[] g = buildVector(dd); - Chebyshev.pcshft(a,b,g); - for (i=0;i=0;j--) val=val*x+g[j]; - y[i]=val; - val=dd[M-1]; - for (j=M-2;j>=0;j--) val=val*xx+dd[j]; - yy[i]=val; - } - localflag = maxel(vecsub(g,dd)) < 1.0; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** pcshft: Polynomial was not shifted"); - - } - - System.out.printf("pcshft: Maximum discrepancy = %f\n", maxel(vecsub(y,yy))); - localflag = maxel(vecsub(y,yy)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** pcshft: Shifted polynomial does not return the same values"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_poldiv.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_poldiv.java deleted file mode 100644 index b0fe3222d2..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_poldiv.java +++ /dev/null @@ -1,59 +0,0 @@ -package com.nr.test.test_chapter5; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.fe.Poly; - -public class Test_poldiv { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double sbeps=2.e-15; - double u[]={1.0,7.0,-10.0,10.0,-5.0,1.0}; // Coefficients of (x-1.0)^5+2.0*(x+1); - double v[]={-3.0,9.0,-9.0,3.0}; // Coefficients of 3.0*(x-1)^3 - double q[]={1.0/3.0,-2.0/3.0,1.0/3.0,0.0,0.0,0.0}; // Quotient is (1/3)*(x-1.0)^2; - double r[]={2.0,2.0,0.0,0.0,0.0,0.0}; // Remainter is 2.0*(x+1) - double[] uu = buildVector(u),vv = buildVector(v),qq=buildVector(q),rr = buildVector(r),s = new double[6],t = new double[6]; - boolean localflag, globalflag=false; - - - - // Test poldiv - System.out.println("Testing poldiv"); - Poly.poldiv(uu,vv,s,t); - System.out.printf("poldiv: Maximum discrepancy in quotient = %f\n", maxel(vecsub(s,qq))); - localflag = maxel(vecsub(s,qq)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** poldiv: Division returns incorrect quotient"); - - } - - System.out.printf("poldiv: Maximum discrepancy in remainder = %f\n", maxel(vecsub(t,rr))); - localflag = maxel(vecsub(t,rr)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** poldiv: Division returns incorrect remainder"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_ratlsq.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_ratlsq.java deleted file mode 100644 index 6a8ae14eca..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter5/Test_ratlsq.java +++ /dev/null @@ -1,73 +0,0 @@ -package com.nr.test.test_chapter5; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.log; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.UniVarRealValueFun; -import com.nr.fe.Ratfn; - -public class Test_ratlsq implements UniVarRealValueFun{ - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=11,M=12; - double fac,x,sbeps=2.e-13; - doubleW dev = new doubleW(0); - double[] c = new double[2*M],y=new double[N],yy=new double[N]; - boolean localflag, globalflag=false; - - - - // Test ratlsq - System.out.println("Testing ratlsq"); - fac=1.0; - for (i=0;i<2*M;i++) { // Series coefficients - c[i]=fac/(double)(i+1); - fac = -fac; - } - Ratfn q=Ratfn.ratlsq(this,0.0,2.0,M,M,dev); // Diagonal works best for this function - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ratlsq: Ratlsq approximation is inaccurate"); - - } - - System.out.printf("ratlsq: Reported maximum absolute deviation from ratlsq = %f\n", dev.val); - localflag = maxel(vecsub(y,yy)) > dev.val; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ratlsq: Error exceeds reported maximum absolute deviation"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - public double funk(double x) { - return(x==0.0 ? 1.0 : log(1.0+x)/x); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Bessel.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Bessel.java deleted file mode 100644 index f5d4d30367..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Bessel.java +++ /dev/null @@ -1,325 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.sf.Bessel; -import com.nr.sf.Bessik; -import com.nr.sf.Bessjy; - -public class Test_Bessel { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @SuppressWarnings("unused") - @Test - public void test() { - int i,j,N=16; - double nnu,xx,sbeps=1.e-14; - double nu[]={0.5,0.5,0.5,0.5,1.5,1.5,1.5,1.5,2.5,2.5,2.5,2.5,3.5,4.5,5.5,6.5}; - double x[]={0.2,0.5,1.0,2.0,0.2,0.5,1.0,2.0,0.2,0.5,1.0,2.0,2.0,2.0,2.0,2.0}; - double u1[]={0.354450744211401103,0.540973789934528091,0.671396707141803090, - 0.513016136561827752,0.0236933040951292395,0.0917016996256513026, - 0.240297839123427011,0.491293778687162345,0.000948817215537489923, - 0.00923640781937972450,0.0494968102284779423,0.223924531468915766, - 0.0685175499851270696,0.0158868934790289778,0.00297347067050333037, - 0.000467195208739339254}; - double u2[]={-1.74856041696187628,-0.990245880243404880,-0.431098868018376080, - 0.234785710406248469,-9.09725282902078249,-2.52146555042133785, - -1.10249557516017917,-0.395623281358703517,-134.710232018349861, - -14.1385474222846222,-2.87638785746216143,-0.828220632444303745, - -1.67492829975205584,-5.03402841668789171,-20.9781995753434569, - -110.346069247701121}; - double u3[]={0.359208417583361390,0.587993086790416325,0.937674888245487647, - 2.04623686308905504,0.0238836108689015129,0.0964034738340167409, - 0.293525326347479800,1.09947318863310968,0.000954254549838696096, - 0.00957224378631588027,0.0570989092030482474,0.397027080139390523, - 0.106905488284633367,0.0228578711431737382,0.00404506814035154520, - 0.000609996371240239640}; - double u4[]={2.29448933979847487,1.07504760349992024,0.461068504447894558, - 0.119937771968061447,13.7669360387908492,3.22514281049976072, - 0.922137008895789117,0.179906657952092171,208.798529921661213, - 20.4259044664984845,3.22747953113526191,0.389797758896199704, - 1.15440105519259143,4.43020145207026971,21.0903075895088051, - 120.426893194368698}; - double[] uu1=buildVector(u1),uu2=buildVector(u2),uu3=buildVector(u3),uu4=buildVector(u4),zz=new double[N],zz1=new double[N],zz2=new double[N]; - boolean localflag, globalflag=false; - - Bessel bess = new Bessel(); - Bessjy bjy = new Bessjy(); - Bessik bik = new Bessik(); - - // Test Bessel (besseljy and besselik) - System.out.println("Testing Bessel (besseljy)"); - - // Test for integer values of nu - sbeps=1.e-10; - for (i=0;i<5;i++) { - nnu=(double)(i); - - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (besseljy,jnu): Incorrect function values, integer order"); - - } - - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (besseljy,ynu): Incorrect function values, integer order"); - - } - - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (besselik,inu): Incorrect function values, integer order"); - - } - - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (besselik,knu): Incorrect function values, integer order"); - - } - } - - // Test some non-integer values of nu - // Test Bessel (besseljy) - System.out.println("Testing Bessel (besseljy),jnu"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (besselij),jnu: Incorrect function values, non-integer order"); - - } - - System.out.println("Testing Bessel (besseljy),ynu"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (besseljy),ynu: Incorrect function values, non-integer order"); - - } - - // Test Bessel (besselik) - System.out.println("Testing Bessel (besselik),inu"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (besselik),inu: Incorrect function values, non-integer order"); - - } - - System.out.println("Testing Bessel (besselik),knu"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (besselik),knu: Incorrect function values, non-integer order"); - - } - - N=17; - double x3[]={-64.0,-32.0,-16.0,-8.0,-4.0,-2.0,-1.0,-0.5,0.0, - 0.5,1.0,2.0,4.0,8.0,16.0,32.0,64.0}; - double y3[]={6.181292862603287e-2,2.066697536442034e-1,-1.430579316691003e-1, - -5.270505035638810e-2,-7.026553294929175e-2,2.274074282016857e-1, - 5.355608832923522e-1,4.757280916105395e-1,3.550280538878172e-1, - 2.316936064808334e-1,1.352924163128815e-1,3.492413042327446e-2, - 9.515638512048023e-4,4.692207616099237e-8,4.156888828917034e-020, - 4.606731112410277e-054,-5.748819722355254e-150}; - double y4[]={-1.896519810390566e-1,-1.164350222348790e-1,2.431231514282269e-1, - -3.312515807511406e-1,3.922347057070000e-1,-4.123025879563988e-1, - 1.039973894969446e-1,3.803526597510537e-1,6.149266274460007e-1, - 8.542770431031557e-1,1.207423594952871,3.298094999978216, - 8.384707140846841e1,1.199586004124440e6,9.572123906049169e17, - 6.107371662410141e51,3.460602472409225e+147}; - double y5[]={1.517458208520610e0,6.602736519705829e-1,-9.747644416212706e-1, - 9.355609381983173e-1,-7.906285753685707e-1,6.182590207416919e-1, - -1.016056711664515e-2,-2.040816703395474e-1,-2.588194037928068e-1, - -2.249105326646840e-1,-1.591474412967932e-1,-5.309038443365637e-2, - -1.958640950204180e-3,-1.341439297906788e-7,-1.669188676838185e-19, - -2.609547331124277e-53,-4.601298677332503e-149}; - double y6[]={4.937628983497952e-1,1.168196625671367e0,-5.684556059761371e-1, - -1.594504978129538e-1,-1.166705674383235e-1,2.787951669211703e-1, - 5.923756264227923e-1,5.059337136238472e-1,4.482883573538264e-1, - 5.445725641405924e-1,9.324359333927754e-1,4.100682049932892e0, - 1.619266835046139e2,3.354342312744483e6,3.813743507121854e+018, - 3.450063137771686e+052,2.767128525086472e+148}; - double[] yy3=buildVector(y3),yy4=buildVector(y4),yy5=buildVector(y5),yy6=buildVector(y6),one=buildVector(N,1.0), - zz3=new double[N],zz4=new double[N],zz5=new double[N],zz6=new double[N]; - - /* - - Bessel2 bess2 = new Bessel2(); - - // Test Bessel (airy) - sbeps=1.e-12; - System.out.println("Testing Bessel (airy_ai, airy_bi, airy_aip, airy_bip)"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (airy_ai): Incorrect function values"); - - } - System.out.printf("Bessel (airy_bi): Maximum discrepancy = %f\n", maxel(vecsub(one,zz4))); - localflag = maxel(vecsub(one,zz4)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (airy_bi): Incorrect function values"); - - } - System.out.printf("Bessel (airy_aip): Maximum discrepancy = %f\n", maxel(vecsub(zz5,yy5))); - localflag = maxel(vecsub(zz5,yy5)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (airy_aip): Incorrect function values"); - - } - System.out.printf("Bessel (airy_bip): Maximum discrepancy = %f\n", maxel(vecsub(one,zz6))); - localflag = maxel(vecsub(one,zz6)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (airy_bip): Incorrect function values"); - - } - - // Test Bessel (sphbes) - System.out.println("Testing Bessel (sphbes)"); - - int M=5; - N=10; - double[] yy7=new double[N],yy8=new double[N],zz7=new double[N],zz8=new double[N]; - double sqrtpio2=sqrt(acos(-1.0)/2); - sbeps=6.e-11; - for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (sphbes), Jnu: Incorrect function values"); - - } - - // Spherical Bessel function yn - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessel (sphbes), Ynu: Incorrect function values"); - - } - } - */ - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Bessel2 extends Bessel - { - double airy_aip(final double x) { - // Simple interface returning Ai'(x) - // if (x != xo) airy(x); // XXX HWH disable it - return aipo; - } - - double airy_bip(final double x) { - // Simple interface returning Bi'(x) - // if (x != xo) airy(x); // XXX HWH disable it - return bipo; - } - }; -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Bessik.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Bessik.java deleted file mode 100644 index d7afd31277..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Bessik.java +++ /dev/null @@ -1,176 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.sf.Bessik; - -public class Test_Bessik { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=17; - double sbeps=1.e-15; - double x[]={-32.0,-16.0,-8.0,-4.0,-2.0,-1.0,-0.5,-0.1,0.0, - 0.1,0.5,1.0,2.0,4.0,8.0,16.0,32.0}; - double y1[]={5.590908381350871e12,8.934462279201048e5,4.275641157218047e2, - 1.130192195213633e1,2.279585302336067,1.266065877752008, - 1.063483370741324,1.002501562934095,1.000000000000000, - 1.002501562934095,1.063483370741324,1.266065877752008, - 2.279585302336067,1.130192195213633e1,4.275641157218047e2, - 8.934462279201048e5,5.590908381350871e12}; - double y2[]={-5.502845511211247e12,-8.650594358548392e5,-3.998731367825601e2, - -9.759465153704449e0,-1.590636854637329e0,-5.651591039924850e-1, - -2.578943053908963e-1,-5.006252604709272e-2,0.0,5.006252604709272e-2, - 2.578943053908963e-1,5.651591039924850e-1,1.590636854637329e0, - 9.759465153704449e0,3.998731367825601e2,8.650594358548392e5, - 5.502845511211247e12}; - double[] yy1=buildVector(y1),yy2=buildVector(y2),zz1=new double[N],zz2=new double[N]; - boolean localflag, globalflag=false; - - - - // Test Bessik (i0) - System.out.println("Testing Bessik (i0)"); - localflag=false; - Bessik bess = new Bessik(); - sbeps=1.e-15; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessik (i0): Incorrect function values"); - - } - - // Test Bessik (i1) - System.out.println("Testing Bessik (i1)"); - localflag=false; - sbeps=1.e-15; - for (i=0;i sbeps; - } - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessik (i1): Incorrect function values"); - - } - - N=10; - double x3[]={0.001,0.01,0.1,0.5,1.0,2.0,4.0,8.0,16.0,32.0}; - double y3[]={7.023688800562382,4.721244730161095,2.427069024702017, - 9.244190712276657e-1,4.210244382407083e-1,1.138938727495334e-1, - 1.115967608585303e-2,1.464707052228154e-4,3.499411663936500e-8, - 2.795057518761980e-15}; - double y4[]={9.999962381560855e2,9.997389411829624e1,9.853844780870606, - 1.656441120003301,6.019072301972346e-1,1.398658818165225e-1, - 1.248349888726843e-2,1.553692118050012e-4,3.607157117528780e-8, - 2.838399271974671e-15}; - double[] yy3=buildVector(y3),yy4=buildVector(y4),zz3=new double[N],zz4=new double[N]; - - // Test Bessik (k0) - System.out.println("Testing Bessik (k0)"); - localflag=false; - sbeps=5.e-15; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessik (k0): Incorrect function values"); - - } - - // Test Bessik (k1) - System.out.println("Testing Bessik (k1)"); - localflag=false; - sbeps=5.e-15; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessik (k1): Incorrect function values"); - - } - - N=16; - int n5[]={2,2,2,2,5,5,5,5,10,10,10,10,20,20,20,20}; - double x5[]={0.01,0.1,1.0,10.0,0.01,0.1,1.0,10.0,0.01,0.1,1.0,10.0,0.01,0.1,1.0,10.0,}; - double y5[]={1.250010416699221e-5,1.251041992241759e-3,1.357476697670383e-1, - 2.281518967726005e3,2.604177517380490e-14,2.605251929893700e-9, - 2.714631559569721e-4,7.771882864032602e2,2.691150571711139e-30, - 2.691756142922153e-20,2.752948039836874e-10,2.189170616372337e1, - 3.919909016180170e-65,3.920371031419948e-45,3.966835985819000e-25, - 1.250799735644947e-4}; - double y6[]={1.999950006838941e4,1.995039646421141e2,1.624838898635177, - 2.150981700693276e-5,3.839976000100000e12,3.837600999583593e7, - 3.609605896012407e2,5.754184998531225e-5,1.857940439048064e28, - 1.857429584630401e18,1.807132899010295e8,1.614255300390669e-3, - 6.377698248601134e62,6.376867526661186e42,6.294369360424536e22, - 1.787442782077055e2}; - double[] yy5=buildVector(y5),yy6=buildVector(y6),zz5=new double[N],zz6=new double[N]; - - - - // Test Bessik (in) - System.out.println("Testing Bessik (in)"); - - localflag=false; - sbeps=5.e-14; - for (i=0;i sbeps; - } - - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessik (in): Incorrect function values"); - - } - - // Test Bessik (kn) - System.out.println("Testing Bessik (kn)"); - localflag=false; - sbeps=5.e-15; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessik (kn): Incorrect function values"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Bessjy.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Bessjy.java deleted file mode 100644 index 73d837572f..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Bessjy.java +++ /dev/null @@ -1,159 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.sf.Bessjy; - -public class Test_Bessjy { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=17; - double sbeps; - double x[]={-32.0,-16.0,-8.0,-4.0,-2.0,-1.0,-0.5,-0.1,0.0, - 0.1,0.5,1.0,2.0,4.0,8.0,16.0,32.0}; - double y1[]={1.380790097465560e-1,-1.748990739836292e-1,1.716508071375539e-1, - -3.971498098638472e-1,2.238907791412356e-1,7.651976865579666e-1, - 9.384698072408130e-1,9.975015620660401e-1,1.0,9.975015620660401e-1, - 9.384698072408130e-1,7.651976865579666e-1,2.238907791412356e-1, - -3.971498098638472e-1,1.716508071375539e-1,-1.748990739836292e-1, - 1.380790097465560e-1}; //,-5.767248077568736e-1 XXX remove it. - double y2[]={2.658902847590528e-2,-9.039717566130416e-2,-2.346363468539147e-1, - 6.604332802354906e-2,-5.767248077568736e-001,-4.400505857449336e-1, - -2.422684576748739e-1,-4.993752603624202e-2,0.0,4.993752603624202e-2, - 2.422684576748739e-1,4.400505857449336e-1,5.767248077568736e-001, - -6.604332802354906e-2,2.346363468539147e-1,9.039717566130416e-2, - -2.658902847590528e-2}; - double[] yy1=buildVector(y1),yy2=buildVector(y2),zz1=new double[N],zz2=new double[N]; - boolean localflag, globalflag=false; - - // Test Bessjy (j0) - System.out.println("Testing Bessjy (j0)"); - Bessjy bess = new Bessjy(); - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessjy (j0): Incorrect function values"); - - } - - // Test Bessjy (j1) - System.out.println("Testing Bessjy (j1)"); - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessjy (j1): Incorrect function values"); - - } - - N=10; - double x3[]={0.001,0.01,0.1,0.5,1.0,2.0,4.0,8.0,16.0,32.0}; - double y3[]={-4.471416611375924,-3.005455637083646,-1.534238651350367, - -4.445187335067066e-1,8.825696421567700e-2,5.103756726497453e-1, - -1.694073932506495e-2,2.235214893875663e-1,9.581099708071243e-2, - -2.874248465443332e-2}; - double y4[]={-6.366221672311394e+002,-6.367859628206066e+001,-6.458951094702027, - -1.471472392670243,-7.812128213002889e-1,-1.070324315409375e-1, - 3.979257105571000e-1,-1.580604617312476e-1,1.779751689394169e-1, - -1.385448315327238e-1}; - double[] yy3=buildVector(y3),yy4=buildVector(y4),zz3=new double[N],zz4=new double[N]; - - // Test Bessjy (y0) - System.out.println("Testing Bessjy (y0)"); - sbeps=1.e-14; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessjy (y0): Incorrect function values"); - - } - - // Test Bessjy (y1) - System.out.println("Testing Bessjy (y1)"); - sbeps=1.5e-13; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessjy (y1): Incorrect function values"); - - } - - N=16; - int n5[]={2,2,2,2,5,5,5,5,10,10,10,10,50,50,50,50}; - double x5[]={0.01,0.1,1.0,10.0,0.01,0.1,1.0,10.0,0.01,0.1,1.0,10.0,0.01,0.1,1.0,10.0,}; - double y5[]={1.249989583365887e-5,1.248958658799919e-3,1.149034849319005e-1, - 2.546303136851206e-1,2.604155815991601e-14,2.603081790964445e-9, - 2.497577302112346e-4,-2.340615281867936e-1,2.691138339236341e-30, - 2.690532895434228e-20,2.630615123687453e-10,2.074861066333589e-1, - 2.920284285406856e-180,2.920142569099765e-130,2.906004948173220e-80, - 1.784513607871616e-30}; - double y6[]={-1.273271380077505e+4,-1.276447832426902e+2,-1.650682606816255, - -5.868082442208572e-3,-2.444635204829711e12,-2.446148450230391e7, - -2.604058666258123e2,1.354030476893622e-1,-1.182808190517663e28, - -1.183133513204520e18,-1.216180142786892e8,-3.598141521834027e-1, - -2.179992503765307e+177,-2.180102618471610e+127,-2.191142812605340e77, - -3.641066501800778e27}; - double[] yy5=buildVector(y5),yy6=buildVector(y6),zz5=new double[N],zz6=new double[N]; - - - - // Test Bessjy (jn) - System.out.println("Testing Bessjy (jn)"); - - sbeps=5.e-14; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessjy (jn): Incorrect function values"); - - } - - // Test Bessjy (yn) - System.out.println("Testing Bessjy (yn)"); - sbeps=5.e-14; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Bessjy (yn): Incorrect function values"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Betadist.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Betadist.java deleted file mode 100644 index 28db246209..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Betadist.java +++ /dev/null @@ -1,183 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Midpnt; -import com.nr.ran.Ran; -import com.nr.sf.Betadist; -import static com.nr.fi.Midpnt.qromo; - -public class Test_Betadist { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=19; - double alpha,beta,u,a,b,integral,sbeps=2.e-15; - double xx[]={0.05,0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.45,0.5,0.55,0.6,0.65,0.7,0.75,0.8,0.85,0.9,0.95}; - double ppexp[]={0.055499225064202982,0.15278874536821926,0.27278247243349879, - 0.40743665431525133,0.55132889542179109,0.70016599098719778, - 0.85021518016199371,0.99801190557910335,1.1401716162949527, - 1.2732395447351601,1.3935430865827199,1.4970178583686551, - 1.5789710488722741,1.6337206456367952,1.6539866862653729, - 1.6297466172610049,1.5457673437898269,1.3750987083139725, - 1.0544852762198569}; - double[] x=buildVector(xx),pexp=buildVector(ppexp),p=new double[N],c=new double[N],d=new double[N]; - boolean localflag=false, globalflag=false; - - - - // Test Betadist - System.out.println("Testing Betadist"); - - // Test special cases - alpha=1.0; beta=1.0; u=0.5; - Betadist norm1 = new Betadist(alpha,beta); - localflag = abs(norm1.p(u)-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Betadist: Special case #1 failed"); - - } - - alpha=1.0; beta=2.0; u=0.5; - Betadist norm2=new Betadist(alpha,beta); - localflag = abs(norm2.p(u)-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Betadist: Special case #2 failed"); - - } - - alpha=2.0; beta=1.0; u=0.5; - Betadist norm3=new Betadist(alpha,beta); - localflag = abs(norm3.p(u)-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Betadist: Special case #3 failed"); - - } - - alpha=2.0; beta=2.0; u=0.5; - Betadist norm4=new Betadist(alpha,beta); - localflag = abs(norm4.p(u)-3.0/2.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Betadist: Special case #4 failed"); - - } - - alpha=2.0; beta=2.0; u=1.0/3.0; - Betadist norm5=new Betadist(alpha,beta); - localflag = abs(norm5.p(u)-4.0/3.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Betadist: Special case #5 failed"); - - } - - // integral of distribution is one - sbeps=2.e-6; - alpha=2.5; beta=1.5; - func_Betadist dist = new func_Betadist(alpha,beta); - Midpnt q2 = new Midpnt(dist,0.0,1.0); - integral=qromo(q2); - localflag = abs(1.0-integral) > sbeps; -// System.out.printf(setprecision(15) << 1.0-integral); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Betadist: Distribution is not normalized to 1.0"); - - } - - // cdf agrees with incomplete integral - sbeps=5.e-6; - alpha=2.5; beta=1.5; - func_Betadist dist2 = new func_Betadist(alpha,beta); - Betadist normcdf =new Betadist(alpha,beta); - localflag=false; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Betadist: cdf does not agree with result of quadrature"); - - } - - // inverse cdf agrees with cdf - alpha=2.5; beta=1.5; - Betadist normc = new Betadist(alpha,beta); - Ran myran = new Ran(17); - sbeps=5.0e-14; - localflag=false; - for (i=0;i<1000;i++) { - u=myran.doub(); - a=normc.cdf(u); - b=normc.invcdf(a); -// if (abs(u-b) > sbeps) { -// System.out.printf(setprecision(15) << u << " %f\n", b << " %f\n", abs(u-b)); -// } - localflag = localflag || abs(u-b) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Betadist: Inverse cdf does not accurately invert the cdf"); - - } - - // Fingerprint test - alpha=2.5; beta=1.5; - Betadist normf = new Betadist(alpha,beta); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Betadist: Fingerprint does not match expectations"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class func_Betadist implements UniVarRealValueFun{ - double alpha,beta; - Betadist normi; - func_Betadist(double aalpha, double bbeta) { - alpha = aalpha; - beta = bbeta; - normi = new Betadist(alpha,beta); - } - - public double funk(final double x) { - return normi.p(x); - } - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Binomialdist.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Binomialdist.java deleted file mode 100644 index d2737da9bf..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Binomialdist.java +++ /dev/null @@ -1,158 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.sf.Binomialdist; - -public class Test_Binomialdist { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,n,ju,jb,M=21; - double p,a,sum,sbeps=2.e-15; - // int kk[]={0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20}; - double ppexp[]={3.6561584400629632e-005,0.00048748779200839343,0.0030874226827198371, - 0.012349690730879482,0.034990790404158277,0.074647019528871122, - 0.12441169921478451,0.16588226561971309,0.17970578775468887, - 0.1597384780041681,0.11714155053638949,0.070994879112963691, - 0.035497439556481721,0.014563052125736135,0.0048543507085786804, - 0.0012944935222876605,0.00026968615047659553,4.2303709878681877e-005, - 4.700412208742411e-006,3.2985348833279697e-007,1.0995116277760029e-008}; - // int[] k = buildVector(kk); - double[] pexp=buildVector(ppexp),pp=new double[M],c=new double[M],d=new double[M]; - boolean localflag=false, globalflag=false; - - - - - // Test Binomialdist - System.out.println("Testing Binomialdist"); - - // Test special cases - - n=1; p=0.5; ju=1; - Binomialdist norm2 = new Binomialdist(n,p); - localflag = abs(norm2.p(ju)-0.5) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Binomialdist: Special case #1 failed"); - - } - - n=2; p=0.5; ju=1; - Binomialdist norm3 = new Binomialdist(n,p); - localflag = abs(norm3.p(ju)-0.5) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Binomialdist: Special case #2 failed"); - - } - - n=2; p=0.5; ju=2; - Binomialdist norm4 = new Binomialdist(n,p); - localflag = abs(norm4.p(ju)-0.25) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Binomialdist: Special case #3 failed"); - - } - - n=3; p=1.0/3.0; ju=2; - Binomialdist norm5 = new Binomialdist(n,p); - localflag = abs(norm5.p(ju)-2.0/9.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Binomialdist: Special case #4 failed"); - - } - - // Sum of distribution is one - sbeps=1.e-14; - n=10; p=0.4; - Binomialdist dist1 = new Binomialdist(n,p); - sum=0.0; - for (i=0;i<=n;i++) - sum += dist1.p(i); - localflag = abs(1.0-sum) > sbeps; -// System.out.printf(setprecision(15) << 1.0-sum); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Binomialdist: Distribution is not normalized to 1.0"); - - } - - // cdf agrees with incomplete integral - sbeps=1.e-14; - n=10; p=0.4; - Binomialdist dist3 =new Binomialdist(n,p); - sum=0.0; - localflag=false; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Binomialdist: cdf does not agree with summation"); - - } - - // inverse cdf agrees with cdf - n=10; p=0.4; - Binomialdist normc=new Binomialdist(n,p); - sbeps=5.0e-14; - localflag=false; - for (i=1;i<10;i++) { - a=normc.cdf(i); - jb=normc.invcdf(a); -// if (abs(i-jb) > sbeps) { -// System.out.printf(setprecision(15) << i << " %f\n", jb << " %f\n", abs(i-jb)); -// } - localflag = localflag || (i-jb) != 0 && (i-jb-1) != 0; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Binomialdist: Inverse cdf does not accurately invert the cdf"); - - } - - // Fingerprint test - n=M-1; p=0.4; - sbeps=2.e-15; - Binomialdist normf=new Binomialdist(n,p); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Binomialdist: Fingerprint does not match expectations"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Cauchydist.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Cauchydist.java deleted file mode 100644 index 0c404d2131..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Cauchydist.java +++ /dev/null @@ -1,199 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static org.junit.Assert.fail; -import static com.nr.fi.Midpnt.qromo; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Midinf; -import com.nr.fi.Midpnt; -import com.nr.ran.Ran; -import com.nr.sf.Cauchydist; - -public class Test_Cauchydist { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=15; - double pi=acos(-1.0),oneoverpi,m,s,u,a,b,integral,sbeps; - double xx[]={-3.0,-2.5,-2.0,-1.5,-1.0,-0.5,0.0,0.5,1.0,1.5,2.0,2.5,3.0,3.5,4.0}; - double ppexp[]={0.032928608915564553,0.042441318157838762,0.056172332855963063, - 0.076394372684109771,0.1061032953945969,0.14691225516174955, - 0.19098593171027439,0.21220659078919379,0.19098593171027439, - 0.14691225516174955,0.1061032953945969,0.076394372684109771, - 0.056172332855963063,0.042441318157838762,0.032928608915564553}; - double[] x=buildVector(xx),pexp=buildVector(ppexp),p= new double[N],c= new double[N],d= new double[N]; - boolean localflag=false, globalflag=false; - - - - // Test Cauchydist - System.out.println("Testing Cauchydist"); - - oneoverpi=1.0/pi; - - sbeps=1.e-15; - // Test special cases - m=0; s=1; u=0; - Cauchydist norm1=new Cauchydist(m,s); - localflag = abs(norm1.p(u)-oneoverpi) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Cauchydist: Special case #1 failed"); - - } - - m=1; s=1; u=m; - Cauchydist norm2=new Cauchydist(m,s); - localflag = abs(norm2.p(u)-oneoverpi) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Cauchydist: Special case #2 failed"); - - } - - m=1; s=1; u=0; - Cauchydist norm3=new Cauchydist(m,s); - localflag = abs(norm3.p(u)-oneoverpi/2.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Cauchydist: Special case #3 failed"); - - } - - m=1; s=2; u=1; - Cauchydist norm4=new Cauchydist(m,s); - localflag = abs(norm4.p(u)-oneoverpi/2.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Cauchydist: Special case #4 failed"); - - } - - m=1; s=2; u=0; - Cauchydist norm5=new Cauchydist(m,s); - localflag = abs(norm5.p(u)-oneoverpi/2.0/(1+1.0/4.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Cauchydist: Special case #5 failed"); - - } - - // integral of distribution is one - sbeps=1.e-8; - m=1.0;s=2.0; - func_Cauchydist dist=new func_Cauchydist(m,s); - Midinf q1 = new Midinf(dist,-1.0e99,-1.0); - Midpnt q2 = new Midpnt(dist,-1.0,1.0); - Midinf q3 = new Midinf(dist,1.0,1.0e99); - integral=qromo(q1)+qromo(q2)+qromo(q3); - localflag = abs(1.0-integral) > sbeps; -// System.out.printf(setprecision(15) << 1.0-integral); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Cauchydist: Distribution is not normalized to 1.0"); - - } - - // cdf agrees with incomplete integral - sbeps=1.e-7; - m=0.5;s=1.5; - func_Cauchydist dist2=new func_Cauchydist(m,s); - Cauchydist normcdf = new Cauchydist(m,s); - localflag=false; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Cauchydist: cdf does not agree with result of quadrature"); - - } - - // inverse cdf agrees with cdf - m=0.5;s=1.5; - Cauchydist normc=new Cauchydist(m,s); - Ran myran = new Ran(17); - sbeps=1.0e-14; - localflag=false; - for (i=0;i<1000;i++) { - u=m-3.0*s+6.0*s*myran.doub(); - a=normc.cdf(u); - b=normc.invcdf(a); -// System.out.printf(setprecision(15) << u << " %f\n", b << " %f\n", abs(u-b)); - localflag = localflag || abs(u-b) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Cauchydist: Inverse cdf does not accurately invert the cdf"); - - } - - // Fingerprint test - m=0.5;s=1.5; - Cauchydist normf=new Cauchydist(m,s); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Cauchydist: Fingerprint does not match expectations"); - - } - - // Symmetry test - localflag=false; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Chisqdist: Special case #1 failed"); - - } - - df=10.0; chisq=2.0; - Chisqdist norm2=new Chisqdist(df); - localflag = abs(norm2.p(chisq)-pow(chisq,df/2.-1.)*exp(-chisq/2.)/pow(2.,df/2.)/factrl((int)(df/2.-1.))) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Chisqdist: Special case #2 failed"); - - } - - df=10.0; chisq=3.0; - Chisqdist norm3=new Chisqdist(df); - localflag = abs(norm3.p(chisq)-pow(chisq,df/2.-1.)*exp(-chisq/2.)/pow(2.,df/2.)/factrl((int)(df/2.-1.))) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Chisqdist: Special case #3 failed"); - - } - - df=6.0; chisq=1.0; - Chisqdist norm4=new Chisqdist(df); - localflag = abs(norm4.p(chisq)-pow(chisq,df/2.-1.)*exp(-chisq/2.)/pow(2.,df/2.)/factrl((int)(df/2.-1.))) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Chisqdist: Special case #4 failed"); - - } - - // integral of distribution is one - sbeps=1.e-8; - df=100.; - func_Chisqdist dist = new func_Chisqdist(df); - Midpnt q2=new Midpnt(dist,0.0,4.0); - Midinf q3=new Midinf(dist,4.0,1.0e99); - integral=qromo(q2)+qromo(q3); - localflag = abs(1.0-integral) > sbeps; -// System.out.printf(setprecision(15) << 1.0-integral); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Chisqdist: Distribution is not normalized to 1.0"); - - } - - // cdf agrees with incomplete integral - sbeps=1.e-7; - df=100.; - func_Chisqdist dist2 = new func_Chisqdist(df); - Chisqdist normcdf=new Chisqdist(df); - localflag=false; - - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Chisqdist: cdf does not agree with result of quadrature"); - - } - - // inverse cdf agrees with cdf - df=100.; - Chisqdist normc=new Chisqdist(df); - Ran myran = new Ran(17); - sbeps=2.0e-12; // XXX 1.0e-12 not pass. - localflag=false; - for (i=0;i<1000;i++) { - chisq=df-3.0*sqrt(df)+6.0*sqrt(df)*myran.doub(); - a=normc.cdf(chisq); - b=normc.invcdf(a); - if (abs(chisq-b) > sbeps) { - System.out.printf("%f %f %f\n",chisq, b ,abs(chisq-b)); - } - localflag = localflag || abs(chisq-b) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Chisqdist: Inverse cdf does not accurately invert the cdf"); - - } - - // Fingerprint test - df=100.; - Chisqdist normf=new Chisqdist(df); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Chisqdist: Fingerprint does not match expectations"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class func_Chisqdist implements UniVarRealValueFun{ - double df; - Chisqdist normi; - func_Chisqdist(double ddf) { - df = ddf; - normi = new Chisqdist(df); - } - public double funk(final double x) { - return normi.p(x); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Erf.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Erf.java deleted file mode 100644 index cf91cf2b06..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Erf.java +++ /dev/null @@ -1,96 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.sf.Erf; - -public class Test_Erf { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=13; - double sbeps; - double x[]={-4.0,-3.0,-2.0,-1.0,-0.5,-0.1,0.0,0.1,0.5,1.0,2.0,3.0,4.0}; - double y1[]={-9.999999845827421e-1,-9.999779095030015e-1,-9.953222650189527e-1, - -8.427007929497148e-1,-5.204998778130465e-1,-1.124629160182849e-1,0.0, - 1.124629160182849e-1,5.204998778130465e-1,8.427007929497148e-1, - 9.953222650189527e-1,9.999779095030015e-1,9.999999845827421e-1}; - double y2[]={1.999999984582742e+000,1.999977909503002e+000,1.995322265018953e+000, - 1.842700792949715e+000,1.520499877813047e+000,1.112462916018285e+000,1.0, - 8.875370839817152e-001,4.795001221869535e-001,1.572992070502852e-001, - 4.677734981047265e-003,2.209049699858543e-005,1.541725790028003e-008}; - double[] xx=buildVector(x),yy1=buildVector(y1),yy2=buildVector(y2),zz1= new double[N],zz2= new double[N],zz3= new double[N],zz4= new double[N]; - boolean localflag, globalflag=false; - - - - // Test Erf - System.out.println("Testing Erf"); - - Erf e = new Erf(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Erf, erf(): Incorrect function values"); - - } - - sbeps=5.e-15; - System.out.printf("Erf, erfc(): Maximum discrepancy = %f\n", maxel(vecsub(zz2,yy2))); - localflag = maxel(vecsub(zz2,yy2)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Erf, erfc(): Incorrect function values"); - - } - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Erf, inverf(): Inversion does not return to original arguments"); - - } - - sbeps=1.e-9; - System.out.printf("Erf, inverfc(): Maximum discrepancy = %f\n", maxel(vecsub(zz4,xx))); - localflag = maxel(vecsub(zz4,xx)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Erf, inverfc(): Inversion does not return to original arguments"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Expondist.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Expondist.java deleted file mode 100644 index e4f169f724..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Expondist.java +++ /dev/null @@ -1,174 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static java.lang.Math.exp; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Midinf; -import com.nr.fi.Midpnt; -import com.nr.ran.Ran; -import com.nr.sf.Expondist; -import static com.nr.fi.Midpnt.qromo; - -public class Test_Expondist { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=21; - double beta,u,a,b,integral,sbeps=1.e-15; - double xx[]={0.0,0.2,0.4,0.6,0.8,1.0,1.2,1.4,1.6,1.8,2.0,2.2,2.4,2.6,2.8,3.0,3.2,3.4,3.6,3.8,4.0}; - double ppexp[]={1.5,1.1112273310225769,0.82321745414103953, - 0.60985448961089872,0.45179131786830307,0.33469524022264474, - 0.24794833233237984,0.18368464237947291,0.13607692993411871, - 0.10080826910962463,0.074680602551795913,0.055324751101859991, - 0.040985583670938852,0.030362867168706571,0.022493365230716576, - 0.016663494807363458,0.012344620573530035,0.0091451198482734569, - 0.0067748714139189989,0.0050189481862069124,0.0037181282649995377}; - double[] x=buildVector(xx),pexp=buildVector(ppexp),p= new double[N],c= new double[N],d= new double[N]; - boolean localflag=false, globalflag=false; - - - - // Test Expondist - System.out.println("Testing Expondist"); - - // Test special cases - beta=1.0; u=0.0; - Expondist norm1=new Expondist(beta); - localflag = abs(norm1.p(u)-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Expondist: Special case #1 failed"); - - } - - beta=1.0; u=1.0; - Expondist norm2=new Expondist(beta); - localflag = abs(norm2.p(u)-exp(-1.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Expondist: Special case #2 failed"); - - } - - beta=2.0; u=0.0; - Expondist norm3=new Expondist(beta); - localflag = abs(norm3.p(u)-2.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Expondist: Special case #3 failed"); - - } - - beta=2.0; u=1.0; - Expondist norm4=new Expondist(beta); - localflag = abs(norm4.p(u)-2.0*exp(-2.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Expondist: Special case #4 failed"); - - } - - // integral of distribution is one - sbeps=1.e-8; - beta=1.5; - func_Expondist dist =new func_Expondist(beta); - Midpnt q2 = new Midpnt(dist,0.0,4.0); - Midinf q3 = new Midinf(dist,4.0,1.0e99); - integral=qromo(q2)+qromo(q3); - localflag = abs(1.0-integral) > sbeps; -// System.out.printf(setprecision(15) << 1.0-integral); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Expondist: Distribution is not normalized to 1.0"); - - } - - // cdf agrees with incomplete integral - sbeps=1.e-7; - beta=1.5; - func_Expondist dist2 = new func_Expondist(beta); - Expondist normcdf=new Expondist(beta); - localflag=false; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Expondist: cdf does not agree with result of quadrature"); - } - - // inverse cdf agrees with cdf - beta=1.5; - Expondist normc=new Expondist(beta); - Ran myran=new Ran(17); - sbeps=5.0e-14; - localflag=false; - for (i=0;i<1000;i++) { - u=3.0*myran.doub(); - a=normc.cdf(u); - b=normc.invcdf(a); -// if (abs(u-b) > sbeps) { -// System.out.printf(setprecision(15) << u << " %f\n", b << " %f\n", abs(u-b)); -// } - localflag = localflag || abs(u-b) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Expondist: Inverse cdf does not accurately invert the cdf"); - - } - - // Fingerprint test - beta=1.5; - Expondist normf=new Expondist(beta); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Expondist: Fingerprint does not match expectations"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class func_Expondist implements UniVarRealValueFun{ - double beta; - Expondist normi; - func_Expondist(double bbeta) { - beta = bbeta; - normi = new Expondist(beta); - } - - public double funk(final double x) { - return normi.p(x); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Fdist.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Fdist.java deleted file mode 100644 index 519d8d0d72..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Fdist.java +++ /dev/null @@ -1,188 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.fi.Midpnt.qromo; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.pow; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Midinf; -import com.nr.fi.Midpnt; -import com.nr.ran.Ran; -import com.nr.sf.Fdist; -public class Test_Fdist { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=20; - double pi,nu1,nu2,u,a,b,integral,sbeps=1.e-15; - double xx[]={0.2,0.4,0.6,0.8,1.0,1.2,1.4,1.6,1.8,2.0,2.2,2.4,2.6,2.8,3.0,3.2,3.4,3.6,3.8,4.0}; - double ppexp[]={0.65903939205294171,0.58692958722433863,0.48156597192304679, - 0.39054186195729862,0.31830988618379047,0.26197671666380806, - 0.21795679194590994,0.18326522386704397,0.15563320920200663, - 0.13338019498623788,0.11526607892303817,0.10037116939735392, - 0.088007419281388721,0.077654806187662545,0.068916111927723928, - 0.061484724623014866,0.055121565493375241,0.049638410886319047, - 0.044885720465175881,0.040743665431525217}; - double[] x=buildVector(xx),pexp=buildVector(ppexp),p= new double[N],c= new double[N],d= new double[N]; - boolean localflag=false, globalflag=false; - - - - // Test Fdist - System.out.println("Testing Fdist"); - - pi=acos(-1.0); - - // Test special cases - nu1=1.0; nu2=1.0; u=1.0; - Fdist norm1=new Fdist(nu1,nu2); - localflag = abs(norm1.p(u)-0.5/pi) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fdist: Special case #1 failed"); - - } - - nu1=1.0; nu2=2.0; u=1.0; - Fdist norm2=new Fdist(nu1,nu2); - localflag = abs(norm2.p(u)-1.0/pow(3.0,1.5)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fdist: Special case #2 failed"); - - } - - nu1=2.0; nu2=1.0; u=1.0; - Fdist norm3=new Fdist(nu1,nu2); - localflag = abs(norm3.p(u)-1.0/pow(3.0,1.5)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fdist: Special case #3 failed"); - - } - - nu1=2.0; nu2=2.0; u=1.0; - Fdist norm4=new Fdist(nu1,nu2); - localflag = abs(norm4.p(u)-0.25) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fdist: Special case #4 failed"); - - } - - nu1=2.0; nu2=2.0; u=2.0; - Fdist norm5=new Fdist(nu1,nu2); - localflag = abs(norm5.p(u)-1.0/9.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fdist: Special case #5 failed"); - - } - - // integral of distribution is one - sbeps=5.e-7; - nu1=5.0; nu2=5.0; - func_Fdist dist = new func_Fdist(nu1,nu2); - Midpnt q2 = new Midpnt(dist,0.0,10.0); - Midinf q3 = new Midinf(dist,10.0,1.0e99); - integral=qromo(q2)+qromo(q3); - localflag = abs(1.0-integral) > sbeps; -// System.out.printf(setprecision(15) << 1.0-integral); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fdist: Distribution is not normalized to 1.0"); - - } - - // cdf agrees with incomplete integral - sbeps=1.e-6; - nu1=5.0; nu2=5.0; - func_Fdist dist2 = new func_Fdist(nu1,nu2); - Fdist normcdf=new Fdist(nu1,nu2); - localflag=false; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fdist: cdf does not agree with result of quadrature"); - - } - - // inverse cdf agrees with cdf - nu1=5.0; nu2=5.0; - Fdist normc=new Fdist(nu1,nu2); - Ran myran = new Ran(17); - sbeps=5.0e-14; - localflag=false; - for (i=0;i<1000;i++) { - u=3.0*myran.doub(); - a=normc.cdf(u); - b=normc.invcdf(a); -// if (abs(u-b) > sbeps) { -// System.out.printf(setprecision(15) << u << " %f\n", b << " %f\n", abs(u-b)); -// } - localflag = localflag || abs(u-b) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fdist: Inverse cdf does not accurately invert the cdf"); - - } - - // Fingerprint test - nu1=3.0; nu2=3.0; - Fdist normf=new Fdist(nu1,nu2); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fdist: Fingerprint does not match expectations"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class func_Fdist implements UniVarRealValueFun{ - double nu1,nu2; - Fdist normi; - - func_Fdist(double nnu1, double nnu2) { - nu1 = nnu1; - nu2 = nnu2; - normi = new Fdist(nu1,nu2); - } - - public double funk(final double x) { - return normi.p(x); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Fermi.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Fermi.java deleted file mode 100644 index 6130f47313..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Fermi.java +++ /dev/null @@ -1,111 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.SQR; -import static com.nr.NRUtil.buildVector; -import static com.nr.sf.Gamma.gammln; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static java.lang.Math.exp; -import static java.lang.Math.log; -import static java.lang.Math.pow; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.sf.Fermi; - -public class Test_Fermi { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=35; - double x,y,u,theta,arg,err,maxerr,sbeps; - double k[]={-0.5,-0.5,-0.5,-0.5,-0.5,0.0,0.0,0.0,0.0,0.0, - 0.5,0.5,0.5,0.5,0.5,1.0,1.0,1.0,1.0,1.0, - 1.5,1.5,1.5,1.5,1.5,2.0,2.0,2.0,2.0,2.0, - 2.5,2.5,2.5,2.5,2.5}; - double eta[]={-4.0,-2.0,0.0,2.0,4.0,-4.0,-2.0,0.0,2.0,4.0, - -4.0,-2.0,0.0,2.0,4.0,-4.0,-2.0,0.0,2.0,4.0, - -4.0,-2.0,0.0,2.0,4.0,-4.0,-2.0,0.0,2.0,4.0, - -4.0,-2.0,0.0,2.0,4.0}; - double llerchphi[]={0.98723954437218395070,0.91377221699828150158,0.60489864342163037025, - 0.19817072295601367000,0.040035599911294837599,0.99095248754732942653, - 0.93787819412221284129,0.69314718055994530942,0.28784840479838595436, - 0.073594983080535873137,0.99358824548351926869,0.95539396843037045842, - 0.76514702462540794537,0.38214911885839316878,0.119263520628480860315, - 0.99545798433477938115,0.96805859921517155120,0.82246703342411321824, - 0.47555757258932435467,0.17631919052265099404,0.99678355180598445962, - 0.97717889296141227425,0.86719988901218413819,0.56372754572416136561, - 0.24287431294359210786,0.99772287456821212285,0.98372520603432318369, - 0.90154267736969571405,0.64369983563986970788,0.31621358700726185813, - 0.99838823665214391464,0.98841134290237239108,0.92755357777394803511, - 0.71384242344355014277,0.39321310731185353334}; - double[] zz= new double[N],lerchphi=buildVector(llerchphi),expect= new double[N]; - boolean localflag, globalflag=false; - - - - // Test Fermi - System.out.println("Testing Fermi"); - - // Test cases with theta=0 - // Fermi(k,eta,0)=exp(eta)*LerchPhi(exp(eta),k+1,1) - Fermi dirac = new Fermi(); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fermi: Incorrect function values"); - - } - - // Limiting cases for large eta and k=1/2 - maxerr=0.0; - for (i=0;i maxerr) maxerr=err; -// System.out.printf(setw(15) << theta << setw(15) << expect[i] << setw(15) << zz[i]; -// System.out.printf(setw(15) << abs(zz[i]/expect[i]-1.0)); - } - sbeps=1.e-4; -// System.out.printf(maxerr); - localflag = maxerr > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Fermi: Incorrect dependence on theta for k=1/2 and large eta"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Gamma.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Gamma.java deleted file mode 100644 index e8c1d1e725..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Gamma.java +++ /dev/null @@ -1,121 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecadd; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.sf.Gamma; - -public class Test_Gamma { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N; - double sbeps; - boolean localflag, globalflag=false; - - - - // Test Gamma - System.out.println("Testing Gamma (gammp, gammq, gser, gcf, invgammp)"); - - Gamma gam = new Gamma(); - - // Test Gamma.gammp, Gamma.gammq (as well as gser, gcf) - N=12; - double a[]={0.5,0.5,0.5,1.0,1.0,1.0,3.0,3.0,3.0,10.0,10.0,10.0}; //,110.0,200.0 - double x[]={0.5,1.0,2.0,0.5,1.0,2.5,2.0,3.5,5.0,7.0,10.0,12.5}; //,100.0,220.0 - double y[]={6.826894921370857e-1,8.427007929497149e-1,9.544997361036406e-1, - 3.934693402873665e-1,6.321205588285578e-1,9.179150013761013e-1, - 3.233235838169363e-1,6.791528011378658e-1,8.753479805169189e-1, - 1.695040627613259e-1,5.420702855281473e-1,7.985688950544638e-1}; - double[] xx=buildVector(x),yy=buildVector(y),zz= new double[N],uu= new double[N],vv= new double[N],c=buildVector(N,1.); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gamma.gammp: Incorrect function values"); - - } - - System.out.printf("Gamma.gammq: Maximum discrepancy = %f\n", maxel(vecsub(vecadd(zz,uu),c))); - sbeps=5.e-15; - localflag = maxel(vecsub(vecadd(zz,uu),c)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gamma.gammq: gammp and gammq do not sum to 1.0"); - - } - - System.out.printf("Gamma.invgammp: Maximum discrepancy = %f\n", maxel(vecsub(xx,vv))); - sbeps=5.e-14; - localflag = maxel(vecsub(xx,vv)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gamma.invgammp: Inverse does not return to original argument x[i]"); - - } - - xx =new double[2];yy =new double[2];zz =new double[2];uu =new double[2];vv =new double[2]; - double[] aa = new double[2],cc=buildVector(2,1.0); - aa[0]=110.0; aa[1]=200.0; - xx[0]=100.0; xx[1]=210.0; - yy[0]=1.705598979081085e-1; yy[1]=7.639696745011632e-1; - zz[0]=gam.gammp(aa[0],xx[0]); zz[1]=gam.gammp(aa[1],xx[1]); - uu[0]=gam.gammq(aa[0],xx[0]); uu[1]=gam.gammq(aa[1],xx[1]); - vv[0]=gam.invgammp(zz[0],aa[0]); vv[1]=gam.invgammp(zz[1],aa[1]); - - System.out.printf("Gamma.gammp from gammpapprox: Maximum discrepancy = %f\n", maxel(vecsub(zz,yy))); - sbeps=5.e-14; - localflag = maxel(vecsub(zz,yy)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gamma.gammp from gammpapprox: Incorrect function values"); - - } - - System.out.printf("Gamma.gammq from gammpapprox: Maximum discrepancy = %f\n", maxel(vecsub(vecadd(zz,uu),cc))); - sbeps=5.e-15; - localflag = maxel(vecsub(vecadd(zz,uu),cc)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gamma.gammq from gammpapprox: gammp and gammq do not sum to 1.0"); - - } - - System.out.printf("Gamma.invgammp: Maximum discrepancy = %f\n", maxel(vecsub(xx,vv))); - sbeps=5.e-13; - localflag = maxel(vecsub(xx,vv)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gamma.invgammp with large a: Inverse does not return to original argument x[i]"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Gammadist.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Gammadist.java deleted file mode 100644 index 7dd100bd73..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Gammadist.java +++ /dev/null @@ -1,187 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static java.lang.Math.exp; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Midinf; -import com.nr.fi.Midpnt; -import com.nr.ran.Ran; -import com.nr.sf.Gammadist; -import static com.nr.fi.Midpnt.qromo; - -public class Test_Gammadist { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=20; - double alpha,beta,u,a,b,integral,sbeps=1.e-15; - double xx[]={0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,2.0}; - double ppexp[]={0.056421908930476883,0.13735630417827352,0.21719074405218716, - 0.28780958001849588,0.34619922631227434,0.39170019681318374, - 0.42484430595288569,0.4467592468238949,0.45883671466221931, - 0.46254098941130778,0.45929855649326967,0.45043668078371302, - 0.43715226875054808,0.42049960233268446,0.40138972612974905, - 0.38059682877263284,0.35876857953338254,0.33643843523417555, - 0.31403863132501508,0.29191303997784868}; - double[] x=buildVector(xx),pexp=buildVector(ppexp),p= new double[N],c= new double[N],d= new double[N]; - boolean localflag=false, globalflag=false; - - - - // Test Gammadist - System.out.println("Testing Gammadist"); - - // Test special cases - alpha=1.0; beta=1.0; u=1.0; - Gammadist norm1 = new Gammadist(alpha,beta); - localflag = abs(norm1.p(u)-exp(-1.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gammadist: Special case #1 failed"); - - } - - alpha=1.0; beta=2.0; u=1.0; - Gammadist norm2 = new Gammadist(alpha,beta); -// System.out.printf(abs(norm2.p(u)-2.0*exp(-2.0)); - localflag = abs(norm2.p(u)-2.0*exp(-2.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gammadist: Special case #2 failed"); - - } - - alpha=2.0; beta=1.0; u=1.0; - Gammadist norm3 = new Gammadist(alpha,beta); -// System.out.printf(abs(norm3.p(u)-x*exp(-1.0)); - localflag = abs(norm3.p(u)-u*exp(-1.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gammadist: Special case #3 failed"); - - } - - alpha=3.0; beta=1.0; u=1.0; - Gammadist norm4 = new Gammadist(alpha,beta); - localflag = abs(norm4.p(u)-u*u*exp(-1.0)/2.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gammadist: Special case #4 failed"); - - } - - alpha=2.0; beta=2.0; u=2.0; - Gammadist norm5 = new Gammadist(alpha,beta); - localflag = abs(norm5.p(u)-4.0*u*exp(-4.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gammadist: Special case #5 failed"); - - } - - // integral of distribution is one - sbeps=2.e-7; - alpha=2.5; beta=1.5; - func_Gammadist dist = new func_Gammadist(alpha,beta); - Midpnt q2 = new Midpnt(dist,0.0,2.0); - Midinf q3 = new Midinf(dist,2.0,1.0e99); - integral=qromo(q2)+qromo(q3); - localflag = abs(1.0-integral) > sbeps; -// System.out.printf(setprecision(15) << 1.0-integral); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gammadist: Distribution is not normalized to 1.0"); - - } - - // cdf agrees with incomplete integral - sbeps=5.e-7; - alpha=2.5; beta=1.5; - func_Gammadist dist2 = new func_Gammadist(alpha,beta); - Gammadist normcdf = new Gammadist(alpha,beta); - localflag=false; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gammadist: cdf does not agree with result of quadrature"); - - } - - // inverse cdf agrees with cdf - alpha=2.5; beta=1.5; - Gammadist normc = new Gammadist(alpha,beta); - Ran myran = new Ran(17); - sbeps=5.0e-14; - localflag=false; - for (i=0;i<1000;i++) { - u=3.0*myran.doub(); - a=normc.cdf(u); - b=normc.invcdf(a); -// if (abs(u-b) > sbeps) { -// System.out.printf(setprecision(15) << u << " %f\n", b << " %f\n", abs(u-b)); -// } - localflag = localflag || abs(u-b) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gammadist: Inverse cdf does not accurately invert the cdf"); - - } - - // Fingerprint test - alpha=2.5; beta=1.5; - Gammadist normf = new Gammadist(alpha,beta); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gammadist: Fingerprint does not match expectations"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class func_Gammadist implements UniVarRealValueFun{ - double alpha,beta; - Gammadist normi; - func_Gammadist(double aalpha, double bbeta) { - alpha=aalpha; - beta=bbeta; - normi = new Gammadist(alpha,beta); - } - - public double funk(final double x) { - return normi.p(x); - } - }; -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_KSdist.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_KSdist.java deleted file mode 100644 index f17975479e..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_KSdist.java +++ /dev/null @@ -1,181 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static java.lang.Math.exp; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; -import com.nr.sf.KSdist; - -public class Test_KSdist { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=21; - double z,a,b,sbeps=1.e-13; // integral - double xx[]={0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,2.0,2.1,2.2,2.3}; - double ppksexp[]={9.3058013345666361e-006,0.0028076732227017387,0.036054756335124914, - 0.13571722094939573,0.28876480497031071,0.45585758842580204, - 0.60726929205934577,0.73000032832264539,0.82228180739359891, - 0.887750333329275,0.93190777815523362,0.96031812046188558, - 0.97778203738347491,0.98804795676080337,0.99382256936555591, - 0.99693237865242035,0.99853639516281267,0.99932907474422028, - 0.99970450327953686,0.99987495699245044,0.99994916130696765}; - double qqksexp[]={0.99999069419866549,0.9971923267772983,0.96394524366487511, - 0.86428277905060424,0.71123519502968935,0.54414241157419796, - 0.39273070794065423,0.26999967167735461,0.17771819260640109, - 0.11224966667072496,0.068092221844766362,0.039681879538114403, - 0.022217962616525127,0.011952043239196616,0.0061774306344441286, - 0.0030676213475797059,0.0014636048371873506,0.00067092525577969533, - 0.00029549672046311421,0.00012504300754960976,5.0838693032397749e-005}; - double[] x=buildVector(xx),pksexp=buildVector(ppksexp),qksexp=buildVector(qqksexp),pks= new double[N],qks= new double[N]; //,c= new double[N],d= new double[N]; - boolean localflag=false, globalflag=false; - - - - // Test KSdist - System.out.println("Testing KSdist"); - - // Test special cases - z=0.0; - KSdist norm = new KSdist(); - localflag = abs(norm.pks(z)-0.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KSdist: Special case #1 failed for Pks"); - - } - - localflag = abs(norm.qks(z)-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KSdist: Special case #1 failed for Qks"); - - } - - z=1.0; -// System.out.printf(setprecision(17) << norm.pks(z) << " %f\n", 1-2.0*exp(-2.0)+2.0*exp(-8.0)-2.0*exp(-18.0)); - localflag = abs(norm.pks(z)-1+2.0*exp(-2.0)-2.0*exp(-8.0)+2.0*exp(-18.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KSdist: Special case #2 failed for Pks"); - - } - - localflag = abs(norm.qks(z)-2.0*exp(-2.0)+2.0*exp(-8.0)-2.0*exp(-18.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KSdist: Special case #2 failed for Qks"); - - } - - z=100.0; - localflag = abs(norm.pks(z)-1.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KSdist: Special case #3 failed for Pks"); - - } - - localflag = abs(norm.qks(z)-0.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KSdist: Special case #3 failed for Qks"); - - } - - // Pks correctly related to Qks - localflag=false; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KSdist: Pks and Qks do not add to 1.0 in all cases"); - - } - - // inverse of Pks agrees with Pks - Ran myran = new Ran(17); - localflag=false; - sbeps=6.e-10; // XXX 5.e-10 not pass - for (i=0;i<10;i++) { - z=0.3+3.0*myran.doub(); - a=norm.pks(z); - b=norm.invpks(a); -// if (abs(z-b) > sbeps) { -// System.out.printf(setprecision(15) << z << " %f\n", b << " %f\n", abs(z-b)); -// } - localflag = localflag || abs(z-b) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KSdist: invPks does not accurately invert the Pks"); - - } - - // inverse of Qks agrees with Qks - localflag=false; - sbeps=5.e-10; - for (i=0;i<1000;i++) { - z=0.3+3.0*myran.doub(); - a=norm.qks(z); - b=norm.invqks(a); -// if (abs(z-b) > sbeps) { -// System.out.printf(setprecision(15) << z << " %f\n", b << " %f\n", abs(z-b)); -// } - localflag = localflag || abs(z-b) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KSdist: invQks does not accurately invert the Qks"); - - } - - // Fingerprint test for Pks - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KSdist: Fingerprint does not match expectations"); - - } - - // Fingerprint test for Qks - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** KSdist: Fingerprint does not match expectations"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Logisticdist.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Logisticdist.java deleted file mode 100644 index 1c15337db2..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Logisticdist.java +++ /dev/null @@ -1,206 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.SQR; -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.cosh; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Midinf; -import com.nr.fi.Midpnt; -import com.nr.ran.Ran; -import com.nr.sf.Logisticdist; -import static com.nr.fi.Midpnt.qromo; - -public class Test_Logisticdist { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=15; - double pi=acos(-1.0),pio4sqrt3,m,s,u,a,b,integral,sbeps=1.e-15; - double xx[]={-3.0,-2.5,-2.0,-1.5,-1.0,-0.5,0.0,0.5,1.0,1.5,2.0,2.5,3.0,3.5,4.0}; - double ppexp[]={0.017059092664760158,0.030497647063658831,0.053500875984749827, - 0.090801643627527795,0.14574392339674236,0.21404650800280242, - 0.27627401928012629,0.30229989403903629,0.27627401928012629, - 0.21404650800280242,0.14574392339674236,0.090801643627527795, - 0.053500875984749827,0.030497647063658831,0.017059092664760158}; - double[] x=buildVector(xx),pexp=buildVector(ppexp),p= new double[N],c= new double[N],d= new double[N]; - boolean localflag=false, globalflag=false; - - - - // Test Logisticdist - System.out.println("Testing Logisticdist"); - - pio4sqrt3=pi/4.0/sqrt(3.0); - - // Test special cases - m=0; s=1; u=0; - Logisticdist norm1 = new Logisticdist(m,s); - localflag = abs(norm1.p(u)-pio4sqrt3/s) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Logisticdist: Special case #1 failed"); - - } - - m=1; s=1; u=m; - Logisticdist norm2 = new Logisticdist(m,s); - localflag = abs(norm2.p(u)-pio4sqrt3) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Logisticdist: Special case #2 failed"); - - } - - m=1; s=1; u=0; - Logisticdist norm3 = new Logisticdist(m,s); -// System.out.printf(abs(norm3.p(u) - pio4sqrt3*SQR(1.0/cosh(2.0*pio4sqrt3)))); - localflag = abs(norm3.p(u)-pio4sqrt3*SQR(1.0/cosh(2.0*pio4sqrt3))) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Logisticdist: Special case #3 failed"); - - } - - m=1; s=2; u=1; - Logisticdist norm4 = new Logisticdist(m,s); - localflag = abs(norm4.p(u)-pio4sqrt3/s) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Logisticdist: Special case #4 failed"); - - } - - m=1; s=2; u=0; - Logisticdist norm5 = new Logisticdist(m,s); - localflag = abs(norm5.p(u)-pio4sqrt3/s/SQR(cosh(pio4sqrt3))) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Logisticdist: Special case #5 failed"); - - } - - // integral of distribution is one - sbeps=1.e-8; - m=1.0;s=2.0; - func_Logisticdist dist = new func_Logisticdist(m,s); - Midinf q1 = new Midinf(dist,-1.0e99,-1.0); - Midpnt q2 = new Midpnt(dist,-1.0,1.0); - Midinf q3 = new Midinf(dist,1.0,1.0e99); - integral=qromo(q1)+qromo(q2)+qromo(q3); - localflag = abs(1.0-integral) > sbeps; -// System.out.printf(setprecision(15) << 1.0-integral); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Logisticdist: Distribution is not normalized to 1.0"); - - } - - // cdf agrees with incomplete integral - sbeps=1.e-7; - m=0.5;s=1.5; - func_Logisticdist dist2 = new func_Logisticdist(m,s); - Logisticdist normcdf = new Logisticdist(m,s); - localflag=false; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Logisticdist: cdf does not agree with result of quadrature"); - - } - - // inverse cdf agrees with cdf - m=0.5;s=1.5; - Logisticdist normc = new Logisticdist(m,s); - Ran myran = new Ran(17); - sbeps=5.0e-14; - localflag=false; - for (i=0;i<1000;i++) { - u=m-3.0*s+6.0*s*myran.doub(); - a=normc.cdf(u); - b=normc.invcdf(a); -// if (abs(u-b) > sbeps) { -// System.out.printf(setprecision(15) << u << " %f\n", b << " %f\n", abs(u-b)); -// } - localflag = localflag || abs(u-b) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Logisticdist: Inverse cdf does not accurately invert the cdf"); - - } - - // Fingerprint test - m=0.5;s=1.5; - Logisticdist normf = new Logisticdist(m,s); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Logisticdist: Fingerprint does not match expectations"); - - } - - // Symmetry test - localflag=false; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Lognormaldist: Special case #1 failed"); - - } - - m=0.0; s=1.0; u=exp(1.0); - Lognormaldist norm2 = new Lognormaldist(m,s); -// System.out.printf(abs(norm2.p(u)-oneoversqt2pi*exp(-0.5)/u)); - localflag = abs(norm2.p(u)-oneoversqt2pi*exp(-0.5)/u) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Lognormaldist: Special case #2 failed"); - - } - - m=1.0; s=1.0; u=exp(0.0); - Lognormaldist norm3 = new Lognormaldist(m,s); -// System.out.printf(abs(norm3.p(u)-oneoversqt2pi*exp(-0.5)/u)); - localflag = abs(norm3.p(u)-oneoversqt2pi*exp(-0.5)/u) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Lognormaldist: Special case #3 failed"); - - } - - m=1.0; s=1.0; u=exp(m); - Lognormaldist norm4 = new Lognormaldist(m,s); - localflag = abs(norm4.p(u)-oneoversqt2pi/u) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Lognormaldist: Special case #4 failed"); - - } - - m=1.0; s=2.0; u=exp(0.0); - Lognormaldist norm5 = new Lognormaldist(m,s); - localflag = abs(norm5.p(u)-oneoversqt2pi*exp(-0.5/SQR(s))/s) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Lognormaldist: Special case #5 failed"); - - } - - // integral of distribution is one - sbeps=5.e-8; - m=0.5; s=1.5; - func_Lognormaldist dist= new func_Lognormaldist(m,s); - Midpnt q2 = new Midpnt(dist,0.0,10.0); - Midinf q3 = new Midinf(dist,10.0,1.0e99); - integral=qromo(q2)+qromo(q3); - localflag = abs(1.0-integral) > sbeps; -// System.out.printf(setprecision(15) << 1.0-integral); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Lognormaldist: Distribution is not normalized to 1.0"); - - } - - // cdf agrees with incomplete integral - sbeps=2.e-7; - m=0.5; s=1.5; - func_Lognormaldist dist2= new func_Lognormaldist(m,s); - Lognormaldist normcdf = new Lognormaldist(m,s); - localflag=false; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Lognormaldist: cdf does not agree with result of quadrature"); - - } - - // inverse cdf agrees with cdf - m=0.5; s=1.5; - Lognormaldist normc = new Lognormaldist(m,s); - Ran myran = new Ran(17); - sbeps=5.0e-14; - localflag=false; - for (i=0;i<1000;i++) { - u=3.0*myran.doub(); - a=normc.cdf(u); - b=normc.invcdf(a); -// if (abs(u-b) > sbeps) { -// System.out.printf(setprecision(15) << u << " %f\n", b << " %f\n", abs(u-b)); -// } - localflag = localflag || abs(u-b) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Lognormaldist: Inverse cdf does not accurately invert the cdf"); - - } - - // Fingerprint test - m=0.5; s=1.5; - Lognormaldist normf = new Lognormaldist(m,s); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Lognormaldist: Fingerprint does not match expectations"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class func_Lognormaldist implements UniVarRealValueFun{ - double m,s; - Lognormaldist normi; - func_Lognormaldist(double mm, double ss) { - m=mm; s=ss; - normi = new Lognormaldist(m,s); - } - public double funk(final double x) { - return normi.p(x); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Normaldist.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Normaldist.java deleted file mode 100644 index 6ec4e4c03c..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Normaldist.java +++ /dev/null @@ -1,185 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.exp; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.ran.Ran; -import com.nr.sf.Normaldist; -import static com.nr.fi.Trapzd.qsimp; - -public class Test_Normaldist { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=15; - double pi=acos(-1.0),invsq2pi,m,s,u,a,b,sbeps; - double xx[]={-3.0,-2.5,-2.0,-1.5,-1.0,-0.5,0.0,0.5,1.0,1.5,2.0,2.5,3.0,3.5,4.0}; - double ppexp[]={0.017481259395806324,0.035993977675458706,0.066318092528499115, - 0.10934004978399577,0.1613138163460956,0.2129653370149015, - 0.25158881846199549,0.26596152026762182,0.25158881846199549, - 0.2129653370149015,0.1613138163460956,0.10934004978399577, - 0.066318092528499115,0.035993977675458706,0.017481259395806324}; - double[] x=buildVector(xx),pexp=buildVector(ppexp),p= new double[N],c= new double[N],d= new double[N]; - boolean localflag=false, globalflag=false; - - - - // Test Normaldist - System.out.println("Testing Normaldist"); - - invsq2pi=1.0/sqrt(2.0*pi); - - // Test special cases - sbeps=1.e-15; - m=0; s=1; u=0; - Normaldist norm1 = new Normaldist(m,s); - localflag = localflag || abs(norm1.p(u) - invsq2pi) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Normaldist: Special case #1 failed"); - - } - - m=1; s=1; u=m; - Normaldist norm2 = new Normaldist(m,s); - localflag = localflag || abs(norm2.p(u) - invsq2pi) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Normaldist: Special case #2 failed"); - - } - - m=1; s=1; u=0; - Normaldist norm3 = new Normaldist(m,s); - localflag = localflag || abs(norm3.p(u) - invsq2pi*exp(-0.5)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Normaldist: Special case #3 failed"); - - } - - m=1; s=2; u=1; - Normaldist norm4 = new Normaldist(m,s); - localflag = localflag || abs(norm4.p(u) - invsq2pi/2.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Normaldist: Special case #4 failed"); - - } - - m=1; s=2; u=0; - Normaldist norm5 = new Normaldist(m,s); - localflag = localflag || abs(norm5.p(u) - invsq2pi/2.0*exp(-1.0/8.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Normaldist: Special case #5 failed"); - - } - - // integral of distribution is one - sbeps=1.e-10; - m=1.0;s=2.0; - func_Normaldist dist = new func_Normaldist(m,s); - localflag = abs(1.0-qsimp(dist,-20.0,20.0)) > sbeps; - // System.out.printf(setprecision(15) << 1.0-qsimp(dist,-20.0,20.0)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Normaldist: Distribution is not normalized to 1.0"); - - } - - // cdf agrees with incomplete integral - sbeps=1.e-10; - m=0.5;s=1.5; - func_Normaldist dist2 =new func_Normaldist(m,s); - Normaldist normcdf = new Normaldist(m,s); - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Normaldist: cdf does not agree with result of quadrature"); - - } - - // inverse cdf agrees with cdf - m=0.5;s=1.5; - Normaldist normc = new Normaldist(m,s); - Ran myran = new Ran(17); - sbeps=5.0e-14; - for (i=0;i<1000;i++) { - u=m-3.0*s+6.0*s*myran.doub(); - a=normc.cdf(u); - b=normc.invcdf(a); -// System.out.printf(setprecision(15) << u << " %f\n", b << " %f\n", abs(u-b)); - localflag = localflag || abs(u-b) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Normaldist: Inverse cdf does not accurately invert the cdf"); - - } - - // Fingerprint test - m=0.5;s=1.5; - Normaldist normf = new Normaldist(m,s); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Normaldist: Fingerprint does not match expectations"); - - } - - // Symmetry test - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poissondist: Special case #1 failed"); - - } - - lambda=1.0; ju=1; - Poissondist norm2 = new Poissondist(lambda); - localflag = abs(norm2.p(ju)-exp(-1.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poissondist: Special case #2 failed"); - - } - - lambda=2.0; ju=0; - Poissondist norm3 = new Poissondist(lambda); - localflag = abs(norm3.p(ju)-exp(-2.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poissondist: Special case #3 failed"); - - } - - lambda=2.0; ju=1; - Poissondist norm4 = new Poissondist(lambda); - localflag = abs(norm4.p(ju)-2.0*exp(-2.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poissondist: Special case #4 failed"); - - } - - lambda=1.0; ju=2; - Poissondist norm5 = new Poissondist(lambda); - localflag = abs(norm5.p(ju)-0.5*exp(-1.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poissondist: Special case #5 failed"); - - } - - lambda=2.0; ju=2; - Poissondist norm6 = new Poissondist(lambda); - localflag = abs(norm6.p(ju)-2.0*exp(-2.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poissondist: Special case #6 failed"); - - } - - // Sum over k is one - sbeps=1.e-15; - lambda=5.0; - sum=0.0; - Poissondist dist = new Poissondist(lambda); - for (i=0;i<50;i++) - sum += dist.p(i); - localflag = abs(1.0-sum) > sbeps; -// System.out.printf(setprecision(15) << 1.0-sum); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poissondist: Distribution is not normalized to 1.0"); - - } - - // cdf agrees with truncated sum - sbeps=1.e-15; - lambda=5.0; - Poissondist dist2 = new Poissondist(lambda); - localflag=false; - sum=0.0; - for (i=0;i<20;i++) { - sum += dist2.p(i); - c[i]=sum; - d[i]=dist2.cdf(i+1); -// System.out.printf(c[i]-d[i]); - localflag = localflag || abs(c[i]-d[i]) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poissondist: cdf does not agree with result of quadrature"); - - } - - // inverse cdf agrees with cdf - lambda=10.0; - Poissondist normc = new Poissondist(lambda); - sbeps=1.0e-12; - localflag=false; - for (i=1;i<20;i++) { - a=normc.cdf(i); - b=normc.invcdf(a); - localflag = localflag || (i-b != 0) && (i-b-1 != 0) ; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poissondist: Inverse cdf does not accurately invert the cdf"); - - } - - // Fingerprint test - lambda=10.0; - Poissondist normf = new Poissondist(lambda); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poissondist: Fingerprint does not match expectations"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Studenttdist.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Studenttdist.java deleted file mode 100644 index 0190a63931..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_Studenttdist.java +++ /dev/null @@ -1,236 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.fi.Midpnt.qromo; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.fi.Midinf; -import com.nr.fi.Midpnt; -import com.nr.ran.Ran; -import com.nr.sf.Studenttdist; -public class Test_Studenttdist { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=15; - double pi=acos(-1.0),oneoverpi,m,s,n,u,a,b,integral,sbeps=1.e-15; - double xx[]={-3.0,-2.5,-2.0,-1.5,-1.0,-0.5,0.0,0.5,1.0,1.5,2.0,2.5,3.0,3.5,4.0}; - double ppexp[]={0.0328216417673656,0.045360921162651474,0.063836610836904312, - 0.090793368604857677,0.12830005981991693,0.17443694974549953, - 0.21734122156158497,0.23570226039551601,0.21734122156158497, - 0.17443694974549953,0.12830005981991693,0.090793368604857677, - 0.063836610836904312,0.045360921162651474,0.0328216417673656}; - double[] x=buildVector(xx),pexp=buildVector(ppexp),p= new double[N],c= new double[N],d= new double[N]; - boolean localflag=false, globalflag=false; - - - - // Test Studenttdist - System.out.println("Testing Studenttdist"); - - oneoverpi=1.0/pi; - - // Test special cases - n=1.0;m=0.0;s=1.0;u=0.0; - Studenttdist norm1 = new Studenttdist(n,m,s); -// System.out.printf(norm1.p(u) << " %f\n", oneoverpi << " %f\n", norm1.p(u)-oneoverpi); - localflag = abs(norm1.p(u)-oneoverpi) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Studenttdist: Special case #1 failed"); - - } - - n=1.0;m=1.0;s=1.0;u=m; - Studenttdist norm2 = new Studenttdist(n,m,s); - localflag = abs(norm2.p(u)-oneoverpi) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Studenttdist: Special case #2 failed"); - - } - - n=1.0;m=1.0;s=1.0;u=0.0; - Studenttdist norm3 = new Studenttdist(n,m,s); - localflag = abs(norm3.p(u)-oneoverpi/2.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Studenttdist: Special case #3 failed"); - - } - - n=1.0;m=1.0;s=2.0;u=1.0; - Studenttdist norm4 = new Studenttdist(n,m,s); - localflag = abs(norm4.p(u)-oneoverpi/2.0) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Studenttdist: Special case #4 failed"); - - } - - n=1.0;m=1.0;s=2.0;u=0.0; - Studenttdist norm5 = new Studenttdist(n,m,s); - localflag = abs(norm5.p(u)-oneoverpi/2.0/(1+1.0/4.0)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Studenttdist: Special case #5 failed"); - - } - - // integral of distribution is one - sbeps=1.e-10; - n=2.0;m=1.0;s=2.0; - func_Studenttdist dist = new func_Studenttdist(n,m,s); - Midinf q1 = new Midinf(dist,-1.0e99,-1.0); - Midpnt q2 = new Midpnt(dist,-1.0,1.0); - Midinf q3 = new Midinf(dist,1.0,1.0e99); - integral=qromo(q1)+qromo(q2)+qromo(q3); - localflag = abs(1.0-integral) > sbeps; -// System.out.printf(setprecision(15) << 1.0-integral); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Studenttdist: Distribution is not normalized to 1.0"); - - } - - // cdf agrees with incomplete integral - sbeps=1.e-8; - n=2.0;m=0.5;s=1.5; - func_Studenttdist dist2 = new func_Studenttdist(n,m,s); - Studenttdist normcdf = new Studenttdist(n,m,s); - localflag=false; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Studenttdist: cdf does not agree with result of quadrature"); - - } - - // inverse cdf agrees with cdf - n=2.0;m=0.5;s=1.5; - Studenttdist normc = new Studenttdist(n,m,s); - Ran myran = new Ran(17); - sbeps=1.0e-13; - localflag=false; - for (i=0;i<1000;i++) { - u=m-3.0*s+6.0*s*myran.doub(); - a=normc.cdf(u); - b=normc.invcdf(a); -// System.out.printf(setprecision(15) << u << " %f\n", b << " %f\n", abs(u-b)); - localflag = localflag || abs(u-b) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Studenttdist: Inverse cdf does not accurately invert the cdf"); - - } - - // Function aa() agrees with incomplete integral - sbeps=1.e-7; - n=2.0;m=0.0;s=1.0; - func_Studenttdist dist3 = new func_Studenttdist(n,m,s); - Studenttdist normaa = new Studenttdist(n,m,s); - localflag=false; - for (i=0;i<10;i++) { - u = 0.5*i; - Midpnt qq1 = new Midpnt(dist3,-u,u); - c[i]=qromo(qq1); - d[i]=normaa.aa(u); -// System.out.printf(setprecision(6) << c[i] << " %f\n", d[i] << " %f\n", c[i]-d[i]); - localflag = localflag || abs(c[i]-d[i]) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Studenttdist: aa() does not agree with result of direct quadrature"); - - } - - // inverse invaa() agrees with aa() - n=2.0;m=0.5;s=1.5; - Studenttdist normaa2 = new Studenttdist(n,m,s); - sbeps=1.0e-13; - localflag=false; - for (i=0;i<1000;i++) { - u=m+3.0*s*myran.doub(); - a=normaa2.aa(u); - b=normaa2.invaa(a); -// System.out.printf(setprecision(15) << u << " %f\n", b << " %f\n", abs(u-b)); - localflag = localflag || abs(u-b) > sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Studenttdist: Inverse invaa() does not accurately invert aa()"); - - } - - // Fingerprint test - n=2.0;m=0.5;s=1.5; - Studenttdist normf = new Studenttdist(n,m,s); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Studenttdist: Fingerprint does not match expectations"); - - } - - // Symmetry test - localflag=false; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** beta: Incorrect function values"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_betai.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_betai.java deleted file mode 100644 index 14b4e80bda..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_betai.java +++ /dev/null @@ -1,91 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; -import com.nr.sf.Beta; - -public class Test_betai { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=21,M=100; - double c,d,u,r,uu,sbeps; - double a[]={0.1,0.1,0.1,0.5,0.5,0.5,1.0,1.0,1.0,2.0,2.0,2.0, - 5.0,5.0,5.0,10.0,10.0,10.0,20.0,20.0,20.0}; - double b[]={0.1,2.0,5.0,0.1,2.0,5.0,0.1,2.0,5.0,0.1,2.0,5.0, - 0.1,2.0,5.0,0.1,2.0,5.0,0.1,2.0,5.0}; - double x[]={0.0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,0.0, - 0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9}; - double y[]={0.0,0.8658177758494670,0.9766004939306013, - 0.1073414121635943,0.8221921916437793,0.9898804402645663, - 8.755646344451919e-2,0.9099999999999999,0.9996800000000000, - 0.1341822241505331,1.0,0.0, - 2.646501824334656e-7,1.600000000000003e-3,9.880866000000001e-2, - 2.079166305336834e-6,5.859375000000002e-3,0.2792569872383998, - 1.527902462384040e-5,5.764607523034282e-2,0.9149251141213293}; - double[] yy=buildVector(y),zz = new double[N]; - boolean localflag, globalflag=false; - - - - // Test betai - System.out.println("Testing betai, invbetai"); - - // Beta bi = new Beta(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** betai: Incorrect function values"); - - } - - // Round trip test - Ran myran = new Ran(17); - sbeps=1.e-8; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** betai: Failure in round-trip test"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_bico.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_bico.java deleted file mode 100644 index eb86667839..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_bico.java +++ /dev/null @@ -1,105 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.sf.Gamma.bico; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -public class Test_bico { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=50; - double sbeps=1.e-12; - double y[]={1.0,5.0,10.0,10.0,5.0,1.0}; - double[] x= new double[N],z= new double[N]; - boolean localflag, globalflag=false; - - - - // Test bico - System.out.println("Testing bico"); - - // Test some small values - localflag = bico(0,0) != 1.0; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** bico: Incorrect value for special case bico(0,0)=1"); - - } - - localflag = bico(1,1) != 1.0; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** bico: Incorrect value for special case bico(1,1)=1"); - - } - - for (i=0;i<6;i++) { - localflag = localflag || bico(5,i) != y[i]; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** bico: Test of bico with small arguments failed"); - - } - } - - // Test recursion in k, for n < 171 - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** bico: Test of recursion in k for n < 171 failed"); - - } - - // Test recursion in k, for n > 171 - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** bico: Test of recursion in k for n > 171 failed"); - - } - - // Test recursion in n - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** bico: Test of recursion in n failed"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_cisi.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_cisi.java deleted file mode 100644 index cb05e523ad..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_cisi.java +++ /dev/null @@ -1,96 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.Complex; -import static com.nr.NRUtil.*; -import static com.nr.sf.Integrals.*; - -public class Test_cisi { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=16; - double sbeps=1.0e-15; - Complex zz1,zz2; - double x[]={0.5,0.6,0.7,0.8,0.9,1.0,1.2,1.4,1.6,1.8,2.0,2.5,3.0,3.5,4.0,4.5}; - double u[]={-0.1777840788066129,-0.02227070695927976,0.1005147070088978, - 0.1982786159524672,0.2760678304677729,0.3374039229009681, - 0.4204591828942405,0.4620065850946773,0.4717325169318778, - 0.4568111294183369,0.4229808287748650,0.2858711963653835, - 0.1196297860080003,-0.03212854851248112,-0.1409816978869304, - -0.1934911221017388}; - double v[]={0.4931074180430667,0.5881288096080801,0.6812222391166113, - 0.7720957854819966,0.8604707107452929,0.9460830703671830, - 1.108047199013719,1.256226732779218,1.389180485870438, - 1.505816780255579,1.605412976802695,1.778520173443827, - 1.848652527999468,1.833125398665997,1.758203138949053, - 1.654140414379244}; - double[] uu=buildVector(u),vv=buildVector(v),zreal = new double[N],zimag = new double[N]; - Complex[] zz = new Complex[N]; - boolean localflag=false, globalflag=false; - - - - // Test cisi - System.out.println("Testing cisi"); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** cisi: Incorrect function values for cosine integral"); - - } - - System.out.printf("cisi: Maximum discrepancy of sine integral = %f\n", maxel(vecsub(zimag,vv))); - localflag = maxel(vecsub(zimag,vv)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** cisi: Incorrect function values for sine integral"); - - } - - // Test symmetries - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** dawson: Incorrect function values"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_ei.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_ei.java deleted file mode 100644 index 7f846e7edf..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_ei.java +++ /dev/null @@ -1,52 +0,0 @@ -package com.nr.test.test_chapter6; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.test.NRTestUtil.*; -import static com.nr.NRUtil.*; -import static com.nr.sf.Integrals.*; - -public class Test_ei { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=10; - double sbeps=1.e-15; - double x[]={0.5e-292,0.5,1.0,2.0,4.0,8.0,16.0,32.0,64.0,128.0}; - double y[]={-6.724707786699197e+002,4.542199048631735e-1,1.895117816355937, - 4.954234356001890,1.963087447005622e1,4.403798995348382e2, - 5.955609986708373e5,2.550043566357786e12,9.899640925974459e25, - 3.061380614342898e+053}; - double[] zz = new double[N],cc =buildVector(N,1.); - boolean localflag, globalflag=false; - - - - // Test ei - System.out.println("Testing ei"); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ei: Incorrect function values"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_elle.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_elle.java deleted file mode 100644 index b892980102..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_elle.java +++ /dev/null @@ -1,92 +0,0 @@ -package com.nr.test.test_chapter6; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.test.NRTestUtil.*; -import static com.nr.sf.Elliptic.*; - -public class Test_elle { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=16,M=10; - double sbeps; - double elle1[]={0.0,0.0998334166468281523,0.198669330795061215,0.295520206661339575, - 0.389418342308650492,0.479425538604203000,0.564642473395035357, - 0.644217687237691054,0.717356090899522762,0.783326909627483388, - 0.841470984807896507,0.891207360061435340,0.932039085967226350, - 0.963558185417192965,0.985449729988460181,0.997494986604054431}; - double elle2[]={0.523598776000000000,0.522691528960261784,0.519952907231629841, - 0.515330345767519975,0.508729236913189576,0.500000000347883381, - 0.488913351004473020,0.475110551307264258,0.457989419291834486, - 0.436367226265627954}; - double elle3[]={0.0,0.0499165830243987898,0.0993306265758595741,0.147729048734116570, - 0.194575897058209209,0.239295761817418877,0.281248556340456227, - 0.319686389142797354,0.353669004307650793,0.381861529207714857, - 0.401819480553494865}; - double[] a= new double[N],b= new double[N],c=new double[M],d=new double[M]; - boolean localflag, globalflag=false; - - - - // Test elle - System.out.println("Testing elle"); - - // Test values vs. phi for k=1 - sbeps=5.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** elle: Incorrect function of phi for k=1"); - - } - - // Test values vs. k for phi=0.523598776 (approx 30 deg) - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** elle: Incorrect function of k for phi=0.523598776 (30 deg)"); - - } - - // Test values vs. k for phi=0.523598776 (approx 30 deg) - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** elle: Incorrect function of phi for k=2"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_ellf.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_ellf.java deleted file mode 100644 index 528a26b065..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_ellf.java +++ /dev/null @@ -1,92 +0,0 @@ -package com.nr.test.test_chapter6; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.test.NRTestUtil.*; -import static com.nr.sf.Elliptic.*; - -public class Test_ellf { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=16,M=10; - double sbeps; - double ellf1[]={0.0,0.100167084547480182,0.201346823567727507,0.304603974401704104, - 0.411114219868596574,0.522238103278440330,0.639622515807764521, - 0.765350458597682954,0.902176698545870355,1.05392311374108558, - 1.22619117088351707,1.42776351721775348,1.67369924955824305, - 1.99339831974637447,2.45799559037297901,3.34067754279831100}; - double ellf2[]={0.523598776000000000,0.524508805698164762,0.527290159585071990, - 0.532106526205558691,0.539268044529137392,0.549306144797899353, - 0.563134596139227132,0.582430260118548007,0.610720592279546591, - 0.657851366229664988}; - double ellf3[]={0.0,0.0500836684734863288,0.1006775690197592557,0.152335159818448609, - 0.205707351112816793,0.261624740315344007,0.321243014549783015, - 0.386340279820085692,0.460042170380593855,0.549140322320619453, - 0.677417538203930387}; - double[] a= new double[N],b= new double[N],c=new double[M],d=new double[M]; - boolean localflag, globalflag=false; - - - - // Test ellf - System.out.println("Testing ellf"); - - // Test values vs. phi for k=1 - sbeps=5.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ellf: Incorrect function of phi for k=1"); - - } - - // Test values vs. k for phi=0.523598776 (approx 30 deg) - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ellf: Incorrect function of k for phi=0.523598776 (30 deg)"); - - } - - // Test values vs. k for phi=0.523598776 (approx 30 deg) - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ellf: Incorrect function of phi for k=2"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_ellpi.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_ellpi.java deleted file mode 100644 index 6b085bf24a..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_ellpi.java +++ /dev/null @@ -1,152 +0,0 @@ -package com.nr.test.test_chapter6; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.test.NRTestUtil.*; -import static com.nr.sf.Elliptic.*; - -public class Test_ellpi { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=16,M=10; - double sbeps,en; - double ellpi1[]={0.0,0.100502764417104114,0.204089873528317272,0.314201094547181115, - 0.435071344871511048,0.572373236468860396,0.734271021897322517, - 0.933304100500074239,1.19002091819793195,1.54058608179260362, - 2.05433293325624867,2.87964064018147283,4.38603767215661825, - 7.72963041510352791,18.2848934716992433,101.345047515285793}; - double ellpi2[]={0.577350269725227267,0.578430405929852887,0.581733633663630267, - 0.5874607596963754851,0.595993115974939418,0.607986406118820100, - 0.624573540241628753,0.647846914950448347,0.682245757590558980, - 0.740309437183358951}; - double ellpi3[]={0.0,0.0501255025975285727,0.1010163386701090373, - 0.153502472640551107,0.208558872308446512,0.267425749123095321, - 0.331818001829399680,0.404347204331590915,0.489536097087013840, - 0.597017539786347541,0.759657207054964912}; - double ellpi4[]={0.0,0.0998354001533643479,0.198731283496840194, - 0.295972908157878589,0.391232663483947057,0.484645541930822404, - 0.576819001486806192,0.668825019188343865,0.762228160389261813, - 0.859207265936498094,0.962856407616018361,1.077849756916385261, - 1.211968082663659937,1.380119771567129244,1.61803271724411808, - 2.06241081470741402}; - double ellpi5[]={0.484169591972923381,0.484961714960443253,0.487381591588874436, - 0.491568024729042223,0.497783554574451842,0.506476877038506087, - 0.518416731663483363,0.535007150197453044,0.559183303289873315, - 0.599067832583639964}; - double ellpi6[]={0.0,0.0500419596493322059,0.100342838645592538, - 0.151198919592696644,0.202989354783613223,0.256242731928117456, - 0.311751967994650342,0.370807081967643963,0.435763040026915024, - 0.511863662072828734,0.617791316339181780}; - double[] a= new double[N],b= new double[N],c=new double[M],d=new double[M]; - boolean localflag, globalflag=false; - - - - // Test ellpi - System.out.println("Testing ellpi"); - - // Test values vs. phi for k=1 and n=-1 - en=-1.0; - sbeps=1.e-13; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ellpi: Incorrect function of phi for k=1 and n=-1"); - - } - - // Test values vs. k for phi=0.523598776 (approx 30 deg) and n=-1 - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ellpi: Incorrect function of k for phi=0.523598776 (30 deg) and n=-1"); - - } - - // Test values vs. k for phi=0.523598776 (approx 30 deg) and n=-1 - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ellpi: Incorrect function of phi for k=2 and n=-1"); - - } - - // Test values vs. phi for k=1 and n=+1 - en=+1.0; - sbeps=1.e-14; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ellpi: Incorrect function of phi for k=1 and n=+1"); - - } - - // Test values vs. k for phi=0.523598776 (approx 30 deg) and n=+1 - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ellpi: Incorrect function of k for phi=0.523598776 (30 deg) and n=+1"); - - } - - // Test values vs. k for phi=0.523598776 (approx 30 deg) and n=+1 - sbeps=1.e-15; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** ellpi: Incorrect function of phi for k=2 and n=+1"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_erfcc.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_erfcc.java deleted file mode 100644 index df8f4545a2..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_erfcc.java +++ /dev/null @@ -1,53 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.sf.Erf; - -public class Test_erfcc { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=13; - double sbeps=2.e-7; - double x[]={-4.0,-3.0,-2.0,-1.0,-0.5,-0.1,0.0,0.1,0.5,1.0,2.0,3.0,4.0}; - double[] yy= new double[N],zz= new double[N]; - boolean localflag, globalflag=false; - - - - // Test erfcc - System.out.println("Testing erfcc"); - - Erf e = new Erf(); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** erfcc: Error exceeds single precision accuracy"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_expint.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_expint.java deleted file mode 100644 index 5ec33ddc8c..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_expint.java +++ /dev/null @@ -1,90 +0,0 @@ -package com.nr.test.test_chapter6; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.test.NRTestUtil.*; -import static com.nr.NRUtil.*; -import static java.lang.Math.*; -import static com.nr.sf.Integrals.*; - -public class Test_expint { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,m,N=22; - double a,b,expect,sbeps=5.e-15; - int n[]={0,0,0,0,0,1,1,1,1,1,2,2,2,2,3,3,4,4,5,5,10,10}; - double x[]={0.01,0.1,0.5,1.0,2.0,0.01,0.1,0.5,1.0,2.0, - 0.0,0.5,1.0,2.0,0.0,1.0,0.0,1.0,0.0,1.0,0.0,1.0}; - double y[]={9.900498337491680e1,9.048374180359595,1.213061319425267, - 3.678794411714423e-1,6.766764161830635e-2,4.037929576538114, - 1.822923958419390,5.597735947761607e-1,2.193839343955203e-1, - 4.890051070806113e-2,1.0,0.32664386232455301773, - 0.14849550677592204,0.037534261820490452,0.5, - 0.10969196719776013,0.33333333333333333,0.086062491324560728, - 0.250,0.070454237461720398,0.11111111111111111, - 0.036393994031416401634}; - double[] yy=buildVector(y),zz = new double[N]; - boolean localflag, globalflag=false; - - - - // Test expint - System.out.println("Testing expint"); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** expint: Incorrect function values"); - - } - - // Test special cases - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** expint: Failure of special case n=0"); - - } - } - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** expint: Failure of special case x=0.0"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_factln.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_factln.java deleted file mode 100644 index e58fd68399..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_factln.java +++ /dev/null @@ -1,50 +0,0 @@ -package com.nr.test.test_chapter6; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.test.NRTestUtil.*; -import static com.nr.NRUtil.*; -import static com.nr.sf.Gamma.*; -public class Test_factln { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=9; - double sbeps=1.e-13; - int x[]={0,1,2,4,8,16,32,64,128}; - double y[]={0.0,0.0,0.6931471805599453,3.178053830347946,1.060460290274525e1, - 3.067186010608067e1,8.155795945611504e1,2.051681994826412e2, - 4.964054784872176e2}; - double[] yy =buildVector(y),z = new double[N]; - boolean localflag, globalflag=false; - - - - // Test factln - System.out.println("Testing factln"); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** factln: Incorrect function values"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_factrl.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_factrl.java deleted file mode 100644 index 0d96612b65..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_factrl.java +++ /dev/null @@ -1,51 +0,0 @@ -package com.nr.test.test_chapter6; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.test.NRTestUtil.*; -import static com.nr.NRUtil.*; -import static com.nr.sf.Gamma.*; - -public class Test_factrl { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=9; - double sbeps=5.e-15; - int x[]={0,1,2,4,8,16,32,64,128}; - double y[]={1.0,1.0,2.0,24.0,40320.0,2.092278988800000e13, - 2.631308369336935e35,1.268869321858842e89, - 3.856204823625803e+215}; - double[] z = new double[N],c = buildVector(N,1.0); - boolean localflag, globalflag=false; - - - - // Test factrl - System.out.println("Testing factrl"); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** factrl: Incorrect function values"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_frenel.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_frenel.java deleted file mode 100644 index d6e082dafa..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_frenel.java +++ /dev/null @@ -1,74 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.sf.Integrals.frenel; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.Complex; - -public class Test_frenel { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=16; - double sbeps=1.0e-15; - double xx[]={0.0,0.2,0.4,0.6,0.8,1.0,1.2,1.4,1.6,1.8,2.0,2.2,2.4,2.6,2.8,3.0}; - double cc[]={0.0,0.1999210575944531,0.3974807591723594,0.5810954469916523, - 0.7228441718963561,0.7798934003768228,0.7154377229230734, - 0.5430957835462564,0.3654616834404877,0.3336329272215571, - 0.4882534060753408,0.6362860449033195,0.5549614058564281, - 0.3889374961919690,0.4674916516989060,0.6057207892976856}; - double ss[]={0.0,0.004187609161656762,0.03335943266061318,0.1105402073593870, - 0.2493413930539178,0.4382591473903548,0.6234009185462497, - 0.7135250773634121,0.6388876835093809,0.4509387692675831, - 0.3434156783636982,0.4557046121246569,0.6196899649456836, - 0.5499893231527195,0.3915284435431718,0.4963129989673750}; - double[] x=buildVector(xx),c=buildVector(cc),s=buildVector(ss),zreal= new double[N],zimag= new double[N]; - Complex[] z= new Complex[N]; - boolean localflag, globalflag=false; - - - - // Test frenel - System.out.println("Testing frenel"); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** frenel: Incorrect function values for C(x)"); - - } - - System.out.printf("frenel: Maximum discrepancy in S(x) = %f\n", maxel(vecsub(zimag,s))); - localflag = maxel(vecsub(zimag,s)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** frenel: Incorrect function values for S(x)"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_gammln.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_gammln.java deleted file mode 100644 index 899d82eff4..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_gammln.java +++ /dev/null @@ -1,49 +0,0 @@ -package com.nr.test.test_chapter6; - -import static org.junit.Assert.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import static com.nr.test.NRTestUtil.*; -import static com.nr.NRUtil.*; -import com.nr.sf.Gamma; -public class Test_gammln { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=10; - double sbeps=5.e-15; - double x[]={0.5,1.0,1.5,2.0,3.0,4.0,5.0,7.0,10.0,20.0}; - double y[]={0.5723649429247001,0.0,-0.1207822376352453,0.0,0.6931471805599454, - 1.791759469228055,3.178053830347945,6.579251212010101,12.80182748008147, - 39.33988418719950}; - double[] yy=buildVector(y),zz = new double[N]; - boolean localflag, globalflag=false; - - - - // Test gammln - System.out.println("Testing gammln"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** gammln: Incorrect function values"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_hypgeo.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_hypgeo.java deleted file mode 100644 index 78060bb7ed..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_hypgeo.java +++ /dev/null @@ -1,210 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.sf.Hypergeo.hypgeo; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.Complex; - -public class Test_hypgeo { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=20,M=100; - double err,errmax,sbeps; - Complex aa,bb,cc,zz,res1,res2; - Complex a[]={new Complex(1.0,0.0), new Complex(0.0,1.0),new Complex(1.0,0.0),new Complex(1.0,0.0), - new Complex(1.0,0.0),new Complex(2.0,0.0),new Complex(3.0,0.0),new Complex(2.0,0.0), - new Complex(2.0,0.0),new Complex(3.0,0.0),new Complex(3.0,0.0),new Complex(2.0,0.0), - new Complex(1.0,0.0),new Complex(0.0,1.0),new Complex(1.0,0.0),new Complex(1.0,0.0), - new Complex(5.0,0.0),new Complex(0.0,3.0),new Complex(0.0,-4.0),new Complex(-5.0,0.0)}; - Complex b[]={new Complex(1.0,0.0),new Complex(1.0,0.0),new Complex(0.0,1.0),new Complex(1.0,0.0), - new Complex(1.0,0.0),new Complex(2.0,0.0),new Complex(3.0,0.0),new Complex(2.0,0.0), - new Complex(2.0,0.0),new Complex(3.0,0.0),new Complex(3.0,0.0),new Complex(2.0,0.0), - new Complex(1.0,0.0),new Complex(0.0,1.0),new Complex(0.0,1.0),new Complex(1.0,0.0), - new Complex(0.0,5.0),new Complex(2.0,0.0),new Complex(0.0,-1.0),new Complex(3.0,0.0)}; - Complex c[]={new Complex(1.0,0.0),new Complex(1.0,0.0),new Complex(1.0,0.0),new Complex(0.0,1.0), - new Complex(1.0,0.0),new Complex(2.0,0.0),new Complex(3.0,0.0),new Complex(2.0,0.0), - new Complex(2.0,0.0),new Complex(3.0,0.0),new Complex(3.0,0.0),new Complex(2.0,0.0), - new Complex(1.0,0.0),new Complex(0.0,1.0),new Complex(1.0,0.0),new Complex(0.0,1.0), - new Complex(0.0,-2.0),new Complex(0.0,-2.0),new Complex(7.0,0.0),new Complex(0.0,7.0)}; - Complex z[]={new Complex(0.5,0.0),new Complex(0.5,0.0),new Complex(0.5,0.0),new Complex(0.5,0.0), - new Complex(0.0,1.0),new Complex(0.0,1.0),new Complex(0.0,1.0),new Complex(0.0,0.0), - new Complex(0.5,0.0),new Complex(0.5,0.0),new Complex(-0.5,0.0),new Complex(-0.5,0.0), - new Complex(-0.5,0.0),new Complex(0.0,1.0),new Complex(1.0,1.0),new Complex(1.0,1.0), - new Complex(1.0,1.0),new Complex(1.0,3.0),new Complex(2.0,-3.0),new Complex(5.0,7.0)}; - Complex eexpect[]={new Complex(2.0,0.0), - new Complex(0.76923890136397212658,0.63896127631363480115), - new Complex(0.76923890136397212658,0.63896127631363480115), - new Complex(0.18874993960184887345,-0.73280804956611519935), - new Complex(0.5,0.5),new Complex(0.0,0.5),new Complex(-0.25,0.25), - new Complex(1.0,0.0),new Complex(4.0,0.0),new Complex(8.0,0.0), - new Complex(0.29629629629629629630,0.0), - new Complex(0.44444444444444444444,0.0), - new Complex(0.66666666666666666667,0.0), - new Complex(0.42882900629436784932,-0.15487175246424677819), - new Complex(0.20787957635076190855,0.0), - new Complex(2.4639512200927103386,5.0258643859042736965), - new Complex(0.000782175555099748119,0.065075199065027035764), - new Complex(-0.31205397840397702583,-0.04344693995132976350), - new Complex(0.34836454596486382673,0.65394630061667130711), - new Complex(617.9369000550522997,2595.6638964158808010)}; - Complex[] y=new Complex[N],expect=new Complex[N]; - System.arraycopy(eexpect, 0,expect,0, N);; - boolean localflag, globalflag=false; - - - - // Test selected values - System.out.println("Testing hypgeo"); - errmax=0.0; - for (i=0;i errmax) errmax=err; - } -// System.out.println("hypgeo: Maximum fractional discrepancy = %f\n", errmax); - sbeps=1.e-10; - localflag = errmax > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** hypgeo: Incorrect function values"); - - } - - // Test symmetry of a and b - sbeps=1.e-15; - localflag=false; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** hypgeo: Lack of symmetry in first two arguments"); - - } - - // Test case a=c, b=1 where hypgeo=1/(1-z) - sbeps=1.e-12; - localflag=false; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** hypgeo: Failure of special case a=c, b=1"); - - } - - // Test a contiguous relationship for aa (Abromowitz & Stegun, 15.2.13) - sbeps=1.e-12; - localflag=false; - for (i=0;i sbeps; - - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** hypgeo: Failure of contiguous relationship for aa"); - - } - - // Test a contiguous relationship for cc (Abromowitz & Stegun, 15.2.27) - sbeps=1.e-10; - localflag=false; - for (i=0;i sbeps; - - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** hypgeo: Failure of contiguous relationship for cc"); - - } - - // Test of mirror symmetry - sbeps=1.e-15; - localflag=false; - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** hypgeo: Function does not follow mirror symmetry rule"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_invxlogx.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_invxlogx.java deleted file mode 100644 index e30545a64c..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_invxlogx.java +++ /dev/null @@ -1,56 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.sf.Integrals.invxlogx; -import static java.lang.Math.abs; -import static java.lang.Math.exp; -import static java.lang.Math.log; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; - -public class Test_invxlogx { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=100000; - double x,y1,y2,sbeps=1.0e-15; - boolean localflag, globalflag=false; - - - - // Test invxlogx - System.out.println("Testing invxlogx"); - - Ran myran = new Ran(17); - for (i=0;isbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** invxlogx: Incorrect function value for y=y1"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_plegendre.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_plegendre.java deleted file mode 100644 index d553e9dec3..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_plegendre.java +++ /dev/null @@ -1,57 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.sf.Legendre; - -public class Test_plegendre { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=15; - double sbeps=1.0e-15; - int l[]={0,1,1,2,2,2,3,3,3,3,5,10,15,20,25}; - int m[]={0,0,1,0,1,2,0,1,2,3,3,5,7,5,3}; - double x[]={0.5,-0.5,0.2,-0.4,0.6,0.2,-0.4,0.6,-0.8,0.7,-0.7,0.4,-0.4,0.1,0.5}; - double y[]={2.820947917738781e-001,-2.443012559514600e-001,-3.385137501286538e-001, - -1.640036139313104e-001,-3.708232339422620e-001,3.708232339422620e-001, - 3.283951726793016e-001,-2.068353178330564e-001,-2.943318172127853e-001, - -1.519582778329822e-001,-4.296502741348962e-001,2.127192227262643e-001, - -2.877479076870877e-001, 2.957240266476461e-001,2.658533041450948e-001}; - double[] yy = buildVector(y),zz = new double[N]; - boolean localflag, globalflag=false; - - - - // Test plegendre - System.out.println("Testing plegendre"); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** plegendre: Incorrect function values"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_rc.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_rc.java deleted file mode 100644 index 3c0721f433..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_rc.java +++ /dev/null @@ -1,82 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.sf.Elliptic.rc; -import static com.nr.sf.Elliptic.rf; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; -public class Test_rc { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=1000,M=15; - double x,y,sbeps; - double xx[]={0.5,0.5,0.5,1.0,1.0,1.0,2.0,2.0,2.0, - 5.0,5.0,5.0,10.0,10.0,10.0}; - double yy[]={0.5,5.0,10.0,0.5,5.0,10.0,0.5,5.0,10.0, - 0.5,5.0,10.0,0.5,5.0,10.0}; - double fingerprint[]={1.4142135623730949,0.58880582378346324,0.43646741450163296, - 1.246450480280461,0.55357435889704532,0.41634859079941822, - 1.0752916200648814,0.51157686594443497,0.39143618306709632, - 0.85722388169844077,0.44721359549995793,0.35124073655203636, - 0.70672482712931073,0.39416225082970491,0.31622776601683794}; - double[] f1= new double[N],f2= new double[N],ff1 = new double[M],expect = buildVector(fingerprint); - boolean localflag, globalflag=false; - - - - // Test rc - System.out.println("Testing rc"); - - // Test values against those of rf(x,y,z); - Ran myran = new Ran(17); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rc: Function rc(x,y) does not equal rf(x,y,y)"); - - } - - // Fingerprint test - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rc: Fuction does not match previously computed fingerprint"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_rd.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_rd.java deleted file mode 100644 index 81d94de05a..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_rd.java +++ /dev/null @@ -1,88 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.sf.Elliptic.rd; -import static com.nr.sf.Elliptic.rj; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; - -public class Test_rd { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=1000,M=15; - double x,y,z,sbeps; - double xx[]={0.5,0.5,0.5,1.0,1.0,1.0,2.0,2.0,2.0, - 5.0,5.0,5.0,10.0,10.0,10.0}; - double yy[]={0.5,5.0,10.0,0.5,5.0,10.0,0.5,5.0,10.0, - 0.5,5.0,10.0,0.5,5.0,10.0}; - double zz[]={0.5,1.0,1.5,2.0,2.5,3.0,3.5,4.0, - 0.5,1.0,1.5,2.0,2.5,3.0,3.5}; - double fingerprint[]={2.828427124746189,0.6761446800665275,0.3561311564429841, - 0.61767396750725501,0.25585876344175834,0.16707403783066954, - 0.28683033981461781,0.14094109198361518,0.57990472541731197, - 0.6761446800665275,0.24574380041928576,0.1516469228750387, - 0.22495805526027765,0.10980936208850103,0.076942538498807111}; - double[] f1= new double[N],f2= new double[N],ff1 = new double[M],expect = buildVector(fingerprint); - boolean localflag, globalflag=false; - - - - // Test rd - System.out.println("Testing rd"); - - // Test values against those of rj(x,y,z); - Ran myran = new Ran(17); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rd: Function rd(x,y,z) does not equal rf(x,y,z,z)"); - - } - - // Fingerprint test - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rd: Fuction does not match previously computed fingerprint"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_rf.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_rf.java deleted file mode 100644 index dd58fe23b6..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_rf.java +++ /dev/null @@ -1,146 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.sf.Elliptic.rf; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; -public class Test_rf { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=1000,M=15; - double x,y,z,lambda,sbeps; - double xx[]={0.5,0.5,0.5,1.0,1.0,1.0,2.0,2.0,2.0, - 5.0,5.0,5.0,10.0,10.0,10.0}; - double yy[]={0.5,5.0,10.0,0.5,5.0,10.0,0.5,5.0,10.0, - 0.5,5.0,10.0,0.5,5.0,10.0}; - double zz[]={0.5,1.0,1.5,2.0,2.5,3.0,3.5,4.0, - 0.5,1.0,1.5,2.0,2.5,3.0,3.5}; - double fingerprint[]={1.4142135623730949,0.78318403980915063,0.61671477142548603, - 0.96885765327245232,0.62910156611289225,0.52066873070659714, - 0.76120858506833289,0.532702194896431,0.59067521087321406, - 0.78318403980915063,0.52979548043855929,0.44484198345350334, - 0.56995656023418362,0.42344785821702513,0.36781365041076669}; - double[] f1= new double[N],f2= new double[N],f3= new double[N],ff1 = new double[M],expect = buildVector(fingerprint); - boolean localflag, globalflag=false; - - - - // Test rf - System.out.println("Testing rf"); - - Ran myran = new Ran(17); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rf: Function rf(x,y,z) does not follow duplication theorem rule 1"); - - } - - sbeps=1.e-14; - localflag = maxel(vecsub(f1,f3)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rf: Function rf(x,y,z) does not follow duplication theorem rule 2"); - - } - - // Test rf(x,x,x) = 1/sqrt(x) - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rf: Function rf(x,x,x) is not equal to 1/sqrt(x)"); - - } - - // Symmetry test - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rf: Function rf(x,y,z) is not equal to rf(y,x,z)"); - - } - - // Symmetry of y and z - System.out.printf("rf: maximum discrepance with swap of y,z = %f\n", maxel(vecsub(f1,f3))); - - sbeps=1.e-14; - localflag = maxel(vecsub(f1,f3)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rf: Function rf(x,y,z) is not equal to rf(x,z,y)"); - - } - - // Fingerprint test - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rf: Fuction does not match previously computed fingerprint"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_rj.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_rj.java deleted file mode 100644 index 388c0c204b..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_rj.java +++ /dev/null @@ -1,162 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.buildVector; -import static com.nr.sf.Elliptic.rj; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.pow; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; - -public class Test_rj { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=1000,M=15; - double x,y,z,p,sbeps; // lambda not used. - double xx[]={0.5,0.5,0.5,1.0,1.0,1.0,2.0,2.0,2.0, - 5.0,5.0,5.0,10.0,10.0,10.0}; - double yy[]={0.5,5.0,10.0,0.5,5.0,10.0,0.5,5.0,10.0, - 0.5,5.0,10.0,0.5,5.0,10.0}; - double zz[]={0.5,1.0,1.5,2.0,2.5,3.0,3.5,4.0, - 0.5,1.0,1.5,2.0,2.5,3.0,3.5}; - double pp[]={0.5,0.5,1.0,1.0,2.0,2.0,5.0,5.0,10.0,10.0, - 0.5,1.0,2.0,5.0,10.0}; - double fingerprint[]={2.8284271247461894,0.98504492018034995,0.44793650058808648, - 0.96012401711294937,0.29241747858151068,0.21151911434681123, - 0.22347653672793238,0.12251370089051629,0.093064515580572826, - 0.13984765109852496,0.41094690289468627,0.21220982894638879, - 0.25740492084525707,0.082096126702519048,0.041707103324323758}; - double[] f1= new double[N],f2= new double[N],f3= new double[N],ff1 = new double[M],expect = buildVector(fingerprint); - boolean localflag, globalflag=false; - - - - // Test rj - System.out.println("Testing rj"); - - Ran myran = new Ran(17); - - // Test rj(x,x,x,x) = 1/x^(3/2) - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rj: Function rj(x,x,x,x) is not equal to 1/x^(3/2)"); - - } - - // Symmetry test - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rj: Function rj(x,y,z,p) is not equal to rj(y,x,z,p)"); - - } - - // Symmetry of y and z - System.out.printf("rj: maximum discrepance with swap of y,z = %f\n", maxel(vecsub(f1,f3))); - - sbeps=1.e-14; - localflag = maxel(vecsub(f1,f3)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rj: Function rj(x,y,z,p) is not equal to rj(x,z,y,p)"); - - } - - // Test symmetry with respect to p - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rj: Function rj(x,x,z,p) is not equal to rj(p,p,z,x)"); - - } - - // Test symmetry with respect to p - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rj: Function rj(x,y,y,p) is not equal to rj(x,p,p,y)"); - - } - - // Fingerprint test - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rj: Fuction does not match previously computed fingerprint"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_sncndn.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_sncndn.java deleted file mode 100644 index 00ca729870..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter6/Test_sncndn.java +++ /dev/null @@ -1,116 +0,0 @@ -package com.nr.test.test_chapter6; - -import static com.nr.NRUtil.SQR; -import static com.nr.NRUtil.buildVector; -import static com.nr.sf.Elliptic.sncndn; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -public class Test_sncndn { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=20; - double sbeps=1.e-15; - double u[]={0.1,0.2,0.5,1.0,2.0,0.1,0.2,0.5,1.0,2.0,0.1,0.2,0.5,1.0,2.0,4.0,-0.2,-0.5,-1.0,-2.0}; - double ksquare[]={0.0,0.0,0.0,0.0,0.0,0.5,0.5,0.5,0.5,0.5,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0}; - double y1[]={0.09983341664682815,0.1986693307950612,0.4794255386042030, - 0.8414709848078965,0.9092974268256817,0.09975068547462484, - 0.1980217429819704,0.4707504736556573,0.8030018248956439, - 0.9946623253580177,0.09966799462495582,0.1973753202249040, - 0.4621171572600098,0.7615941559557649,0.9640275800758169, - 0.9993292997390670,-0.1973753202249040,-0.4621171572600098, - -0.7615941559557649,-0.9640275800758169}; - double y2[]={0.9950041652780258,0.9800665778412416,0.8775825618903727, - 0.5403023058681397,-0.4161468365471424,0.9950124626090582, - 0.9801976276784098,0.8822663948904403,0.5959765676721407, - -0.1031836155277618,0.9950207489532265,0.9803279976447253, - 0.8868188839700739,0.6480542736638854,0.2658022288340797, - 0.03661899347368653,0.9803279976447253,0.8868188839700739, - 0.6480542736638854,0.2658022288340797}; - double y3[]={1.000000000000000,1.000000000000000,1.000000000000000, - 1.000000000000000,1.000000000000000,0.9975093485144243, - 0.9901483195224800,0.9429724257773857,0.8231610016315963, - 0.7108610477840873,0.9950207489532265,0.9803279976447253, - 0.8868188839700739,0.6480542736638854,0.2658022288340797, - 0.03661899347368653,0.9803279976447253,0.8868188839700739, - 0.6480542736638854,0.2658022288340797}; - double[] yy1=buildVector(y1),yy2=buildVector(y2),yy3=buildVector(y3),zz1= new double[N],zz2= new double[N],zz3= new double[N]; - double[] one=buildVector(N,1.0),test1= new double[N],test2= new double[N]; - boolean localflag, globalflag=false; - - - - // Test sncndn - System.out.println("Testing sncndn"); - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** sncndn: Test for relation between sn and cn failed"); - - } - - System.out.printf("test2: Maximum discrepancy = %f\n", maxel(vecsub(one,test2))); - localflag = maxel(vecsub(one,test2)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** sncndn: Test for relation between sn and dn failed"); - - } - - System.out.printf("sncndn (sn): Maximum discrepancy = %f\n", maxel(vecsub(zz1,yy1))); - localflag = maxel(vecsub(zz1,yy1)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** sncndn: Incorrect function values for sn"); - - } - - System.out.printf("sncndn (cn): Maximum discrepancy = %f\n", maxel(vecsub(zz2,yy2))); - localflag = maxel(vecsub(zz2,yy2)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** sncndn: Incorrect function values for cn"); - - } - - System.out.printf("sncndn (dn): Maximum discrepancy = %f\n", maxel(vecsub(zz3,yy3))); - localflag = maxel(vecsub(zz3,yy3)) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** sncndn: Incorrect function values for dn"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Binomialdev.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Binomialdev.java deleted file mode 100644 index f6b6f876c8..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Binomialdev.java +++ /dev/null @@ -1,79 +0,0 @@ -package com.nr.test.test_chapter7; - -import static com.nr.NRUtil.buildVector; -import static com.nr.stat.Stattests.chsone; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.ran.Binomialdev; -import com.nr.sf.Binomialdist; - -public class Test_Binomialdev { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,nbin,N=100000,M=20; - doubleW df = new doubleW(0); - doubleW chisq = new doubleW(0); - doubleW prob = new doubleW(0); - - double pp; - int fpr[]={12,10,9,8,9,13,5,10,9,7}; - int[] fingerprint =buildVector(fpr); - double[] bins = new double[M],ebins = new double[M]; // x=new double[M] - boolean localflag, globalflag=false; - - - - // Test Binomialdev - System.out.println("Testing Binomialdev"); - - // Check fingerprint of doub() - pp=0.5; - Binomialdev myran = new Binomialdev(M,pp,17); - localflag=false; - for (i=0;i<10;i++) -// System.out.printf(setw(25) << setprecision(20) << myran.dev()); - localflag=localflag || (myran.dev() != fingerprint[i]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Binomialdev: dev() does not match fingerprint"); - - } - - // Check statistics - Binomialdist expect = new Binomialdist(M,pp); - for (i=0;i= 0) && (nbin < M)) bins[nbin] += 1; - } - chsone(bins,ebins,df,chisq,prob); - System.out.printf(" chisq,dev(): %f\n prob: %f\n",chisq.val, prob.val); - localflag = (prob.val < 0.05); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Binomialdev: dev() does not give distribution with correct variance"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Cauchydev.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Cauchydev.java deleted file mode 100644 index fba3868a08..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Cauchydev.java +++ /dev/null @@ -1,90 +0,0 @@ -package com.nr.test.test_chapter7; - -import static com.nr.NRUtil.buildVector; -import static com.nr.stat.Stattests.chsone; -import static java.lang.Math.abs; -import static java.lang.Math.floor; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.ran.Cauchydev; -import com.nr.sf.Cauchydist; - -public class Test_Cauchydev { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @SuppressWarnings("unused") - @Test - public void test() { - int i,nbin,N=100000,M=1000; - doubleW df = new doubleW(0); - doubleW chisq = new doubleW(0); - doubleW prob = new doubleW(0); - double range=10.0,xl,xu,mu,sig,binsize,sbeps=1.e-15; - double fpr[]={-5.4660758319305183,-0.30564072790788632,-0.44755371579220488, - -1.9442849501644124,0.66387554413406102,-0.004358322069596801, - 0.50260252584448173,9.5625234809339883,0.33471895222248255, - -0.18486043134925173}; - double[] fingerprint = buildVector(fpr); - double[] x = new double[M],bins = new double[M],ebins = new double[M]; - boolean localflag, globalflag=false; - - - - // Test Cauchydev - System.out.println("Testing Cauchydev"); - - // Check fingerprint of doub() - mu=0.0; - sig=1.0; - Cauchydev myran = new Cauchydev(mu,sig,17); - localflag=false; - for (i=0;i<10;i++) { - //System.out.printf("%.20f %.20f\n", myran.dev(), fingerprint[i]); - localflag=localflag || abs(myran.dev()-fingerprint[i])>sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - // fail("*** Cauchydev: dev() does not match fingerprint"); - - } - - // Check statistics - Cauchydist expect = new Cauchydist(mu,sig); - xl=mu-range/2.0; - xu=mu+range/2.0; - binsize=range/(M); - for (i=0;i= 0) && (nbin < M)) bins[nbin] += 1; - } - chsone(bins,ebins,df,chisq,prob); - System.out.printf(" chisq,dev(): %f prob: %f\n",chisq.val, prob.val); - localflag = (prob.val < 0.05); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Cauchydev: dev() does not give distribution with correct variance"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Expondev.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Expondev.java deleted file mode 100644 index 27aa69cde5..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Expondev.java +++ /dev/null @@ -1,82 +0,0 @@ -package com.nr.test.test_chapter7; - -import static com.nr.NRUtil.buildVector; -import static com.nr.stat.Stattests.chsone; -import static java.lang.Math.abs; -import static java.lang.Math.floor; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.ran.Expondev; -import com.nr.sf.Expondist; -public class Test_Expondev { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,nbin,N=100000,M=1000; - doubleW df = new doubleW(0); - doubleW chisq = new doubleW(0); - doubleW prob = new doubleW(0); - double range=10.0,binsize,beta=1.0,sbeps=1.e-15; - double fpr[]={4.2243978049659718,0.90295803506245254,0.12403099453814931, - 0.079329948033191738,1.3165010419652894,2.4667405038323449, - 0.95549662657685031,0.28104150659487703,4.8108667409405195, - 0.82390385975005687}; - double[] fingerprint = buildVector(fpr); - double[] x = new double[M],bins =new double[M],ebins = new double[M]; - boolean localflag, globalflag=false; - - - - // Test Expondev - System.out.println("Testing Expondev"); - - // Check fingerprint of doub() - Expondev myran = new Expondev(beta,17); - localflag=false; - for (i=0;i<10;i++) - localflag=localflag || abs(myran.dev()-fingerprint[i])>sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Expondev: dev() does not match fingerprint"); - - } - - // Check statistics - Expondist expect = new Expondist(beta); - binsize=range/(M); - for (i=0;isbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gammadev: dev() does not match fingerprint"); - - } - - // Check statistics - Gammadist expect=new Gammadist(alpha,beta); - binsize=range/M; - for (i=0;i= 0) && (nbin < M)) bins[nbin] += 1; - } - chsone(bins,ebins,df,chisq,prob); - System.out.printf(" chisq,dev(): %f prob: %f\n",chisq.val, prob.val); - localflag = (prob.val < 0.05); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Gammadev: dev() does not give distribution with correct variance"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Hash.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Hash.java deleted file mode 100644 index 0c43d081a9..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Hash.java +++ /dev/null @@ -1,94 +0,0 @@ -package com.nr.test.test_chapter7; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Hash; -import com.nr.ran.Hashfn2; - -public class Test_Hash { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=8; - String names[]={"Charles Babbage","Marie Antoinette","Jane Austen", - "Andrew Jackson","Ludwig van Beethoven","Samuel Morse", - "John Quincy Adams","James Buchanan"}; - int dates[]={1791,1755,1775,1767,1770,1791,1767,1791}; - boolean localflag, globalflag=false; - - - - // Test Hash - System.out.println("Testing Hash"); - - Hash year = new Hash(100,100){ - Hashfn2 hashfn2 = new Hashfn2(); - public long fn(String k){ - return hashfn2.fn(k.getBytes()); - } - }; - - // Test operator[] - for (i=0;i hash = new Hashtable(N,2*N){ - Hashfn2 hashfn2 = new Hashfn2(); - public long fn(atom k) { - - return hashfn2.fn(k.toByte()); - } - }; - - // Test simple iset(), iget() - i=hash.iset(chart[5]); -// System.out.printf(i); - localflag = (i != 0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Hashtable: First iset() did not return index 0"); - - } - - i=hash.iget(chart[5]); -// System.out.printf(i); - localflag = (i != 0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Hashtable: iget() did not return correct index"); - - } - - // Test simple ierase() - i=hash.ierase(chart[5]); - localflag = (i != 0); -// System.out.printf(i); - localflag = (i != 0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Hashtable: ierase() did not return correct index"); - - } - - i=hash.iget(chart[5]); -// System.out.printf(i); - localflag = (i != -1); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Hashtable: iget() from erased key should return -1"); - - } - - // Test garbage collector - i=hash.iset(chart[5]); // Return hashes for 3 keys -// System.out.printf(i); - i=hash.iset(chart[2]); -// System.out.printf(i); - i=hash.iset(chart[7]); -// System.out.printf(i); - ia=hash.ierase(chart[2]); // erase two keys -// System.out.printf(i); - ib=hash.ierase(chart[7]); -// System.out.printf(i); - - // Following two iset()'s should use indices just erased - i=hash.iset(chart[1]); // store two more keys -// System.out.printf(i); - localflag = (i != ib); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Hashtable: iset() should use hash of last erased key"); - - } - - i=hash.iset(chart[9]); -// System.out.printf(i); - localflag = (i != ia); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Hashtable: iset() should use hash of penultimate erased key"); - - } - - // Test multiple iset() on same keys. They should return same index. - Ran myran = new Ran(17); - int j; - for (i=0;i<100;i++) { - j=myran.int32p()%N; - hash.iset(chart[j]); - } - - // N keys should always use only the first N indices - int[] expect =buildVector(N,1); - int[] check = buildVector(N,0); - for (i=0;isbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Logisticdev: dev() does not match fingerprint"); - - } - - // Check statistics - Logisticdist expect = new Logisticdist(mu,sig); - xl=mu-range/2.0; - xu=mu+range/2.0; - binsize=range/M; - for (i=0;i= 0) && (nbin < M)) bins[nbin] += 1; - } - chsone(bins,ebins,df,chisq,prob); - System.out.printf(" chisq,dev(): %f prob: %f\n", chisq.val, prob.val); - localflag = (prob.val < 0.05); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Logisticdev: dev() does not give distribution with correct variance"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_MCintegrate.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_MCintegrate.java deleted file mode 100644 index 01a5357bd5..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_MCintegrate.java +++ /dev/null @@ -1,161 +0,0 @@ -package com.nr.test.test_chapter7; - -import static com.nr.NRUtil.SQR; -import static com.nr.NRUtil.buildVector; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.pow; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.MCintegrate; - -public class Test_MCintegrate { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - double R1=3.0,R2=1.0,PI=acos(-1.0); - double[] xlo = new double[3],xhi = new double[3],slo = new double[3],shi = new double[3]; - boolean localflag, globalflag=false; - - - - // Test MCintegrate - System.out.println("Testing MCintegrate"); - - xlo[0]=0.0; - xhi[0]=4.0; - xlo[1]=-4.0; - xhi[1]=4.0; - xlo[2]=-1.0; - xhi[2]=1.0; - MCintegrate mymc = new MCintegrate(xlo,xhi,17,false){ - - @Override - public double[] funcs(final double[] x){ - return torusfuncs(x); - } - - @Override - public boolean inregion(final double[] x) { - return torusregion(x); - } - - @Override - public double[] xmap(final double[] x){ - return null; - } - }; - mymc.step(1000000); - mymc.calcanswers(); -// for (i=0;i<4;i++) -// System.out.printf(mymc.ff[i] << " %f\n", mymc.fferr[i]); - - localflag = abs(mymc.ff[0]-SQR(PI)*R1*SQR(R2)) > 2.0*mymc.fferr[0]; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MCintegrate: Calculation of hemitorus volume is inaccurate"); - - } - - localflag = abs(mymc.ff[1]-2.0*PI*SQR(R1)*SQR(R2)*(1+SQR(R2/R1)/4.0)) > 2.0*mymc.fferr[1]; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MCintegrate: Calculation of x moment of hemitorus is inaccurate"); - - } - - localflag = abs(mymc.ff[2]) > 2.0*mymc.fferr[2]; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MCintegrate: Calculation of y moment of hemitorus is inaccurate"); - - } - - localflag=abs(mymc.ff[3]) > 2.0*mymc.fferr[3]; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MCintegrate: Calculation of z moment of hemitorus is inaccurate"); - - } - - // Test MCintegrate with change of variables for weighting by z^2 - slo[0]=0.0; - shi[0]=4.0; - slo[1]=-4.0; - shi[1]=4.0; - slo[2]=-1.0/3.0; - shi[2]=1.0/3.0; - //MCintegrate mymc2(slo,shi,torusfuncs,torusregion,torusmap2,17); - MCintegrate mymc2 = new MCintegrate(xlo,xhi,17,true){ - - @Override - public double[] funcs(final double[] x){ - return torusfuncs(x); - } - - @Override - public boolean inregion(final double[] x) { - return torusregion(x); - } - - @Override - public double[] xmap(final double[] x){ - return torusmap2(x); - } - }; - mymc2.step(1000000); - mymc2.calcanswers(); -// for (i=0;i<4;i++) -// System.out.printf(mymc2.ff[i] << " %f\n", mymc2.fferr[i]); - - localflag = abs(mymc2.ff[0]-SQR(PI)*R1*SQR(SQR(R2))/4.0) > 2.0*mymc2.fferr[0]; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MCintegrate: Incorrect weighted volume calculation with change of variables"); - - } - - localflag = abs(mymc2.ff[1]-PI*SQR(R1)*SQR(SQR(R2))*(1+SQR(R2/R1)/6.0)/2.0) > 2.0*mymc2.fferr[1]; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MCintegrate: Incorrect weighted x moment with change of variables"); - - } - - localflag = abs(mymc2.ff[2]) > 2.0*mymc2.fferr[2]; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MCintegrate: Incorrect weighted y moment with change of variables"); - - } - - localflag=abs(mymc2.ff[3]) > 2.0*mymc2.fferr[3]; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** MCintegrate: Incorrect weighted z moment with change of variables"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - double[] torusmap2(final double[] s) { - double[] xx = buildVector(s); - xx[2]=(s[2] < 0.0 ? -pow(abs(3.0*s[2]),1.0/3.0) : pow(3.0*s[2],1.0/3.0)); - return xx; - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Mhash.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Mhash.java deleted file mode 100644 index f62e3c9122..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Mhash.java +++ /dev/null @@ -1,140 +0,0 @@ -package com.nr.test.test_chapter7; - -import static com.nr.NRUtil.buildVector; -import static org.junit.Assert.fail; -import static com.nr.test.NRTestUtil.*; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Hashfn2; -import com.nr.ran.Mhash; - -public class Test_Mhash { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,count,N=8; - String[] str = new String[1]; - String names[]={"Charles Babbage","Marie Antoinette","Jane Austen", - "Andrew Jackson","Ludwig van Beethoven","Samuel Morse", - "John Quincy Adams","James Buchanan"}; - int dates[]={1791,1755,1775,1767,1770,1791,1767,1791}; - boolean localflag, globalflag=false; - - - - // Test Mhash - System.out.println("Testing Mhash"); - - //Mhash person(100,100); - Mhash person = new Mhash(100,100){ - Hashfn2 hashfn2 = new Hashfn2(); - public long fn(Integer k){ - int kk = k; - byte[] b = new byte[4]; - b[0] = (byte)(kk >>>24); - b[1] = (byte)(kk >>>16); - b[2] = (byte)(kk >>>8); - b[3] = (byte)kk; - - return hashfn2.fn(b); - } - }; - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Multinormaldev: Mean value of x does not match target value"); - - } - - localflag = abs(1.0-yave/mean[1]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Multinormaldev: Mean value of y does not match target value"); - - } - - localflag = abs(1.0-zave/mean[2]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Multinormaldev: Mean value of z does not match target value"); - - } - - localflag = abs(1.0-xvar/covar[0][0]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Multinormaldev: Variance of x does not match target value"); - - } - - localflag = abs(1.0-yvar/covar[1][1]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Multinormaldev: Variance of y does not match target value"); - - } - - localflag = abs(1.0-zvar/covar[2][2]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Multinormaldev: Variance of z does not match target value"); - - } - - localflag = abs(1.0-covxy/covar[0][1]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Multinormaldev: Covariance does not match target value"); - - } - - localflag = abs(1.0-covxz/covar[0][2]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Multinormaldev: Covariance does not match target value"); - - } - - localflag = abs(1.0-covyz/covar[1][2]) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Multinormaldev: Covariance does not match target value"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Normaldev.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Normaldev.java deleted file mode 100644 index 89f20161e6..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Normaldev.java +++ /dev/null @@ -1,88 +0,0 @@ -package com.nr.test.test_chapter7; - -import static com.nr.NRUtil.buildVector; -import static com.nr.stat.Stattests.chsone; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.ran.Normaldev; -import com.nr.sf.Normaldist; -import static java.lang.Math.*; - -public class Test_Normaldev { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @SuppressWarnings("unused") - @Test - public void test() { - int i,nbin,N=100000,M=1000; - doubleW df = new doubleW(0); - doubleW chisq = new doubleW(0); - doubleW prob = new doubleW(0); - double range=10.0,xl,xu,mu,sig,binsize,sbeps=1.e-15; - double fpr[]={1.1374125522420115,-0.35950397273931667,-1.6105670258529632, - 0.42167950591239073,0.42086816489557621,0.71359860938979924, - 0.56718836082663404,0.10148179520762551,0.47465403328436934, - -0.4866388952851291}; - double[] fingerprint=buildVector(fpr); - double[] x=new double[M],bins =new double[M],ebins =new double[M]; - boolean localflag, globalflag=false; - - - - // Test Normaldev - System.out.println("Testing Normaldev"); - - // Check fingerprint of doub() - mu=0.0; - sig=1.0; - Normaldev myran = new Normaldev(mu,sig,17); - localflag=false; - for (i=0;i<10;i++) -// System.out.printf(setw(25) << setprecision(20) << myran.dev()); - localflag=localflag || abs(myran.dev()-fingerprint[i])>sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Normaldev: dev() does not match fingerprint"); - - } - - // Check statistics - Normaldist expect = new Normaldist(mu,sig); - xl=mu-range/2.0; - xu=mu+range/2.0; - binsize=range/M; - for (i=0;i= 0) && (nbin < M)) bins[nbin] += 1; - } - chsone(bins,ebins,df,chisq,prob); - System.out.printf(" chisq,dev(): %f prob: %f\n", chisq.val, prob.val); - localflag = (prob.val < 0.05); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Normaldev: dev() does not give distribution with correct variance"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Normaldev_BM.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Normaldev_BM.java deleted file mode 100644 index 6ed6135f3d..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Normaldev_BM.java +++ /dev/null @@ -1,88 +0,0 @@ -package com.nr.test.test_chapter7; - -import static com.nr.NRUtil.buildVector; -import static com.nr.stat.Stattests.chsone; -import static java.lang.Math.abs; -import static java.lang.Math.floor; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.ran.Normaldev_BM; -import com.nr.sf.Normaldist; -public class Test_Normaldev_BM { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @SuppressWarnings("unused") - @Test - public void test() { - int i,nbin,N=100000,M=1000; - doubleW df = new doubleW(0); - doubleW chisq = new doubleW(0); - doubleW prob = new doubleW(0); - double range=10.0,xl,xu,mu,sig,binsize,sbeps=1.e-15; - double fpr[]={-0.040234259938936714,-0.20636252953342041,-0.39109108994808306, - -0.2184933724157597,1.3879841011885372,-0.62802347682638449, - -0.023082200554415865,-0.18525427215527071,-1.5890668800145005, - -1.728054800100431}; - double[] fingerprint=buildVector(fpr); - double[] x=new double[M],bins =new double[M],ebins =new double[M]; - boolean localflag, globalflag=false; - - - - // Test Normaldev_BM - System.out.println("Testing Normaldev_BM"); - - // Check fingerprint of doub() - mu=0.0; - sig=1.0; - Normaldev_BM myran = new Normaldev_BM(mu,sig,17); - localflag=false; - for (i=0;i<10;i++) -// System.out.printf(setw(25) << setprecision(20) << myran.dev()); - localflag=localflag || abs(myran.dev()-fingerprint[i])>sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Normaldev_BM: dev() does not match fingerprint"); - - } - - // Check statistics - Normaldist expect = new Normaldist(mu,sig); - xl=mu-range/2.0; - xu=mu+range/2.0; - binsize=range/M; - for (i=0;i= 0) && (nbin < M)) bins[nbin] += 1; - } - chsone(bins,ebins,df,chisq,prob); - System.out.printf(" chisq,dev(): %f prob: %f\n",chisq.val, prob.val); - localflag = (prob.val < 0.05); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Normaldev_BM: dev() does not give distribution with correct variance"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Poissondev.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Poissondev.java deleted file mode 100644 index 31951a037b..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Poissondev.java +++ /dev/null @@ -1,79 +0,0 @@ -package com.nr.test.test_chapter7; - -import static com.nr.NRUtil.buildVector; -import static com.nr.stat.Stattests.chsone; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.ran.Poissondev; -import com.nr.sf.Poissondist; - -public class Test_Poissondev { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,nbin,N=100000,M=10; - doubleW df = new doubleW(0); - doubleW chisq = new doubleW(0); - doubleW prob = new doubleW(0); - double lambda; - int fpr[]={0,4,2,3,4,4,3,3,7,2}; - int[] fingerprint=buildVector(fpr); - double[] bins =new double[M],ebins =new double[M]; // x is not used - - boolean localflag, globalflag=false; - - - - // Test Poissondev - System.out.println("Testing Poissondev"); - - // Check fingerprint of doub() - lambda=3.0; - Poissondev myran = new Poissondev(lambda,17); - localflag=false; - for (i=0;i<10;i++) -// System.out.printf(setw(25) << setprecision(20) << myran.dev()); - localflag=localflag || (myran.dev() != fingerprint[i]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poissondev: dev() does not match fingerprint"); - - } - - // Check statistics - Poissondist expect = new Poissondist(lambda); - for (i=0;i= 0) && (nbin < M)) bins[nbin] += 1; - } - chsone(bins,ebins,df,chisq,prob); - System.out.printf(" chisq,dev(): %f prob: %f\n",chisq.val, prob.val); - localflag = (prob.val < 0.05); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Poissondev: dev() does not give distribution with correct variance"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Primpolytest.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Primpolytest.java deleted file mode 100644 index bd7ce424a0..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_Primpolytest.java +++ /dev/null @@ -1,64 +0,0 @@ -package com.nr.test.test_chapter7; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Primpolytest; -import com.nr.ran.Ran; - -public class Test_Primpolytest { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,nflag,N=11; - long mask; - int pp[]={2046052277,1186898897,221421833,55334070,1225518245, - 216563424,1532859853,1735381519,2049267032,1363072601, - 130420448}; - // double sbeps=5.e-15; not used - boolean localflag=false, globalflag=false; - - - - // Test Primpolytest - System.out.println("Testing Primpolytest"); - - Primpolytest ptest = new Primpolytest(); - for (i=0;i> 1); - for (i=0;i sbeps; - } - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Ran: doub() does not match fingerprint"); - } - - // Check statistics - for (i=0;isbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Ranbyte: doub() does not match fingerprint"); - - } - - // Check statistics - for (i=0;isbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Ranfib: doub() does not match fingerprint"); - - } - - // Check statistics - for (i=0;isbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Ranhash: doub() does not match fingerprint"); - - } - - // Check statistics - for (i=0;isbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Ranlim32: doub() does not match fingerprint"); - - } - - // Check statistics - for (i=0;isbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Ranq1: doub() does not match fingerprint"); - - } - - // Check statistics - for (i=0;isbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Ranq2: doub() does not match fingerprint"); - - } - - // Check statistics - for (i=0;i 0.1; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** mcmc: Inaccurate estimate for rate lambda1"); - - } - - localflag = abs(s.lam2-lambda2)/lambda2 > 0.1; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** mcmc: Inaccurate estimate for rate lambda2"); - - } - - localflag = (s.k1 != k1); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** mcmc: integer parameter k1 was not correctly determined"); - - } - - localflag = (s.k2 != k2); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** mcmc: integer parameter k2 was not correctly determined"); - - } - - localflag = abs(s.tc-tc)/tc > 0.1; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** mcmc: Inaccurate estimate for critical time tc"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_miser.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_miser.java deleted file mode 100644 index 1417cd64fc..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_miser.java +++ /dev/null @@ -1,131 +0,0 @@ -package com.nr.test.test_chapter7; - -import static com.nr.NRUtil.SQR; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.RealValueFun; -import com.nr.ran.Miser; - -public class Test_miser { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i; - doubleW ave= new doubleW(0),var= new doubleW(0); - double tgral,vol,sd,PI=acos(-1.0),R1=3.0,R2=1.0; - double[] regn = new double[6]; - boolean localflag, globalflag=false; - - - - // Test miser - System.out.println("Testing miser"); - - regn[0]=0.0; - regn[1]=-4.0; - regn[2]=-1.0; - regn[3]=4.0; - regn[4]=4.0; - regn[5]=1.0; - vol=1.0; - for (i=0;i<3;i++) vol *= (regn[i+3]-regn[i]); - - torusfunc1 torusfunc1 = new torusfunc1(); - // Test #1: Compute volume of hemitorus - Miser.miser(torusfunc1,regn,1000000,0.0,ave,var); - tgral=ave.val*vol; - sd=sqrt(var.val)*vol; - -// System.out.printf(tgral << " %f\n", sd); -// System.out.printf(SQR(PI)*R1*SQR(R2)); - localflag = abs(tgral-SQR(PI)*R1*SQR(R2)) > 2.0*sd; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** miser: Computation of hemitoroid volume is inaccurate"); - - } - - torusfunc2 torusfunc2 = new torusfunc2(); - // Test #2: Weight the integral by x - Miser.miser(torusfunc2,regn,1000000,0.0,ave,var); - tgral=ave.val*vol; - sd=sqrt(var.val)*vol; - -// System.out.printf(tgral << " %f\n", sd); -// System.out.printf(2.0*PI*SQR(R1)*SQR(R2)*(1+SQR(R2/R1)/4.0)); - localflag = abs(tgral-2.0*PI*SQR(R1)*SQR(R2)*(1+SQR(R2/R1)/4.0)) > 2.0*sd; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** miser: Computation of hemitoroid weighted by x is inaccurate"); - - } - - torusfunc3 torusfunc3 = new torusfunc3(); - // Test #3: Weight the integral by z^2 - Miser.miser(torusfunc3,regn,1000000,0.0,ave,var); - tgral=ave.val*vol; - sd=sqrt(var.val)*vol; - -// System.out.printf(tgral << " %f\n", sd); -// System.out.printf(SQR(PI)*R1*SQR(SQR(R2))/4.0); - localflag = abs(tgral-SQR(PI)*R1*SQR(SQR(R2))/4.0) > 2.0*sd; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** miser: Computation of hemitoroid weighted by z^2 is inaccurate"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - - class torusfunc1 implements RealValueFun { - public double funk(final double[] x) { - double R1 = 3.0, R2 = 1.0; - - if (SQR(x[2]) + SQR(sqrt(SQR(x[0]) + SQR(x[1])) - R1) <= R2) - return 1.0; - else - return 0.; - } - } - - class torusfunc2 implements RealValueFun { - public double funk(final double[] x) { - double R1 = 3.0, R2 = 1.0; - - if (SQR(x[2]) + SQR(sqrt(SQR(x[0]) + SQR(x[1])) - R1) <= R2) - return x[0]; - else - return 0.; - } - } - - class torusfunc3 implements RealValueFun { - public double funk(final double[] x) { - double R1 = 3.0, R2 = 1.0; - - if (SQR(x[2]) + SQR(sqrt(SQR(x[0]) + SQR(x[1])) - R1) <= R2) - return SQR(x[2]); - else - return 0.; - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_psdes.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_psdes.java deleted file mode 100644 index 1bb6ba8188..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_psdes.java +++ /dev/null @@ -1,63 +0,0 @@ -package com.nr.test.test_chapter7; - -import static com.nr.NRUtil.buildVector; -import static com.nr.stat.Stattests.chsone; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; -import org.netlib.util.intW; - -import com.nr.ran.HashAll; -public class Test_psdes { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @SuppressWarnings("unused") - @Test - public void test() { - int i,M=1024,N=100*M; - intW lword = new intW(0),rword = new intW(0); - doubleW dfW=new doubleW(0),chisqW=new doubleW(0),probW=new doubleW(0); - double df,chisq,prob,average; - double[] bins = new double[M]; - boolean localflag, globalflag=false; - - - - // Test psdes - System.out.println("Testing psdes"); - - average=N/(double)(M); - double[] ebins = buildVector(M,average); - - for (i=0;i 0.02; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** sobseq: Error in volume calculation is not approaching 1/N"); - - } - - localflag = sumerr[3]/sumerr[1] > 0.02; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** sobseq: Error in integral calculation is not approaching 1/N"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_vegas.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_vegas.java deleted file mode 100644 index 6d74861f5d..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter7/Test_vegas.java +++ /dev/null @@ -1,147 +0,0 @@ -package com.nr.test.test_chapter7; - -import static com.nr.NRUtil.SQR; -import static java.lang.Math.abs; -import static java.lang.Math.acos; -import static java.lang.Math.sqrt; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.ran.VEGAS; - -public class Test_vegas { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - doubleW tgral= new doubleW(0),sd= new doubleW(0),chi2a= new doubleW(0); - double R1=3.0,R2=1,PI=acos(-1.0); - double[] regn =new double[6]; - boolean localflag, globalflag=false; - - - - // Test vegas - System.out.println("Testing vegas"); - - regn[0]=0.0; - regn[1]=-4.0; - regn[2]=-1.0; - regn[3]=4.0; - regn[4]=4.0; - regn[5]=1.0; - - // Test #1: Compute volume of hemitorus - VEGAS vegas = new VEGAS() { - public double fxn(final double[] x, final double wgt){ - return torusfunc1(x, wgt); - } - }; - vegas.vegas(regn,0,1000,100,-1,tgral,sd,chi2a); -// System.out.printf(chi2a); - localflag = chi2a.val > 1.2; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** vegas: chi-square for test #1 is too high"); - - } - - vegas.vegas(regn,1,100000,1,-1,tgral,sd,chi2a); - -// System.out.printf(tgral << " %f\n", sd << " %f\n", chi2a); -// System.out.printf(SQR(PI)*R1*SQR(R2)); - localflag = abs(tgral.val-SQR(PI)*R1*SQR(R2)) > 2.0*sd.val; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** vegas: Computation of hemitoroid volume is inaccurate"); - - } - - // Test #2: Weight the integral by x - vegas = new VEGAS() { - public double fxn(final double[] x, final double wgt){ - return torusfunc2(x, wgt); - } - }; - vegas.vegas(regn,0,1000,100,-1,tgral,sd,chi2a); -// System.out.printf(chi2a); - localflag = chi2a.val > 1.2; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** vegas: chi-square for test #2 is too high"); - - } - - vegas.vegas(regn,1,100000,1,-1,tgral,sd,chi2a); - -// System.out.printf(tgral << " %f\n", sd << " %f\n", chi2a); -// System.out.printf(2.0*PI*SQR(R1)*SQR(R2)*(1+SQR(R2/R1)/4.0)); - localflag = abs(tgral.val-2.0*PI*SQR(R1)*SQR(R2)*(1+SQR(R2/R1)/4.0)) > 2.0*sd.val; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** vegas: Computation of hemitoroid weighted by x is inaccurate"); - - } - - // Test #3: Weight the integral by z^2 - vegas = new VEGAS() { - public double fxn(final double[] x, final double wgt){ - return torusfunc3(x, wgt); - } - }; - vegas.vegas(regn,0,1000,100,-1,tgral,sd,chi2a); -// System.out.printf(chi2a); - localflag = chi2a.val > 1.2; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** vegas: chi-square for test #3 is too high"); - - } - - vegas.vegas(regn,1,100000,1,-1,tgral,sd,chi2a); - -// System.out.printf(tgral << " %f\n", sd << " %f\n", chi2a); -// System.out.printf(SQR(PI)*R1*SQR(SQR(R2))/4.0); - localflag = abs(tgral.val-SQR(PI)*R1*SQR(SQR(R2))/4.0) > 2.0*sd.val; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** vegas: Computation of hemitoroid weighted by z^2 is inaccurate"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - double torusfunc1(final double[] x, final double wgt) { - double R1=3.0,R2=1.0; - - if (SQR(x[2])+SQR(sqrt(SQR(x[0])+SQR(x[1]))-R1) <= R2) return 1.0; - else return 0.; - } - - double torusfunc2(final double[] x, final double wgt) { - double R1=3.0,R2=1.0; - - if (SQR(x[2])+SQR(sqrt(SQR(x[0])+SQR(x[1]))-R1) <= R2) return x[0]; - else return 0.; - } - - double torusfunc3(final double[] x, final double wgt) { - double R1=3.0,R2=1.0; - - if (SQR(x[2])+SQR(sqrt(SQR(x[0])+SQR(x[1]))-R1) <= R2) return SQR(x[2]); - else return 0.; - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_Heapselect.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_Heapselect.java deleted file mode 100644 index 8292cab1dc..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_Heapselect.java +++ /dev/null @@ -1,71 +0,0 @@ -package com.nr.test.test_chapter8; - -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; -import com.nr.sort.Heapselect; -import com.nr.sort.Sorter; - -public class Test_Heapselect { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=1000,M=100; - double xm,val; - double[] x = new double[M],y = new double[M]; - boolean localflag, globalflag=false; - - - - // Test Heapselect - System.out.println("Testing Heapselect"); - Heapselect heap = new Heapselect(M); - Ran myran = new Ran(17); - // Find top 100 values in 1000 random numbers - for (i=0;i= xm) { - if (j < M) y[j]=val; - j++; - } - } - localflag = (j != M); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Heapselect: The Mth largest was not correctly identified"); - - } - - Sorter.sort(y); - localflag = (maxel(vecsub(x,y))!=0.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Heapselect: The M largest elements are not correctly ordered"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_IQagent.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_IQagent.java deleted file mode 100644 index a5a1e188dd..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_IQagent.java +++ /dev/null @@ -1,76 +0,0 @@ -package com.nr.test.test_chapter8; - -import static com.nr.NRUtil.buildVector; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; -import com.nr.sort.IQagent; - -public class Test_IQagent { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=1000,M=100; - double var,sbeps; - double uu[]={1.0,25.0,50.0,75.0,100.0}; - double[] u=buildVector(uu),x = new double[11],y=new double[11],z = new double[5]; - boolean localflag, globalflag=false; - - - - // Test IQagent - System.out.println("Testing IQagent"); - IQagent iq = new IQagent(); - Ran myran = new Ran(17); - for (j=0;j sbeps); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** IQagent: Percentiles of uniform distribution are suspiciously nonuniform"); - - } - - // Artificial distribution - IQagent iq2 = new IQagent(); - for (j=0;j xx[i+1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Indexx: Array sorted according to index is incorrectly ordered"); - - } - - // Test member function sort() on another array - for (i=0;i yy[i]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Indexx: Independent array sorted according to index is incorrectly ordered"); - - } - - // Test member function el() - for (i=0;i sbeps); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Indexx: Member function el() does not sort inverted array into reverse order"); - - } - - // Test l-value version of member function el() - for (i=0;i sbeps); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** Indexx: l-value version of member function el() does not sort inverted array into reverse order"); - - } - - // Test member function rank() - idx.rank(zi); - idx.sort(zi); - for (i=0;i x[i+1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** hpsort: Sorted values are not correctly ordered"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_piksr2.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_piksr2.java deleted file mode 100644 index b87a59e493..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_piksr2.java +++ /dev/null @@ -1,66 +0,0 @@ -package com.nr.test.test_chapter8; - -import static com.nr.NRUtil.buildVector; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; -import com.nr.sort.Sorter; - -public class Test_piksr2 { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=100; - double[] x= new double[N],y= new double[N]; - boolean localflag=false, globalflag=false; - - - - // Test piksr2 - System.out.println("Testing piksr2"); - Ran myran = new Ran(17); - for (i=0;i x[i+1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** piksr2: First array is not correctly ordered"); - - } - - for (i=0;i x[i+1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** piksrt: Sorted values are not correctly ordered"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_select.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_select.java deleted file mode 100644 index 30574169b8..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_select.java +++ /dev/null @@ -1,67 +0,0 @@ -package com.nr.test.test_chapter8; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; -import com.nr.sort.Sorter; - -public class Test_select { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,k,N=100,M=20; - double xsel; - double[] x=new double[N]; - boolean localflag, globalflag=false; - - - - // Test select - System.out.println("Testing select"); - Ran myran = new Ran(17); - for (i=0;i x[k]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** select: Some array positions below k have values above a[k]"); - - } - - localflag = false; - for (j=k+1;j xsel) count++; - localflag = (count != (N-k-1)); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** selip: There are not k values less or equal to selected value"); - - } - - // Test that array was not altered - localflag = (maxel(vecsub(x,xx)) != 0.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** selip: Array was altered by selip"); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_shell.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_shell.java deleted file mode 100644 index 06487a5303..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_shell.java +++ /dev/null @@ -1,65 +0,0 @@ -package com.nr.test.test_chapter8; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; -import com.nr.sort.Sorter; - -public class Test_shell { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=100; - double[] x= new double[N],y= new double[N]; - boolean localflag,globalflag=false; - - - - // Test shell - System.out.println("Testing shell"); - localflag=false; - Ran myran = new Ran(17); - for (i=0;i x[i+1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** shell: Sorted values are not correctly ordered"); - - } - - localflag=false; - for (i=0;i y[i+1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** shell: First half of array is not correctly ordered"); - - } - - localflag=false; - for (i=N/2;i y[i]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** shell: Second half of array is not correctly ordered"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_sort.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_sort.java deleted file mode 100644 index 8a31f78083..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_sort.java +++ /dev/null @@ -1,65 +0,0 @@ -package com.nr.test.test_chapter8; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; -import com.nr.sort.Sorter; - -public class Test_sort { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=100; - double[] x= new double[N],y= new double[N]; - boolean localflag,globalflag=false; - - - - // Test sort - System.out.println("Testing sort"); - localflag=false; - Ran myran = new Ran(17); - for (i=0;i x[i+1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** sort: Sorted values are not correctly ordered"); - - } - - localflag=false; - for (i=0;i y[i+1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** sort: First half of array is not correctly ordered"); - - } - - localflag=false; - for (i=N/2;i y[i]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** sort: Second half of array is not correctly ordered"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_sort2.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_sort2.java deleted file mode 100644 index bd93c5ae5e..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter8/Test_sort2.java +++ /dev/null @@ -1,66 +0,0 @@ -package com.nr.test.test_chapter8; - -import static com.nr.NRUtil.buildVector; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.ran.Ran; -import com.nr.sort.Sorter; - -public class Test_sort2 { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=100; - double[] x= new double[N],y= new double[N]; - boolean localflag=false, globalflag=false; - - - - // Test sort2 - System.out.println("Testing sort2"); - Ran myran = new Ran(17); - for (i=0;i x[i+1]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** sort2: First array is not correctly ordered"); - - } - - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** broydn: Inaccurate roots"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Func_broydn implements RealMultiValueFun { - public double[] funk(final double[] x) { - double[] fvec = new double[4]; - - fvec[0] = -SQR(x[0])-SQR(x[1])-SQR(x[2])+x[3]; - fvec[1] = SQR(x[0])+SQR(x[1])+SQR(x[2])+SQR(x[3])-1.0; - fvec[2] = x[0]-x[1]; - fvec[3] = x[1]-x[2]; - return fvec; - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_laguer.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_laguer.java deleted file mode 100644 index 23ccc2e2ea..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_laguer.java +++ /dev/null @@ -1,74 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.root.Roots.laguer; -import static com.nr.test.NRTestUtil.maxel; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.intW; - -import com.nr.Complex; -import com.nr.ran.Ran; - -public class Test_laguer { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - intW its = new intW(0); - int i,M=5,N=20; - double sbeps=1.e-14; - Complex x = new Complex(),re1 = new Complex(1.0,0.0),im1=new Complex(0.0,1.0); - Complex a[]={ - re1.mul(2.0).add(im1), - im1.mul(2.0), - re1.mul(3.0).add(im1), - re1.add(im1.mul(2.0)), - re1.sub(im1), - new Complex(1.0) - }; - Complex[] aa = new Complex[M+1];System.arraycopy(a, 0, aa, 0 , M+1); - double[] dy = new double[N]; - boolean localflag, globalflag=false; - - - - // Test laguer - System.out.println("Testing laguer"); - // Roots of polynomial x^5+(1-i)x^4+(1+2i)x^3+(3+i)x^2+(2i)x+(2+i)" - // Roots are x=i, x=-i, x=sqrt(2i), x=-i*sqrt(2i), x=(i-1) - Ran myran =new Ran(17); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** laguer: Incorrect roots"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_lnsrch.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_lnsrch.java deleted file mode 100644 index 9739ad1f06..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_lnsrch.java +++ /dev/null @@ -1,102 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.NRUtil.SQR; -import static com.nr.root.Roots.lnsrch; -import static com.nr.test.NRTestUtil.maxel; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.booleanW; -import org.netlib.util.doubleW; - -import com.nr.RealMultiValueFun; -import com.nr.RealValueFun; - -public class Test_lnsrch { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,NDIM=4,M=10; // NTRIAL=6, not used. - doubleW fnew = new doubleW(0); - double fold,stpmax=1.0,sbeps=1.e-14; - double x0[]={0.5,-0.5,1.0,1.0,1.0,0.5,-1.0,-1.0,-1.0,-0.5}; - double x1[]={0.5,-0.5,1.0,1.0,0.5,1.0,-1.0,-1.0,-0.5,-1.0}; - double x2[]={0.5,-0.5,1.0,0.5,1.0,1.0,-1.0,-0.5,-1.0,-1.0}; - double x3[]={0.5,-0.5,0.9,1.0,1.0,1.0,-0.9,-1.0,-1.0,-1.0}; - double p0[]={1.0,-1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,-1.0}; - double p1[]={1.0,-1.0,0.0,0.0,1.0,0.0,0.0,0.0,-1.0,0.0}; - double p2[]={1.0,-1.0,0.0,1.0,0.0,0.0,0.0,-1.0,0.0,0.0}; - double p3[]={1.0,-1.0,1.0,0.0,0.0,0.0,-1.0,0.0,0.0,0.0}; - double[] xold=new double[NDIM],gold=new double[NDIM],p=new double[NDIM],xnew=new double[NDIM]; - double[] dy = new double[(M)]; - boolean localflag, globalflag=false; - - - - // Test lnsrch - System.out.println("Testing lnsrch"); - - Func_lnsrch f = new Func_lnsrch(); // function - Funcd_lnsrch g = new Funcd_lnsrch(); // gradiant - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** lnsrch: Inaccurate minima"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Func_lnsrch implements RealValueFun{ - public double funk(final double[] x) { - return(SQR(x[0]-x[1])+SQR(x[1]-x[2])+SQR(x[2]-x[3])+SQR(x[3]-1)*SQR(x[3]+1)); - } // Minima of 0.0 at x0=x1=x2=x3= +- 1; - }; - - class Funcd_lnsrch implements RealMultiValueFun { - public double[] funk(final double[] x) { - double[] g = new double[4]; - g[0]= 2.0*(x[0]-x[1]); - g[1]= -2.0*(x[0]-x[1])+2.0*(x[1]-x[2]); - g[2]= -2.0*(x[1]-x[2])+2.0*(x[2]-x[3]); - g[3]= -2.0*(x[2]-x[3])+2.0*(x[3]-1)*SQR(x[3]+1)+2.0*(x[3]+1)*SQR(x[3]-1); - return(g); - } - }; -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_mnewt.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_mnewt.java deleted file mode 100644 index 237b7c8ebb..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_mnewt.java +++ /dev/null @@ -1,91 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.NRUtil.SQR; -import static com.nr.test.NRTestUtil.maxel; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.root.MNEWT; - -public class Test_mnewt { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,NTRIAL=6,NDIM=4,M=8; - double tolx=1.0e-14,tolf=1.0e-14,sbeps=1.e-14; - double x0[]={0.5,0.4,0.6,0.5,-0.5,-0.4,-0.5,-0.4}; - double x1[]={0.6,0.6,0.4,0.4,-0.4,-0.5,-0.6,-0.6}; - double x2[]={0.4,0.5,0.5,0.6,-0.6,-0.6,-0.4,-0.5}; - double x3[]={0.0,1.4,0.0,1.6,0.0,1.3,0.0,1.7}; - double[] fvec=new double[NDIM],x=new double[NDIM],dy = new double[M]; - double[][] fjac=new double[NDIM][NDIM]; - boolean localflag, globalflag=false; - - - - // Test mnewt - System.out.println("Testing mnewt"); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** mnewt: Inaccurate roots"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - void usrfun(double[] x, double[] fvec, double[][] fjac) { - int i; - - int n=x.length; - fjac[0][0] = -2.0*x[0]; - fjac[0][1] = -2.0*x[1]; - fjac[0][2] = -2.0*x[2]; - fjac[0][3] = 1.0; - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** newt: Inaccurate roots"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Func_newt implements RealMultiValueFun { - public double[] funk(final double[] x) { - double[] fvec =new double[4]; - - fvec[0] = -SQR(x[0])-SQR(x[1])-SQR(x[2])+x[3]; - fvec[1] = SQR(x[0])+SQR(x[1])+SQR(x[2])+SQR(x[3])-1.0; - fvec[2] = x[0]-x[1]; - fvec[3] = x[1]-x[2]; - return fvec; - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_qroot.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_qroot.java deleted file mode 100644 index 645506e7f7..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_qroot.java +++ /dev/null @@ -1,102 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.NRUtil.buildVector; -import static com.nr.root.Roots.qroot; -import static com.nr.root.Roots.zroots; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.Complex; - -public class Test_qroot { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int j,N=6; - boolean polish=true; - double eps=1.e-10,err,sbeps=1.e-14; - doubleW b = new doubleW(0); - doubleW c = new doubleW(0); - - Complex pp[]={ - new Complex(2.0), - new Complex(-2.0), - new Complex(7.0), - new Complex(1.0), - new Complex(-3.0), - new Complex(5.0)}; - double ppr[]={2.0,-2.0,7.0,1.0,-3.0,5.0}; - Complex[] p=new Complex[N];System.arraycopy(pp, 0, p, 0, N); - double[] pr=buildVector(ppr); - Complex[] rts=new Complex[N-1],rts2 =new Complex[2]; - boolean localflag, globalflag=false; - - - - // Test qroot - System.out.println("Testing qroot"); - // Ran myran = new Ran(17); not use it - zroots(p,rts,!polish); // Find actual roots - // for (j=0;j sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** qroot: Quadratic is not a factor of the polynomial"); - } - - c.val=1.3; // Constructed another guess from actual roots - b.val=-1.4; - qroot(pr,b,c,eps); - a[0]=new Complex(c.val); a[1]=new Complex(b.val); a[2]=new Complex(1.0); // Now test result - zroots(a,rts2,polish); - err=0.0; - for (j=0;j<2;j++) { - Complex r = p[4].add(rts2[j].mul(p[5])); - r = p[3].add(rts2[j].mul(r)); - r = p[2].add(rts2[j].mul(r)); - r = p[1].add(rts2[j].mul(r)); - r = p[0].add(rts2[j].mul(r)); - err += r.abs(); - } - System.out.printf("qroot: Discrepancy = %f\n", abs(err)); - localflag = abs(err) > sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** qroot: Quadratic is not a factor of the polynomial"); - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtbis.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtbis.java deleted file mode 100644 index e58e88d176..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtbis.java +++ /dev/null @@ -1,74 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.NRUtil.buildVector; -import static com.nr.root.Roots.rtbis; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.root.Roots.Zbrak; -import com.nr.sf.Bessjy; - -public class Test_rtbis { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i; - int nroot = 0; - double[] xb1,xb2; - double sbeps=1.e-12,xacc=0.0; - double x1=1.0,x2=50.0; - double y[]={2.404825557695773,5.520078110286311,8.653727912911013, - 1.179153443901428e1,1.493091770848779e1,1.807106396791092e1, - 2.121163662987926e1,2.435247153074930e1,2.749347913204025e1, - 3.063460646843198e1,3.377582021357357e1,3.691709835366405e1, - 4.005842576462825e1,4.319979171317673e1,4.634118837166182e1, - 4.948260989739782e1}; - double[] yy =buildVector(y); - boolean localflag, globalflag=false; - - - - // Test rtbis - System.out.println("Testing rtbis"); - Func_rtbis fx = new Func_rtbis(); - Zbrak z = new Zbrak(); z.zbrak(fx,x1,x2,100); - xb1= z.xb1;xb2=z.xb2;nroot = z.nroot; - double[] root = new double[nroot]; - for (i=0;i xacc; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rtbis: Incorrect roots"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Func_rtbis implements UniVarRealValueFun { - Bessjy b = new Bessjy(); - public double funk (final double x) { - return b.j0(x); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtflsp.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtflsp.java deleted file mode 100644 index 16c1966163..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtflsp.java +++ /dev/null @@ -1,75 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.NRUtil.buildVector; -import static com.nr.root.Roots.rtflsp; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.root.Roots.Zbrak; -import com.nr.sf.Bessjy; - -public class Test_rtflsp { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i; - int nroot = 0; - double[] xb1,xb2; - double sbeps=1.e-13,xacc=0.0; - double x1=1.0,x2=50.0; - double y[]={2.404825557695773,5.520078110286311,8.653727912911013, - 1.179153443901428e1,1.493091770848779e1,1.807106396791092e1, - 2.121163662987926e1,2.435247153074930e1,2.749347913204025e1, - 3.063460646843198e1,3.377582021357357e1,3.691709835366405e1, - 4.005842576462825e1,4.319979171317673e1,4.634118837166182e1, - 4.948260989739782e1}; - double[] yy = buildVector(y); - boolean localflag, globalflag=false; - - - - // Test rtflsp - System.out.println("Testing rtflsp"); - Func_rtflsp fx = new Func_rtflsp(); - Zbrak z = new Zbrak(); z.zbrak(fx,x1,x2,100); - xb1= z.xb1;xb2=z.xb2;nroot = z.nroot; - - double[] root = new double[nroot]; - for (i=0;i xacc; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rtflsp: Incorrect roots"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Func_rtflsp implements UniVarRealValueFun{ - Bessjy b = new Bessjy(); - public double funk (final double x) { - return b.j0(x); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtnewt.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtnewt.java deleted file mode 100644 index e830f5a172..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtnewt.java +++ /dev/null @@ -1,76 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.NRUtil.buildVector; -import static com.nr.root.Roots.rtnewt; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniValRealValueFunWithDiff; -import com.nr.root.Roots.Zbrak; -import com.nr.sf.Bessjy; - -public class Test_rtnewt { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i; - int nroot = 0; - double[] xb1,xb2; - double sbeps=1.e-12,xacc=0.; - double x1=1.0,x2=50.0; - double y[]={2.404825557695773,5.520078110286311,8.653727912911013, - 1.179153443901428e1,1.493091770848779e1,1.807106396791092e1, - 2.121163662987926e1,2.435247153074930e1,2.749347913204025e1, - 3.063460646843198e1,3.377582021357357e1,3.691709835366405e1, - 4.005842576462825e1,4.319979171317673e1,4.634118837166182e1, - 4.948260989739782e1}; - double[] yy=buildVector(y); - boolean localflag, globalflag=false; - - - - // Test rtnewt - System.out.println("Testing rtnewt"); - Funcd_rtnewt fxd = new Funcd_rtnewt(); - Zbrak z = new Zbrak(); z.zbrak(fxd,x1,x2,100); - xb1= z.xb1;xb2=z.xb2;nroot = z.nroot; - double[] root = new double[nroot]; - for (i=0;i xacc; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rtnewt: Incorrect roots"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class Funcd_rtnewt implements UniValRealValueFunWithDiff{ - Bessjy b = new Bessjy(); - public double funk (final double x) { - return b.j0(x); - } - public double df(final double x) { - return -b.j1(x); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtsafe.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtsafe.java deleted file mode 100644 index f3d9b145a4..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtsafe.java +++ /dev/null @@ -1,75 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.NRUtil.buildVector; -import static com.nr.root.Roots.rtsafe; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniValRealValueFunWithDiff; -import com.nr.root.Roots.Zbrak; -import com.nr.sf.Bessjy; - -public class Test_rtsafe { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i; - int nroot = 0; - double[] xb1,xb2; - double sbeps=1.e-13,xacc=0.0; - double x1=1.0,x2=50.0; - double y[]={2.404825557695773,5.520078110286311,8.653727912911013, - 1.179153443901428e1,1.493091770848779e1,1.807106396791092e1, - 2.121163662987926e1,2.435247153074930e1,2.749347913204025e1, - 3.063460646843198e1,3.377582021357357e1,3.691709835366405e1, - 4.005842576462825e1,4.319979171317673e1,4.634118837166182e1, - 4.948260989739782e1}; - double[] yy=buildVector(y); - boolean localflag, globalflag=false; - - // Test rtsafe - System.out.println("Testing rtsafe"); - Funcd_rtsafe fxd = new Funcd_rtsafe(); - Zbrak z = new Zbrak(); z.zbrak(fxd,x1,x2,100); - xb1= z.xb1;xb2=z.xb2;nroot = z.nroot; - double[] root = new double[nroot]; - for (i=0;i xacc; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rtsafe: Incorrect roots"); - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Funcd_rtsafe implements UniValRealValueFunWithDiff { - Bessjy b = new Bessjy(); - public double funk (final double x) { - return b.j0(x); - } - public double df(final double x) { - return -b.j1(x); - } - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtsec.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtsec.java deleted file mode 100644 index 4fe0adcc73..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_rtsec.java +++ /dev/null @@ -1,74 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.NRUtil.buildVector; -import static com.nr.root.Roots.rtsec; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.root.Roots.Zbrak; -import com.nr.sf.Bessjy; - -public class Test_rtsec { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i; - int nroot = 0; - double[] xb1,xb2; - double sbeps=1.e-12,xacc=0.; - double x1=1.0,x2=50.0; - double y[]={2.404825557695773,5.520078110286311,8.653727912911013, - 1.179153443901428e1,1.493091770848779e1,1.807106396791092e1, - 2.121163662987926e1,2.435247153074930e1,2.749347913204025e1, - 3.063460646843198e1,3.377582021357357e1,3.691709835366405e1, - 4.005842576462825e1,4.319979171317673e1,4.634118837166182e1, - 4.948260989739782e1}; - double[] yy=buildVector(y); - boolean localflag, globalflag=false; - - - - // Test rtsec - System.out.println("Testing rtsec"); - Func_rtsec fx = new Func_rtsec(); - Zbrak z = new Zbrak(); z.zbrak(fx,x1,x2,100); - xb1= z.xb1;xb2=z.xb2;nroot = z.nroot; - double[] root = new double[nroot]; - for (i=0;i xacc; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** rtsec: Incorrect roots"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Func_rtsec implements UniVarRealValueFun { - Bessjy b = new Bessjy(); - public double funk (final double x) { - return b.j0(x); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zbrac.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zbrac.java deleted file mode 100644 index 5000350cab..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zbrac.java +++ /dev/null @@ -1,81 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.root.Roots.zbrac; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; -import org.netlib.util.doubleW; - -import com.nr.UniVarRealValueFun; -import com.nr.sf.Bessjy; - -public class Test_zbrac { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - boolean success; - int i,j,N=16,M=50; - doubleW x1=new doubleW(0),x2=new doubleW(0); - double y[]={2.404825557695773,5.520078110286311,8.653727912911013, - 1.179153443901428e1,1.493091770848779e1,1.807106396791092e1, - 2.121163662987926e1,2.435247153074930e1,2.749347913204025e1, - 3.063460646843198e1,3.377582021357357e1,3.691709835366405e1, - 4.005842576462825e1,4.319979171317673e1,4.634118837166182e1, - 4.948260989739782e1}; - boolean localflag, globalflag=false; - - - - // Test zbrac - System.out.println("Testing zbrac"); - Func_zbrac fx = new Func_zbrac(); - for (i=1;i= 0.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** zbrac: An identified bracketing interval does not actually bracket a root."); - - } - - for (j=0;j x1.val) && (y[j] < x2.val); - localflag = !localflag; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** zbrac: No known root of bessj0 falls witning one of the identified brackets."); - - } - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Func_zbrac implements UniVarRealValueFun{ - Bessjy b =new Bessjy(); - public double funk (final double x) { - return b.j0(x); - } - } -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zbrak.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zbrak.java deleted file mode 100644 index 3f93e49654..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zbrak.java +++ /dev/null @@ -1,73 +0,0 @@ -package com.nr.test.test_chapter9; - -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.root.Roots.Zbrak; -import com.nr.sf.Bessjy; - -public class Test_zbrak { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i; - int nroot = 0; - double[] xb1,xb2; - double x1=1.0,x2=50.0; - double y[]={2.404825557695773,5.520078110286311,8.653727912911013, - 1.179153443901428e1,1.493091770848779e1,1.807106396791092e1, - 2.121163662987926e1,2.435247153074930e1,2.749347913204025e1, - 3.063460646843198e1,3.377582021357357e1,3.691709835366405e1, - 4.005842576462825e1,4.319979171317673e1,4.634118837166182e1, - 4.948260989739782e1}; - - - boolean localflag=false, globalflag=false; - - - - // Test zbrak - System.out.println("Testing zbrak"); - Func_zbrak fx = new Func_zbrak(); - Zbrak z = new Zbrak(); z.zbrak(fx,x1,x2,100); - xb1= z.xb1;xb2=z.xb2;nroot = z.nroot; - for (i=0;i= 0.0); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** zbrak: One of the returned intervals does not contain a root."); - - } - - for (i=0;i xb2[i]); - globalflag = globalflag || localflag; - if (localflag) { - fail("*** zbrak: A known root of bessj0 does not fall in the identified intervals."); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Func_zbrak implements UniVarRealValueFun { - Bessjy b = new Bessjy(); - - public double funk (final double x) { - return b.j0(x); - } - }; -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zbrent.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zbrent.java deleted file mode 100644 index 9d4babfbfe..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zbrent.java +++ /dev/null @@ -1,73 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.NRUtil.buildVector; -import static com.nr.root.Roots.zbrent; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.root.Roots.Zbrak; -import com.nr.sf.Bessjy; -public class Test_zbrent { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i; - int nroot = 0; - double[] xb1,xb2; - double sbeps=1.e-15,xacc=0; - double x1=1.0,x2=50.0; - double y[]={2.404825557695773,5.520078110286311,8.653727912911013, - 1.179153443901428e1,1.493091770848779e1,1.807106396791092e1, - 2.121163662987926e1,2.435247153074930e1,2.749347913204025e1, - 3.063460646843198e1,3.377582021357357e1,3.691709835366405e1, - 4.005842576462825e1,4.319979171317673e1,4.634118837166182e1, - 4.948260989739782e1}; - double[] yy = buildVector(y); - boolean localflag, globalflag=false; - - - - // Test zbrent - System.out.println("Testing zbrent"); - Func_zbrent fx = new Func_zbrent(); - Zbrak z = new Zbrak(); z.zbrak(fx,x1,x2,100); - xb1= z.xb1;xb2=z.xb2;nroot = z.nroot; - double[] root=new double[nroot]; - for (i=0;i xacc; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** zbrent: Incorrect roots"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - class Func_zbrent implements UniVarRealValueFun { - Bessjy b = new Bessjy(); - public double funk (final double x) { - return b.j0(x); - } - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zrhqr.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zrhqr.java deleted file mode 100644 index d2b1b3d273..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zrhqr.java +++ /dev/null @@ -1,56 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.NRUtil.buildVector; -import static com.nr.root.Roots.zrhqr; -import static com.nr.test.NRTestUtil.maxel; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.Complex; - -public class Test_zrhqr { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,j,N=5; - double sbeps=5.e-14; - double a[]={2.0,-2.0,7.0,1.0,-3.0,5.0}; - Complex b = new Complex(); - double[] aa= buildVector(a),dy = new double[N]; - Complex[] rts = new Complex[N]; - boolean localflag, globalflag=false; - - // Test zrhqr - System.out.println("Testing zrhqr"); - // Roots of polynomial - zrhqr(aa,rts); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** zrhqr: Incorrect roots"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zriddr.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zriddr.java deleted file mode 100644 index 27f482366c..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zriddr.java +++ /dev/null @@ -1,75 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.NRUtil.buildVector; -import static com.nr.root.Roots.zriddr; -import static com.nr.test.NRTestUtil.maxel; -import static com.nr.test.NRTestUtil.vecsub; -import static java.lang.Math.abs; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.UniVarRealValueFun; -import com.nr.root.Roots.Zbrak; -import com.nr.sf.Bessjy; - -public class Test_zriddr { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i; - int nroot = 0; - double[] xb1,xb2; - - double sbeps=1.e-15,xacc=0.; - double x1=1.0,x2=50.0; - - double y[]={2.404825557695773,5.520078110286311,8.653727912911013, - 1.179153443901428e1,1.493091770848779e1,1.807106396791092e1, - 2.121163662987926e1,2.435247153074930e1,2.749347913204025e1, - 3.063460646843198e1,3.377582021357357e1,3.691709835366405e1, - 4.005842576462825e1,4.319979171317673e1,4.634118837166182e1, - 4.948260989739782e1}; - double[] yy = buildVector(y); - boolean localflag, globalflag=false; - - - // Test zriddr - System.out.println("Testing zriddr"); - Func_zriddr fx = new Func_zriddr(); - Zbrak z = new Zbrak(); z.zbrak(fx,x1,x2,100); - xb1= z.xb1;xb2=z.xb2;nroot = z.nroot; - double[] root =new double[(nroot)]; - for (i=0;i xacc; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** zriddr: Incorrect roots"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - - class Func_zriddr implements UniVarRealValueFun{ - Bessjy b = new Bessjy(); - public double funk (final double x) { - return b.j0(x); - } - }; -} diff --git a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zroots.java b/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zroots.java deleted file mode 100644 index 41dc826f13..0000000000 --- a/common-tools/cnuphys/numRec/test/com/nr/test/test_chapter9/Test_zroots.java +++ /dev/null @@ -1,72 +0,0 @@ -package com.nr.test.test_chapter9; - -import static com.nr.root.Roots.zroots; -import static com.nr.test.NRTestUtil.maxel; -import static org.junit.Assert.fail; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.nr.Complex; - - -public class Test_zroots { - - @Before - public void setUp() throws Exception { - } - - @After - public void tearDown() throws Exception { - } - - @Test - public void test() { - int i,N=5; - boolean polish=true; - double sbeps=1.e-14; - Complex re1 = new Complex(1.0,0.0),im1=new Complex(0.0,1.0); - Complex a[]={ - re1.mul(2.0).add(im1), - im1.mul(2.0), - re1.mul(3.0).add(im1), - re1.add(im1.mul(2.0)), - re1.sub(im1), - new Complex(1.0) - }; - - Complex[] aa = new Complex[N+1];System.arraycopy(a, 0, aa, 0 , N+1); - - Complex[] rts = new Complex[N]; - double[] dy=new double[N]; - boolean localflag, globalflag=false; - - - - // Test zroots - System.out.println("Testing zroots"); - // Roots of polynomial x^5+(1-i)x^4+(1+2i)x^3+(3+i)x^2+(2i)x+(2+i)" - // Roots are x=i, x=-i, x=sqrt(2i), x=-i*sqrt(2i), x=(i-1) - zroots(aa,rts,polish); - for (i=0;i sbeps; - globalflag = globalflag || localflag; - if (localflag) { - fail("*** zroots: Incorrect roots"); - - } - - if (globalflag) System.out.println("Failed\n"); - else System.out.println("Passed\n"); - } - -} diff --git a/common-tools/cnuphys/pom.xml b/common-tools/cnuphys/pom.xml deleted file mode 100644 index 6161774821..0000000000 --- a/common-tools/cnuphys/pom.xml +++ /dev/null @@ -1,23 +0,0 @@ - - - 4.0.0 - - cnuphys - clas12 - 13.8.4-SNAPSHOT - pom - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - splot - snr - magfield - swimmer - - - diff --git a/common-tools/cnuphys/snr/pom.xml b/common-tools/cnuphys/snr/pom.xml deleted file mode 100644 index 90f23dfcbc..0000000000 --- a/common-tools/cnuphys/snr/pom.xml +++ /dev/null @@ -1,16 +0,0 @@ - - - 4.0.0 - - cnuphys - snr - 13.8.4-SNAPSHOT - jar - - - cnuphys - clas12 - 13.8.4-SNAPSHOT - - - diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/.gitignore b/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/.gitignore deleted file mode 100644 index ddef73b84d..0000000000 --- a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/.gitignore +++ /dev/null @@ -1,3 +0,0 @@ -/ExtendedWord.class -/GeoConstants.class -/NoiseReductionParameters.class diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/clas12/.gitignore b/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/clas12/.gitignore deleted file mode 100644 index 43cfef8650..0000000000 --- a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/clas12/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -/Clas12NoiseAnalysis.class -/Clas12NoiseResult.class diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/.gitignore b/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/.gitignore deleted file mode 100644 index b242f2ebde..0000000000 --- a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/.gitignore +++ /dev/null @@ -1,18 +0,0 @@ -/ChamberTest.class -/CompositeChamber.class -/DetectorTest$1.class -/DetectorTest$2.class -/DetectorTest$DisplayOption.class -/DetectorTest.class -/HitTest$HitType.class -/HitTest.class -/NoiseTest$1.class -/NoiseTest$2.class -/NoiseTest$3.class -/NoiseTest$4.class -/NoiseTest$5.class -/NoiseTest$6.class -/NoiseTest.class -/TestParameters.class -/TestSupport.class -/TrackTest.class diff --git a/common-tools/cnuphys/splot/pom.xml b/common-tools/cnuphys/splot/pom.xml deleted file mode 100644 index 26ee79a55f..0000000000 --- a/common-tools/cnuphys/splot/pom.xml +++ /dev/null @@ -1,29 +0,0 @@ - - - 4.0.0 - - cnuphys - splot - 13.8.4-SNAPSHOT - jar - - - cnuphys - clas12 - 13.8.4-SNAPSHOT - - - - - cnuphys - numRec - 1.0 - - - cnuphys - f2jutil - 1.0 - - - - diff --git a/common-tools/cnuphys/splot/src/main/java/build.xml b/common-tools/cnuphys/splot/src/main/java/build.xml deleted file mode 100644 index fc8ef50771..0000000000 --- a/common-tools/cnuphys/splot/src/main/java/build.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - - - - - - - Building splot image jar - - - - - Building splot jar - - - - - - - - - - - - - diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/.gitignore b/common-tools/cnuphys/splot/src/main/java/cnuphys/.gitignore deleted file mode 100644 index ae3c172604..0000000000 --- a/common-tools/cnuphys/splot/src/main/java/cnuphys/.gitignore +++ /dev/null @@ -1 +0,0 @@ -/bin/ diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/.gitignore b/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/.gitignore deleted file mode 100644 index 1888bce86c..0000000000 --- a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/.gitignore +++ /dev/null @@ -1,26 +0,0 @@ -/ButtonPanel.class -/ColorDialog$1.class -/ColorDialog.class -/ColorLabel$1.class -/ColorLabel.class -/ColorPanel$1.class -/ColorPanel.class -/CurveDataModel.class -/CurveEditorDialog.class -/CurveEditorPanel$1.class -/CurveEditorPanel$2.class -/CurveEditorPanel.class -/CurveTable$1.class -/CurveTable$2.class -/CurveTable$3.class -/CurveTable$4.class -/CurveTable.class -/DataEditor.class -/DialogUtilities.class -/IColorChangeListener.class -/PlotPreferencesDialog.class -/SimpleDialog$1.class -/SimpleDialog$2.class -/SimpleDialog.class -/VerticalFlowLayout$AlignedComponent.class -/VerticalFlowLayout.class diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/.gitignore b/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/.gitignore deleted file mode 100644 index 381c7714e2..0000000000 --- a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/.gitignore +++ /dev/null @@ -1,36 +0,0 @@ -/AExample$1.class -/AExample.class -/APlotDialog.class -/AnotherGaussian$1.class -/AnotherGaussian.class -/ErfTest$1.class -/ErfTest.class -/ErfcTest$1.class -/ErfcTest.class -/Gaussians$1.class -/Gaussians.class -/Grid.class -/GrowingHisto.class -/Histo.class -/LineWithXAndYErrors$1.class -/LineWithXAndYErrors.class -/MemoryUsageDialog.class -/OneXThreeY$1.class -/OneXThreeY.class -/Scatter$1.class -/Scatter.class -/StraightLine$1.class -/StraightLine.class -/StripChart$1.class -/StripChart.class -/TripleGaussian$1.class -/TripleGaussian.class -/TwoHisto.class -/TwoLinesWithErrors$1.class -/TwoLinesWithErrors.class -/Grid$1.class -/Grid$2.class -/Grid$3.class -/GrowingHisto$1.class -/Histo$1.class -/TwoHisto$1.class diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/.gitignore b/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/.gitignore deleted file mode 100644 index b3a616fed4..0000000000 --- a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/.gitignore +++ /dev/null @@ -1,35 +0,0 @@ -/ANonlinearFit.class -/AltPolynomialFit.class -/CubicSpline.class -/ErfFit.class -/ErfcFit.class -/FErf.class -/FErfc.class -/FGaussPoly.class -/FGaussian.class -/FPoly.class -/Fit$ErrorType.class -/Fit.class -/FitEditorPanel$1.class -/FitEditorPanel$2.class -/FitEditorPanel$3.class -/FitEditorPanel$4.class -/FitEditorPanel$5.class -/FitEditorPanel.class -/FitHold.class -/FitType.class -/FitUtilities$1.class -/FitUtilities.class -/GaussianFit.class -/IValueGetter.class -/LineFit.class -/LinearExyFit.class -/PolyAndGaussianFit.class -/PolyFit.class -/Polynomial.class -/CubicSpline$1.class -/CubicSpline$2.class -/CubicSpline$3.class -/PolyFit$1.class -/Polynomial$1.class -/Polynomial$2.class diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/.gitignore b/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/.gitignore deleted file mode 100644 index fbfa9d2b9d..0000000000 --- a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/.gitignore +++ /dev/null @@ -1,14 +0,0 @@ -/DataChangeListener.class -/DataColumn.class -/DataColumnType.class -/DataSet.class -/DataSetException.class -/DataSetType.class -/DataTable$1.class -/DataTable$MyTableCellEditor.class -/DataTable.class -/GrowableArray.class -/HistoData.class -/NiceScale.class -/StripData$1.class -/StripData.class diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/.gitignore b/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/.gitignore deleted file mode 100644 index 214190be67..0000000000 --- a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/.gitignore +++ /dev/null @@ -1,34 +0,0 @@ -/APreferencePanel.class -/CommonBorder.class -/CurveDrawer.class -/DataDrawer.class -/DoubleFormat.class -/Draggable.class -/Environment.class -/FloatingLabel.class -/GeneralPlotParamPanel.class -/GraphicsUtilities.class -/HorizontalLine.class -/ImageManager.class -/Legend.class -/PlotCanvas$1.class -/PlotCanvas$2.class -/PlotCanvas.class -/PlotGrid.class -/PlotGridDialog.class -/PlotLine.class -/PlotPanel$1.class -/PlotPanel$2.class -/PlotPanel$3.class -/PlotPanel.class -/PlotParameters.class -/PlotPopupMenu.class -/PlotTicks.class -/PrintUtilities.class -/SplotMenus.class -/TextFieldSlider$1.class -/TextFieldSlider.class -/UnicodeSupport.class -/VerticalLabelUI.class -/VerticalLine.class -/X11Colors.class diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/rubberband/.gitignore b/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/rubberband/.gitignore deleted file mode 100644 index d840aef4ce..0000000000 --- a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/rubberband/.gitignore +++ /dev/null @@ -1,5 +0,0 @@ -/IRubberbanded.class -/Rubberband$1.class -/Rubberband$2.class -/Rubberband$Policy.class -/Rubberband.class diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/.gitignore b/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/.gitignore deleted file mode 100644 index 7bd53ebfb7..0000000000 --- a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/.gitignore +++ /dev/null @@ -1,10 +0,0 @@ -/EnumComboBox.class -/IStyled.class -/LineStyle$1.class -/LineStyle.class -/StyleEditorPanel$1.class -/StyleEditorPanel.class -/Styled.class -/SymbolDraw.class -/SymbolType$1.class -/SymbolType.class diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/toolbar/.gitignore b/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/toolbar/.gitignore deleted file mode 100644 index 4ba771825c..0000000000 --- a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/toolbar/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -/CommonToolBar.class -/IToolBarListener.class -/ToolBarButton.class -/ToolBarToggleButton.class diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/xml/.gitignore b/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/xml/.gitignore deleted file mode 100644 index 84deee7eae..0000000000 --- a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/xml/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -/XmlDomParser.class -/XmlPrintStreamWritable.class -/XmlPrintStreamWriter.class -/XmlSupport.class diff --git a/common-tools/cnuphys/swimmer/pom.xml b/common-tools/cnuphys/swimmer/pom.xml deleted file mode 100644 index 33a857bbfc..0000000000 --- a/common-tools/cnuphys/swimmer/pom.xml +++ /dev/null @@ -1,31 +0,0 @@ - - - 4.0.0 - - cnuphys - swimmer - 13.8.4-SNAPSHOT - jar - - - cnuphys - clas12 - 13.8.4-SNAPSHOT - - - - - cnuphys - magfield - 13.8.4-SNAPSHOT - - - - cnuphys - splot - 13.8.4-SNAPSHOT - - - - - diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/bin/cnuphys/lund/.gitignore b/common-tools/cnuphys/swimmer/src/main/java/cnuphys/bin/cnuphys/lund/.gitignore deleted file mode 100644 index 6b232bce45..0000000000 --- a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/bin/cnuphys/lund/.gitignore +++ /dev/null @@ -1,21 +0,0 @@ -/DoubleFormat.class -/GeneratedParticleRecord.class -/LundComboBox$LundComboBoxItem.class -/LundComboBox.class -/LundId$1.class -/LundId.class -/LundStyle.class -/LundSupport.class -/LundTrackDialog$CommonBorder.class -/LundTrackDialog.class -/SwimTrajectoryListener.class -/TrajectoryRowData.class -/TrajectoryTable.class -/TrajectoryTableModel.class -/X11Colors.class -/LundTrackDialog$1.class -/LundTrackDialog$2.class -/LundTrackDialog$3.class -/LundTrackDialog$4.class -/LundTrackDialog$5.class -/LundTrackDialog$6.class diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/bin/cnuphys/rk4/.gitignore b/common-tools/cnuphys/swimmer/src/main/java/cnuphys/bin/cnuphys/rk4/.gitignore deleted file mode 100644 index 3002a59e45..0000000000 --- a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/bin/cnuphys/rk4/.gitignore +++ /dev/null @@ -1,15 +0,0 @@ -/ButcherTableau.class -/DefaultStopper.class -/IAdvance.class -/IDerivative.class -/IRk4Listener.class -/IStopper.class -/RungeKutta4$1.class -/RungeKutta4$2.class -/RungeKutta4$3.class -/RungeKutta4$4.class -/RungeKutta4$ButcherTableauAdvance.class -/RungeKutta4$HalfStepAdvance.class -/RungeKutta4$UniformAdvance.class -/RungeKutta4.class -/RungeKuttaException.class diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/bin/cnuphys/swim/.gitignore b/common-tools/cnuphys/swimmer/src/main/java/cnuphys/bin/cnuphys/swim/.gitignore deleted file mode 100644 index d59a1d35f7..0000000000 --- a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/bin/cnuphys/swim/.gitignore +++ /dev/null @@ -1,21 +0,0 @@ -/Bxdl.class -/DefaultDerivative.class -/DefaultListener.class -/DefaultSwimStopper.class -/Example.class -/IProjector.class -/SwimMenu$1.class -/SwimMenu$2.class -/SwimMenu$3.class -/SwimMenu$4.class -/SwimMenu$5.class -/SwimMenu$6.class -/SwimMenu$7.class -/SwimMenu.class -/SwimTrajectory.class -/SwimTrajectory2D.class -/Swimmer.class -/Swimming.class -/TerminalPlot.class -/Swimmer$1.class -/Swimming$1.class diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/bin/cnuphys/swimZ/.gitignore b/common-tools/cnuphys/swimmer/src/main/java/cnuphys/bin/cnuphys/swimZ/.gitignore deleted file mode 100644 index 472f5fb335..0000000000 --- a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/bin/cnuphys/swimZ/.gitignore +++ /dev/null @@ -1,7 +0,0 @@ -/SwimZ.class -/SwimZDerivative.class -/SwimZException.class -/SwimZRange.class -/SwimZResult.class -/SwimZStateVector.class -/SwimZTest.class diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/.gitignore b/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/.gitignore deleted file mode 100644 index 6b232bce45..0000000000 --- a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/.gitignore +++ /dev/null @@ -1,21 +0,0 @@ -/DoubleFormat.class -/GeneratedParticleRecord.class -/LundComboBox$LundComboBoxItem.class -/LundComboBox.class -/LundId$1.class -/LundId.class -/LundStyle.class -/LundSupport.class -/LundTrackDialog$CommonBorder.class -/LundTrackDialog.class -/SwimTrajectoryListener.class -/TrajectoryRowData.class -/TrajectoryTable.class -/TrajectoryTableModel.class -/X11Colors.class -/LundTrackDialog$1.class -/LundTrackDialog$2.class -/LundTrackDialog$3.class -/LundTrackDialog$4.class -/LundTrackDialog$5.class -/LundTrackDialog$6.class diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/.gitignore b/common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/.gitignore deleted file mode 100644 index 3002a59e45..0000000000 --- a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/.gitignore +++ /dev/null @@ -1,15 +0,0 @@ -/ButcherTableau.class -/DefaultStopper.class -/IAdvance.class -/IDerivative.class -/IRk4Listener.class -/IStopper.class -/RungeKutta4$1.class -/RungeKutta4$2.class -/RungeKutta4$3.class -/RungeKutta4$4.class -/RungeKutta4$ButcherTableauAdvance.class -/RungeKutta4$HalfStepAdvance.class -/RungeKutta4$UniformAdvance.class -/RungeKutta4.class -/RungeKuttaException.class diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/.gitignore b/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/.gitignore deleted file mode 100644 index d59a1d35f7..0000000000 --- a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/.gitignore +++ /dev/null @@ -1,21 +0,0 @@ -/Bxdl.class -/DefaultDerivative.class -/DefaultListener.class -/DefaultSwimStopper.class -/Example.class -/IProjector.class -/SwimMenu$1.class -/SwimMenu$2.class -/SwimMenu$3.class -/SwimMenu$4.class -/SwimMenu$5.class -/SwimMenu$6.class -/SwimMenu$7.class -/SwimMenu.class -/SwimTrajectory.class -/SwimTrajectory2D.class -/Swimmer.class -/Swimming.class -/TerminalPlot.class -/Swimmer$1.class -/Swimming$1.class diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/.gitignore b/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/.gitignore deleted file mode 100644 index 472f5fb335..0000000000 --- a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/.gitignore +++ /dev/null @@ -1,7 +0,0 @@ -/SwimZ.class -/SwimZDerivative.class -/SwimZException.class -/SwimZRange.class -/SwimZResult.class -/SwimZStateVector.class -/SwimZTest.class diff --git a/common-tools/coat-libs/pom.xml b/common-tools/coat-libs/pom.xml deleted file mode 100644 index 345723ee7f..0000000000 --- a/common-tools/coat-libs/pom.xml +++ /dev/null @@ -1,278 +0,0 @@ - - - 4.0.0 - - org.jlab.coat - coat-libs - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - freehep-repo-public - https://clasweb.jlab.org/.clas12maven/ - - - - - - - - org.jlab.coda - jevio - jar-with-dependencies - - - - org.jlab.coda - et - 14.0 - - - - j4ml - j4ml-neuroph - - - - j4ml - j4ml-clas12 - - - - org.jama - jamapack - 1.0 - - - - org.jlab.plugins - trackfitter - 1.0 - - - - org.jlab.plugins - jMath - 1.0 - - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clara-io - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-logging - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-jcsg - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-analysis - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-math - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - - org.jlab.clas - swim-tools - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-tracking - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-decay-tools - 13.8.4-SNAPSHOT - - - - cnuphys - snr - 13.8.4-SNAPSHOT - - - - org.freehep - jminuit - - - - de.erichseifert - vectorgraphics2d - 1.0 - - - - net.objecthunter - exp4j - - - - - - - - - src/main/resources - true - - **/pom.properties - - - - - - - - - org.apache.maven.plugins - maven-shade-plugin - 3.6.2 - - - package - - shade - - - - - false - - - cnuphys:cnuphys - cnuphys:jogl-all - cnuphys:jogl - cnuphys:gluegen - org.jlab.coda:jclara - org.jacoco - - - - - *:* - - - META-INF/*.SF - META-INF/*.DSA - META-INF/*.RSA - - META-INF/maven/** - - module-info.class - - .DS_Store - .classpath - .factorypath - .project - .settings - - - - - - - ${project.artifactId} - ${project.version} - ${project.artifactId} - ${project.version} - ${project.groupId} - - - - - - - - - org.codehaus.mojo - flatten-maven-plugin - - - org.apache.maven.plugins - maven-deploy-plugin - - - - - org.apache.maven.plugins - maven-dependency-plugin - - true - - - - - - - - - - ${project.artifactId} - ${coat.deployment.url} - - - - diff --git a/common-tools/pom.xml b/common-tools/pom.xml deleted file mode 100644 index 809fb7afe3..0000000000 --- a/common-tools/pom.xml +++ /dev/null @@ -1,35 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - pom - - - org.jlab.clas - coatjava - 13.8.4-SNAPSHOT - - - - clas-utils - clas-physics - clas-io - clas-logging - clas-geometry - clas-jcsg - clas-detector - cnuphys - clas-reco - swim-tools - clas-analysis - clas-math - clara-io - clas-tracking - clas-decay-tools - coat-libs - - - diff --git a/common-tools/swim-tools/pom.xml b/common-tools/swim-tools/pom.xml deleted file mode 100644 index dcf4a09be7..0000000000 --- a/common-tools/swim-tools/pom.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - 4.0.0 - - org.jlab.clas - swim-tools - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas - common-tools - 13.8.4-SNAPSHOT - - - - - org.apache.commons - commons-math3 - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - cnuphys - magfield - 13.8.4-SNAPSHOT - - - cnuphys - swimmer - 13.8.4-SNAPSHOT - - - - diff --git a/deploy-coatjava.sh b/deploy-coatjava.sh index 2a33ba4acc..c85ff3f58b 100755 --- a/deploy-coatjava.sh +++ b/deploy-coatjava.sh @@ -127,9 +127,10 @@ fi # change the version number, if different # NOTE: `maven-release-plugin` could be used to better automate the versioning -# here, but since this deployment is _only_ done in the `coat-libs` POM (the -# shaded JAR), and we also want to make a tarball with _all_ of the POMs at the -# correct version number, we may as well do the version bump here +# here, but since the deployment publishes a single coordinate +# (org.jlab.coat:coat-libs:) and we also want to make a tarball with the +# install tree at the correct version number, we may as well do the version +# bump here if [ "$ver_current" != "$ver_deploy" ]; then log "change version number $ver_current -> $ver_deploy" $src_dir/libexec/version-bump.sh $ver_deploy @@ -140,15 +141,33 @@ log "cleanly rebuild coatjava" $src_dir/build-coatjava.sh --clean $src_dir/build-coatjava.sh -# deploy locally; no need to `clean deploy`, since we have already cleaned and re-built -log "local deployment of coatjava version $ver_deploy" -pom_files=( - $src_dir/common-tools/coat-libs/pom.xml - $src_dir/reconstruction/pom.xml -) -for pom_file in ${pom_files[@]}; do - mvn deploy -Dmaven.test.skip=true -f $pom_file -done +# deploy locally; no need to `clean deploy`, since we have already cleaned and re-built. +# +# Post-merge (T19), the project is a single root POM that produces: +# - target/coatjava-.jar (primary thin jar; NOT deployed) +# - target/coatjava--coat-libs.jar (shaded uber-jar, attached via +# maven-shade-plugin classifier) +# - target/.flattened-pom.xml (clean, external-deps-only POM +# from flatten-maven-plugin) +# +# The default `mvn deploy` lifecycle is suppressed in the root POM (see +# maven-deploy-plugin true) because it would publish the wrong +# GAV (org.jlab.coat:coatjava with a `coat-libs` classifier) rather than the +# freestanding GAV org.jlab.coat:coat-libs that downstream consumers depend +# on. Instead, we explicitly invoke `deploy:deploy-file` to publish the +# shaded jar under the correct standalone artifactId, with the flattened POM +# as its published .pom. +log "local deployment of coat-libs version $ver_deploy" +mvn deploy:deploy-file \ + -Dmaven.test.skip=true \ + -DrepositoryId=coat-libs \ + -Durl=file://$deploy_dir \ + -DgroupId=org.jlab.coat \ + -DartifactId=coat-libs \ + -Dversion=$ver_deploy \ + -Dpackaging=jar \ + -Dfile=$src_dir/target/coatjava-${ver_deploy}-coat-libs.jar \ + -DgeneratePom=true # make a tarball too deploy_tarball=coatjava-${ver_deploy}.tar.gz @@ -168,7 +187,6 @@ print_deployment if ! $dry_run; then log "now deploying..." scp -r $deploy_dir/org/jlab/coat/coat-libs/* $deployment_user@$deployment_host:/group/clas/www/clasweb/html/clas12maven/org/jlab/coat/coat-libs/. - scp -r $deploy_dir/org/jlab/clas12/detector/* $deployment_user@$deployment_host:/group/clas/www/clasweb/html/clas12maven/org/jlab/clas12/detector/. scp $deploy_tarball $deployment_user@$deployment_host:/group/clas/www/clasweb/html/clas12offline/distribution/coatjava/. log "...done" else diff --git a/libexec/build-javadocs.sh b/libexec/build-javadocs.sh index 3cea6aca2a..8d972bd61f 100755 --- a/libexec/build-javadocs.sh +++ b/libexec/build-javadocs.sh @@ -1,5 +1,4 @@ #!/usr/bin/env bash # analyze maven dependencies -# NOTE: skips `coat-libs`, the shaded JAR module set -euo pipefail -mvn javadoc:aggregate -pl '!org.jlab.coat:coat-libs' --no-transfer-progress +mvn javadoc:javadoc --no-transfer-progress diff --git a/libexec/version-bump.sh b/libexec/version-bump.sh index 3d610dd992..2b0cff7ef5 100755 --- a/libexec/version-bump.sh +++ b/libexec/version-bump.sh @@ -4,6 +4,6 @@ set -euo pipefail ver=$1 echo ">>> bumping version number to: $ver" pom_file=$(cd $(dirname ${BASH_SOURCE[0]:-$0})/.. && pwd -P)/pom.xml -mvn versions:set -DnewVersion=$ver -DprocessAllModules=true -f $pom_file -mvn versions:commit -DprocessAllModules=true -f $pom_file +mvn versions:set -DnewVersion=$ver -f $pom_file +mvn versions:commit -f $pom_file echo ">>> bumped version number to: $ver" diff --git a/pom.xml b/pom.xml index 7b2cf7486b..a9f2b6c80c 100644 --- a/pom.xml +++ b/pom.xml @@ -2,10 +2,18 @@ 4.0.0 - org.jlab.clas + + + org.jlab.coat coatjava 13.8.4-SNAPSHOT - pom + jar UTF-8 @@ -13,11 +21,6 @@ file://myLocalMvnRepo - - common-tools - reconstruction - - clas12maven @@ -29,6 +32,13 @@ + + + ${project.artifactId} + ${coat.deployment.url} + + + skip-tests @@ -247,6 +257,214 @@ + + + + + + + org.jlab.coda + jevio + jar-with-dependencies + + + org.jlab.coda + et + 14.0 + + + org.jlab.coda + jclara + + + org.jlab.coda + jtools + 2.2 + + + org.jlab.coda + xmsg + 2.3 + + + org.jlab.jnp + jnp-hipo + + + org.jlab.jnp + jnp-hipo4 + + + org.jlab.ccdbrcdb + ccdbrcdb + + + + + gov.nist.math + jama + + + org.jama + jamapack + 1.0 + + + org.jlab.plugins + jMath + 1.0 + + + org.jlab.plugins + trackfitter + 1.0 + + + org.apache.commons + commons-math3 + + + org.apache.commons + commons-lang3 + + + org.apache.commons + commons-text + 1.15.0 + + + org.ejml + ejml-simple + + + org.freehep + jminuit + + + java3d + vecmath + 1.3.1 + + + + + j4ml + j4ml-neuroph + + + j4ml + j4ml-data + + + j4ml + j4ml-clas12 + + + ai.djl + api + + + + ai.djl + model-zoo + runtime + + + ai.djl.pytorch + pytorch-model-zoo + runtime + + + ai.djl.pytorch + pytorch-engine + runtime + + + ai.djl.pytorch + pytorch-native-cpu + linux-x86_64 + runtime + + + ai.djl.pytorch + pytorch-jni + runtime + + + + + org.jlab + groot + + + org.openjfx + javafx-base + linux + + + org.openjfx + javafx-graphics + linux + + + org.openjfx + javafx-fxml + linux + + + de.erichseifert + vectorgraphics2d + 1.0 + + + + + cnuphys + f2jutil + 1.0 + + + + + net.objecthunter + exp4j + + + org.json + json + + + org.yaml + snakeyaml + + + org.slf4j + slf4j-api + + + jakarta.annotation + jakarta.annotation-api + + + + + junit + junit + + + + @@ -259,9 +477,27 @@ + + + + src/main/resources + true + + **/pom.properties + + + + src/main/resources + false + + **/pom.properties + + + + - + @@ -284,14 +520,6 @@ UTF-8 none - - - aggregate - - aggregate - - - @@ -313,7 +541,7 @@ - + org.apache.maven.plugins maven-jar-plugin @@ -338,7 +566,29 @@ - + + + org.apache.maven.plugins + maven-surefire-plugin + 3.5.3 + + ${project.build.directory}/surefire-cwd + + + + org.apache.maven.plugins maven-dependency-plugin @@ -355,14 +605,37 @@ true + ai.djl:model-zoo ai.djl.pytorch:pytorch-model-zoo ai.djl.pytorch:pytorch-engine ai.djl.pytorch:pytorch-native-cpu ai.djl.pytorch:pytorch-jni + + de.erichseifert:vectorgraphics2d + net.objecthunter:exp4j + org.jama:jamapack + org.jlab.plugins:jMath + + copy-djl-runtime-jars + package + + copy-dependencies + + + ${project.build.directory}/lib/services + ai.djl + + @@ -421,43 +694,234 @@ + + + org.apache.maven.plugins + maven-shade-plugin + 3.6.2 + + + shade-coat-libs + package + + shade + + + + false + + true + coat-libs + + + + org.jlab.coda:jclara + + org.jacoco + + ai.djl:* + ai.djl.pytorch:* + + net.java.dev.jna:jna + org.apache.commons:commons-compress + commons-codec:commons-codec + commons-io:commons-io + jakarta.annotation:jakarta.annotation-api + + + + + *:* + + + META-INF/*.SF + META-INF/*.DSA + META-INF/*.RSA + + META-INF/maven/** + + module-info.class + + .DS_Store + .classpath + .factorypath + .project + .settings + + + + + ${project.groupId}:${project.artifactId} + + org/jlab/rec/ahdc/** + org/jlab/rec/ai/** + org/jlab/rec/alert/** + org/jlab/rec/atof/** + org/jlab/rec/band/** + org/jlab/rec/cnd/** + org/jlab/rec/ctof/** + org/jlab/rec/cvt/** + org/jlab/rec/dc/** + org/jlab/rec/eb/** + org/jlab/rec/fmt/** + org/jlab/rec/ft/** + org/jlab/rec/ftof/** + org/jlab/rec/htcc/** + org/jlab/rec/mucal/** + org/jlab/rec/muhd/** + org/jlab/rec/muvt/** + org/jlab/rec/rich/** + org/jlab/rec/rtpc/** + org/jlab/rec/tof/** + + org/jlab/service/ahdc/** + org/jlab/service/ai/** + org/jlab/service/alert/** + org/jlab/service/atof/** + org/jlab/service/band/** + org/jlab/service/bg/** + org/jlab/service/cnd/** + org/jlab/service/ctof/** + org/jlab/service/dc/** + org/jlab/service/eb/** + org/jlab/service/ec/** + org/jlab/service/fmt/** + org/jlab/service/ftof/** + org/jlab/service/htcc/** + org/jlab/service/ltcc/** + org/jlab/service/mc/** + org/jlab/service/mltn/** + org/jlab/service/postproc/** + org/jlab/service/raster/** + org/jlab/service/recoil/** + org/jlab/service/rich/** + org/jlab/service/rtpc/** + org/jlab/service/swaps/** + org/jlab/service/swim/** + org/jlab/service/uber/** + org/jlab/service/urwt/** + + org/jlab/display/** + org/jlab/calibration/** + + + + + + + + coat-libs + ${project.version} + coat-libs + ${project.version} + ${project.groupId} + + + + + + + + + + + org.codehaus.mojo + flatten-maven-plugin + 1.7.3 + + fatjar + + + + flatten + package + + flatten + + + + + + + + org.apache.maven.plugins + maven-deploy-plugin + 3.1.4 + + + + default-deploy + + true + + + + + - - - - - org.codehaus.mojo - flatten-maven-plugin - 1.7.3 - - fatjar - - - - flatten - package - - flatten - - - - - - - - org.apache.maven.plugins - maven-deploy-plugin - 3.1.4 - - - ${project.build.directory}/.flattened-pom.xml - - - + + diff --git a/reconstruction/ai/pom.xml b/reconstruction/ai/pom.xml deleted file mode 100644 index 4bebb2c65c..0000000000 --- a/reconstruction/ai/pom.xml +++ /dev/null @@ -1,43 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-ai - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - - ai.djl - api - - - - - diff --git a/reconstruction/alert/pom.xml b/reconstruction/alert/pom.xml deleted file mode 100644 index 69c0e1a864..0000000000 --- a/reconstruction/alert/pom.xml +++ /dev/null @@ -1,148 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-alert - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - gov.nist.math - jama - - - org.apache.commons - commons-math3 - - - org.apache.commons - commons-lang3 - compile - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - compile - - - org.jlab.clas - clas-analysis - 13.8.4-SNAPSHOT - test - - - org.jlab.clas - clas-tracking - 13.8.4-SNAPSHOT - compile - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - compile - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - compile - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - compile - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - compile - - - org.jlab.clas - swim-tools - 13.8.4-SNAPSHOT - compile - - - junit - junit - - - ai.djl - api - - - - - - ai.djl - model-zoo - runtime - - - - ai.djl.pytorch - pytorch-model-zoo - runtime - - - - ai.djl.pytorch - pytorch-engine - runtime - - - ai.djl.pytorch - pytorch-native-cpu - linux-x86_64 - runtime - - - ai.djl.pytorch - pytorch-jni - runtime - - - - - - - - org.apache.maven.plugins - maven-dependency-plugin - 3.10.0 - - - copy-dependencies - package - - copy-dependencies - - - ${project.build.directory}/lib/services - ai.djl - - - - - - - - diff --git a/reconstruction/band/pom.xml b/reconstruction/band/pom.xml deleted file mode 100644 index a985e8bcd6..0000000000 --- a/reconstruction/band/pom.xml +++ /dev/null @@ -1,39 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-band - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/bg/pom.xml b/reconstruction/bg/pom.xml deleted file mode 100644 index 3f862882d7..0000000000 --- a/reconstruction/bg/pom.xml +++ /dev/null @@ -1,38 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-bg - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-analysis - 13.8.4-SNAPSHOT - - - - - diff --git a/reconstruction/calib/pom.xml b/reconstruction/calib/pom.xml deleted file mode 100644 index 8e800e62f9..0000000000 --- a/reconstruction/calib/pom.xml +++ /dev/null @@ -1,39 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-calib - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/cnd/pom.xml b/reconstruction/cnd/pom.xml deleted file mode 100644 index 13ec3a10a4..0000000000 --- a/reconstruction/cnd/pom.xml +++ /dev/null @@ -1,49 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-cnd - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab.clas12.detector - clas12detector-cvt - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/cvt/pom.xml b/reconstruction/cvt/pom.xml deleted file mode 100644 index 258c6ed025..0000000000 --- a/reconstruction/cvt/pom.xml +++ /dev/null @@ -1,100 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-cvt - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - java3d - vecmath - 1.3.1 - - - org.jlab - groot - - - cnuphys - magfield - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-jcsg - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-analysis - 13.8.4-SNAPSHOT - test - - - org.jlab.clas - clas-tracking - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - org.jlab.clas - swim-tools - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-eb - 13.8.4-SNAPSHOT - test - jar - - - org.jlab.plugins - trackfitter - 1.0 - - - junit - junit - - - - diff --git a/reconstruction/dc/pom.xml b/reconstruction/dc/pom.xml deleted file mode 100644 index 2724d7d10b..0000000000 --- a/reconstruction/dc/pom.xml +++ /dev/null @@ -1,116 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-dc - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab.jnp - jnp-hipo - - - org.jlab - groot - - - gov.nist.math - jama - - - org.apache.commons - commons-math3 - - - cnuphys - magfield - 13.8.4-SNAPSHOT - test - - - org.jlab.clas - clas-tracking - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-ai - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-jcsg - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-analysis - 13.8.4-SNAPSHOT - test - - - org.jlab.clas - clas-math - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - cnuphys - snr - 13.8.4-SNAPSHOT - - - org.jlab.plugins - trackfitter - 1.0 - - - org.jlab.clas - swim-tools - 13.8.4-SNAPSHOT - - - junit - junit - - - - diff --git a/reconstruction/eb/pom.xml b/reconstruction/eb/pom.xml deleted file mode 100644 index ddcb8c21fe..0000000000 --- a/reconstruction/eb/pom.xml +++ /dev/null @@ -1,100 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-eb - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab.jnp - jnp-hipo - - - cnuphys - magfield - 13.8.4-SNAPSHOT - test - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-analysis - 13.8.4-SNAPSHOT - test - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - org.jlab.clas - swim-tools - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-dc - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-ec - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-tof - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-htcc - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-ltcc - 13.8.4-SNAPSHOT - - - junit - junit - - - - - diff --git a/reconstruction/ec/pom.xml b/reconstruction/ec/pom.xml deleted file mode 100644 index aedc1a47e5..0000000000 --- a/reconstruction/ec/pom.xml +++ /dev/null @@ -1,63 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-ec - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab - groot - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-analysis - 13.8.4-SNAPSHOT - test - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - junit - junit - - - - diff --git a/reconstruction/fmt/pom.xml b/reconstruction/fmt/pom.xml deleted file mode 100644 index 633fbb24e2..0000000000 --- a/reconstruction/fmt/pom.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-fmt - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab.jnp - jnp-hipo - - - org.jlab.clas - swim-tools - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/ft/pom.xml b/reconstruction/ft/pom.xml deleted file mode 100644 index 77ca4bc8ad..0000000000 --- a/reconstruction/ft/pom.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-ft - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab - groot - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/htcc/pom.xml b/reconstruction/htcc/pom.xml deleted file mode 100644 index 6269c5b7e8..0000000000 --- a/reconstruction/htcc/pom.xml +++ /dev/null @@ -1,39 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-htcc - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/htcc/src/main/java/org/jlab/rec/htcc/.gitignore b/reconstruction/htcc/src/main/java/org/jlab/rec/htcc/.gitignore deleted file mode 100644 index a966e3ae6d..0000000000 --- a/reconstruction/htcc/src/main/java/org/jlab/rec/htcc/.gitignore +++ /dev/null @@ -1,9 +0,0 @@ -/Geom$Ellipse.class -/Geom$FindIntersect.class -/Geom$Rotate3D.class -/Geom$line.class -/Geom.class -/HTCCCluster.class -/HTCCReconstruction$ReconstructionParameters.class -/HTCCReconstruction.class -/package-info.class diff --git a/reconstruction/htcc/src/main/java/org/jlab/service/htcc/.gitignore b/reconstruction/htcc/src/main/java/org/jlab/service/htcc/.gitignore deleted file mode 100644 index 01852213a5..0000000000 --- a/reconstruction/htcc/src/main/java/org/jlab/service/htcc/.gitignore +++ /dev/null @@ -1 +0,0 @@ -/HTCCReconstructionService.class diff --git a/reconstruction/ltcc/pom.xml b/reconstruction/ltcc/pom.xml deleted file mode 100644 index b56d01d75e..0000000000 --- a/reconstruction/ltcc/pom.xml +++ /dev/null @@ -1,57 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-ltcc - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.openjfx - javafx-base - linux - - - jakarta.annotation - jakarta.annotation-api - - - org.jlab - groot - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/mc/pom.xml b/reconstruction/mc/pom.xml deleted file mode 100644 index c5be978515..0000000000 --- a/reconstruction/mc/pom.xml +++ /dev/null @@ -1,39 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-mc - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/mltn/pom.xml b/reconstruction/mltn/pom.xml deleted file mode 100644 index 2fe2256f97..0000000000 --- a/reconstruction/mltn/pom.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-mltn - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - - org.jlab.jnp - jnp-hipo4 - - - - j4ml - j4ml-neuroph - - - - j4ml - j4ml-data - - - - j4ml - j4ml-clas12 - - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - - - diff --git a/reconstruction/mu/pom.xml b/reconstruction/mu/pom.xml deleted file mode 100644 index 79a1b3bddf..0000000000 --- a/reconstruction/mu/pom.xml +++ /dev/null @@ -1,67 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-mu - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab.jnp - jnp-hipo - - - org.jlab - groot - - - org.jlab.clas - swim-tools - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-jcsg - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/pom.xml b/reconstruction/pom.xml deleted file mode 100644 index 0befecee4b..0000000000 --- a/reconstruction/pom.xml +++ /dev/null @@ -1,71 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - pom - - - org.jlab.clas - coatjava - 13.8.4-SNAPSHOT - - - - ai - dc - tof - cvt - ft - ec - ltcc - htcc - cnd - rich - fmt - eb - band - mc - rtpc - mltn - swaps - raster - vtx - urwt - alert - bg - postproc - recoil - calib - uber - mu - - - - - - - org.apache.maven.plugins - maven-deploy-plugin - - - org.codehaus.mojo - flatten-maven-plugin - - - - - - - ${project.artifactId} - ${coat.deployment.url} - - - - diff --git a/reconstruction/postproc/pom.xml b/reconstruction/postproc/pom.xml deleted file mode 100644 index dfb46c0607..0000000000 --- a/reconstruction/postproc/pom.xml +++ /dev/null @@ -1,38 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-postproc - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-analysis - 13.8.4-SNAPSHOT - - - - - diff --git a/reconstruction/raster/pom.xml b/reconstruction/raster/pom.xml deleted file mode 100644 index a0e997b026..0000000000 --- a/reconstruction/raster/pom.xml +++ /dev/null @@ -1,43 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-raster - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab - groot - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/recoil/pom.xml b/reconstruction/recoil/pom.xml deleted file mode 100644 index 7a8ed1c523..0000000000 --- a/reconstruction/recoil/pom.xml +++ /dev/null @@ -1,48 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-recoil - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab - groot - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-jcsg - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/rich/pom.xml b/reconstruction/rich/pom.xml deleted file mode 100644 index 5c81bdf09a..0000000000 --- a/reconstruction/rich/pom.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-rich - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.freehep - jminuit - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-jcsg - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/rtpc/pom.xml b/reconstruction/rtpc/pom.xml deleted file mode 100644 index 181992fc12..0000000000 --- a/reconstruction/rtpc/pom.xml +++ /dev/null @@ -1,59 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-rtpc - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - cnuphys - magfield - 13.8.4-SNAPSHOT - - - org.apache.commons - commons-math3 - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-tracking - 13.8.4-SNAPSHOT - compile - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/swaps/pom.xml b/reconstruction/swaps/pom.xml deleted file mode 100644 index 8de6b7310d..0000000000 --- a/reconstruction/swaps/pom.xml +++ /dev/null @@ -1,38 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-swaps - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - - - diff --git a/reconstruction/tof/pom.xml b/reconstruction/tof/pom.xml deleted file mode 100644 index 3ff73e323f..0000000000 --- a/reconstruction/tof/pom.xml +++ /dev/null @@ -1,62 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-tof - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - - org.jlab.clas - clas-jcsg - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-physics - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-utils - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - - - diff --git a/reconstruction/uber/pom.xml b/reconstruction/uber/pom.xml deleted file mode 100644 index f033ed8ff1..0000000000 --- a/reconstruction/uber/pom.xml +++ /dev/null @@ -1,114 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-uber - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - swim-tools - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-dc - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-ec - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-tof - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-htcc - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-ltcc - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-ft - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-cnd - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-band - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-cvt - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-raster - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-vtx - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-calib - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-rtpc - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-rich - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-eb - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-mltn - 13.8.4-SNAPSHOT - - - org.jlab.clas12.detector - clas12detector-fmt - 13.8.4-SNAPSHOT - - - - diff --git a/reconstruction/urwt/pom.xml b/reconstruction/urwt/pom.xml deleted file mode 100644 index a1a86403fe..0000000000 --- a/reconstruction/urwt/pom.xml +++ /dev/null @@ -1,48 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-urwt - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab - groot - - - org.jlab.clas - clas-detector - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-jcsg - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - clas12detector-urwt - diff --git a/reconstruction/vtx/pom.xml b/reconstruction/vtx/pom.xml deleted file mode 100644 index a787878ef4..0000000000 --- a/reconstruction/vtx/pom.xml +++ /dev/null @@ -1,45 +0,0 @@ - - - 4.0.0 - - org.jlab.clas12.detector - clas12detector-vtx - 13.8.4-SNAPSHOT - jar - - - org.jlab.clas12 - reconstruction - 13.8.4-SNAPSHOT - - - - - org.jlab.clas - swim-tools - 13.8.4-SNAPSHOT - jar - - - cnuphys - swimmer - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-reco - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-io - 13.8.4-SNAPSHOT - - - org.jlab.clas - clas-geometry - 13.8.4-SNAPSHOT - - - - diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AAdaptiveStopper.java b/src/main/java/cnuphys/adaptiveSwim/AAdaptiveStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AAdaptiveStopper.java rename to src/main/java/cnuphys/adaptiveSwim/AAdaptiveStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveCylinderStopper.java b/src/main/java/cnuphys/adaptiveSwim/AdaptiveCylinderStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveCylinderStopper.java rename to src/main/java/cnuphys/adaptiveSwim/AdaptiveCylinderStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveDefaultStopper.java b/src/main/java/cnuphys/adaptiveSwim/AdaptiveDefaultStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveDefaultStopper.java rename to src/main/java/cnuphys/adaptiveSwim/AdaptiveDefaultStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveLineStopper.java b/src/main/java/cnuphys/adaptiveSwim/AdaptiveLineStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveLineStopper.java rename to src/main/java/cnuphys/adaptiveSwim/AdaptiveLineStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptivePlaneStopper.java b/src/main/java/cnuphys/adaptiveSwim/AdaptivePlaneStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptivePlaneStopper.java rename to src/main/java/cnuphys/adaptiveSwim/AdaptivePlaneStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveRhoStopper.java b/src/main/java/cnuphys/adaptiveSwim/AdaptiveRhoStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveRhoStopper.java rename to src/main/java/cnuphys/adaptiveSwim/AdaptiveRhoStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveSStopper.java b/src/main/java/cnuphys/adaptiveSwim/AdaptiveSStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveSStopper.java rename to src/main/java/cnuphys/adaptiveSwim/AdaptiveSStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveSphereStopper.java b/src/main/java/cnuphys/adaptiveSwim/AdaptiveSphereStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveSphereStopper.java rename to src/main/java/cnuphys/adaptiveSwim/AdaptiveSphereStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveStepResult.java b/src/main/java/cnuphys/adaptiveSwim/AdaptiveStepResult.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveStepResult.java rename to src/main/java/cnuphys/adaptiveSwim/AdaptiveStepResult.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimException.java b/src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimException.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimException.java rename to src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimException.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimResult.java b/src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimResult.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimResult.java rename to src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimResult.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimUtilities.java b/src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimUtilities.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimUtilities.java rename to src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimUtilities.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimmer.java b/src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimmer.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimmer.java rename to src/main/java/cnuphys/adaptiveSwim/AdaptiveSwimmer.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveZStopper.java b/src/main/java/cnuphys/adaptiveSwim/AdaptiveZStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/AdaptiveZStopper.java rename to src/main/java/cnuphys/adaptiveSwim/AdaptiveZStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/ButcherAdvance.java b/src/main/java/cnuphys/adaptiveSwim/ButcherAdvance.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/ButcherAdvance.java rename to src/main/java/cnuphys/adaptiveSwim/ButcherAdvance.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/IAdaptiveAdvance.java b/src/main/java/cnuphys/adaptiveSwim/IAdaptiveAdvance.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/IAdaptiveAdvance.java rename to src/main/java/cnuphys/adaptiveSwim/IAdaptiveAdvance.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/IAdaptiveStopper.java b/src/main/java/cnuphys/adaptiveSwim/IAdaptiveStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/IAdaptiveStopper.java rename to src/main/java/cnuphys/adaptiveSwim/IAdaptiveStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/RK4HalfStepAdvance.java b/src/main/java/cnuphys/adaptiveSwim/RK4HalfStepAdvance.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/RK4HalfStepAdvance.java rename to src/main/java/cnuphys/adaptiveSwim/RK4HalfStepAdvance.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Constants.java b/src/main/java/cnuphys/adaptiveSwim/geometry/Constants.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Constants.java rename to src/main/java/cnuphys/adaptiveSwim/geometry/Constants.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Cylinder.java b/src/main/java/cnuphys/adaptiveSwim/geometry/Cylinder.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Cylinder.java rename to src/main/java/cnuphys/adaptiveSwim/geometry/Cylinder.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Line.java b/src/main/java/cnuphys/adaptiveSwim/geometry/Line.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Line.java rename to src/main/java/cnuphys/adaptiveSwim/geometry/Line.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Plane.java b/src/main/java/cnuphys/adaptiveSwim/geometry/Plane.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Plane.java rename to src/main/java/cnuphys/adaptiveSwim/geometry/Plane.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Point.java b/src/main/java/cnuphys/adaptiveSwim/geometry/Point.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Point.java rename to src/main/java/cnuphys/adaptiveSwim/geometry/Point.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Sphere.java b/src/main/java/cnuphys/adaptiveSwim/geometry/Sphere.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Sphere.java rename to src/main/java/cnuphys/adaptiveSwim/geometry/Sphere.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Vector.java b/src/main/java/cnuphys/adaptiveSwim/geometry/Vector.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/geometry/Vector.java rename to src/main/java/cnuphys/adaptiveSwim/geometry/Vector.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/AdaptiveBeamlineSwimTest.java b/src/main/java/cnuphys/adaptiveSwim/test/AdaptiveBeamlineSwimTest.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/AdaptiveBeamlineSwimTest.java rename to src/main/java/cnuphys/adaptiveSwim/test/AdaptiveBeamlineSwimTest.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/AdaptiveResultDiff.java b/src/main/java/cnuphys/adaptiveSwim/test/AdaptiveResultDiff.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/AdaptiveResultDiff.java rename to src/main/java/cnuphys/adaptiveSwim/test/AdaptiveResultDiff.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/AdaptiveSectorSwimTest.java b/src/main/java/cnuphys/adaptiveSwim/test/AdaptiveSectorSwimTest.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/AdaptiveSectorSwimTest.java rename to src/main/java/cnuphys/adaptiveSwim/test/AdaptiveSectorSwimTest.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/AdaptiveTests.java b/src/main/java/cnuphys/adaptiveSwim/test/AdaptiveTests.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/AdaptiveTests.java rename to src/main/java/cnuphys/adaptiveSwim/test/AdaptiveTests.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/InitialValues.java b/src/main/java/cnuphys/adaptiveSwim/test/InitialValues.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/InitialValues.java rename to src/main/java/cnuphys/adaptiveSwim/test/InitialValues.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/LineTestPlotGrid.java b/src/main/java/cnuphys/adaptiveSwim/test/LineTestPlotGrid.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/LineTestPlotGrid.java rename to src/main/java/cnuphys/adaptiveSwim/test/LineTestPlotGrid.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/ZTestPlotGrid.java b/src/main/java/cnuphys/adaptiveSwim/test/ZTestPlotGrid.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/adaptiveSwim/test/ZTestPlotGrid.java rename to src/main/java/cnuphys/adaptiveSwim/test/ZTestPlotGrid.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/AsciiReadSupport.java b/src/main/java/cnuphys/lund/AsciiReadSupport.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/AsciiReadSupport.java rename to src/main/java/cnuphys/lund/AsciiReadSupport.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/AsciiReader.java b/src/main/java/cnuphys/lund/AsciiReader.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/AsciiReader.java rename to src/main/java/cnuphys/lund/AsciiReader.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/DoubleFormat.java b/src/main/java/cnuphys/lund/DoubleFormat.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/DoubleFormat.java rename to src/main/java/cnuphys/lund/DoubleFormat.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/GeneratedParticleRecord.java b/src/main/java/cnuphys/lund/GeneratedParticleRecord.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/GeneratedParticleRecord.java rename to src/main/java/cnuphys/lund/GeneratedParticleRecord.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/HeaderRenderer.java b/src/main/java/cnuphys/lund/HeaderRenderer.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/HeaderRenderer.java rename to src/main/java/cnuphys/lund/HeaderRenderer.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/LundComboBox.java b/src/main/java/cnuphys/lund/LundComboBox.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/LundComboBox.java rename to src/main/java/cnuphys/lund/LundComboBox.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/LundFileSupport.java b/src/main/java/cnuphys/lund/LundFileSupport.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/LundFileSupport.java rename to src/main/java/cnuphys/lund/LundFileSupport.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/LundId.java b/src/main/java/cnuphys/lund/LundId.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/LundId.java rename to src/main/java/cnuphys/lund/LundId.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/LundStyle.java b/src/main/java/cnuphys/lund/LundStyle.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/LundStyle.java rename to src/main/java/cnuphys/lund/LundStyle.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/LundSupport.java b/src/main/java/cnuphys/lund/LundSupport.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/LundSupport.java rename to src/main/java/cnuphys/lund/LundSupport.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/LundTrackDialog.java b/src/main/java/cnuphys/lund/LundTrackDialog.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/LundTrackDialog.java rename to src/main/java/cnuphys/lund/LundTrackDialog.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/SimpleRenderer.java b/src/main/java/cnuphys/lund/SimpleRenderer.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/SimpleRenderer.java rename to src/main/java/cnuphys/lund/SimpleRenderer.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/SwimTrajectoryListener.java b/src/main/java/cnuphys/lund/SwimTrajectoryListener.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/SwimTrajectoryListener.java rename to src/main/java/cnuphys/lund/SwimTrajectoryListener.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/TrajectoryRowData.java b/src/main/java/cnuphys/lund/TrajectoryRowData.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/TrajectoryRowData.java rename to src/main/java/cnuphys/lund/TrajectoryRowData.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/TrajectoryTable.java b/src/main/java/cnuphys/lund/TrajectoryTable.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/TrajectoryTable.java rename to src/main/java/cnuphys/lund/TrajectoryTable.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/TrajectoryTableModel.java b/src/main/java/cnuphys/lund/TrajectoryTableModel.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/TrajectoryTableModel.java rename to src/main/java/cnuphys/lund/TrajectoryTableModel.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/X11Colors.java b/src/main/java/cnuphys/lund/X11Colors.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/lund/X11Colors.java rename to src/main/java/cnuphys/lund/X11Colors.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/AngularUnit.java b/src/main/java/cnuphys/magfield/AngularUnit.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/AngularUnit.java rename to src/main/java/cnuphys/magfield/AngularUnit.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/Cell2D.java b/src/main/java/cnuphys/magfield/Cell2D.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/Cell2D.java rename to src/main/java/cnuphys/magfield/Cell2D.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/Cell3D.java b/src/main/java/cnuphys/magfield/Cell3D.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/Cell3D.java rename to src/main/java/cnuphys/magfield/Cell3D.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/ColorScaleModel.java b/src/main/java/cnuphys/magfield/ColorScaleModel.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/ColorScaleModel.java rename to src/main/java/cnuphys/magfield/ColorScaleModel.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/Comparison.java b/src/main/java/cnuphys/magfield/Comparison.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/Comparison.java rename to src/main/java/cnuphys/magfield/Comparison.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/ComponentZoomer.java b/src/main/java/cnuphys/magfield/ComponentZoomer.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/ComponentZoomer.java rename to src/main/java/cnuphys/magfield/ComponentZoomer.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CompositeField.java b/src/main/java/cnuphys/magfield/CompositeField.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CompositeField.java rename to src/main/java/cnuphys/magfield/CompositeField.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CompositeProbe.java b/src/main/java/cnuphys/magfield/CompositeProbe.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CompositeProbe.java rename to src/main/java/cnuphys/magfield/CompositeProbe.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CoordinateSystem.java b/src/main/java/cnuphys/magfield/CoordinateSystem.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/CoordinateSystem.java rename to src/main/java/cnuphys/magfield/CoordinateSystem.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/FastMath.java b/src/main/java/cnuphys/magfield/FastMath.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/FastMath.java rename to src/main/java/cnuphys/magfield/FastMath.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/FieldProbe.java b/src/main/java/cnuphys/magfield/FieldProbe.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/FieldProbe.java rename to src/main/java/cnuphys/magfield/FieldProbe.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/FieldUnit.java b/src/main/java/cnuphys/magfield/FieldUnit.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/FieldUnit.java rename to src/main/java/cnuphys/magfield/FieldUnit.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/FloatVect.java b/src/main/java/cnuphys/magfield/FloatVect.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/FloatVect.java rename to src/main/java/cnuphys/magfield/FloatVect.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/GEMCCompare.java b/src/main/java/cnuphys/magfield/GEMCCompare.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/GEMCCompare.java rename to src/main/java/cnuphys/magfield/GEMCCompare.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/GridCoordinate.java b/src/main/java/cnuphys/magfield/GridCoordinate.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/GridCoordinate.java rename to src/main/java/cnuphys/magfield/GridCoordinate.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/IComponentZoomable.java b/src/main/java/cnuphys/magfield/IComponentZoomable.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/IComponentZoomable.java rename to src/main/java/cnuphys/magfield/IComponentZoomable.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/IField.java b/src/main/java/cnuphys/magfield/IField.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/IField.java rename to src/main/java/cnuphys/magfield/IField.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/IMagField.java b/src/main/java/cnuphys/magfield/IMagField.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/IMagField.java rename to src/main/java/cnuphys/magfield/IMagField.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/Icecore.java b/src/main/java/cnuphys/magfield/Icecore.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/Icecore.java rename to src/main/java/cnuphys/magfield/Icecore.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/LengthUnit.java b/src/main/java/cnuphys/magfield/LengthUnit.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/LengthUnit.java rename to src/main/java/cnuphys/magfield/LengthUnit.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MagTests.java b/src/main/java/cnuphys/magfield/MagTests.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MagTests.java rename to src/main/java/cnuphys/magfield/MagTests.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MagneticField.java b/src/main/java/cnuphys/magfield/MagneticField.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MagneticField.java rename to src/main/java/cnuphys/magfield/MagneticField.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MagneticFieldCanvas.java b/src/main/java/cnuphys/magfield/MagneticFieldCanvas.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MagneticFieldCanvas.java rename to src/main/java/cnuphys/magfield/MagneticFieldCanvas.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MagneticFieldChangeListener.java b/src/main/java/cnuphys/magfield/MagneticFieldChangeListener.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MagneticFieldChangeListener.java rename to src/main/java/cnuphys/magfield/MagneticFieldChangeListener.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MagneticFieldInitializationException.java b/src/main/java/cnuphys/magfield/MagneticFieldInitializationException.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MagneticFieldInitializationException.java rename to src/main/java/cnuphys/magfield/MagneticFieldInitializationException.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MagneticFields.java b/src/main/java/cnuphys/magfield/MagneticFields.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MagneticFields.java rename to src/main/java/cnuphys/magfield/MagneticFields.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MisplacedPanel.java b/src/main/java/cnuphys/magfield/MisplacedPanel.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/MisplacedPanel.java rename to src/main/java/cnuphys/magfield/MisplacedPanel.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/RotatedCompositeField.java b/src/main/java/cnuphys/magfield/RotatedCompositeField.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/RotatedCompositeField.java rename to src/main/java/cnuphys/magfield/RotatedCompositeField.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/RotatedCompositeProbe.java b/src/main/java/cnuphys/magfield/RotatedCompositeProbe.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/RotatedCompositeProbe.java rename to src/main/java/cnuphys/magfield/RotatedCompositeProbe.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/ScaleFieldPanel.java b/src/main/java/cnuphys/magfield/ScaleFieldPanel.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/ScaleFieldPanel.java rename to src/main/java/cnuphys/magfield/ScaleFieldPanel.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/Solenoid.java b/src/main/java/cnuphys/magfield/Solenoid.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/Solenoid.java rename to src/main/java/cnuphys/magfield/Solenoid.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/SolenoidProbe.java b/src/main/java/cnuphys/magfield/SolenoidProbe.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/SolenoidProbe.java rename to src/main/java/cnuphys/magfield/SolenoidProbe.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/StandardSolenoid.java b/src/main/java/cnuphys/magfield/StandardSolenoid.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/StandardSolenoid.java rename to src/main/java/cnuphys/magfield/StandardSolenoid.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/StandardSolenoidProbe.java b/src/main/java/cnuphys/magfield/StandardSolenoidProbe.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/StandardSolenoidProbe.java rename to src/main/java/cnuphys/magfield/StandardSolenoidProbe.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/TestData.java b/src/main/java/cnuphys/magfield/TestData.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/TestData.java rename to src/main/java/cnuphys/magfield/TestData.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/ToAscii.java b/src/main/java/cnuphys/magfield/ToAscii.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/ToAscii.java rename to src/main/java/cnuphys/magfield/ToAscii.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/Torus.java b/src/main/java/cnuphys/magfield/Torus.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/Torus.java rename to src/main/java/cnuphys/magfield/Torus.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/TorusProbe.java b/src/main/java/cnuphys/magfield/TorusProbe.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/TorusProbe.java rename to src/main/java/cnuphys/magfield/TorusProbe.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/TransverseSolenoid.java b/src/main/java/cnuphys/magfield/TransverseSolenoid.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/TransverseSolenoid.java rename to src/main/java/cnuphys/magfield/TransverseSolenoid.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/TransverseSolenoidProbe.java b/src/main/java/cnuphys/magfield/TransverseSolenoidProbe.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/TransverseSolenoidProbe.java rename to src/main/java/cnuphys/magfield/TransverseSolenoidProbe.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/ZeroProbe.java b/src/main/java/cnuphys/magfield/ZeroProbe.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/ZeroProbe.java rename to src/main/java/cnuphys/magfield/ZeroProbe.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/converter/AsciiReadSupport.java b/src/main/java/cnuphys/magfield/converter/AsciiReadSupport.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/converter/AsciiReadSupport.java rename to src/main/java/cnuphys/magfield/converter/AsciiReadSupport.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/converter/AsciiReader.java b/src/main/java/cnuphys/magfield/converter/AsciiReader.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/converter/AsciiReader.java rename to src/main/java/cnuphys/magfield/converter/AsciiReader.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/converter/Converter.java b/src/main/java/cnuphys/magfield/converter/Converter.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/converter/Converter.java rename to src/main/java/cnuphys/magfield/converter/Converter.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/converter/ConverterSolenoid.java b/src/main/java/cnuphys/magfield/converter/ConverterSolenoid.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/converter/ConverterSolenoid.java rename to src/main/java/cnuphys/magfield/converter/ConverterSolenoid.java diff --git a/common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/converter/ZFile.java b/src/main/java/cnuphys/magfield/converter/ZFile.java similarity index 100% rename from common-tools/cnuphys/magfield/src/main/java/cnuphys/magfield/converter/ZFile.java rename to src/main/java/cnuphys/magfield/converter/ZFile.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/ButcherTableau.java b/src/main/java/cnuphys/rk4/ButcherTableau.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/ButcherTableau.java rename to src/main/java/cnuphys/rk4/ButcherTableau.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/DefaultStopper.java b/src/main/java/cnuphys/rk4/DefaultStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/DefaultStopper.java rename to src/main/java/cnuphys/rk4/DefaultStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/IAdvance.java b/src/main/java/cnuphys/rk4/IAdvance.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/IAdvance.java rename to src/main/java/cnuphys/rk4/IAdvance.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/IDerivative.java b/src/main/java/cnuphys/rk4/IDerivative.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/IDerivative.java rename to src/main/java/cnuphys/rk4/IDerivative.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/IRkListener.java b/src/main/java/cnuphys/rk4/IRkListener.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/IRkListener.java rename to src/main/java/cnuphys/rk4/IRkListener.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/IStopper.java b/src/main/java/cnuphys/rk4/IStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/IStopper.java rename to src/main/java/cnuphys/rk4/IStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/RkTest.java b/src/main/java/cnuphys/rk4/RkTest.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/RkTest.java rename to src/main/java/cnuphys/rk4/RkTest.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/RungeKutta.java b/src/main/java/cnuphys/rk4/RungeKutta.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/RungeKutta.java rename to src/main/java/cnuphys/rk4/RungeKutta.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/RungeKuttaException.java b/src/main/java/cnuphys/rk4/RungeKuttaException.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/RungeKuttaException.java rename to src/main/java/cnuphys/rk4/RungeKuttaException.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/RungeKuttaZ.java b/src/main/java/cnuphys/rk4/RungeKuttaZ.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/rk4/RungeKuttaZ.java rename to src/main/java/cnuphys/rk4/RungeKuttaZ.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/Adjacency.java b/src/main/java/cnuphys/snr/Adjacency.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/Adjacency.java rename to src/main/java/cnuphys/snr/Adjacency.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/ExtendedWord.java b/src/main/java/cnuphys/snr/ExtendedWord.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/ExtendedWord.java rename to src/main/java/cnuphys/snr/ExtendedWord.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/NoiseReductionParameters.java b/src/main/java/cnuphys/snr/NoiseReductionParameters.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/NoiseReductionParameters.java rename to src/main/java/cnuphys/snr/NoiseReductionParameters.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/SNRAnalysisLevel.java b/src/main/java/cnuphys/snr/SNRAnalysisLevel.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/SNRAnalysisLevel.java rename to src/main/java/cnuphys/snr/SNRAnalysisLevel.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/SNRCluster.java b/src/main/java/cnuphys/snr/SNRCluster.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/SNRCluster.java rename to src/main/java/cnuphys/snr/SNRCluster.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/SNRClusterFinder.java b/src/main/java/cnuphys/snr/SNRClusterFinder.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/SNRClusterFinder.java rename to src/main/java/cnuphys/snr/SNRClusterFinder.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/SegmentStartList.java b/src/main/java/cnuphys/snr/SegmentStartList.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/SegmentStartList.java rename to src/main/java/cnuphys/snr/SegmentStartList.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/WireList.java b/src/main/java/cnuphys/snr/WireList.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/WireList.java rename to src/main/java/cnuphys/snr/WireList.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/clas12/Clas12Constants.java b/src/main/java/cnuphys/snr/clas12/Clas12Constants.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/clas12/Clas12Constants.java rename to src/main/java/cnuphys/snr/clas12/Clas12Constants.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/clas12/Clas12NoiseAnalysis.java b/src/main/java/cnuphys/snr/clas12/Clas12NoiseAnalysis.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/clas12/Clas12NoiseAnalysis.java rename to src/main/java/cnuphys/snr/clas12/Clas12NoiseAnalysis.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/clas12/Clas12NoiseResult.java b/src/main/java/cnuphys/snr/clas12/Clas12NoiseResult.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/clas12/Clas12NoiseResult.java rename to src/main/java/cnuphys/snr/clas12/Clas12NoiseResult.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/BasicStroke.java b/src/main/java/cnuphys/snr/test/BasicStroke.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/BasicStroke.java rename to src/main/java/cnuphys/snr/test/BasicStroke.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/ChamberTest.java b/src/main/java/cnuphys/snr/test/ChamberTest.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/ChamberTest.java rename to src/main/java/cnuphys/snr/test/ChamberTest.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/DetectorTest.java b/src/main/java/cnuphys/snr/test/DetectorTest.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/DetectorTest.java rename to src/main/java/cnuphys/snr/test/DetectorTest.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/HitTest.java b/src/main/java/cnuphys/snr/test/HitTest.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/HitTest.java rename to src/main/java/cnuphys/snr/test/HitTest.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/LineStyle.java b/src/main/java/cnuphys/snr/test/LineStyle.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/LineStyle.java rename to src/main/java/cnuphys/snr/test/LineStyle.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/NoiseTest.java b/src/main/java/cnuphys/snr/test/NoiseTest.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/NoiseTest.java rename to src/main/java/cnuphys/snr/test/NoiseTest.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/TestParameters.java b/src/main/java/cnuphys/snr/test/TestParameters.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/TestParameters.java rename to src/main/java/cnuphys/snr/test/TestParameters.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/TestSupport.java b/src/main/java/cnuphys/snr/test/TestSupport.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/TestSupport.java rename to src/main/java/cnuphys/snr/test/TestSupport.java diff --git a/common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/TrackTest.java b/src/main/java/cnuphys/snr/test/TrackTest.java similarity index 100% rename from common-tools/cnuphys/snr/src/main/java/cnuphys/snr/test/TrackTest.java rename to src/main/java/cnuphys/snr/test/TrackTest.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/AxesLimitsPanel.java b/src/main/java/cnuphys/splot/edit/AxesLimitsPanel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/AxesLimitsPanel.java rename to src/main/java/cnuphys/splot/edit/AxesLimitsPanel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/ButtonPanel.java b/src/main/java/cnuphys/splot/edit/ButtonPanel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/ButtonPanel.java rename to src/main/java/cnuphys/splot/edit/ButtonPanel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/ColorDialog.java b/src/main/java/cnuphys/splot/edit/ColorDialog.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/ColorDialog.java rename to src/main/java/cnuphys/splot/edit/ColorDialog.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/ColorLabel.java b/src/main/java/cnuphys/splot/edit/ColorLabel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/ColorLabel.java rename to src/main/java/cnuphys/splot/edit/ColorLabel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/ColorPanel.java b/src/main/java/cnuphys/splot/edit/ColorPanel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/ColorPanel.java rename to src/main/java/cnuphys/splot/edit/ColorPanel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/CurveDataModel.java b/src/main/java/cnuphys/splot/edit/CurveDataModel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/CurveDataModel.java rename to src/main/java/cnuphys/splot/edit/CurveDataModel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/CurveEditorDialog.java b/src/main/java/cnuphys/splot/edit/CurveEditorDialog.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/CurveEditorDialog.java rename to src/main/java/cnuphys/splot/edit/CurveEditorDialog.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/CurveEditorPanel.java b/src/main/java/cnuphys/splot/edit/CurveEditorPanel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/CurveEditorPanel.java rename to src/main/java/cnuphys/splot/edit/CurveEditorPanel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/CurveTable.java b/src/main/java/cnuphys/splot/edit/CurveTable.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/CurveTable.java rename to src/main/java/cnuphys/splot/edit/CurveTable.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/DataEditor.java b/src/main/java/cnuphys/splot/edit/DataEditor.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/DataEditor.java rename to src/main/java/cnuphys/splot/edit/DataEditor.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/DialogUtilities.java b/src/main/java/cnuphys/splot/edit/DialogUtilities.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/DialogUtilities.java rename to src/main/java/cnuphys/splot/edit/DialogUtilities.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/IColorChangeListener.java b/src/main/java/cnuphys/splot/edit/IColorChangeListener.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/IColorChangeListener.java rename to src/main/java/cnuphys/splot/edit/IColorChangeListener.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/OneAxisLimitsPanel.java b/src/main/java/cnuphys/splot/edit/OneAxisLimitsPanel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/OneAxisLimitsPanel.java rename to src/main/java/cnuphys/splot/edit/OneAxisLimitsPanel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/PlotPreferencesDialog.java b/src/main/java/cnuphys/splot/edit/PlotPreferencesDialog.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/PlotPreferencesDialog.java rename to src/main/java/cnuphys/splot/edit/PlotPreferencesDialog.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/SimpleDialog.java b/src/main/java/cnuphys/splot/edit/SimpleDialog.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/SimpleDialog.java rename to src/main/java/cnuphys/splot/edit/SimpleDialog.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/edit/VerticalFlowLayout.java b/src/main/java/cnuphys/splot/edit/VerticalFlowLayout.java similarity index 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common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/AnotherGaussian.java rename to src/main/java/cnuphys/splot/example/AnotherGaussian.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/ErfTest.java b/src/main/java/cnuphys/splot/example/ErfTest.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/ErfTest.java rename to src/main/java/cnuphys/splot/example/ErfTest.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/ErfcTest.java b/src/main/java/cnuphys/splot/example/ErfcTest.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/ErfcTest.java rename to src/main/java/cnuphys/splot/example/ErfcTest.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/Gaussians.java b/src/main/java/cnuphys/splot/example/Gaussians.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/Gaussians.java rename to src/main/java/cnuphys/splot/example/Gaussians.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/Grid.java b/src/main/java/cnuphys/splot/example/Grid.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/Grid.java rename to src/main/java/cnuphys/splot/example/Grid.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/GrowingHisto.java b/src/main/java/cnuphys/splot/example/GrowingHisto.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/GrowingHisto.java rename to src/main/java/cnuphys/splot/example/GrowingHisto.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/Histo.java b/src/main/java/cnuphys/splot/example/Histo.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/Histo.java rename to src/main/java/cnuphys/splot/example/Histo.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/Histo2D.java b/src/main/java/cnuphys/splot/example/Histo2D.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/Histo2D.java rename to src/main/java/cnuphys/splot/example/Histo2D.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/LineWithXAndYErrors.java b/src/main/java/cnuphys/splot/example/LineWithXAndYErrors.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/LineWithXAndYErrors.java rename to src/main/java/cnuphys/splot/example/LineWithXAndYErrors.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/MemoryUsageDialog.java b/src/main/java/cnuphys/splot/example/MemoryUsageDialog.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/MemoryUsageDialog.java rename to src/main/java/cnuphys/splot/example/MemoryUsageDialog.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/OneXThreeY.java b/src/main/java/cnuphys/splot/example/OneXThreeY.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/OneXThreeY.java rename to src/main/java/cnuphys/splot/example/OneXThreeY.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/Scatter.java b/src/main/java/cnuphys/splot/example/Scatter.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/Scatter.java rename to src/main/java/cnuphys/splot/example/Scatter.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/StraightLine.java b/src/main/java/cnuphys/splot/example/StraightLine.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/StraightLine.java rename to src/main/java/cnuphys/splot/example/StraightLine.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/StripChart.java b/src/main/java/cnuphys/splot/example/StripChart.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/StripChart.java rename to src/main/java/cnuphys/splot/example/StripChart.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/TripleGaussian.java b/src/main/java/cnuphys/splot/example/TripleGaussian.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/TripleGaussian.java rename to src/main/java/cnuphys/splot/example/TripleGaussian.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/TwoHisto.java b/src/main/java/cnuphys/splot/example/TwoHisto.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/TwoHisto.java rename to src/main/java/cnuphys/splot/example/TwoHisto.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/TwoLinesWithErrors.java b/src/main/java/cnuphys/splot/example/TwoLinesWithErrors.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/example/TwoLinesWithErrors.java rename to src/main/java/cnuphys/splot/example/TwoLinesWithErrors.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/ANonlinearFit.java b/src/main/java/cnuphys/splot/fit/ANonlinearFit.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/ANonlinearFit.java rename to src/main/java/cnuphys/splot/fit/ANonlinearFit.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/AltPolynomialFit.java b/src/main/java/cnuphys/splot/fit/AltPolynomialFit.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/AltPolynomialFit.java rename to src/main/java/cnuphys/splot/fit/AltPolynomialFit.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/CubicSpline.java b/src/main/java/cnuphys/splot/fit/CubicSpline.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/CubicSpline.java rename to src/main/java/cnuphys/splot/fit/CubicSpline.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/ErfFit.java b/src/main/java/cnuphys/splot/fit/ErfFit.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/ErfFit.java rename to src/main/java/cnuphys/splot/fit/ErfFit.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/ErfcFit.java b/src/main/java/cnuphys/splot/fit/ErfcFit.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/ErfcFit.java rename to src/main/java/cnuphys/splot/fit/ErfcFit.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FErf.java b/src/main/java/cnuphys/splot/fit/FErf.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FErf.java rename to src/main/java/cnuphys/splot/fit/FErf.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FErfc.java b/src/main/java/cnuphys/splot/fit/FErfc.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FErfc.java rename to src/main/java/cnuphys/splot/fit/FErfc.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FGaussPoly.java b/src/main/java/cnuphys/splot/fit/FGaussPoly.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FGaussPoly.java rename to src/main/java/cnuphys/splot/fit/FGaussPoly.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FGaussian.java b/src/main/java/cnuphys/splot/fit/FGaussian.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FGaussian.java rename to src/main/java/cnuphys/splot/fit/FGaussian.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FPoly.java b/src/main/java/cnuphys/splot/fit/FPoly.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FPoly.java rename to src/main/java/cnuphys/splot/fit/FPoly.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/Fit.java b/src/main/java/cnuphys/splot/fit/Fit.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/Fit.java rename to src/main/java/cnuphys/splot/fit/Fit.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FitEditorPanel.java b/src/main/java/cnuphys/splot/fit/FitEditorPanel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FitEditorPanel.java rename to src/main/java/cnuphys/splot/fit/FitEditorPanel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FitHold.java b/src/main/java/cnuphys/splot/fit/FitHold.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FitHold.java rename to src/main/java/cnuphys/splot/fit/FitHold.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FitType.java b/src/main/java/cnuphys/splot/fit/FitType.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FitType.java rename to src/main/java/cnuphys/splot/fit/FitType.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FitUtilities.java b/src/main/java/cnuphys/splot/fit/FitUtilities.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/FitUtilities.java rename to src/main/java/cnuphys/splot/fit/FitUtilities.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/GaussianFit.java b/src/main/java/cnuphys/splot/fit/GaussianFit.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/GaussianFit.java rename to src/main/java/cnuphys/splot/fit/GaussianFit.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/IValueGetter.java b/src/main/java/cnuphys/splot/fit/IValueGetter.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/IValueGetter.java rename to src/main/java/cnuphys/splot/fit/IValueGetter.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/LineFit.java b/src/main/java/cnuphys/splot/fit/LineFit.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/LineFit.java rename to src/main/java/cnuphys/splot/fit/LineFit.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/LinearExyFit.java b/src/main/java/cnuphys/splot/fit/LinearExyFit.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/LinearExyFit.java rename to src/main/java/cnuphys/splot/fit/LinearExyFit.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/PolyAndGaussianFit.java b/src/main/java/cnuphys/splot/fit/PolyAndGaussianFit.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/PolyAndGaussianFit.java rename to src/main/java/cnuphys/splot/fit/PolyAndGaussianFit.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/PolyFit.java b/src/main/java/cnuphys/splot/fit/PolyFit.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/PolyFit.java rename to src/main/java/cnuphys/splot/fit/PolyFit.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/Polynomial.java b/src/main/java/cnuphys/splot/fit/Polynomial.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/fit/Polynomial.java rename to src/main/java/cnuphys/splot/fit/Polynomial.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataChangeListener.java b/src/main/java/cnuphys/splot/pdata/DataChangeListener.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataChangeListener.java rename to src/main/java/cnuphys/splot/pdata/DataChangeListener.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataColumn.java b/src/main/java/cnuphys/splot/pdata/DataColumn.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataColumn.java rename to src/main/java/cnuphys/splot/pdata/DataColumn.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataColumnType.java b/src/main/java/cnuphys/splot/pdata/DataColumnType.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataColumnType.java rename to src/main/java/cnuphys/splot/pdata/DataColumnType.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataSet.java b/src/main/java/cnuphys/splot/pdata/DataSet.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataSet.java rename to src/main/java/cnuphys/splot/pdata/DataSet.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataSetException.java b/src/main/java/cnuphys/splot/pdata/DataSetException.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataSetException.java rename to src/main/java/cnuphys/splot/pdata/DataSetException.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataSetType.java b/src/main/java/cnuphys/splot/pdata/DataSetType.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataSetType.java rename to src/main/java/cnuphys/splot/pdata/DataSetType.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataTable.java b/src/main/java/cnuphys/splot/pdata/DataTable.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/DataTable.java rename to src/main/java/cnuphys/splot/pdata/DataTable.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/GrowableArray.java b/src/main/java/cnuphys/splot/pdata/GrowableArray.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/GrowableArray.java rename to src/main/java/cnuphys/splot/pdata/GrowableArray.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/Histo2DData.java b/src/main/java/cnuphys/splot/pdata/Histo2DData.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/Histo2DData.java rename to src/main/java/cnuphys/splot/pdata/Histo2DData.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/HistoData.java b/src/main/java/cnuphys/splot/pdata/HistoData.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/HistoData.java rename to src/main/java/cnuphys/splot/pdata/HistoData.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/NiceScale.java b/src/main/java/cnuphys/splot/pdata/NiceScale.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/NiceScale.java rename to src/main/java/cnuphys/splot/pdata/NiceScale.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/StripData.java b/src/main/java/cnuphys/splot/pdata/StripData.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/pdata/StripData.java rename to src/main/java/cnuphys/splot/pdata/StripData.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/APreferencePanel.java b/src/main/java/cnuphys/splot/plot/APreferencePanel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/APreferencePanel.java rename to src/main/java/cnuphys/splot/plot/APreferencePanel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/ColorScaleModel.java b/src/main/java/cnuphys/splot/plot/ColorScaleModel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/ColorScaleModel.java rename to src/main/java/cnuphys/splot/plot/ColorScaleModel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/CommonBorder.java b/src/main/java/cnuphys/splot/plot/CommonBorder.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/CommonBorder.java rename to src/main/java/cnuphys/splot/plot/CommonBorder.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/CurveDrawer.java b/src/main/java/cnuphys/splot/plot/CurveDrawer.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/CurveDrawer.java rename to src/main/java/cnuphys/splot/plot/CurveDrawer.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/DataDrawer.java b/src/main/java/cnuphys/splot/plot/DataDrawer.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/DataDrawer.java rename to src/main/java/cnuphys/splot/plot/DataDrawer.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/DoubleFormat.java b/src/main/java/cnuphys/splot/plot/DoubleFormat.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/DoubleFormat.java rename to src/main/java/cnuphys/splot/plot/DoubleFormat.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/Draggable.java b/src/main/java/cnuphys/splot/plot/Draggable.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/Draggable.java rename to src/main/java/cnuphys/splot/plot/Draggable.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/DraggableRectangle.java b/src/main/java/cnuphys/splot/plot/DraggableRectangle.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/DraggableRectangle.java rename to src/main/java/cnuphys/splot/plot/DraggableRectangle.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/Environment.java b/src/main/java/cnuphys/splot/plot/Environment.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/Environment.java rename to src/main/java/cnuphys/splot/plot/Environment.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/ExtraText.java b/src/main/java/cnuphys/splot/plot/ExtraText.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/ExtraText.java rename to src/main/java/cnuphys/splot/plot/ExtraText.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/FloatingLabel.java b/src/main/java/cnuphys/splot/plot/FloatingLabel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/FloatingLabel.java rename to src/main/java/cnuphys/splot/plot/FloatingLabel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/GeneralPlotParamPanel.java b/src/main/java/cnuphys/splot/plot/GeneralPlotParamPanel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/GeneralPlotParamPanel.java rename to src/main/java/cnuphys/splot/plot/GeneralPlotParamPanel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/Gradient.java b/src/main/java/cnuphys/splot/plot/Gradient.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/Gradient.java rename to src/main/java/cnuphys/splot/plot/Gradient.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/GraphicsUtilities.java b/src/main/java/cnuphys/splot/plot/GraphicsUtilities.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/GraphicsUtilities.java rename to src/main/java/cnuphys/splot/plot/GraphicsUtilities.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/HorizontalLine.java b/src/main/java/cnuphys/splot/plot/HorizontalLine.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/HorizontalLine.java rename to src/main/java/cnuphys/splot/plot/HorizontalLine.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/ImageManager.java b/src/main/java/cnuphys/splot/plot/ImageManager.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/ImageManager.java rename to src/main/java/cnuphys/splot/plot/ImageManager.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/Legend.java b/src/main/java/cnuphys/splot/plot/Legend.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/Legend.java rename to src/main/java/cnuphys/splot/plot/Legend.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/LimitsMethod.java b/src/main/java/cnuphys/splot/plot/LimitsMethod.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/LimitsMethod.java rename to src/main/java/cnuphys/splot/plot/LimitsMethod.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotCanvas.java b/src/main/java/cnuphys/splot/plot/PlotCanvas.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotCanvas.java rename to src/main/java/cnuphys/splot/plot/PlotCanvas.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotGrid.java b/src/main/java/cnuphys/splot/plot/PlotGrid.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotGrid.java rename to src/main/java/cnuphys/splot/plot/PlotGrid.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotGridDialog.java b/src/main/java/cnuphys/splot/plot/PlotGridDialog.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotGridDialog.java rename to src/main/java/cnuphys/splot/plot/PlotGridDialog.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotLine.java b/src/main/java/cnuphys/splot/plot/PlotLine.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotLine.java rename to src/main/java/cnuphys/splot/plot/PlotLine.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotPanel.java b/src/main/java/cnuphys/splot/plot/PlotPanel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotPanel.java rename to src/main/java/cnuphys/splot/plot/PlotPanel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotParameters.java b/src/main/java/cnuphys/splot/plot/PlotParameters.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotParameters.java rename to src/main/java/cnuphys/splot/plot/PlotParameters.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotPopupMenu.java b/src/main/java/cnuphys/splot/plot/PlotPopupMenu.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotPopupMenu.java rename to src/main/java/cnuphys/splot/plot/PlotPopupMenu.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotTicks.java b/src/main/java/cnuphys/splot/plot/PlotTicks.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PlotTicks.java rename to src/main/java/cnuphys/splot/plot/PlotTicks.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PrintUtilities.java b/src/main/java/cnuphys/splot/plot/PrintUtilities.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/PrintUtilities.java rename to src/main/java/cnuphys/splot/plot/PrintUtilities.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/SplotMenus.java b/src/main/java/cnuphys/splot/plot/SplotMenus.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/SplotMenus.java rename to src/main/java/cnuphys/splot/plot/SplotMenus.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/StripChartPanel.java b/src/main/java/cnuphys/splot/plot/StripChartPanel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/StripChartPanel.java rename to src/main/java/cnuphys/splot/plot/StripChartPanel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/TextFieldSlider.java b/src/main/java/cnuphys/splot/plot/TextFieldSlider.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/TextFieldSlider.java rename to src/main/java/cnuphys/splot/plot/TextFieldSlider.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/UnicodeSupport.java b/src/main/java/cnuphys/splot/plot/UnicodeSupport.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/UnicodeSupport.java rename to src/main/java/cnuphys/splot/plot/UnicodeSupport.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/VerticalLabelUI.java b/src/main/java/cnuphys/splot/plot/VerticalLabelUI.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/VerticalLabelUI.java rename to src/main/java/cnuphys/splot/plot/VerticalLabelUI.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/VerticalLine.java b/src/main/java/cnuphys/splot/plot/VerticalLine.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/VerticalLine.java rename to src/main/java/cnuphys/splot/plot/VerticalLine.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/X11Colors.java b/src/main/java/cnuphys/splot/plot/X11Colors.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/plot/X11Colors.java rename to src/main/java/cnuphys/splot/plot/X11Colors.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/rubberband/IRubberbanded.java b/src/main/java/cnuphys/splot/rubberband/IRubberbanded.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/rubberband/IRubberbanded.java rename to src/main/java/cnuphys/splot/rubberband/IRubberbanded.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/rubberband/Rubberband.java b/src/main/java/cnuphys/splot/rubberband/Rubberband.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/rubberband/Rubberband.java rename to src/main/java/cnuphys/splot/rubberband/Rubberband.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/EnumComboBox.java b/src/main/java/cnuphys/splot/style/EnumComboBox.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/EnumComboBox.java rename to src/main/java/cnuphys/splot/style/EnumComboBox.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/IStyled.java b/src/main/java/cnuphys/splot/style/IStyled.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/IStyled.java rename to src/main/java/cnuphys/splot/style/IStyled.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/LineStyle.java b/src/main/java/cnuphys/splot/style/LineStyle.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/LineStyle.java rename to src/main/java/cnuphys/splot/style/LineStyle.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/StyleEditorPanel.java b/src/main/java/cnuphys/splot/style/StyleEditorPanel.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/StyleEditorPanel.java rename to src/main/java/cnuphys/splot/style/StyleEditorPanel.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/Styled.java b/src/main/java/cnuphys/splot/style/Styled.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/Styled.java rename to src/main/java/cnuphys/splot/style/Styled.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/SymbolDraw.java b/src/main/java/cnuphys/splot/style/SymbolDraw.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/SymbolDraw.java rename to src/main/java/cnuphys/splot/style/SymbolDraw.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/SymbolType.java b/src/main/java/cnuphys/splot/style/SymbolType.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/style/SymbolType.java rename to src/main/java/cnuphys/splot/style/SymbolType.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/toolbar/CommonToolBar.java b/src/main/java/cnuphys/splot/toolbar/CommonToolBar.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/toolbar/CommonToolBar.java rename to src/main/java/cnuphys/splot/toolbar/CommonToolBar.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/toolbar/IToolBarListener.java b/src/main/java/cnuphys/splot/toolbar/IToolBarListener.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/toolbar/IToolBarListener.java rename to src/main/java/cnuphys/splot/toolbar/IToolBarListener.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/toolbar/ToolBarButton.java b/src/main/java/cnuphys/splot/toolbar/ToolBarButton.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/toolbar/ToolBarButton.java rename to src/main/java/cnuphys/splot/toolbar/ToolBarButton.java diff --git a/common-tools/cnuphys/splot/src/main/java/cnuphys/splot/toolbar/ToolBarToggleButton.java b/src/main/java/cnuphys/splot/toolbar/ToolBarToggleButton.java similarity index 100% rename from common-tools/cnuphys/splot/src/main/java/cnuphys/splot/toolbar/ToolBarToggleButton.java rename to src/main/java/cnuphys/splot/toolbar/ToolBarToggleButton.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/BeamLineStopper.java b/src/main/java/cnuphys/swim/BeamLineStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/BeamLineStopper.java rename to src/main/java/cnuphys/swim/BeamLineStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/Bxdl.java b/src/main/java/cnuphys/swim/Bxdl.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/Bxdl.java rename to src/main/java/cnuphys/swim/Bxdl.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultCylinderStopper.java b/src/main/java/cnuphys/swim/DefaultCylinderStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultCylinderStopper.java rename to src/main/java/cnuphys/swim/DefaultCylinderStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultDerivative.java b/src/main/java/cnuphys/swim/DefaultDerivative.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultDerivative.java rename to src/main/java/cnuphys/swim/DefaultDerivative.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultListener.java b/src/main/java/cnuphys/swim/DefaultListener.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultListener.java rename to src/main/java/cnuphys/swim/DefaultListener.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultPlaneStopper.java b/src/main/java/cnuphys/swim/DefaultPlaneStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultPlaneStopper.java rename to src/main/java/cnuphys/swim/DefaultPlaneStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultRhoStopper.java b/src/main/java/cnuphys/swim/DefaultRhoStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultRhoStopper.java rename to src/main/java/cnuphys/swim/DefaultRhoStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultSwimStopper.java b/src/main/java/cnuphys/swim/DefaultSwimStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultSwimStopper.java rename to src/main/java/cnuphys/swim/DefaultSwimStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultZStopper.java b/src/main/java/cnuphys/swim/DefaultZStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/DefaultZStopper.java rename to src/main/java/cnuphys/swim/DefaultZStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/Example.java b/src/main/java/cnuphys/swim/Example.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/Example.java rename to src/main/java/cnuphys/swim/Example.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/IProjector.java b/src/main/java/cnuphys/swim/IProjector.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/IProjector.java rename to src/main/java/cnuphys/swim/IProjector.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/NewPlaneStopper.java b/src/main/java/cnuphys/swim/NewPlaneStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/NewPlaneStopper.java rename to src/main/java/cnuphys/swim/NewPlaneStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/NumStepStopper.java b/src/main/java/cnuphys/swim/NumStepStopper.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/NumStepStopper.java rename to src/main/java/cnuphys/swim/NumStepStopper.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/SectorDerivative.java b/src/main/java/cnuphys/swim/SectorDerivative.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/SectorDerivative.java rename to src/main/java/cnuphys/swim/SectorDerivative.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/SwimMenu.java b/src/main/java/cnuphys/swim/SwimMenu.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/SwimMenu.java rename to src/main/java/cnuphys/swim/SwimMenu.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/SwimTrajectory.java b/src/main/java/cnuphys/swim/SwimTrajectory.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/SwimTrajectory.java rename to src/main/java/cnuphys/swim/SwimTrajectory.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/SwimTrajectory2D.java b/src/main/java/cnuphys/swim/SwimTrajectory2D.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/SwimTrajectory2D.java rename to src/main/java/cnuphys/swim/SwimTrajectory2D.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/Swimmer.java b/src/main/java/cnuphys/swim/Swimmer.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/Swimmer.java rename to src/main/java/cnuphys/swim/Swimmer.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/Swimming.java b/src/main/java/cnuphys/swim/Swimming.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/Swimming.java rename to src/main/java/cnuphys/swim/Swimming.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/TrajectoryCompare.java b/src/main/java/cnuphys/swim/TrajectoryCompare.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/TrajectoryCompare.java rename to src/main/java/cnuphys/swim/TrajectoryCompare.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/util/Plane.java b/src/main/java/cnuphys/swim/util/Plane.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/util/Plane.java rename to src/main/java/cnuphys/swim/util/Plane.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/util/SerialIO.java b/src/main/java/cnuphys/swim/util/SerialIO.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/util/SerialIO.java rename to src/main/java/cnuphys/swim/util/SerialIO.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/util/TerminalPlot.java b/src/main/java/cnuphys/swim/util/TerminalPlot.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/util/TerminalPlot.java rename to src/main/java/cnuphys/swim/util/TerminalPlot.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/util/TrajectorySummary.java b/src/main/java/cnuphys/swim/util/TrajectorySummary.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/util/TrajectorySummary.java rename to src/main/java/cnuphys/swim/util/TrajectorySummary.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/util/VectorSupport.java b/src/main/java/cnuphys/swim/util/VectorSupport.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swim/util/VectorSupport.java rename to src/main/java/cnuphys/swim/util/VectorSupport.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SectorSwimZDerivative.java b/src/main/java/cnuphys/swimZ/SectorSwimZDerivative.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SectorSwimZDerivative.java rename to src/main/java/cnuphys/swimZ/SectorSwimZDerivative.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZ.java b/src/main/java/cnuphys/swimZ/SwimZ.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZ.java rename to src/main/java/cnuphys/swimZ/SwimZ.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZDerivative.java b/src/main/java/cnuphys/swimZ/SwimZDerivative.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZDerivative.java rename to src/main/java/cnuphys/swimZ/SwimZDerivative.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZException.java b/src/main/java/cnuphys/swimZ/SwimZException.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZException.java rename to src/main/java/cnuphys/swimZ/SwimZException.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZRange.java b/src/main/java/cnuphys/swimZ/SwimZRange.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZRange.java rename to src/main/java/cnuphys/swimZ/SwimZRange.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZResult.java b/src/main/java/cnuphys/swimZ/SwimZResult.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZResult.java rename to src/main/java/cnuphys/swimZ/SwimZResult.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZStateVector.java b/src/main/java/cnuphys/swimZ/SwimZStateVector.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZStateVector.java rename to src/main/java/cnuphys/swimZ/SwimZStateVector.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZTest.java b/src/main/java/cnuphys/swimZ/SwimZTest.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimZ/SwimZTest.java rename to src/main/java/cnuphys/swimZ/SwimZTest.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/CreateTestTrajectories.java b/src/main/java/cnuphys/swimtest/CreateTestTrajectories.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/CreateTestTrajectories.java rename to src/main/java/cnuphys/swimtest/CreateTestTrajectories.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/RandomData.java b/src/main/java/cnuphys/swimtest/RandomData.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/RandomData.java rename to src/main/java/cnuphys/swimtest/RandomData.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/SectorTest.java b/src/main/java/cnuphys/swimtest/SectorTest.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/SectorTest.java rename to src/main/java/cnuphys/swimtest/SectorTest.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/SmallDZTest.java b/src/main/java/cnuphys/swimtest/SmallDZTest.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/SmallDZTest.java rename to src/main/java/cnuphys/swimtest/SmallDZTest.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/SwimTest.java b/src/main/java/cnuphys/swimtest/SwimTest.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/SwimTest.java rename to src/main/java/cnuphys/swimtest/SwimTest.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/SwimTestData.java b/src/main/java/cnuphys/swimtest/SwimTestData.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/SwimTestData.java rename to src/main/java/cnuphys/swimtest/SwimTestData.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/TestTrajectories.java b/src/main/java/cnuphys/swimtest/TestTrajectories.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/TestTrajectories.java rename to src/main/java/cnuphys/swimtest/TestTrajectories.java diff --git a/common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/ThreadTest.java b/src/main/java/cnuphys/swimtest/ThreadTest.java similarity index 100% rename from common-tools/cnuphys/swimmer/src/main/java/cnuphys/swimtest/ThreadTest.java rename to src/main/java/cnuphys/swimtest/ThreadTest.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/Complex.java b/src/main/java/com/nr/Complex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/Complex.java rename to src/main/java/com/nr/Complex.java diff --git a/common-tools/cnuphys/numRec/LICENSE.txt b/src/main/java/com/nr/LICENSE.txt similarity index 100% rename from common-tools/cnuphys/numRec/LICENSE.txt rename to src/main/java/com/nr/LICENSE.txt diff --git a/common-tools/cnuphys/numRec/NAMES.txt b/src/main/java/com/nr/NAMES.txt similarity index 100% rename from common-tools/cnuphys/numRec/NAMES.txt rename to src/main/java/com/nr/NAMES.txt diff --git a/common-tools/cnuphys/numRec/src/com/nr/NRUtil.java b/src/main/java/com/nr/NRUtil.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/NRUtil.java rename to src/main/java/com/nr/NRUtil.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/RealMultiValueFun.java b/src/main/java/com/nr/RealMultiValueFun.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/RealMultiValueFun.java rename to src/main/java/com/nr/RealMultiValueFun.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/RealValueFun.java b/src/main/java/com/nr/RealValueFun.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/RealValueFun.java rename to src/main/java/com/nr/RealValueFun.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/RealValueFunWithDiff.java b/src/main/java/com/nr/RealValueFunWithDiff.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/RealValueFunWithDiff.java rename to src/main/java/com/nr/RealValueFunWithDiff.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/UniValRealValueFunWithDiff.java b/src/main/java/com/nr/UniValRealValueFunWithDiff.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/UniValRealValueFunWithDiff.java rename to src/main/java/com/nr/UniValRealValueFunWithDiff.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/UniVarRealMultiValueFun.java b/src/main/java/com/nr/UniVarRealMultiValueFun.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/UniVarRealMultiValueFun.java rename to src/main/java/com/nr/UniVarRealMultiValueFun.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/UniVarRealValueFun.java b/src/main/java/com/nr/UniVarRealValueFun.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/UniVarRealValueFun.java rename to src/main/java/com/nr/UniVarRealValueFun.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/bvp/Difeq.java b/src/main/java/com/nr/bvp/Difeq.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/bvp/Difeq.java rename to src/main/java/com/nr/bvp/Difeq.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/bvp/Shoot.java b/src/main/java/com/nr/bvp/Shoot.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/bvp/Shoot.java rename to src/main/java/com/nr/bvp/Shoot.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/bvp/Shootf.java b/src/main/java/com/nr/bvp/Shootf.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/bvp/Shootf.java rename to src/main/java/com/nr/bvp/Shootf.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/bvp/Solvde.java b/src/main/java/com/nr/bvp/Solvde.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/bvp/Solvde.java rename to src/main/java/com/nr/bvp/Solvde.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/Box.java b/src/main/java/com/nr/cg/Box.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/Box.java rename to src/main/java/com/nr/cg/Box.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/Boxnode.java b/src/main/java/com/nr/cg/Boxnode.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/Boxnode.java rename to src/main/java/com/nr/cg/Boxnode.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/Circle.java b/src/main/java/com/nr/cg/Circle.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/Circle.java rename to src/main/java/com/nr/cg/Circle.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/Convexhull.java b/src/main/java/com/nr/cg/Convexhull.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/Convexhull.java rename to src/main/java/com/nr/cg/Convexhull.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/Delaunay.java b/src/main/java/com/nr/cg/Delaunay.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/Delaunay.java rename to src/main/java/com/nr/cg/Delaunay.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/KDtree.java b/src/main/java/com/nr/cg/KDtree.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/KDtree.java rename to src/main/java/com/nr/cg/KDtree.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/Minspantree.java b/src/main/java/com/nr/cg/Minspantree.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/Minspantree.java rename to src/main/java/com/nr/cg/Minspantree.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/Nearpoints.java b/src/main/java/com/nr/cg/Nearpoints.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/Nearpoints.java rename to src/main/java/com/nr/cg/Nearpoints.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/Point.java b/src/main/java/com/nr/cg/Point.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/Point.java rename to src/main/java/com/nr/cg/Point.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/Polygon.java b/src/main/java/com/nr/cg/Polygon.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/Polygon.java rename to src/main/java/com/nr/cg/Polygon.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/Qotree.java b/src/main/java/com/nr/cg/Qotree.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/Qotree.java rename to src/main/java/com/nr/cg/Qotree.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/Sphcirc.java b/src/main/java/com/nr/cg/Sphcirc.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/Sphcirc.java rename to src/main/java/com/nr/cg/Sphcirc.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/Triel.java b/src/main/java/com/nr/cg/Triel.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/Triel.java rename to src/main/java/com/nr/cg/Triel.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/cg/Voronoi.java b/src/main/java/com/nr/cg/Voronoi.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/cg/Voronoi.java rename to src/main/java/com/nr/cg/Voronoi.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Gaumixmod.java b/src/main/java/com/nr/ci/Gaumixmod.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Gaumixmod.java rename to src/main/java/com/nr/ci/Gaumixmod.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/HMM.java b/src/main/java/com/nr/ci/HMM.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/HMM.java rename to src/main/java/com/nr/ci/HMM.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Kmeans.java b/src/main/java/com/nr/ci/Kmeans.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Kmeans.java rename to src/main/java/com/nr/ci/Kmeans.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Phylagglom.java b/src/main/java/com/nr/ci/Phylagglom.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Phylagglom.java rename to src/main/java/com/nr/ci/Phylagglom.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Phylagglomnode.java b/src/main/java/com/nr/ci/Phylagglomnode.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Phylagglomnode.java rename to src/main/java/com/nr/ci/Phylagglomnode.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Phylo_clc.java b/src/main/java/com/nr/ci/Phylo_clc.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Phylo_clc.java rename to src/main/java/com/nr/ci/Phylo_clc.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Phylo_nj.java b/src/main/java/com/nr/ci/Phylo_nj.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Phylo_nj.java rename to src/main/java/com/nr/ci/Phylo_nj.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Phylo_slc.java b/src/main/java/com/nr/ci/Phylo_slc.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Phylo_slc.java rename to src/main/java/com/nr/ci/Phylo_slc.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Phylo_upgma.java b/src/main/java/com/nr/ci/Phylo_upgma.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Phylo_upgma.java rename to src/main/java/com/nr/ci/Phylo_upgma.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Phylo_wpgma.java b/src/main/java/com/nr/ci/Phylo_wpgma.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Phylo_wpgma.java rename to src/main/java/com/nr/ci/Phylo_wpgma.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Svm.java b/src/main/java/com/nr/ci/Svm.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Svm.java rename to src/main/java/com/nr/ci/Svm.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Svmgausskernel.java b/src/main/java/com/nr/ci/Svmgausskernel.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Svmgausskernel.java rename to src/main/java/com/nr/ci/Svmgausskernel.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Svmgenkernel.java b/src/main/java/com/nr/ci/Svmgenkernel.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Svmgenkernel.java rename to src/main/java/com/nr/ci/Svmgenkernel.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Svmlinkernel.java b/src/main/java/com/nr/ci/Svmlinkernel.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Svmlinkernel.java rename to src/main/java/com/nr/ci/Svmlinkernel.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ci/Svmpolykernel.java b/src/main/java/com/nr/ci/Svmpolykernel.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ci/Svmpolykernel.java rename to src/main/java/com/nr/ci/Svmpolykernel.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/eig/Jacobi.java b/src/main/java/com/nr/eig/Jacobi.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/eig/Jacobi.java rename to src/main/java/com/nr/eig/Jacobi.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/eig/Symmeig.java b/src/main/java/com/nr/eig/Symmeig.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/eig/Symmeig.java rename to src/main/java/com/nr/eig/Symmeig.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/eig/Unsymmeig.java b/src/main/java/com/nr/eig/Unsymmeig.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/eig/Unsymmeig.java rename to src/main/java/com/nr/eig/Unsymmeig.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/Bandec_Ex.java b/src/main/java/com/nr/example/Bandec_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/Bandec_Ex.java rename to src/main/java/com/nr/example/Bandec_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/Chebyshev_Ex.java b/src/main/java/com/nr/example/Chebyshev_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/Chebyshev_Ex.java rename to src/main/java/com/nr/example/Chebyshev_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/Cholesky_Ex.java b/src/main/java/com/nr/example/Cholesky_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/Cholesky_Ex.java rename to src/main/java/com/nr/example/Cholesky_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/Cyclic_Ex.java b/src/main/java/com/nr/example/Cyclic_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/Cyclic_Ex.java rename to src/main/java/com/nr/example/Cyclic_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/FFT_Ex.java b/src/main/java/com/nr/example/FFT_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/FFT_Ex.java rename to src/main/java/com/nr/example/FFT_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/GaussJordan_Ex.java b/src/main/java/com/nr/example/GaussJordan_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/GaussJordan_Ex.java rename to src/main/java/com/nr/example/GaussJordan_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/LUdcmp_Ex.java b/src/main/java/com/nr/example/LUdcmp_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/LUdcmp_Ex.java rename to src/main/java/com/nr/example/LUdcmp_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/Levin_Ex.java b/src/main/java/com/nr/example/Levin_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/Levin_Ex.java rename to src/main/java/com/nr/example/Levin_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/QRdcmp_Ex.java b/src/main/java/com/nr/example/QRdcmp_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/QRdcmp_Ex.java rename to src/main/java/com/nr/example/QRdcmp_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/SVD_Ex.java b/src/main/java/com/nr/example/SVD_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/SVD_Ex.java rename to src/main/java/com/nr/example/SVD_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/Solvde_Ex.java b/src/main/java/com/nr/example/Solvde_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/Solvde_Ex.java rename to src/main/java/com/nr/example/Solvde_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/Toepltz_Ex.java b/src/main/java/com/nr/example/Toepltz_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/Toepltz_Ex.java rename to src/main/java/com/nr/example/Toepltz_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/Trigag_Ex.java b/src/main/java/com/nr/example/Trigag_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/Trigag_Ex.java rename to src/main/java/com/nr/example/Trigag_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/Vander_Ex.java b/src/main/java/com/nr/example/Vander_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/Vander_Ex.java rename to src/main/java/com/nr/example/Vander_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/Zrhqr_Ex.java b/src/main/java/com/nr/example/Zrhqr_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/Zrhqr_Ex.java rename to src/main/java/com/nr/example/Zrhqr_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/example/Zroots_Ex.java b/src/main/java/com/nr/example/Zroots_Ex.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/example/Zroots_Ex.java rename to src/main/java/com/nr/example/Zroots_Ex.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fe/Chebyshev.java b/src/main/java/com/nr/fe/Chebyshev.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fe/Chebyshev.java rename to src/main/java/com/nr/fe/Chebyshev.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fe/Dfridr.java b/src/main/java/com/nr/fe/Dfridr.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fe/Dfridr.java rename to src/main/java/com/nr/fe/Dfridr.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fe/Epsalg.java b/src/main/java/com/nr/fe/Epsalg.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fe/Epsalg.java rename to src/main/java/com/nr/fe/Epsalg.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fe/Eulsum.java b/src/main/java/com/nr/fe/Eulsum.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fe/Eulsum.java rename to src/main/java/com/nr/fe/Eulsum.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fe/Levin.java b/src/main/java/com/nr/fe/Levin.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fe/Levin.java rename to src/main/java/com/nr/fe/Levin.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fe/Poly.java b/src/main/java/com/nr/fe/Poly.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fe/Poly.java rename to src/main/java/com/nr/fe/Poly.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fe/Ratfn.java b/src/main/java/com/nr/fe/Ratfn.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fe/Ratfn.java rename to src/main/java/com/nr/fe/Ratfn.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fft/FFT.java b/src/main/java/com/nr/fft/FFT.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fft/FFT.java rename to src/main/java/com/nr/fft/FFT.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fft/WrapVecDoub.java b/src/main/java/com/nr/fft/WrapVecDoub.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fft/WrapVecDoub.java rename to src/main/java/com/nr/fft/WrapVecDoub.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/Adapt.java b/src/main/java/com/nr/fi/Adapt.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/Adapt.java rename to src/main/java/com/nr/fi/Adapt.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/DErule.java b/src/main/java/com/nr/fi/DErule.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/DErule.java rename to src/main/java/com/nr/fi/DErule.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/GaussianWeights.java b/src/main/java/com/nr/fi/GaussianWeights.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/GaussianWeights.java rename to src/main/java/com/nr/fi/GaussianWeights.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/Midexp.java b/src/main/java/com/nr/fi/Midexp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/Midexp.java rename to src/main/java/com/nr/fi/Midexp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/Midinf.java b/src/main/java/com/nr/fi/Midinf.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/Midinf.java rename to src/main/java/com/nr/fi/Midinf.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/Midpnt.java b/src/main/java/com/nr/fi/Midpnt.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/Midpnt.java rename to src/main/java/com/nr/fi/Midpnt.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/Midsql.java b/src/main/java/com/nr/fi/Midsql.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/Midsql.java rename to src/main/java/com/nr/fi/Midsql.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/Midsqu.java b/src/main/java/com/nr/fi/Midsqu.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/Midsqu.java rename to src/main/java/com/nr/fi/Midsqu.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/NRf1.java b/src/main/java/com/nr/fi/NRf1.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/NRf1.java rename to src/main/java/com/nr/fi/NRf1.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/NRf2.java b/src/main/java/com/nr/fi/NRf2.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/NRf2.java rename to src/main/java/com/nr/fi/NRf2.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/NRf3.java b/src/main/java/com/nr/fi/NRf3.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/NRf3.java rename to src/main/java/com/nr/fi/NRf3.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/Quadrature.java b/src/main/java/com/nr/fi/Quadrature.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/Quadrature.java rename to src/main/java/com/nr/fi/Quadrature.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/Stiel.java b/src/main/java/com/nr/fi/Stiel.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/Stiel.java rename to src/main/java/com/nr/fi/Stiel.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/fi/Trapzd.java b/src/main/java/com/nr/fi/Trapzd.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/fi/Trapzd.java rename to src/main/java/com/nr/fi/Trapzd.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/BaryRat_interp.java b/src/main/java/com/nr/interp/BaryRat_interp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/BaryRat_interp.java rename to src/main/java/com/nr/interp/BaryRat_interp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/Base_interp.java b/src/main/java/com/nr/interp/Base_interp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/Base_interp.java rename to src/main/java/com/nr/interp/Base_interp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/Bilin_interp.java b/src/main/java/com/nr/interp/Bilin_interp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/Bilin_interp.java rename to src/main/java/com/nr/interp/Bilin_interp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/Curve_interp.java b/src/main/java/com/nr/interp/Curve_interp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/Curve_interp.java rename to src/main/java/com/nr/interp/Curve_interp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/Krig.java b/src/main/java/com/nr/interp/Krig.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/Krig.java rename to src/main/java/com/nr/interp/Krig.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/Laplace_interp.java b/src/main/java/com/nr/interp/Laplace_interp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/Laplace_interp.java rename to src/main/java/com/nr/interp/Laplace_interp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/Linear_interp.java b/src/main/java/com/nr/interp/Linear_interp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/Linear_interp.java rename to src/main/java/com/nr/interp/Linear_interp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/PolCoef.java b/src/main/java/com/nr/interp/PolCoef.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/PolCoef.java rename to src/main/java/com/nr/interp/PolCoef.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/Poly2D_interp.java b/src/main/java/com/nr/interp/Poly2D_interp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/Poly2D_interp.java rename to src/main/java/com/nr/interp/Poly2D_interp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/Poly_interp.java b/src/main/java/com/nr/interp/Poly_interp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/Poly_interp.java rename to src/main/java/com/nr/interp/Poly_interp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/Powvargram.java b/src/main/java/com/nr/interp/Powvargram.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/Powvargram.java rename to src/main/java/com/nr/interp/Powvargram.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/RBF_fn.java b/src/main/java/com/nr/interp/RBF_fn.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/RBF_fn.java rename to src/main/java/com/nr/interp/RBF_fn.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/RBF_gauss.java b/src/main/java/com/nr/interp/RBF_gauss.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/RBF_gauss.java rename to src/main/java/com/nr/interp/RBF_gauss.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/RBF_interp.java b/src/main/java/com/nr/interp/RBF_interp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/RBF_interp.java rename to src/main/java/com/nr/interp/RBF_interp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/RBF_inversemultiquadric.java b/src/main/java/com/nr/interp/RBF_inversemultiquadric.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/RBF_inversemultiquadric.java rename to src/main/java/com/nr/interp/RBF_inversemultiquadric.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/RBF_multiquadric.java b/src/main/java/com/nr/interp/RBF_multiquadric.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/RBF_multiquadric.java rename to src/main/java/com/nr/interp/RBF_multiquadric.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/RBF_thinplate.java b/src/main/java/com/nr/interp/RBF_thinplate.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/RBF_thinplate.java rename to src/main/java/com/nr/interp/RBF_thinplate.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/Rational_interp.java b/src/main/java/com/nr/interp/Rational_interp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/Rational_interp.java rename to src/main/java/com/nr/interp/Rational_interp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/Shep_interp.java b/src/main/java/com/nr/interp/Shep_interp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/Shep_interp.java rename to src/main/java/com/nr/interp/Shep_interp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/Spline2D_interp.java b/src/main/java/com/nr/interp/Spline2D_interp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/Spline2D_interp.java rename to src/main/java/com/nr/interp/Spline2D_interp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/interp/Spline_interp.java b/src/main/java/com/nr/interp/Spline_interp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/interp/Spline_interp.java rename to src/main/java/com/nr/interp/Spline_interp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/inv/Fred2.java b/src/main/java/com/nr/inv/Fred2.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/inv/Fred2.java rename to src/main/java/com/nr/inv/Fred2.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/inv/Quad_matrix.java b/src/main/java/com/nr/inv/Quad_matrix.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/inv/Quad_matrix.java rename to src/main/java/com/nr/inv/Quad_matrix.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/inv/Volterra.java b/src/main/java/com/nr/inv/Volterra.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/inv/Volterra.java rename to src/main/java/com/nr/inv/Volterra.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/inv/Wwghts.java b/src/main/java/com/nr/inv/Wwghts.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/inv/Wwghts.java rename to src/main/java/com/nr/inv/Wwghts.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/ADAT.java b/src/main/java/com/nr/la/ADAT.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/ADAT.java rename to src/main/java/com/nr/la/ADAT.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/Bandec.java b/src/main/java/com/nr/la/Bandec.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/Bandec.java rename to src/main/java/com/nr/la/Bandec.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/Cholesky.java b/src/main/java/com/nr/la/Cholesky.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/Cholesky.java rename to src/main/java/com/nr/la/Cholesky.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/GaussJordan.java b/src/main/java/com/nr/la/GaussJordan.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/GaussJordan.java rename to src/main/java/com/nr/la/GaussJordan.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/LUdcmp.java b/src/main/java/com/nr/la/LUdcmp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/LUdcmp.java rename to src/main/java/com/nr/la/LUdcmp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/Linbcg.java b/src/main/java/com/nr/la/Linbcg.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/Linbcg.java rename to src/main/java/com/nr/la/Linbcg.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/NRsparseCol.java b/src/main/java/com/nr/la/NRsparseCol.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/NRsparseCol.java rename to src/main/java/com/nr/la/NRsparseCol.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/NRsparseLinbcg.java b/src/main/java/com/nr/la/NRsparseLinbcg.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/NRsparseLinbcg.java rename to src/main/java/com/nr/la/NRsparseLinbcg.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/NRsparseMat.java b/src/main/java/com/nr/la/NRsparseMat.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/NRsparseMat.java rename to src/main/java/com/nr/la/NRsparseMat.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/QRdcmp.java b/src/main/java/com/nr/la/QRdcmp.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/QRdcmp.java rename to src/main/java/com/nr/la/QRdcmp.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/SVD.java b/src/main/java/com/nr/la/SVD.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/SVD.java rename to src/main/java/com/nr/la/SVD.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/Toepltz.java b/src/main/java/com/nr/la/Toepltz.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/Toepltz.java rename to src/main/java/com/nr/la/Toepltz.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/Tridag.java b/src/main/java/com/nr/la/Tridag.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/Tridag.java rename to src/main/java/com/nr/la/Tridag.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/la/Vander.java b/src/main/java/com/nr/la/Vander.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/la/Vander.java rename to src/main/java/com/nr/la/Vander.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/lna/Arithcode.java b/src/main/java/com/nr/lna/Arithcode.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/lna/Arithcode.java rename to src/main/java/com/nr/lna/Arithcode.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/lna/Gray.java b/src/main/java/com/nr/lna/Gray.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/lna/Gray.java rename to src/main/java/com/nr/lna/Gray.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/lna/Huffcode.java b/src/main/java/com/nr/lna/Huffcode.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/lna/Huffcode.java rename to src/main/java/com/nr/lna/Huffcode.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/lna/Icrc.java b/src/main/java/com/nr/lna/Icrc.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/lna/Icrc.java rename to src/main/java/com/nr/lna/Icrc.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/lna/MParith.java b/src/main/java/com/nr/lna/MParith.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/lna/MParith.java rename to src/main/java/com/nr/lna/MParith.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/lna/Machar.java b/src/main/java/com/nr/lna/Machar.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/lna/Machar.java rename to src/main/java/com/nr/lna/Machar.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/lna/PSpage.java b/src/main/java/com/nr/lna/PSpage.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/lna/PSpage.java rename to src/main/java/com/nr/lna/PSpage.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/lna/PSplot.java b/src/main/java/com/nr/lna/PSplot.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/lna/PSplot.java rename to src/main/java/com/nr/lna/PSplot.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Amebsa.java b/src/main/java/com/nr/min/Amebsa.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Amebsa.java rename to src/main/java/com/nr/min/Amebsa.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Amoeba.java b/src/main/java/com/nr/min/Amoeba.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Amoeba.java rename to src/main/java/com/nr/min/Amoeba.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Anneal.java b/src/main/java/com/nr/min/Anneal.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Anneal.java rename to src/main/java/com/nr/min/Anneal.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Bracketmethod.java b/src/main/java/com/nr/min/Bracketmethod.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Bracketmethod.java rename to src/main/java/com/nr/min/Bracketmethod.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Brent.java b/src/main/java/com/nr/min/Brent.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Brent.java rename to src/main/java/com/nr/min/Brent.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Dbrent.java b/src/main/java/com/nr/min/Dbrent.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Dbrent.java rename to src/main/java/com/nr/min/Dbrent.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Df1dim.java b/src/main/java/com/nr/min/Df1dim.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Df1dim.java rename to src/main/java/com/nr/min/Df1dim.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Dlinemethod.java b/src/main/java/com/nr/min/Dlinemethod.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Dlinemethod.java rename to src/main/java/com/nr/min/Dlinemethod.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Dynpro.java b/src/main/java/com/nr/min/Dynpro.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Dynpro.java rename to src/main/java/com/nr/min/Dynpro.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/F1dim.java b/src/main/java/com/nr/min/F1dim.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/F1dim.java rename to src/main/java/com/nr/min/F1dim.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Frprmn.java b/src/main/java/com/nr/min/Frprmn.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Frprmn.java rename to src/main/java/com/nr/min/Frprmn.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Funcd.java b/src/main/java/com/nr/min/Funcd.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Funcd.java rename to src/main/java/com/nr/min/Funcd.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Golden.java b/src/main/java/com/nr/min/Golden.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Golden.java rename to src/main/java/com/nr/min/Golden.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Linemethod.java b/src/main/java/com/nr/min/Linemethod.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Linemethod.java rename to src/main/java/com/nr/min/Linemethod.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/Powell.java b/src/main/java/com/nr/min/Powell.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/Powell.java rename to src/main/java/com/nr/min/Powell.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/QuasiNewton.java b/src/main/java/com/nr/min/QuasiNewton.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/QuasiNewton.java rename to src/main/java/com/nr/min/QuasiNewton.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/min/StringAlign.java b/src/main/java/com/nr/min/StringAlign.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/min/StringAlign.java rename to src/main/java/com/nr/min/StringAlign.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/model/FGauss.java b/src/main/java/com/nr/model/FGauss.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/model/FGauss.java rename to src/main/java/com/nr/model/FGauss.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/model/Fitab.java b/src/main/java/com/nr/model/Fitab.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/model/Fitab.java rename to src/main/java/com/nr/model/Fitab.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/model/Fitexy.java b/src/main/java/com/nr/model/Fitexy.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/model/Fitexy.java rename to src/main/java/com/nr/model/Fitexy.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/model/Fitlin.java b/src/main/java/com/nr/model/Fitlin.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/model/Fitlin.java rename to src/main/java/com/nr/model/Fitlin.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/model/Fitmed.java b/src/main/java/com/nr/model/Fitmed.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/model/Fitmed.java rename to src/main/java/com/nr/model/Fitmed.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/model/Fitmrq.java b/src/main/java/com/nr/model/Fitmrq.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/model/Fitmrq.java rename to src/main/java/com/nr/model/Fitmrq.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/model/Fitsvd.java b/src/main/java/com/nr/model/Fitsvd.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/model/Fitsvd.java rename to src/main/java/com/nr/model/Fitsvd.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/model/MultiFuncd.java b/src/main/java/com/nr/model/MultiFuncd.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/model/MultiFuncd.java rename to src/main/java/com/nr/model/MultiFuncd.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/model/Plog.java b/src/main/java/com/nr/model/Plog.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/model/Plog.java rename to src/main/java/com/nr/model/Plog.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/model/Proposal.java b/src/main/java/com/nr/model/Proposal.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/model/Proposal.java rename to src/main/java/com/nr/model/Proposal.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/model/State.java b/src/main/java/com/nr/model/State.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/model/State.java rename to src/main/java/com/nr/model/State.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ode/DerivativeInf.java b/src/main/java/com/nr/ode/DerivativeInf.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ode/DerivativeInf.java rename to src/main/java/com/nr/ode/DerivativeInf.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ode/Hypderiv.java b/src/main/java/com/nr/ode/Hypderiv.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ode/Hypderiv.java rename to src/main/java/com/nr/ode/Hypderiv.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ode/Odeint.java b/src/main/java/com/nr/ode/Odeint.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ode/Odeint.java rename to src/main/java/com/nr/ode/Odeint.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ode/Output.java b/src/main/java/com/nr/ode/Output.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ode/Output.java rename to src/main/java/com/nr/ode/Output.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ode/StepperBS.java b/src/main/java/com/nr/ode/StepperBS.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ode/StepperBS.java rename to src/main/java/com/nr/ode/StepperBS.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ode/StepperBase.java b/src/main/java/com/nr/ode/StepperBase.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ode/StepperBase.java rename to src/main/java/com/nr/ode/StepperBase.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ode/StepperDopr5.java b/src/main/java/com/nr/ode/StepperDopr5.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ode/StepperDopr5.java rename to src/main/java/com/nr/ode/StepperDopr5.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ode/StepperDopr853.java b/src/main/java/com/nr/ode/StepperDopr853.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ode/StepperDopr853.java rename to src/main/java/com/nr/ode/StepperDopr853.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ode/StepperRoss.java b/src/main/java/com/nr/ode/StepperRoss.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ode/StepperRoss.java rename to src/main/java/com/nr/ode/StepperRoss.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ode/StepperSie.java b/src/main/java/com/nr/ode/StepperSie.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ode/StepperSie.java rename to src/main/java/com/nr/ode/StepperSie.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ode/StepperStoerm.java b/src/main/java/com/nr/ode/StepperStoerm.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ode/StepperStoerm.java rename to src/main/java/com/nr/ode/StepperStoerm.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ode/Stochsim.java b/src/main/java/com/nr/ode/Stochsim.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ode/Stochsim.java rename to src/main/java/com/nr/ode/Stochsim.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/pde/Mgfas.java b/src/main/java/com/nr/pde/Mgfas.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/pde/Mgfas.java rename to src/main/java/com/nr/pde/Mgfas.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/pde/Mglin.java b/src/main/java/com/nr/pde/Mglin.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/pde/Mglin.java rename to src/main/java/com/nr/pde/Mglin.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/pde/Relaxation.java b/src/main/java/com/nr/pde/Relaxation.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/pde/Relaxation.java rename to src/main/java/com/nr/pde/Relaxation.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/pde/Weights.java b/src/main/java/com/nr/pde/Weights.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/pde/Weights.java rename to src/main/java/com/nr/pde/Weights.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Binomialdev.java b/src/main/java/com/nr/ran/Binomialdev.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Binomialdev.java rename to src/main/java/com/nr/ran/Binomialdev.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Cauchydev.java b/src/main/java/com/nr/ran/Cauchydev.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Cauchydev.java rename to src/main/java/com/nr/ran/Cauchydev.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Expondev.java b/src/main/java/com/nr/ran/Expondev.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Expondev.java rename to src/main/java/com/nr/ran/Expondev.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Gammadev.java b/src/main/java/com/nr/ran/Gammadev.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Gammadev.java rename to src/main/java/com/nr/ran/Gammadev.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Hash.java b/src/main/java/com/nr/ran/Hash.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Hash.java rename to src/main/java/com/nr/ran/Hash.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/HashAll.java b/src/main/java/com/nr/ran/HashAll.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/HashAll.java rename to src/main/java/com/nr/ran/HashAll.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Hashfn1.java b/src/main/java/com/nr/ran/Hashfn1.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Hashfn1.java rename to src/main/java/com/nr/ran/Hashfn1.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Hashfn2.java b/src/main/java/com/nr/ran/Hashfn2.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Hashfn2.java rename to src/main/java/com/nr/ran/Hashfn2.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Hashtable.java b/src/main/java/com/nr/ran/Hashtable.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Hashtable.java rename to src/main/java/com/nr/ran/Hashtable.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Logisticdev.java b/src/main/java/com/nr/ran/Logisticdev.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Logisticdev.java rename to src/main/java/com/nr/ran/Logisticdev.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/MCintegrate.java b/src/main/java/com/nr/ran/MCintegrate.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/MCintegrate.java rename to src/main/java/com/nr/ran/MCintegrate.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Mhash.java b/src/main/java/com/nr/ran/Mhash.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Mhash.java rename to src/main/java/com/nr/ran/Mhash.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Miser.java b/src/main/java/com/nr/ran/Miser.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Miser.java rename to src/main/java/com/nr/ran/Miser.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Multinormaldev.java b/src/main/java/com/nr/ran/Multinormaldev.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Multinormaldev.java rename to src/main/java/com/nr/ran/Multinormaldev.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Normaldev.java b/src/main/java/com/nr/ran/Normaldev.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Normaldev.java rename to src/main/java/com/nr/ran/Normaldev.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Normaldev_BM.java b/src/main/java/com/nr/ran/Normaldev_BM.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Normaldev_BM.java rename to src/main/java/com/nr/ran/Normaldev_BM.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Poissondev.java b/src/main/java/com/nr/ran/Poissondev.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Poissondev.java rename to src/main/java/com/nr/ran/Poissondev.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Primpolytest.java b/src/main/java/com/nr/ran/Primpolytest.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Primpolytest.java rename to src/main/java/com/nr/ran/Primpolytest.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Ran.java b/src/main/java/com/nr/ran/Ran.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Ran.java rename to src/main/java/com/nr/ran/Ran.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Ranbyte.java b/src/main/java/com/nr/ran/Ranbyte.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Ranbyte.java rename to src/main/java/com/nr/ran/Ranbyte.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Ranfib.java b/src/main/java/com/nr/ran/Ranfib.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Ranfib.java rename to src/main/java/com/nr/ran/Ranfib.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Ranhash.java b/src/main/java/com/nr/ran/Ranhash.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Ranhash.java rename to src/main/java/com/nr/ran/Ranhash.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Ranlim32.java b/src/main/java/com/nr/ran/Ranlim32.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Ranlim32.java rename to src/main/java/com/nr/ran/Ranlim32.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Ranq1.java b/src/main/java/com/nr/ran/Ranq1.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Ranq1.java rename to src/main/java/com/nr/ran/Ranq1.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Ranq2.java b/src/main/java/com/nr/ran/Ranq2.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Ranq2.java rename to src/main/java/com/nr/ran/Ranq2.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/Sobol.java b/src/main/java/com/nr/ran/Sobol.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/Sobol.java rename to src/main/java/com/nr/ran/Sobol.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/ran/VEGAS.java b/src/main/java/com/nr/ran/VEGAS.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/ran/VEGAS.java rename to src/main/java/com/nr/ran/VEGAS.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/root/MNEWT.java b/src/main/java/com/nr/root/MNEWT.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/root/MNEWT.java rename to src/main/java/com/nr/root/MNEWT.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/root/NRfdjac.java b/src/main/java/com/nr/root/NRfdjac.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/root/NRfdjac.java rename to src/main/java/com/nr/root/NRfdjac.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/root/NRfmin.java b/src/main/java/com/nr/root/NRfmin.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/root/NRfmin.java rename to src/main/java/com/nr/root/NRfmin.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/root/Roots.java b/src/main/java/com/nr/root/Roots.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/root/Roots.java rename to src/main/java/com/nr/root/Roots.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Bessel.java b/src/main/java/com/nr/sf/Bessel.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Bessel.java rename to src/main/java/com/nr/sf/Bessel.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Bessik.java b/src/main/java/com/nr/sf/Bessik.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Bessik.java rename to src/main/java/com/nr/sf/Bessik.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Bessjy.java b/src/main/java/com/nr/sf/Bessjy.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Bessjy.java rename to src/main/java/com/nr/sf/Bessjy.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Beta.java b/src/main/java/com/nr/sf/Beta.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Beta.java rename to src/main/java/com/nr/sf/Beta.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Betadist.java b/src/main/java/com/nr/sf/Betadist.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Betadist.java rename to src/main/java/com/nr/sf/Betadist.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Binomialdist.java b/src/main/java/com/nr/sf/Binomialdist.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Binomialdist.java rename to src/main/java/com/nr/sf/Binomialdist.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Cauchydist.java b/src/main/java/com/nr/sf/Cauchydist.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Cauchydist.java rename to src/main/java/com/nr/sf/Cauchydist.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Chisqdist.java b/src/main/java/com/nr/sf/Chisqdist.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Chisqdist.java rename to src/main/java/com/nr/sf/Chisqdist.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Elliptic.java b/src/main/java/com/nr/sf/Elliptic.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Elliptic.java rename to src/main/java/com/nr/sf/Elliptic.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Erf.java b/src/main/java/com/nr/sf/Erf.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Erf.java rename to src/main/java/com/nr/sf/Erf.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Expondist.java b/src/main/java/com/nr/sf/Expondist.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Expondist.java rename to src/main/java/com/nr/sf/Expondist.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Fdist.java b/src/main/java/com/nr/sf/Fdist.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Fdist.java rename to src/main/java/com/nr/sf/Fdist.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Fermi.java b/src/main/java/com/nr/sf/Fermi.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Fermi.java rename to src/main/java/com/nr/sf/Fermi.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Gamma.java b/src/main/java/com/nr/sf/Gamma.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Gamma.java rename to src/main/java/com/nr/sf/Gamma.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Gammadist.java b/src/main/java/com/nr/sf/Gammadist.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Gammadist.java rename to src/main/java/com/nr/sf/Gammadist.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Gauleg18.java b/src/main/java/com/nr/sf/Gauleg18.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Gauleg18.java rename to src/main/java/com/nr/sf/Gauleg18.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Hypergeo.java b/src/main/java/com/nr/sf/Hypergeo.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Hypergeo.java rename to src/main/java/com/nr/sf/Hypergeo.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Integrals.java b/src/main/java/com/nr/sf/Integrals.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Integrals.java rename to src/main/java/com/nr/sf/Integrals.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/KSdist.java b/src/main/java/com/nr/sf/KSdist.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/KSdist.java rename to src/main/java/com/nr/sf/KSdist.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Legendre.java b/src/main/java/com/nr/sf/Legendre.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Legendre.java rename to src/main/java/com/nr/sf/Legendre.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Logisticdist.java b/src/main/java/com/nr/sf/Logisticdist.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Logisticdist.java rename to src/main/java/com/nr/sf/Logisticdist.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Lognormaldist.java b/src/main/java/com/nr/sf/Lognormaldist.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Lognormaldist.java rename to src/main/java/com/nr/sf/Lognormaldist.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Normaldist.java b/src/main/java/com/nr/sf/Normaldist.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Normaldist.java rename to src/main/java/com/nr/sf/Normaldist.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Poissondist.java b/src/main/java/com/nr/sf/Poissondist.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Poissondist.java rename to src/main/java/com/nr/sf/Poissondist.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sf/Studenttdist.java b/src/main/java/com/nr/sf/Studenttdist.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sf/Studenttdist.java rename to src/main/java/com/nr/sf/Studenttdist.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sort/EClass.java b/src/main/java/com/nr/sort/EClass.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sort/EClass.java rename to src/main/java/com/nr/sort/EClass.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sort/EquivalenceInf.java b/src/main/java/com/nr/sort/EquivalenceInf.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sort/EquivalenceInf.java rename to src/main/java/com/nr/sort/EquivalenceInf.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sort/Heapselect.java b/src/main/java/com/nr/sort/Heapselect.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sort/Heapselect.java rename to src/main/java/com/nr/sort/Heapselect.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sort/IQagent.java b/src/main/java/com/nr/sort/IQagent.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sort/IQagent.java rename to src/main/java/com/nr/sort/IQagent.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sort/Indexx.java b/src/main/java/com/nr/sort/Indexx.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sort/Indexx.java rename to src/main/java/com/nr/sort/Indexx.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sort/Sorter.java b/src/main/java/com/nr/sort/Sorter.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sort/Sorter.java rename to src/main/java/com/nr/sort/Sorter.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/BartlettWin.java b/src/main/java/com/nr/sp/BartlettWin.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/BartlettWin.java rename to src/main/java/com/nr/sp/BartlettWin.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/Daub4.java b/src/main/java/com/nr/sp/Daub4.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/Daub4.java rename to src/main/java/com/nr/sp/Daub4.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/Daub4i.java b/src/main/java/com/nr/sp/Daub4i.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/Daub4i.java rename to src/main/java/com/nr/sp/Daub4i.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/Daubs.java b/src/main/java/com/nr/sp/Daubs.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/Daubs.java rename to src/main/java/com/nr/sp/Daubs.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/DftInt.java b/src/main/java/com/nr/sp/DftInt.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/DftInt.java rename to src/main/java/com/nr/sp/DftInt.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/Fourier.java b/src/main/java/com/nr/sp/Fourier.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/Fourier.java rename to src/main/java/com/nr/sp/Fourier.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/Hann.java b/src/main/java/com/nr/sp/Hann.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/Hann.java rename to src/main/java/com/nr/sp/Hann.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/Slepian.java b/src/main/java/com/nr/sp/Slepian.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/Slepian.java rename to src/main/java/com/nr/sp/Slepian.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/Slepwindow.java b/src/main/java/com/nr/sp/Slepwindow.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/Slepwindow.java rename to src/main/java/com/nr/sp/Slepwindow.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/Spectolap.java b/src/main/java/com/nr/sp/Spectolap.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/Spectolap.java rename to src/main/java/com/nr/sp/Spectolap.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/Spectreg.java b/src/main/java/com/nr/sp/Spectreg.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/Spectreg.java rename to src/main/java/com/nr/sp/Spectreg.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/SquareWin.java b/src/main/java/com/nr/sp/SquareWin.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/SquareWin.java rename to src/main/java/com/nr/sp/SquareWin.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/Wavelet.java b/src/main/java/com/nr/sp/Wavelet.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/Wavelet.java rename to src/main/java/com/nr/sp/Wavelet.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/WelchWin.java b/src/main/java/com/nr/sp/WelchWin.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/WelchWin.java rename to src/main/java/com/nr/sp/WelchWin.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/sp/WindowFun.java b/src/main/java/com/nr/sp/WindowFun.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/sp/WindowFun.java rename to src/main/java/com/nr/sp/WindowFun.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/stat/Moment.java b/src/main/java/com/nr/stat/Moment.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/stat/Moment.java rename to src/main/java/com/nr/stat/Moment.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/stat/Quadvl.java b/src/main/java/com/nr/stat/Quadvl.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/stat/Quadvl.java rename to src/main/java/com/nr/stat/Quadvl.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/stat/QuadvlInf.java b/src/main/java/com/nr/stat/QuadvlInf.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/stat/QuadvlInf.java rename to src/main/java/com/nr/stat/QuadvlInf.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/stat/SavitzkyGolayFilter.java b/src/main/java/com/nr/stat/SavitzkyGolayFilter.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/stat/SavitzkyGolayFilter.java rename to src/main/java/com/nr/stat/SavitzkyGolayFilter.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/stat/Stattests.java b/src/main/java/com/nr/stat/Stattests.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/stat/Stattests.java rename to src/main/java/com/nr/stat/Stattests.java diff --git a/common-tools/cnuphys/numRec/src/com/nr/util/Calendar.java b/src/main/java/com/nr/util/Calendar.java similarity index 100% rename from common-tools/cnuphys/numRec/src/com/nr/util/Calendar.java rename to src/main/java/com/nr/util/Calendar.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Bounds.java b/src/main/java/eu/mihosoft/vrl/v3d/Bounds.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Bounds.java rename to src/main/java/eu/mihosoft/vrl/v3d/Bounds.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/CSG.java b/src/main/java/eu/mihosoft/vrl/v3d/CSG.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/CSG.java rename to src/main/java/eu/mihosoft/vrl/v3d/CSG.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Cube.java b/src/main/java/eu/mihosoft/vrl/v3d/Cube.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Cube.java rename to src/main/java/eu/mihosoft/vrl/v3d/Cube.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Cylinder.java b/src/main/java/eu/mihosoft/vrl/v3d/Cylinder.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Cylinder.java rename to src/main/java/eu/mihosoft/vrl/v3d/Cylinder.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Edge.java b/src/main/java/eu/mihosoft/vrl/v3d/Edge.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Edge.java rename to src/main/java/eu/mihosoft/vrl/v3d/Edge.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Extrude.java b/src/main/java/eu/mihosoft/vrl/v3d/Extrude.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Extrude.java rename to src/main/java/eu/mihosoft/vrl/v3d/Extrude.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/FileUtil.java b/src/main/java/eu/mihosoft/vrl/v3d/FileUtil.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/FileUtil.java rename to src/main/java/eu/mihosoft/vrl/v3d/FileUtil.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Intersection.java b/src/main/java/eu/mihosoft/vrl/v3d/Intersection.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Intersection.java rename to src/main/java/eu/mihosoft/vrl/v3d/Intersection.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Main.java b/src/main/java/eu/mihosoft/vrl/v3d/Main.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Main.java rename to src/main/java/eu/mihosoft/vrl/v3d/Main.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Matrix3d.java b/src/main/java/eu/mihosoft/vrl/v3d/Matrix3d.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Matrix3d.java rename to src/main/java/eu/mihosoft/vrl/v3d/Matrix3d.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/MeshContainer.java b/src/main/java/eu/mihosoft/vrl/v3d/MeshContainer.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/MeshContainer.java rename to src/main/java/eu/mihosoft/vrl/v3d/MeshContainer.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Modifier.java b/src/main/java/eu/mihosoft/vrl/v3d/Modifier.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Modifier.java rename to src/main/java/eu/mihosoft/vrl/v3d/Modifier.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Node.java b/src/main/java/eu/mihosoft/vrl/v3d/Node.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Node.java rename to src/main/java/eu/mihosoft/vrl/v3d/Node.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ObjFile.java b/src/main/java/eu/mihosoft/vrl/v3d/ObjFile.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ObjFile.java rename to src/main/java/eu/mihosoft/vrl/v3d/ObjFile.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Plane.java b/src/main/java/eu/mihosoft/vrl/v3d/Plane.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Plane.java rename to src/main/java/eu/mihosoft/vrl/v3d/Plane.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Polygon.java b/src/main/java/eu/mihosoft/vrl/v3d/Polygon.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Polygon.java rename to src/main/java/eu/mihosoft/vrl/v3d/Polygon.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Polyhedron.java b/src/main/java/eu/mihosoft/vrl/v3d/Polyhedron.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Polyhedron.java rename to src/main/java/eu/mihosoft/vrl/v3d/Polyhedron.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Primitive.java b/src/main/java/eu/mihosoft/vrl/v3d/Primitive.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Primitive.java rename to src/main/java/eu/mihosoft/vrl/v3d/Primitive.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/PropertyStorage.java b/src/main/java/eu/mihosoft/vrl/v3d/PropertyStorage.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/PropertyStorage.java rename to src/main/java/eu/mihosoft/vrl/v3d/PropertyStorage.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/RoundedCube.java b/src/main/java/eu/mihosoft/vrl/v3d/RoundedCube.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/RoundedCube.java rename to src/main/java/eu/mihosoft/vrl/v3d/RoundedCube.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/STL.java b/src/main/java/eu/mihosoft/vrl/v3d/STL.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/STL.java rename to src/main/java/eu/mihosoft/vrl/v3d/STL.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Sphere.java b/src/main/java/eu/mihosoft/vrl/v3d/Sphere.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Sphere.java rename to src/main/java/eu/mihosoft/vrl/v3d/Sphere.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Transform.java b/src/main/java/eu/mihosoft/vrl/v3d/Transform.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Transform.java rename to src/main/java/eu/mihosoft/vrl/v3d/Transform.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/UnityModifier.java b/src/main/java/eu/mihosoft/vrl/v3d/UnityModifier.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/UnityModifier.java rename to src/main/java/eu/mihosoft/vrl/v3d/UnityModifier.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/VFX3DUtil.java b/src/main/java/eu/mihosoft/vrl/v3d/VFX3DUtil.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/VFX3DUtil.java rename to src/main/java/eu/mihosoft/vrl/v3d/VFX3DUtil.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Vector3d.java b/src/main/java/eu/mihosoft/vrl/v3d/Vector3d.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Vector3d.java rename to src/main/java/eu/mihosoft/vrl/v3d/Vector3d.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Vertex.java b/src/main/java/eu/mihosoft/vrl/v3d/Vertex.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/Vertex.java rename to src/main/java/eu/mihosoft/vrl/v3d/Vertex.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/WeightFunction.java b/src/main/java/eu/mihosoft/vrl/v3d/WeightFunction.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/WeightFunction.java rename to src/main/java/eu/mihosoft/vrl/v3d/WeightFunction.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/XModifier.java b/src/main/java/eu/mihosoft/vrl/v3d/XModifier.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/XModifier.java rename to src/main/java/eu/mihosoft/vrl/v3d/XModifier.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/YModifier.java b/src/main/java/eu/mihosoft/vrl/v3d/YModifier.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/YModifier.java rename to src/main/java/eu/mihosoft/vrl/v3d/YModifier.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ZModifier.java b/src/main/java/eu/mihosoft/vrl/v3d/ZModifier.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ZModifier.java rename to src/main/java/eu/mihosoft/vrl/v3d/ZModifier.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/imagej/STLLoader.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/imagej/STLLoader.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/imagej/STLLoader.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/imagej/STLLoader.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Importer.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Importer.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Importer.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Importer.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Importer3D.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Importer3D.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Importer3D.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Importer3D.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/ImporterFinder.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/ImporterFinder.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/ImporterFinder.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/ImporterFinder.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Optimizer.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Optimizer.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Optimizer.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Optimizer.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/SmoothingGroups.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/SmoothingGroups.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/SmoothingGroups.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/SmoothingGroups.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Validator.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Validator.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Validator.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/Validator.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/FloatArrayList.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/FloatArrayList.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/FloatArrayList.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/FloatArrayList.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/IntegerArrayList.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/IntegerArrayList.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/IntegerArrayList.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/IntegerArrayList.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/MtlReader.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/MtlReader.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/MtlReader.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/MtlReader.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/ObjImporter.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/ObjImporter.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/ObjImporter.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/ObjImporter.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/ObjOrPolyObjImporter.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/ObjOrPolyObjImporter.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/ObjOrPolyObjImporter.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/ObjOrPolyObjImporter.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/PolyObjImporter.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/PolyObjImporter.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/PolyObjImporter.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/PolyObjImporter.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/PolygonMesh.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/PolygonMesh.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/PolygonMesh.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/PolygonMesh.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/PolygonMeshView.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/PolygonMeshView.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/PolygonMeshView.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/PolygonMeshView.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/SubdivisionMesh.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/SubdivisionMesh.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/SubdivisionMesh.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/SubdivisionMesh.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/OriginalPointArray.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/OriginalPointArray.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/OriginalPointArray.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/OriginalPointArray.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SubdividedPointArray.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SubdividedPointArray.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SubdividedPointArray.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SubdividedPointArray.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SymbolicPointArray.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SymbolicPointArray.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SymbolicPointArray.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SymbolicPointArray.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SymbolicPolygonMesh.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SymbolicPolygonMesh.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SymbolicPolygonMesh.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SymbolicPolygonMesh.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SymbolicSubdivisionBuilder.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SymbolicSubdivisionBuilder.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SymbolicSubdivisionBuilder.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/shape3d/symbolic/SymbolicSubdivisionBuilder.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/utils3d/DragSupport.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/utils3d/DragSupport.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/utils3d/DragSupport.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/utils3d/DragSupport.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AdvancingFront.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AdvancingFront.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AdvancingFront.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AdvancingFront.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AdvancingFrontIndex.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AdvancingFrontIndex.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AdvancingFrontIndex.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AdvancingFrontIndex.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AdvancingFrontNode.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AdvancingFrontNode.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AdvancingFrontNode.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AdvancingFrontNode.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AnyToXYTransform.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AnyToXYTransform.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AnyToXYTransform.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/AnyToXYTransform.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/ConstrainedPointSet.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/ConstrainedPointSet.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/ConstrainedPointSet.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/ConstrainedPointSet.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/CoordinateTransform.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/CoordinateTransform.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/CoordinateTransform.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/CoordinateTransform.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweep.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweep.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweep.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweep.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepConstraint.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepConstraint.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepConstraint.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepConstraint.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepContext.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepContext.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepContext.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepContext.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepDebugContext.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepDebugContext.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepDebugContext.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepDebugContext.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepPointComparator.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepPointComparator.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepPointComparator.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DTSweepPointComparator.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DelaunayTriangle.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DelaunayTriangle.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DelaunayTriangle.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/DelaunayTriangle.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Edge.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Edge.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Edge.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Edge.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/FloatBufferPoint.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/FloatBufferPoint.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/FloatBufferPoint.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/FloatBufferPoint.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Matrix3Transform.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Matrix3Transform.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Matrix3Transform.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Matrix3Transform.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/NoTransform.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/NoTransform.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/NoTransform.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/NoTransform.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Point.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Point.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Point.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Point.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PointGenerator.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PointGenerator.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PointGenerator.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PointGenerator.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PointOnEdgeException.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PointOnEdgeException.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PointOnEdgeException.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PointOnEdgeException.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PointSet.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PointSet.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PointSet.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PointSet.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Poly2Tri.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Poly2Tri.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Poly2Tri.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Poly2Tri.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Polygon.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Polygon.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Polygon.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Polygon.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonGenerator.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonGenerator.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonGenerator.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonGenerator.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonPoint.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonPoint.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonPoint.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonPoint.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonSet.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonSet.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonSet.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonSet.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonUtil.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonUtil.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonUtil.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/PolygonUtil.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TPoint.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TPoint.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TPoint.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TPoint.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Triangulatable.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Triangulatable.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Triangulatable.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Triangulatable.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationAlgorithm.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationAlgorithm.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationAlgorithm.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationAlgorithm.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationConstraint.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationConstraint.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationConstraint.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationConstraint.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationContext.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationContext.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationContext.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationContext.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationDebugContext.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationDebugContext.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationDebugContext.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationDebugContext.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationMode.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationMode.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationMode.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationMode.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationPoint.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationPoint.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationPoint.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationPoint.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationProcess.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationProcess.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationProcess.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationProcess.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationProcessEvent.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationProcessEvent.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationProcessEvent.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationProcessEvent.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationProcessListener.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationProcessListener.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationProcessListener.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationProcessListener.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationUtil.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationUtil.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationUtil.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/TriangulationUtil.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Tuple2.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Tuple2.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Tuple2.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Tuple2.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Tuple3.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Tuple3.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Tuple3.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/Tuple3.java diff --git a/common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/XYToAnyTransform.java b/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/XYToAnyTransform.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/XYToAnyTransform.java rename to src/main/java/eu/mihosoft/vrl/v3d/ext/org/poly2tri/XYToAnyTransform.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/efficiency/Truth.java b/src/main/java/org/jlab/analysis/efficiency/Truth.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/efficiency/Truth.java rename to src/main/java/org/jlab/analysis/efficiency/Truth.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/ADCTDCMerger.java b/src/main/java/org/jlab/analysis/eventmerger/ADCTDCMerger.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/ADCTDCMerger.java rename to src/main/java/org/jlab/analysis/eventmerger/ADCTDCMerger.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/EventMerger.java b/src/main/java/org/jlab/analysis/eventmerger/EventMerger.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/EventMerger.java rename to src/main/java/org/jlab/analysis/eventmerger/EventMerger.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/EventMergerConstants.java b/src/main/java/org/jlab/analysis/eventmerger/EventMergerConstants.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/EventMergerConstants.java rename to src/main/java/org/jlab/analysis/eventmerger/EventMergerConstants.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/EventMergerEnum.java b/src/main/java/org/jlab/analysis/eventmerger/EventMergerEnum.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/EventMergerEnum.java rename to src/main/java/org/jlab/analysis/eventmerger/EventMergerEnum.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/FilterBankSize.java b/src/main/java/org/jlab/analysis/eventmerger/FilterBankSize.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/FilterBankSize.java rename to src/main/java/org/jlab/analysis/eventmerger/FilterBankSize.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/FilterFcup.java b/src/main/java/org/jlab/analysis/eventmerger/FilterFcup.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/FilterFcup.java rename to src/main/java/org/jlab/analysis/eventmerger/FilterFcup.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/FilterTrigger.java b/src/main/java/org/jlab/analysis/eventmerger/FilterTrigger.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/FilterTrigger.java rename to src/main/java/org/jlab/analysis/eventmerger/FilterTrigger.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/RandomTriggerFilter.java b/src/main/java/org/jlab/analysis/eventmerger/RandomTriggerFilter.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/RandomTriggerFilter.java rename to src/main/java/org/jlab/analysis/eventmerger/RandomTriggerFilter.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/RandomTriggerSplit.java b/src/main/java/org/jlab/analysis/eventmerger/RandomTriggerSplit.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/RandomTriggerSplit.java rename to src/main/java/org/jlab/analysis/eventmerger/RandomTriggerSplit.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/SortedWriterUtils.java b/src/main/java/org/jlab/analysis/eventmerger/SortedWriterUtils.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/SortedWriterUtils.java rename to src/main/java/org/jlab/analysis/eventmerger/SortedWriterUtils.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/math/ClasMath.java b/src/main/java/org/jlab/analysis/math/ClasMath.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/math/ClasMath.java rename to src/main/java/org/jlab/analysis/math/ClasMath.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/physics/TestEvent.java b/src/main/java/org/jlab/analysis/physics/TestEvent.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/physics/TestEvent.java rename to src/main/java/org/jlab/analysis/physics/TestEvent.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/Processor.java b/src/main/java/org/jlab/analysis/postprocess/Processor.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/Processor.java rename to src/main/java/org/jlab/analysis/postprocess/Processor.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/RebuildScalers.java b/src/main/java/org/jlab/analysis/postprocess/RebuildScalers.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/RebuildScalers.java rename to src/main/java/org/jlab/analysis/postprocess/RebuildScalers.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/Tag1ToEvent.java b/src/main/java/org/jlab/analysis/postprocess/Tag1ToEvent.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/Tag1ToEvent.java rename to src/main/java/org/jlab/analysis/postprocess/Tag1ToEvent.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/Util.java b/src/main/java/org/jlab/analysis/postprocess/Util.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/Util.java rename to src/main/java/org/jlab/analysis/postprocess/Util.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/Dictionary.java b/src/main/java/org/jlab/analysis/roads/Dictionary.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/Dictionary.java rename to src/main/java/org/jlab/analysis/roads/Dictionary.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/DictionaryCreator.java b/src/main/java/org/jlab/analysis/roads/DictionaryCreator.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/DictionaryCreator.java rename to src/main/java/org/jlab/analysis/roads/DictionaryCreator.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/DictionaryGenerator.java b/src/main/java/org/jlab/analysis/roads/DictionaryGenerator.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/DictionaryGenerator.java rename to src/main/java/org/jlab/analysis/roads/DictionaryGenerator.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/DictionaryMerger.java b/src/main/java/org/jlab/analysis/roads/DictionaryMerger.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/DictionaryMerger.java rename to src/main/java/org/jlab/analysis/roads/DictionaryMerger.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/DictionaryValidator.java b/src/main/java/org/jlab/analysis/roads/DictionaryValidator.java similarity index 100% rename from common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/DictionaryValidator.java rename to src/main/java/org/jlab/analysis/roads/DictionaryValidator.java diff --git a/common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/README.md 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a/reconstruction/calib/src/main/java/org/jlab/calibration/detectors/RICHBankBuilder.java b/src/main/java/org/jlab/calibration/detectors/RICHBankBuilder.java similarity index 100% rename from reconstruction/calib/src/main/java/org/jlab/calibration/detectors/RICHBankBuilder.java rename to src/main/java/org/jlab/calibration/detectors/RICHBankBuilder.java diff --git a/reconstruction/calib/src/main/java/org/jlab/calibration/service/CalibBanksEngine.java b/src/main/java/org/jlab/calibration/service/CalibBanksEngine.java similarity index 100% rename from reconstruction/calib/src/main/java/org/jlab/calibration/service/CalibBanksEngine.java rename to src/main/java/org/jlab/calibration/service/CalibBanksEngine.java diff --git a/common-tools/clas-math/src/main/java/org/jlab/clas/clas/math/FastMath.java b/src/main/java/org/jlab/clas/clas/math/FastMath.java similarity index 100% rename from common-tools/clas-math/src/main/java/org/jlab/clas/clas/math/FastMath.java rename to 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a/common-tools/clas-math/src/main/java/org/jlab/clas/clas/math/Riven.java b/src/main/java/org/jlab/clas/clas/math/Riven.java similarity index 100% rename from common-tools/clas-math/src/main/java/org/jlab/clas/clas/math/Riven.java rename to src/main/java/org/jlab/clas/clas/math/Riven.java diff --git a/common-tools/clas-math/src/main/java/org/jlab/clas/clas/math/Test.java b/src/main/java/org/jlab/clas/clas/math/Test.java similarity index 100% rename from common-tools/clas-math/src/main/java/org/jlab/clas/clas/math/Test.java rename to src/main/java/org/jlab/clas/clas/math/Test.java diff --git a/common-tools/clas-decay-tools/src/main/java/org/jlab/clas/decay/analysis/Analysis.java b/src/main/java/org/jlab/clas/decay/analysis/Analysis.java similarity index 100% rename from common-tools/clas-decay-tools/src/main/java/org/jlab/clas/decay/analysis/Analysis.java rename to src/main/java/org/jlab/clas/decay/analysis/Analysis.java diff --git a/common-tools/clas-decay-tools/src/main/java/org/jlab/clas/decay/analysis/AnalysisEngine.java b/src/main/java/org/jlab/clas/decay/analysis/AnalysisEngine.java similarity index 100% rename from common-tools/clas-decay-tools/src/main/java/org/jlab/clas/decay/analysis/AnalysisEngine.java rename to src/main/java/org/jlab/clas/decay/analysis/AnalysisEngine.java diff --git a/common-tools/clas-decay-tools/src/main/java/org/jlab/clas/decay/analysis/Constants.java b/src/main/java/org/jlab/clas/decay/analysis/Constants.java similarity index 100% rename from common-tools/clas-decay-tools/src/main/java/org/jlab/clas/decay/analysis/Constants.java rename to src/main/java/org/jlab/clas/decay/analysis/Constants.java diff --git a/common-tools/clas-decay-tools/src/main/java/org/jlab/clas/decay/analysis/Decay.java b/src/main/java/org/jlab/clas/decay/analysis/Decay.java similarity index 100% rename from common-tools/clas-decay-tools/src/main/java/org/jlab/clas/decay/analysis/Decay.java rename to 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a/common-tools/clas-reco/src/main/java/org/jlab/clas/detector/DetectorResponseComparators.java b/src/main/java/org/jlab/clas/detector/DetectorResponseComparators.java similarity index 100% rename from common-tools/clas-reco/src/main/java/org/jlab/clas/detector/DetectorResponseComparators.java rename to src/main/java/org/jlab/clas/detector/DetectorResponseComparators.java diff --git a/common-tools/clas-reco/src/main/java/org/jlab/clas/detector/DetectorResponseFactory.java b/src/main/java/org/jlab/clas/detector/DetectorResponseFactory.java similarity index 100% rename from common-tools/clas-reco/src/main/java/org/jlab/clas/detector/DetectorResponseFactory.java rename to src/main/java/org/jlab/clas/detector/DetectorResponseFactory.java diff --git a/common-tools/clas-reco/src/main/java/org/jlab/clas/detector/DetectorTrack.java b/src/main/java/org/jlab/clas/detector/DetectorTrack.java similarity index 100% rename from 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b/src/main/java/org/jlab/clas/physics/LorentzVector.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/clas/physics/LorentzVector.java rename to src/main/java/org/jlab/clas/physics/LorentzVector.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/clas/physics/Particle.java b/src/main/java/org/jlab/clas/physics/Particle.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/clas/physics/Particle.java rename to src/main/java/org/jlab/clas/physics/Particle.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/clas/physics/ParticleFinder.java b/src/main/java/org/jlab/clas/physics/ParticleFinder.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/clas/physics/ParticleFinder.java rename to src/main/java/org/jlab/clas/physics/ParticleFinder.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/clas/physics/ParticleGenerator.java 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a/common-tools/clas-physics/src/main/java/org/jlab/clas/physics/PhysicsEvent.java b/src/main/java/org/jlab/clas/physics/PhysicsEvent.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/clas/physics/PhysicsEvent.java rename to src/main/java/org/jlab/clas/physics/PhysicsEvent.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/clas/physics/PhysicsKinematics.java b/src/main/java/org/jlab/clas/physics/PhysicsKinematics.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/clas/physics/PhysicsKinematics.java rename to src/main/java/org/jlab/clas/physics/PhysicsKinematics.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/clas/physics/Vector3.java b/src/main/java/org/jlab/clas/physics/Vector3.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/clas/physics/Vector3.java rename to src/main/java/org/jlab/clas/physics/Vector3.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/clas/reactions/DecayKinematics.java b/src/main/java/org/jlab/clas/reactions/DecayKinematics.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/clas/reactions/DecayKinematics.java rename to src/main/java/org/jlab/clas/reactions/DecayKinematics.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/clas/reactions/IDecay.java b/src/main/java/org/jlab/clas/reactions/IDecay.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/clas/reactions/IDecay.java rename to src/main/java/org/jlab/clas/reactions/IDecay.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/clas/reactions/TransMatrix.java b/src/main/java/org/jlab/clas/reactions/TransMatrix.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/clas/reactions/TransMatrix.java rename to src/main/java/org/jlab/clas/reactions/TransMatrix.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/clas/reactions/TwoBodyDecay.java b/src/main/java/org/jlab/clas/reactions/TwoBodyDecay.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/clas/reactions/TwoBodyDecay.java rename to src/main/java/org/jlab/clas/reactions/TwoBodyDecay.java diff --git a/common-tools/clas-reco/src/main/java/org/jlab/clas/reco/Clas12Types.java b/src/main/java/org/jlab/clas/reco/Clas12Types.java similarity index 100% rename from common-tools/clas-reco/src/main/java/org/jlab/clas/reco/Clas12Types.java rename to src/main/java/org/jlab/clas/reco/Clas12Types.java diff --git a/common-tools/clas-reco/src/main/java/org/jlab/clas/reco/EngineProcessor.java b/src/main/java/org/jlab/clas/reco/EngineProcessor.java similarity index 100% rename from common-tools/clas-reco/src/main/java/org/jlab/clas/reco/EngineProcessor.java rename to src/main/java/org/jlab/clas/reco/EngineProcessor.java diff --git a/common-tools/clas-reco/src/main/java/org/jlab/clas/reco/ReconstructionEngine.java b/src/main/java/org/jlab/clas/reco/ReconstructionEngine.java similarity index 100% rename from common-tools/clas-reco/src/main/java/org/jlab/clas/reco/ReconstructionEngine.java rename to src/main/java/org/jlab/clas/reco/ReconstructionEngine.java diff --git a/common-tools/clas-reco/src/main/java/org/jlab/clas/reco/UberEngine.java b/src/main/java/org/jlab/clas/reco/UberEngine.java similarity index 100% rename from common-tools/clas-reco/src/main/java/org/jlab/clas/reco/UberEngine.java rename to src/main/java/org/jlab/clas/reco/UberEngine.java diff --git a/common-tools/swim-tools/src/main/java/org/jlab/clas/swimtools/MagFieldsEngine.java b/src/main/java/org/jlab/clas/swimtools/MagFieldsEngine.java similarity index 100% rename from common-tools/swim-tools/src/main/java/org/jlab/clas/swimtools/MagFieldsEngine.java rename to src/main/java/org/jlab/clas/swimtools/MagFieldsEngine.java diff --git a/common-tools/swim-tools/src/main/java/org/jlab/clas/swimtools/ProbeCollection.java b/src/main/java/org/jlab/clas/swimtools/ProbeCollection.java similarity index 100% rename from common-tools/swim-tools/src/main/java/org/jlab/clas/swimtools/ProbeCollection.java rename to src/main/java/org/jlab/clas/swimtools/ProbeCollection.java diff --git a/common-tools/swim-tools/src/main/java/org/jlab/clas/swimtools/Swim.java b/src/main/java/org/jlab/clas/swimtools/Swim.java similarity index 100% rename from common-tools/swim-tools/src/main/java/org/jlab/clas/swimtools/Swim.java rename to src/main/java/org/jlab/clas/swimtools/Swim.java diff --git a/common-tools/swim-tools/src/main/java/org/jlab/clas/swimtools/Swimmer.java b/src/main/java/org/jlab/clas/swimtools/Swimmer.java similarity index 100% rename from common-tools/swim-tools/src/main/java/org/jlab/clas/swimtools/Swimmer.java rename to src/main/java/org/jlab/clas/swimtools/Swimmer.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/AKFitter.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/AKFitter.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/AKFitter.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/AKFitter.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/AMeasVecs.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/AMeasVecs.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/AMeasVecs.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/AMeasVecs.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/AStateVecs.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/AStateVecs.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/AStateVecs.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/AStateVecs.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/AStateVector.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/AStateVector.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/AStateVector.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/AStateVector.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/KFCovMatOps.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/KFCovMatOps.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/KFCovMatOps.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/KFCovMatOps.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/Material.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/Material.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/Material.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/Material.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/Surface.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/Surface.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/Surface.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/Surface.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/Type.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/Type.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/Type.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/Type.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/Units.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/Units.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/Units.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/Units.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/helical/KFitter.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/helical/KFitter.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/helical/KFitter.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/helical/KFitter.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/helical/MeasVecs.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/helical/MeasVecs.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/helical/MeasVecs.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/helical/MeasVecs.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/helical/StateVecs.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/helical/StateVecs.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/helical/StateVecs.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/helical/StateVecs.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/straight/KFitter.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/straight/KFitter.java similarity index 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a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/zReference/KFitter.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/zReference/KFitter.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/zReference/KFitter.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/zReference/KFitter.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/zReference/KFitterStraight.java b/src/main/java/org/jlab/clas/tracking/kalmanfilter/zReference/KFitterStraight.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/zReference/KFitterStraight.java rename to src/main/java/org/jlab/clas/tracking/kalmanfilter/zReference/KFitterStraight.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/zReference/MeasVecs.java 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a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/trackrep/Helix.java b/src/main/java/org/jlab/clas/tracking/trackrep/Helix.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/trackrep/Helix.java rename to src/main/java/org/jlab/clas/tracking/trackrep/Helix.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/trackrep/Seed.java b/src/main/java/org/jlab/clas/tracking/trackrep/Seed.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/trackrep/Seed.java rename to src/main/java/org/jlab/clas/tracking/trackrep/Seed.java diff --git a/common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/trackrep/Trajectory.java b/src/main/java/org/jlab/clas/tracking/trackrep/Trajectory.java similarity index 100% rename from common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/trackrep/Trajectory.java rename to 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b/src/main/java/org/jlab/detector/banks/FilteredBank.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/banks/FilteredBank.java rename to src/main/java/org/jlab/detector/banks/FilteredBank.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/banks/RawBank.java b/src/main/java/org/jlab/detector/banks/RawBank.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/banks/RawBank.java rename to src/main/java/org/jlab/detector/banks/RawBank.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/banks/RawDataBank.java b/src/main/java/org/jlab/detector/banks/RawDataBank.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/banks/RawDataBank.java rename to src/main/java/org/jlab/detector/banks/RawDataBank.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/base/DetectorCollection.java 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a/common-tools/clas-detector/src/main/java/org/jlab/detector/base/DetectorType.java b/src/main/java/org/jlab/detector/base/DetectorType.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/base/DetectorType.java rename to src/main/java/org/jlab/detector/base/DetectorType.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/base/GeometryFactory.java b/src/main/java/org/jlab/detector/base/GeometryFactory.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/base/GeometryFactory.java rename to src/main/java/org/jlab/detector/base/GeometryFactory.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/calib/tasks/CalibrationEngine.java b/src/main/java/org/jlab/detector/calib/tasks/CalibrationEngine.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/calib/tasks/CalibrationEngine.java rename to src/main/java/org/jlab/detector/calib/tasks/CalibrationEngine.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/calib/tasks/CalibrationEngineTask.java b/src/main/java/org/jlab/detector/calib/tasks/CalibrationEngineTask.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/calib/tasks/CalibrationEngineTask.java rename to src/main/java/org/jlab/detector/calib/tasks/CalibrationEngineTask.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/calib/tasks/CalibrationEngineView.java b/src/main/java/org/jlab/detector/calib/tasks/CalibrationEngineView.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/calib/tasks/CalibrationEngineView.java rename to src/main/java/org/jlab/detector/calib/tasks/CalibrationEngineView.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/CalibrationConstants.java b/src/main/java/org/jlab/detector/calib/utils/CalibrationConstants.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/CalibrationConstants.java rename to src/main/java/org/jlab/detector/calib/utils/CalibrationConstants.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/CalibrationConstantsListener.java b/src/main/java/org/jlab/detector/calib/utils/CalibrationConstantsListener.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/CalibrationConstantsListener.java rename to src/main/java/org/jlab/detector/calib/utils/CalibrationConstantsListener.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/CalibrationConstantsView.java b/src/main/java/org/jlab/detector/calib/utils/CalibrationConstantsView.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/CalibrationConstantsView.java rename to src/main/java/org/jlab/detector/calib/utils/CalibrationConstantsView.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/ConstantsManager.java b/src/main/java/org/jlab/detector/calib/utils/ConstantsManager.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/ConstantsManager.java rename to src/main/java/org/jlab/detector/calib/utils/ConstantsManager.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/DatabaseConstantProvider.java b/src/main/java/org/jlab/detector/calib/utils/DatabaseConstantProvider.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/DatabaseConstantProvider.java rename to src/main/java/org/jlab/detector/calib/utils/DatabaseConstantProvider.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/RCDBConstants.java b/src/main/java/org/jlab/detector/calib/utils/RCDBConstants.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/RCDBConstants.java rename to src/main/java/org/jlab/detector/calib/utils/RCDBConstants.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/RCDBProvider.java b/src/main/java/org/jlab/detector/calib/utils/RCDBProvider.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/calib/utils/RCDBProvider.java rename to src/main/java/org/jlab/detector/calib/utils/RCDBProvider.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CLASDecoder.java b/src/main/java/org/jlab/detector/decode/CLASDecoder.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CLASDecoder.java rename to src/main/java/org/jlab/detector/decode/CLASDecoder.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CLASDecoder4.java b/src/main/java/org/jlab/detector/decode/CLASDecoder4.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CLASDecoder4.java rename to src/main/java/org/jlab/detector/decode/CLASDecoder4.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CLASDecoder4U.java b/src/main/java/org/jlab/detector/decode/CLASDecoder4U.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CLASDecoder4U.java rename to src/main/java/org/jlab/detector/decode/CLASDecoder4U.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CodaDecoders.java b/src/main/java/org/jlab/detector/decode/CodaDecoders.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CodaDecoders.java rename to src/main/java/org/jlab/detector/decode/CodaDecoders.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CodaEventDecoder.java b/src/main/java/org/jlab/detector/decode/CodaEventDecoder.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CodaEventDecoder.java rename to src/main/java/org/jlab/detector/decode/CodaEventDecoder.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/DetectorBankDgtz.java b/src/main/java/org/jlab/detector/decode/DetectorBankDgtz.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/decode/DetectorBankDgtz.java rename to src/main/java/org/jlab/detector/decode/DetectorBankDgtz.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/DetectorDataDgtz.java b/src/main/java/org/jlab/detector/decode/DetectorDataDgtz.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/decode/DetectorDataDgtz.java rename to src/main/java/org/jlab/detector/decode/DetectorDataDgtz.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/DetectorDataFilter.java b/src/main/java/org/jlab/detector/decode/DetectorDataFilter.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/decode/DetectorDataFilter.java rename to src/main/java/org/jlab/detector/decode/DetectorDataFilter.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/DetectorDecoderDebug.java b/src/main/java/org/jlab/detector/decode/DetectorDecoderDebug.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/decode/DetectorDecoderDebug.java rename to src/main/java/org/jlab/detector/decode/DetectorDecoderDebug.java diff 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common-tools/clas-detector/src/main/java/org/jlab/detector/decode/ExtendedFADCFitter.java rename to src/main/java/org/jlab/detector/decode/ExtendedFADCFitter.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/FADCData.java b/src/main/java/org/jlab/detector/decode/FADCData.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/decode/FADCData.java rename to src/main/java/org/jlab/detector/decode/FADCData.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/IFADCFitter.java b/src/main/java/org/jlab/detector/decode/IFADCFitter.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/decode/IFADCFitter.java rename to src/main/java/org/jlab/detector/decode/IFADCFitter.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/MVTFitter.java b/src/main/java/org/jlab/detector/decode/MVTFitter.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/decode/MVTFitter.java rename to src/main/java/org/jlab/detector/decode/MVTFitter.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/TranslationTable.java b/src/main/java/org/jlab/detector/decode/TranslationTable.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/decode/TranslationTable.java rename to src/main/java/org/jlab/detector/decode/TranslationTable.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/epics/Epics.java b/src/main/java/org/jlab/detector/epics/Epics.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/epics/Epics.java rename to src/main/java/org/jlab/detector/epics/Epics.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/epics/EpicsSequence.java b/src/main/java/org/jlab/detector/epics/EpicsSequence.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/epics/EpicsSequence.java rename to src/main/java/org/jlab/detector/epics/EpicsSequence.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/examples/DaqPulsePlotter.java b/src/main/java/org/jlab/detector/examples/DaqPulsePlotter.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/examples/DaqPulsePlotter.java rename to src/main/java/org/jlab/detector/examples/DaqPulsePlotter.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/examples/DetectorTiming.java b/src/main/java/org/jlab/detector/examples/DetectorTiming.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/examples/DetectorTiming.java rename to src/main/java/org/jlab/detector/examples/DetectorTiming.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/examples/RawEventViewer.java b/src/main/java/org/jlab/detector/examples/RawEventViewer.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/examples/RawEventViewer.java rename to src/main/java/org/jlab/detector/examples/RawEventViewer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/detector/geant4/BSTGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/BSTGeant4Factory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/detector/geant4/BSTGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/BSTGeant4Factory.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/detector/geant4/DCGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/DCGeant4Factory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/detector/geant4/DCGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/DCGeant4Factory.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/detector/geant4/ECGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/ECGeant4Factory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/detector/geant4/ECGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/ECGeant4Factory.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/detector/geant4/FTOFGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/FTOFGeant4Factory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/detector/geant4/FTOFGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/FTOFGeant4Factory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/CTOFGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/v2/CTOFGeant4Factory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/CTOFGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/v2/CTOFGeant4Factory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/DCGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/v2/DCGeant4Factory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/DCGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/v2/DCGeant4Factory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/ECGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/v2/ECGeant4Factory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/ECGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/v2/ECGeant4Factory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/FTOFGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/v2/FTOFGeant4Factory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/FTOFGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/v2/FTOFGeant4Factory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/Geant4Factory.java b/src/main/java/org/jlab/detector/geant4/v2/Geant4Factory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/Geant4Factory.java rename to src/main/java/org/jlab/detector/geant4/v2/Geant4Factory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/MUVT/MUVTConstants.java b/src/main/java/org/jlab/detector/geant4/v2/MPGD/MUVT/MUVTConstants.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/MUVT/MUVTConstants.java rename to src/main/java/org/jlab/detector/geant4/v2/MPGD/MUVT/MUVTConstants.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/MUVT/MUVTGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/v2/MPGD/MUVT/MUVTGeant4Factory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/MUVT/MUVTGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/v2/MPGD/MUVT/MUVTGeant4Factory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/MUVT/MUVTStripFactory.java b/src/main/java/org/jlab/detector/geant4/v2/MPGD/MUVT/MUVTStripFactory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/MUVT/MUVTStripFactory.java rename to src/main/java/org/jlab/detector/geant4/v2/MPGD/MUVT/MUVTStripFactory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/URWT/URWTConstants.java b/src/main/java/org/jlab/detector/geant4/v2/MPGD/URWT/URWTConstants.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/URWT/URWTConstants.java rename to src/main/java/org/jlab/detector/geant4/v2/MPGD/URWT/URWTConstants.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/URWT/URWTGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/v2/MPGD/URWT/URWTGeant4Factory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/URWT/URWTGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/v2/MPGD/URWT/URWTGeant4Factory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/URWT/URWTStripFactory.java b/src/main/java/org/jlab/detector/geant4/v2/MPGD/URWT/URWTStripFactory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/URWT/URWTStripFactory.java rename to src/main/java/org/jlab/detector/geant4/v2/MPGD/URWT/URWTStripFactory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/trapezoid/MPGDTrapezoidConstants.java b/src/main/java/org/jlab/detector/geant4/v2/MPGD/trapezoid/MPGDTrapezoidConstants.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/trapezoid/MPGDTrapezoidConstants.java rename to src/main/java/org/jlab/detector/geant4/v2/MPGD/trapezoid/MPGDTrapezoidConstants.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/trapezoid/MPGDTrapezoidGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/v2/MPGD/trapezoid/MPGDTrapezoidGeant4Factory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/trapezoid/MPGDTrapezoidGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/v2/MPGD/trapezoid/MPGDTrapezoidGeant4Factory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/trapezoid/MPGDTrapezoidStripFactory.java b/src/main/java/org/jlab/detector/geant4/v2/MPGD/trapezoid/MPGDTrapezoidStripFactory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/MPGD/trapezoid/MPGDTrapezoidStripFactory.java rename to src/main/java/org/jlab/detector/geant4/v2/MPGD/trapezoid/MPGDTrapezoidStripFactory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/PCALGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/v2/PCALGeant4Factory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/PCALGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/v2/PCALGeant4Factory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/RICHGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/v2/RICHGeant4Factory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/RICHGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/v2/RICHGeant4Factory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/AlignmentFactory.java b/src/main/java/org/jlab/detector/geant4/v2/SVT/AlignmentFactory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/AlignmentFactory.java rename to src/main/java/org/jlab/detector/geant4/v2/SVT/AlignmentFactory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/Matrix.java b/src/main/java/org/jlab/detector/geant4/v2/SVT/Matrix.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/Matrix.java rename to src/main/java/org/jlab/detector/geant4/v2/SVT/Matrix.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/SVTAlignmentFactory.java b/src/main/java/org/jlab/detector/geant4/v2/SVT/SVTAlignmentFactory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/SVTAlignmentFactory.java rename to src/main/java/org/jlab/detector/geant4/v2/SVT/SVTAlignmentFactory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/SVTConstants.java b/src/main/java/org/jlab/detector/geant4/v2/SVT/SVTConstants.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/SVTConstants.java rename to src/main/java/org/jlab/detector/geant4/v2/SVT/SVTConstants.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/SVTStripFactory.java b/src/main/java/org/jlab/detector/geant4/v2/SVT/SVTStripFactory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/SVTStripFactory.java rename to src/main/java/org/jlab/detector/geant4/v2/SVT/SVTStripFactory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/SVTVolumeFactory.java b/src/main/java/org/jlab/detector/geant4/v2/SVT/SVTVolumeFactory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/SVTVolumeFactory.java rename to src/main/java/org/jlab/detector/geant4/v2/SVT/SVTVolumeFactory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/Util.java b/src/main/java/org/jlab/detector/geant4/v2/SVT/Util.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/Util.java rename to src/main/java/org/jlab/detector/geant4/v2/SVT/Util.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVTGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/v2/SVTGeant4Factory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVTGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/v2/SVTGeant4Factory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/recoil/RecoilConstants.java b/src/main/java/org/jlab/detector/geant4/v2/recoil/RecoilConstants.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/recoil/RecoilConstants.java rename to src/main/java/org/jlab/detector/geant4/v2/recoil/RecoilConstants.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/recoil/RecoilGeant4Factory.java b/src/main/java/org/jlab/detector/geant4/v2/recoil/RecoilGeant4Factory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/recoil/RecoilGeant4Factory.java rename to src/main/java/org/jlab/detector/geant4/v2/recoil/RecoilGeant4Factory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/recoil/RecoilStripFactory.java b/src/main/java/org/jlab/detector/geant4/v2/recoil/RecoilStripFactory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/recoil/RecoilStripFactory.java rename to src/main/java/org/jlab/detector/geant4/v2/recoil/RecoilStripFactory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHComponent.java b/src/main/java/org/jlab/detector/geom/RICH/RICHComponent.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHComponent.java rename to src/main/java/org/jlab/detector/geom/RICH/RICHComponent.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHFrame.java b/src/main/java/org/jlab/detector/geom/RICH/RICHFrame.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHFrame.java rename to src/main/java/org/jlab/detector/geom/RICH/RICHFrame.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHGeoCalibration.java b/src/main/java/org/jlab/detector/geom/RICH/RICHGeoCalibration.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHGeoCalibration.java rename to src/main/java/org/jlab/detector/geom/RICH/RICHGeoCalibration.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHGeoConstants.java b/src/main/java/org/jlab/detector/geom/RICH/RICHGeoConstants.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHGeoConstants.java rename to src/main/java/org/jlab/detector/geom/RICH/RICHGeoConstants.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHGeoFactory.java b/src/main/java/org/jlab/detector/geom/RICH/RICHGeoFactory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHGeoFactory.java rename to src/main/java/org/jlab/detector/geom/RICH/RICHGeoFactory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHGeoParameters.java b/src/main/java/org/jlab/detector/geom/RICH/RICHGeoParameters.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHGeoParameters.java rename to src/main/java/org/jlab/detector/geom/RICH/RICHGeoParameters.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHIntersection.java b/src/main/java/org/jlab/detector/geom/RICH/RICHIntersection.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHIntersection.java rename to src/main/java/org/jlab/detector/geom/RICH/RICHIntersection.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHLayer.java b/src/main/java/org/jlab/detector/geom/RICH/RICHLayer.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHLayer.java rename to src/main/java/org/jlab/detector/geom/RICH/RICHLayer.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHLayerType.java b/src/main/java/org/jlab/detector/geom/RICH/RICHLayerType.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHLayerType.java rename to src/main/java/org/jlab/detector/geom/RICH/RICHLayerType.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHPixel.java b/src/main/java/org/jlab/detector/geom/RICH/RICHPixel.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHPixel.java rename to src/main/java/org/jlab/detector/geom/RICH/RICHPixel.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHPixelMap.java b/src/main/java/org/jlab/detector/geom/RICH/RICHPixelMap.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHPixelMap.java rename to src/main/java/org/jlab/detector/geom/RICH/RICHPixelMap.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHRay.java b/src/main/java/org/jlab/detector/geom/RICH/RICHRay.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/RICH/RICHRay.java rename to src/main/java/org/jlab/detector/geom/RICH/RICHRay.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/dc/DCGeantFactory.java b/src/main/java/org/jlab/detector/geom/dc/DCGeantFactory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/dc/DCGeantFactory.java rename to src/main/java/org/jlab/detector/geom/dc/DCGeantFactory.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/dc/GeantFactory.java b/src/main/java/org/jlab/detector/geom/dc/GeantFactory.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/geom/dc/GeantFactory.java rename to src/main/java/org/jlab/detector/geom/dc/GeantFactory.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/DecoderBoardTest.java b/src/main/java/org/jlab/detector/helicity/DecoderBoardTest.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/DecoderBoardTest.java rename to src/main/java/org/jlab/detector/helicity/DecoderBoardTest.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/DecoderBoardUtil.java b/src/main/java/org/jlab/detector/helicity/DecoderBoardUtil.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/DecoderBoardUtil.java rename to src/main/java/org/jlab/detector/helicity/DecoderBoardUtil.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicityAnalysisSimple.java b/src/main/java/org/jlab/detector/helicity/HelicityAnalysisSimple.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicityAnalysisSimple.java rename to src/main/java/org/jlab/detector/helicity/HelicityAnalysisSimple.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicityBit.java b/src/main/java/org/jlab/detector/helicity/HelicityBit.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicityBit.java rename to src/main/java/org/jlab/detector/helicity/HelicityBit.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicityGenerator.java b/src/main/java/org/jlab/detector/helicity/HelicityGenerator.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicityGenerator.java rename to src/main/java/org/jlab/detector/helicity/HelicityGenerator.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicityInterval.java b/src/main/java/org/jlab/detector/helicity/HelicityInterval.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicityInterval.java rename to src/main/java/org/jlab/detector/helicity/HelicityInterval.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicityPattern.java b/src/main/java/org/jlab/detector/helicity/HelicityPattern.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicityPattern.java rename to src/main/java/org/jlab/detector/helicity/HelicityPattern.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicitySequence.java b/src/main/java/org/jlab/detector/helicity/HelicitySequence.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicitySequence.java rename to src/main/java/org/jlab/detector/helicity/HelicitySequence.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicitySequenceDelayed.java b/src/main/java/org/jlab/detector/helicity/HelicitySequenceDelayed.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicitySequenceDelayed.java rename to src/main/java/org/jlab/detector/helicity/HelicitySequenceDelayed.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicitySequenceManager.java b/src/main/java/org/jlab/detector/helicity/HelicitySequenceManager.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicitySequenceManager.java rename to src/main/java/org/jlab/detector/helicity/HelicitySequenceManager.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicityState.java b/src/main/java/org/jlab/detector/helicity/HelicityState.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicityState.java rename to src/main/java/org/jlab/detector/helicity/HelicityState.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/SequenceUtil.java b/src/main/java/org/jlab/detector/helicity/SequenceUtil.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/SequenceUtil.java rename to src/main/java/org/jlab/detector/helicity/SequenceUtil.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/hits/CTOFDetHit.java b/src/main/java/org/jlab/detector/hits/CTOFDetHit.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/hits/CTOFDetHit.java rename to src/main/java/org/jlab/detector/hits/CTOFDetHit.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/hits/DetHit.java b/src/main/java/org/jlab/detector/hits/DetHit.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/hits/DetHit.java rename to src/main/java/org/jlab/detector/hits/DetHit.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/hits/DetId.java b/src/main/java/org/jlab/detector/hits/DetId.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/hits/DetId.java rename to src/main/java/org/jlab/detector/hits/DetId.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/hits/FTOFDetHit.java b/src/main/java/org/jlab/detector/hits/FTOFDetHit.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/hits/FTOFDetHit.java rename to src/main/java/org/jlab/detector/hits/FTOFDetHit.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/hits/PCALDetHit.java b/src/main/java/org/jlab/detector/hits/PCALDetHit.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/hits/PCALDetHit.java rename to src/main/java/org/jlab/detector/hits/PCALDetHit.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/HipoExtractor.java b/src/main/java/org/jlab/detector/pulse/HipoExtractor.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/HipoExtractor.java rename to src/main/java/org/jlab/detector/pulse/HipoExtractor.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/IExtractor.java b/src/main/java/org/jlab/detector/pulse/IExtractor.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/IExtractor.java rename to src/main/java/org/jlab/detector/pulse/IExtractor.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/Mode3.java b/src/main/java/org/jlab/detector/pulse/Mode3.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/Mode3.java rename to src/main/java/org/jlab/detector/pulse/Mode3.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/Mode7.java b/src/main/java/org/jlab/detector/pulse/Mode7.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/Mode7.java rename to src/main/java/org/jlab/detector/pulse/Mode7.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/ModeAHDC.java b/src/main/java/org/jlab/detector/pulse/ModeAHDC.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/ModeAHDC.java rename to src/main/java/org/jlab/detector/pulse/ModeAHDC.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/Pulse.java b/src/main/java/org/jlab/detector/pulse/Pulse.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/Pulse.java rename to src/main/java/org/jlab/detector/pulse/Pulse.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/qadb/QadbBin.java b/src/main/java/org/jlab/detector/qadb/QadbBin.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/qadb/QadbBin.java rename to src/main/java/org/jlab/detector/qadb/QadbBin.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/qadb/QadbBinSequence.java b/src/main/java/org/jlab/detector/qadb/QadbBinSequence.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/qadb/QadbBinSequence.java rename to src/main/java/org/jlab/detector/qadb/QadbBinSequence.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/scalers/DaqScaler.java b/src/main/java/org/jlab/detector/scalers/DaqScaler.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/scalers/DaqScaler.java rename to src/main/java/org/jlab/detector/scalers/DaqScaler.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/scalers/DaqScalers.java b/src/main/java/org/jlab/detector/scalers/DaqScalers.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/scalers/DaqScalers.java rename to src/main/java/org/jlab/detector/scalers/DaqScalers.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/scalers/DaqScalersSequence.java b/src/main/java/org/jlab/detector/scalers/DaqScalersSequence.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/scalers/DaqScalersSequence.java rename to src/main/java/org/jlab/detector/scalers/DaqScalersSequence.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/scalers/Dsc2Scaler.java b/src/main/java/org/jlab/detector/scalers/Dsc2Scaler.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/scalers/Dsc2Scaler.java rename to src/main/java/org/jlab/detector/scalers/Dsc2Scaler.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/scalers/StruckScaler.java b/src/main/java/org/jlab/detector/scalers/StruckScaler.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/scalers/StruckScaler.java rename to src/main/java/org/jlab/detector/scalers/StruckScaler.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/scalers/StruckScalers.java b/src/main/java/org/jlab/detector/scalers/StruckScalers.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/scalers/StruckScalers.java rename to src/main/java/org/jlab/detector/scalers/StruckScalers.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/swaps/SwapManager.java b/src/main/java/org/jlab/detector/swaps/SwapManager.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/swaps/SwapManager.java rename to src/main/java/org/jlab/detector/swaps/SwapManager.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/swaps/SwapTable.java b/src/main/java/org/jlab/detector/swaps/SwapTable.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/swaps/SwapTable.java rename to src/main/java/org/jlab/detector/swaps/SwapTable.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/units/Measurement.java b/src/main/java/org/jlab/detector/units/Measurement.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/units/Measurement.java rename to src/main/java/org/jlab/detector/units/Measurement.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/units/SystemOfUnits.java b/src/main/java/org/jlab/detector/units/SystemOfUnits.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/units/SystemOfUnits.java rename to src/main/java/org/jlab/detector/units/SystemOfUnits.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/view/DetectorListener.java b/src/main/java/org/jlab/detector/view/DetectorListener.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/view/DetectorListener.java rename to src/main/java/org/jlab/detector/view/DetectorListener.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/view/DetectorPane2D.java b/src/main/java/org/jlab/detector/view/DetectorPane2D.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/view/DetectorPane2D.java rename to src/main/java/org/jlab/detector/view/DetectorPane2D.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/view/DetectorShape2D.java b/src/main/java/org/jlab/detector/view/DetectorShape2D.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/view/DetectorShape2D.java rename to src/main/java/org/jlab/detector/view/DetectorShape2D.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/view/DetectorView2D.java b/src/main/java/org/jlab/detector/view/DetectorView2D.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/view/DetectorView2D.java rename to src/main/java/org/jlab/detector/view/DetectorView2D.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/view/ViewWorld.java b/src/main/java/org/jlab/detector/view/ViewWorld.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/view/ViewWorld.java rename to src/main/java/org/jlab/detector/view/ViewWorld.java diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/view/ViewerTests.java b/src/main/java/org/jlab/detector/view/ViewerTests.java similarity index 100% rename from common-tools/clas-detector/src/main/java/org/jlab/detector/view/ViewerTests.java rename to src/main/java/org/jlab/detector/view/ViewerTests.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Box.java b/src/main/java/org/jlab/detector/volume/G4Box.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Box.java rename to src/main/java/org/jlab/detector/volume/G4Box.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Operation.java b/src/main/java/org/jlab/detector/volume/G4Operation.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Operation.java rename to src/main/java/org/jlab/detector/volume/G4Operation.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Pgon.java b/src/main/java/org/jlab/detector/volume/G4Pgon.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Pgon.java rename to src/main/java/org/jlab/detector/volume/G4Pgon.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Stl.java b/src/main/java/org/jlab/detector/volume/G4Stl.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Stl.java rename to src/main/java/org/jlab/detector/volume/G4Stl.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Trap.java b/src/main/java/org/jlab/detector/volume/G4Trap.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Trap.java rename to src/main/java/org/jlab/detector/volume/G4Trap.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Trd.java b/src/main/java/org/jlab/detector/volume/G4Trd.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Trd.java rename to src/main/java/org/jlab/detector/volume/G4Trd.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Tubs.java b/src/main/java/org/jlab/detector/volume/G4Tubs.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4Tubs.java rename to src/main/java/org/jlab/detector/volume/G4Tubs.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4World.java b/src/main/java/org/jlab/detector/volume/G4World.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/G4World.java rename to src/main/java/org/jlab/detector/volume/G4World.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/Geant4Basic.java b/src/main/java/org/jlab/detector/volume/Geant4Basic.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/Geant4Basic.java rename to src/main/java/org/jlab/detector/volume/Geant4Basic.java diff --git a/reconstruction/ec/src/main/java/org/jlab/display/ec/ECDisplay.java b/src/main/java/org/jlab/display/ec/ECDisplay.java similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/display/ec/ECDisplay.java rename to src/main/java/org/jlab/display/ec/ECDisplay.java diff --git a/reconstruction/ec/src/main/java/org/jlab/display/ec/ECMonitor.java b/src/main/java/org/jlab/display/ec/ECMonitor.java similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/display/ec/ECMonitor.java rename to src/main/java/org/jlab/display/ec/ECMonitor.java diff --git a/reconstruction/ec/src/main/java/org/jlab/display/ec/ECPion.java-DISABLED b/src/main/java/org/jlab/display/ec/ECPion.java-DISABLED similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/display/ec/ECPion.java-DISABLED rename to src/main/java/org/jlab/display/ec/ECPion.java-DISABLED diff --git a/reconstruction/ec/src/main/java/org/jlab/display/ec/ECPionFinder.java b/src/main/java/org/jlab/display/ec/ECPionFinder.java similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/display/ec/ECPionFinder.java rename to src/main/java/org/jlab/display/ec/ECPionFinder.java diff --git a/reconstruction/ec/src/main/java/org/jlab/display/ec/ECRECMonitor.java b/src/main/java/org/jlab/display/ec/ECRECMonitor.java similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/display/ec/ECRECMonitor.java rename to src/main/java/org/jlab/display/ec/ECRECMonitor.java diff --git a/reconstruction/ec/src/main/java/org/jlab/display/ec/Renderer.java b/src/main/java/org/jlab/display/ec/Renderer.java similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/display/ec/Renderer.java rename to src/main/java/org/jlab/display/ec/Renderer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/CoordinateSystem.java b/src/main/java/org/jlab/geom/CoordinateSystem.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/CoordinateSystem.java rename to src/main/java/org/jlab/geom/CoordinateSystem.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/DetectorHit.java b/src/main/java/org/jlab/geom/DetectorHit.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/DetectorHit.java rename to src/main/java/org/jlab/geom/DetectorHit.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/DetectorId.java b/src/main/java/org/jlab/geom/DetectorId.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/DetectorId.java rename to src/main/java/org/jlab/geom/DetectorId.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/G4Volume.java b/src/main/java/org/jlab/geom/G4Volume.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/G4Volume.java rename to src/main/java/org/jlab/geom/G4Volume.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/G4VolumeMap.java b/src/main/java/org/jlab/geom/G4VolumeMap.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/G4VolumeMap.java rename to src/main/java/org/jlab/geom/G4VolumeMap.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/Showable.java b/src/main/java/org/jlab/geom/Showable.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/Showable.java rename to src/main/java/org/jlab/geom/Showable.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/abs/AbstractComponent.java b/src/main/java/org/jlab/geom/abs/AbstractComponent.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/abs/AbstractComponent.java rename to src/main/java/org/jlab/geom/abs/AbstractComponent.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/abs/AbstractDetector.java b/src/main/java/org/jlab/geom/abs/AbstractDetector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/abs/AbstractDetector.java rename to src/main/java/org/jlab/geom/abs/AbstractDetector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/abs/AbstractLayer.java b/src/main/java/org/jlab/geom/abs/AbstractLayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/abs/AbstractLayer.java rename to src/main/java/org/jlab/geom/abs/AbstractLayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/abs/AbstractSector.java b/src/main/java/org/jlab/geom/abs/AbstractSector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/abs/AbstractSector.java rename to src/main/java/org/jlab/geom/abs/AbstractSector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/abs/AbstractSuperlayer.java b/src/main/java/org/jlab/geom/abs/AbstractSuperlayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/abs/AbstractSuperlayer.java rename to src/main/java/org/jlab/geom/abs/AbstractSuperlayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/abs/MeshComponent.java b/src/main/java/org/jlab/geom/abs/MeshComponent.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/abs/MeshComponent.java rename to src/main/java/org/jlab/geom/abs/MeshComponent.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/base/Component.java b/src/main/java/org/jlab/geom/base/Component.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/base/Component.java rename to src/main/java/org/jlab/geom/base/Component.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/base/ConstantProvider.java b/src/main/java/org/jlab/geom/base/ConstantProvider.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/base/ConstantProvider.java rename to src/main/java/org/jlab/geom/base/ConstantProvider.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/base/Detector.java b/src/main/java/org/jlab/geom/base/Detector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/base/Detector.java rename to src/main/java/org/jlab/geom/base/Detector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/base/DetectorTransformation.java b/src/main/java/org/jlab/geom/base/DetectorTransformation.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/base/DetectorTransformation.java rename to src/main/java/org/jlab/geom/base/DetectorTransformation.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/base/Factory.java b/src/main/java/org/jlab/geom/base/Factory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/base/Factory.java rename to src/main/java/org/jlab/geom/base/Factory.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/base/Layer.java b/src/main/java/org/jlab/geom/base/Layer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/base/Layer.java rename to src/main/java/org/jlab/geom/base/Layer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/base/Sector.java b/src/main/java/org/jlab/geom/base/Sector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/base/Sector.java rename to src/main/java/org/jlab/geom/base/Sector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/base/Superlayer.java b/src/main/java/org/jlab/geom/base/Superlayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/base/Superlayer.java rename to src/main/java/org/jlab/geom/base/Superlayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/component/DriftChamberWire.java b/src/main/java/org/jlab/geom/component/DriftChamberWire.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/component/DriftChamberWire.java rename to src/main/java/org/jlab/geom/component/DriftChamberWire.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/component/PrismaticComponent.java b/src/main/java/org/jlab/geom/component/PrismaticComponent.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/component/PrismaticComponent.java rename to src/main/java/org/jlab/geom/component/PrismaticComponent.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/component/RectangularComponent.java b/src/main/java/org/jlab/geom/component/RectangularComponent.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/component/RectangularComponent.java rename to src/main/java/org/jlab/geom/component/RectangularComponent.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/component/ScintillatorMesh.java b/src/main/java/org/jlab/geom/component/ScintillatorMesh.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/component/ScintillatorMesh.java rename to src/main/java/org/jlab/geom/component/ScintillatorMesh.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/component/ScintillatorPaddle.java b/src/main/java/org/jlab/geom/component/ScintillatorPaddle.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/component/ScintillatorPaddle.java rename to src/main/java/org/jlab/geom/component/ScintillatorPaddle.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/component/SiStrip.java b/src/main/java/org/jlab/geom/component/SiStrip.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/component/SiStrip.java rename to src/main/java/org/jlab/geom/component/SiStrip.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/component/TrackerStrip.java b/src/main/java/org/jlab/geom/component/TrackerStrip.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/component/TrackerStrip.java rename to src/main/java/org/jlab/geom/component/TrackerStrip.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCDetector.java b/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCDetector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCDetector.java rename to src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCDetector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCFactory.java b/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCFactory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCFactory.java rename to src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCFactory.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCLayer.java b/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCLayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCLayer.java rename to src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCLayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCSector.java b/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCSector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCSector.java rename to src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCSector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCSuperlayer.java b/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCSuperlayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCSuperlayer.java rename to src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCSuperlayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCWire.java b/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCWire.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCWire.java rename to src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCWire.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/ConcaveComponent.java b/src/main/java/org/jlab/geom/detector/alert/AHDC/ConcaveComponent.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/ConcaveComponent.java rename to src/main/java/org/jlab/geom/detector/alert/AHDC/ConcaveComponent.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFDetector.java b/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFDetector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFDetector.java rename to src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFDetector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFFactory.java b/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFFactory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFFactory.java rename to src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFFactory.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFLayer.java b/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFLayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFLayer.java rename to src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFLayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFSector.java b/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFSector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFSector.java rename to src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFSector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFSuperlayer.java b/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFSuperlayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFSuperlayer.java rename to src/main/java/org/jlab/geom/detector/alert/ATOF/AlertTOFSuperlayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/bst/BSTDetector.java b/src/main/java/org/jlab/geom/detector/bst/BSTDetector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/bst/BSTDetector.java rename to src/main/java/org/jlab/geom/detector/bst/BSTDetector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/bst/BSTFactory.java b/src/main/java/org/jlab/geom/detector/bst/BSTFactory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/bst/BSTFactory.java rename to src/main/java/org/jlab/geom/detector/bst/BSTFactory.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/bst/BSTLayer.java b/src/main/java/org/jlab/geom/detector/bst/BSTLayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/bst/BSTLayer.java rename to src/main/java/org/jlab/geom/detector/bst/BSTLayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/bst/BSTRing.java b/src/main/java/org/jlab/geom/detector/bst/BSTRing.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/bst/BSTRing.java rename to src/main/java/org/jlab/geom/detector/bst/BSTRing.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/bst/BSTSector.java b/src/main/java/org/jlab/geom/detector/bst/BSTSector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/bst/BSTSector.java rename to src/main/java/org/jlab/geom/detector/bst/BSTSector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/bst/BSTSuperlayer.java b/src/main/java/org/jlab/geom/detector/bst/BSTSuperlayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/bst/BSTSuperlayer.java rename to src/main/java/org/jlab/geom/detector/bst/BSTSuperlayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/cnd/CNDDetector.java b/src/main/java/org/jlab/geom/detector/cnd/CNDDetector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/cnd/CNDDetector.java rename to src/main/java/org/jlab/geom/detector/cnd/CNDDetector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/cnd/CNDFactory.java b/src/main/java/org/jlab/geom/detector/cnd/CNDFactory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/cnd/CNDFactory.java rename to src/main/java/org/jlab/geom/detector/cnd/CNDFactory.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/cnd/CNDLayer.java b/src/main/java/org/jlab/geom/detector/cnd/CNDLayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/cnd/CNDLayer.java rename to src/main/java/org/jlab/geom/detector/cnd/CNDLayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/cnd/CNDSector.java b/src/main/java/org/jlab/geom/detector/cnd/CNDSector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/cnd/CNDSector.java rename to src/main/java/org/jlab/geom/detector/cnd/CNDSector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/cnd/CNDSuperlayer.java b/src/main/java/org/jlab/geom/detector/cnd/CNDSuperlayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/cnd/CNDSuperlayer.java rename to src/main/java/org/jlab/geom/detector/cnd/CNDSuperlayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DCDetector.java b/src/main/java/org/jlab/geom/detector/dc/DCDetector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DCDetector.java rename to src/main/java/org/jlab/geom/detector/dc/DCDetector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DCFactory.java b/src/main/java/org/jlab/geom/detector/dc/DCFactory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DCFactory.java rename to src/main/java/org/jlab/geom/detector/dc/DCFactory.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DCFactoryUpdated.java b/src/main/java/org/jlab/geom/detector/dc/DCFactoryUpdated.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DCFactoryUpdated.java rename to src/main/java/org/jlab/geom/detector/dc/DCFactoryUpdated.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DCLayer.java b/src/main/java/org/jlab/geom/detector/dc/DCLayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DCLayer.java rename to src/main/java/org/jlab/geom/detector/dc/DCLayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DCSector.java b/src/main/java/org/jlab/geom/detector/dc/DCSector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DCSector.java rename to src/main/java/org/jlab/geom/detector/dc/DCSector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DCSuperlayer.java b/src/main/java/org/jlab/geom/detector/dc/DCSuperlayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DCSuperlayer.java rename to src/main/java/org/jlab/geom/detector/dc/DCSuperlayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DriftChamber.java b/src/main/java/org/jlab/geom/detector/dc/DriftChamber.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/DriftChamber.java rename to src/main/java/org/jlab/geom/detector/dc/DriftChamber.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/Layer.java b/src/main/java/org/jlab/geom/detector/dc/Layer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/Layer.java rename to src/main/java/org/jlab/geom/detector/dc/Layer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/Region.java b/src/main/java/org/jlab/geom/detector/dc/Region.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/Region.java rename to src/main/java/org/jlab/geom/detector/dc/Region.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/Sector.java b/src/main/java/org/jlab/geom/detector/dc/Sector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/Sector.java rename to src/main/java/org/jlab/geom/detector/dc/Sector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/Superlayer.java b/src/main/java/org/jlab/geom/detector/dc/Superlayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/dc/Superlayer.java rename to src/main/java/org/jlab/geom/detector/dc/Superlayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ec/ECDetector.java b/src/main/java/org/jlab/geom/detector/ec/ECDetector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ec/ECDetector.java rename to src/main/java/org/jlab/geom/detector/ec/ECDetector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ec/ECDetectorDraw.java b/src/main/java/org/jlab/geom/detector/ec/ECDetectorDraw.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ec/ECDetectorDraw.java rename to src/main/java/org/jlab/geom/detector/ec/ECDetectorDraw.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ec/ECFactory.java b/src/main/java/org/jlab/geom/detector/ec/ECFactory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ec/ECFactory.java rename to src/main/java/org/jlab/geom/detector/ec/ECFactory.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ec/ECLayer.java b/src/main/java/org/jlab/geom/detector/ec/ECLayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ec/ECLayer.java rename to src/main/java/org/jlab/geom/detector/ec/ECLayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ec/ECSector.java b/src/main/java/org/jlab/geom/detector/ec/ECSector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ec/ECSector.java rename to src/main/java/org/jlab/geom/detector/ec/ECSector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ec/ECSuperlayer.java b/src/main/java/org/jlab/geom/detector/ec/ECSuperlayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ec/ECSuperlayer.java rename to src/main/java/org/jlab/geom/detector/ec/ECSuperlayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/fmt/FMTDetector.java b/src/main/java/org/jlab/geom/detector/fmt/FMTDetector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/fmt/FMTDetector.java rename to src/main/java/org/jlab/geom/detector/fmt/FMTDetector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/fmt/FMTFactory.java b/src/main/java/org/jlab/geom/detector/fmt/FMTFactory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/fmt/FMTFactory.java rename to src/main/java/org/jlab/geom/detector/fmt/FMTFactory.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/fmt/FMTLayer.java b/src/main/java/org/jlab/geom/detector/fmt/FMTLayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/fmt/FMTLayer.java rename to src/main/java/org/jlab/geom/detector/fmt/FMTLayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/fmt/FMTSector.java b/src/main/java/org/jlab/geom/detector/fmt/FMTSector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/fmt/FMTSector.java rename to src/main/java/org/jlab/geom/detector/fmt/FMTSector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/fmt/FMTSuperlayer.java b/src/main/java/org/jlab/geom/detector/fmt/FMTSuperlayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/fmt/FMTSuperlayer.java rename to src/main/java/org/jlab/geom/detector/fmt/FMTSuperlayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ft/FTCALDetector.java b/src/main/java/org/jlab/geom/detector/ft/FTCALDetector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ft/FTCALDetector.java rename to src/main/java/org/jlab/geom/detector/ft/FTCALDetector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ft/FTCALFactory.java b/src/main/java/org/jlab/geom/detector/ft/FTCALFactory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ft/FTCALFactory.java rename to src/main/java/org/jlab/geom/detector/ft/FTCALFactory.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ft/FTCALLayer.java b/src/main/java/org/jlab/geom/detector/ft/FTCALLayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ft/FTCALLayer.java rename to src/main/java/org/jlab/geom/detector/ft/FTCALLayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ft/FTCALSector.java b/src/main/java/org/jlab/geom/detector/ft/FTCALSector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ft/FTCALSector.java rename to src/main/java/org/jlab/geom/detector/ft/FTCALSector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ft/FTCALSuperlayer.java b/src/main/java/org/jlab/geom/detector/ft/FTCALSuperlayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ft/FTCALSuperlayer.java rename to src/main/java/org/jlab/geom/detector/ft/FTCALSuperlayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFDetector.java b/src/main/java/org/jlab/geom/detector/ftof/FTOFDetector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFDetector.java rename to src/main/java/org/jlab/geom/detector/ftof/FTOFDetector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFDetectorMesh.java b/src/main/java/org/jlab/geom/detector/ftof/FTOFDetectorMesh.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFDetectorMesh.java rename to src/main/java/org/jlab/geom/detector/ftof/FTOFDetectorMesh.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFFactory.java b/src/main/java/org/jlab/geom/detector/ftof/FTOFFactory.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFFactory.java rename to src/main/java/org/jlab/geom/detector/ftof/FTOFFactory.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFLayer.java b/src/main/java/org/jlab/geom/detector/ftof/FTOFLayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFLayer.java rename to src/main/java/org/jlab/geom/detector/ftof/FTOFLayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFLayerMesh.java b/src/main/java/org/jlab/geom/detector/ftof/FTOFLayerMesh.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFLayerMesh.java rename to src/main/java/org/jlab/geom/detector/ftof/FTOFLayerMesh.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFSector.java b/src/main/java/org/jlab/geom/detector/ftof/FTOFSector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFSector.java rename to src/main/java/org/jlab/geom/detector/ftof/FTOFSector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFSectorMesh.java b/src/main/java/org/jlab/geom/detector/ftof/FTOFSectorMesh.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFSectorMesh.java rename to src/main/java/org/jlab/geom/detector/ftof/FTOFSectorMesh.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFSuperlayer.java b/src/main/java/org/jlab/geom/detector/ftof/FTOFSuperlayer.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFSuperlayer.java rename to src/main/java/org/jlab/geom/detector/ftof/FTOFSuperlayer.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFSuperlayerMesh.java b/src/main/java/org/jlab/geom/detector/ftof/FTOFSuperlayerMesh.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/FTOFSuperlayerMesh.java rename to src/main/java/org/jlab/geom/detector/ftof/FTOFSuperlayerMesh.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/ForwardTOF.java b/src/main/java/org/jlab/geom/detector/ftof/ForwardTOF.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/ForwardTOF.java rename to src/main/java/org/jlab/geom/detector/ftof/ForwardTOF.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/Paddle.java b/src/main/java/org/jlab/geom/detector/ftof/Paddle.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/Paddle.java rename to src/main/java/org/jlab/geom/detector/ftof/Paddle.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/Panel.java b/src/main/java/org/jlab/geom/detector/ftof/Panel.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/Panel.java rename to src/main/java/org/jlab/geom/detector/ftof/Panel.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/Sector.java b/src/main/java/org/jlab/geom/detector/ftof/Sector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/ftof/Sector.java rename to src/main/java/org/jlab/geom/detector/ftof/Sector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/DetectoMesh2DViewApp.java-BAK b/src/main/java/org/jlab/geom/fx/DetectoMesh2DViewApp.java-BAK similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/DetectoMesh2DViewApp.java-BAK rename to src/main/java/org/jlab/geom/fx/DetectoMesh2DViewApp.java-BAK diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/DetectorEventHandler.java-BAK b/src/main/java/org/jlab/geom/fx/DetectorEventHandler.java-BAK similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/DetectorEventHandler.java-BAK rename to src/main/java/org/jlab/geom/fx/DetectorEventHandler.java-BAK diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/DetectorMesh2D.java-BAK b/src/main/java/org/jlab/geom/fx/DetectorMesh2D.java-BAK similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/DetectorMesh2D.java-BAK rename to src/main/java/org/jlab/geom/fx/DetectorMesh2D.java-BAK diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/DetectorMesh2DCanvas.java-BAK b/src/main/java/org/jlab/geom/fx/DetectorMesh2DCanvas.java-BAK similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/DetectorMesh2DCanvas.java-BAK rename to src/main/java/org/jlab/geom/fx/DetectorMesh2DCanvas.java-BAK diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/DetectorMesh2DLayer.java-BAK b/src/main/java/org/jlab/geom/fx/DetectorMesh2DLayer.java-BAK similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/DetectorMesh2DLayer.java-BAK rename to src/main/java/org/jlab/geom/fx/DetectorMesh2DLayer.java-BAK diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/DetectorTabView.java-BAK b/src/main/java/org/jlab/geom/fx/DetectorTabView.java-BAK similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/DetectorTabView.java-BAK rename to src/main/java/org/jlab/geom/fx/DetectorTabView.java-BAK diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/Mesh3D.java-BAK b/src/main/java/org/jlab/geom/fx/Mesh3D.java-BAK similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/Mesh3D.java-BAK rename to src/main/java/org/jlab/geom/fx/Mesh3D.java-BAK diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/PopupText.java-BAK b/src/main/java/org/jlab/geom/fx/PopupText.java-BAK similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/fx/PopupText.java-BAK rename to src/main/java/org/jlab/geom/fx/PopupText.java-BAK diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/G4BaseVolume.java b/src/main/java/org/jlab/geom/geant/G4BaseVolume.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/G4BaseVolume.java rename to src/main/java/org/jlab/geom/geant/G4BaseVolume.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/G4Material.java b/src/main/java/org/jlab/geom/geant/G4Material.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/G4Material.java rename to src/main/java/org/jlab/geom/geant/G4Material.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/G4Trd.java b/src/main/java/org/jlab/geom/geant/G4Trd.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/G4Trd.java rename to src/main/java/org/jlab/geom/geant/G4Trd.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/Geant4Basic.java b/src/main/java/org/jlab/geom/geant/Geant4Basic.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/Geant4Basic.java rename to src/main/java/org/jlab/geom/geant/Geant4Basic.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/Geant4Box.java b/src/main/java/org/jlab/geom/geant/Geant4Box.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/Geant4Box.java rename to src/main/java/org/jlab/geom/geant/Geant4Box.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/Geant4Mesh.java b/src/main/java/org/jlab/geom/geant/Geant4Mesh.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/Geant4Mesh.java rename to src/main/java/org/jlab/geom/geant/Geant4Mesh.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/GemcTestProgram.java b/src/main/java/org/jlab/geom/geant/GemcTestProgram.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/GemcTestProgram.java rename to src/main/java/org/jlab/geom/geant/GemcTestProgram.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/IG4Volume.java b/src/main/java/org/jlab/geom/geant/IG4Volume.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/IG4Volume.java rename to src/main/java/org/jlab/geom/geant/IG4Volume.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/IGeant4Volume.java b/src/main/java/org/jlab/geom/geant/IGeant4Volume.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/geant/IGeant4Volume.java rename to src/main/java/org/jlab/geom/geant/IGeant4Volume.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gemc/GemcBank.java b/src/main/java/org/jlab/geom/gemc/GemcBank.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gemc/GemcBank.java rename to src/main/java/org/jlab/geom/gemc/GemcBank.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gemc/GemcDetector.java b/src/main/java/org/jlab/geom/gemc/GemcDetector.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gemc/GemcDetector.java rename to src/main/java/org/jlab/geom/gemc/GemcDetector.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gemc/GemcHit.java b/src/main/java/org/jlab/geom/gemc/GemcHit.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gemc/GemcHit.java rename to src/main/java/org/jlab/geom/gemc/GemcHit.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gemc/GemcMaterial.java b/src/main/java/org/jlab/geom/gemc/GemcMaterial.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gemc/GemcMaterial.java rename to src/main/java/org/jlab/geom/gemc/GemcMaterial.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gemc/GemcPropertyMap.java b/src/main/java/org/jlab/geom/gemc/GemcPropertyMap.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gemc/GemcPropertyMap.java rename to src/main/java/org/jlab/geom/gemc/GemcPropertyMap.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gemc/GemcPropertyMaps.java b/src/main/java/org/jlab/geom/gemc/GemcPropertyMaps.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gemc/GemcPropertyMaps.java rename to src/main/java/org/jlab/geom/gemc/GemcPropertyMaps.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorComponentUI.java b/src/main/java/org/jlab/geom/gui/DetectorComponentUI.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorComponentUI.java rename to src/main/java/org/jlab/geom/gui/DetectorComponentUI.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorLayerPanel.java b/src/main/java/org/jlab/geom/gui/DetectorLayerPanel.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorLayerPanel.java rename to src/main/java/org/jlab/geom/gui/DetectorLayerPanel.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorLayerUI.java b/src/main/java/org/jlab/geom/gui/DetectorLayerUI.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorLayerUI.java rename to src/main/java/org/jlab/geom/gui/DetectorLayerUI.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorShape3D.java b/src/main/java/org/jlab/geom/gui/DetectorShape3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorShape3D.java rename to src/main/java/org/jlab/geom/gui/DetectorShape3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorShape3DPanel.java b/src/main/java/org/jlab/geom/gui/DetectorShape3DPanel.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorShape3DPanel.java rename to src/main/java/org/jlab/geom/gui/DetectorShape3DPanel.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorShape3DStore.java b/src/main/java/org/jlab/geom/gui/DetectorShape3DStore.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorShape3DStore.java rename to src/main/java/org/jlab/geom/gui/DetectorShape3DStore.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorViewPanel.java b/src/main/java/org/jlab/geom/gui/DetectorViewPanel.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/DetectorViewPanel.java rename to src/main/java/org/jlab/geom/gui/DetectorViewPanel.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/GeometryFrame.java b/src/main/java/org/jlab/geom/gui/GeometryFrame.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/GeometryFrame.java rename to src/main/java/org/jlab/geom/gui/GeometryFrame.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/GeometryPanel.java b/src/main/java/org/jlab/geom/gui/GeometryPanel.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/GeometryPanel.java rename to src/main/java/org/jlab/geom/gui/GeometryPanel.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/GeometryProfiler.java b/src/main/java/org/jlab/geom/gui/GeometryProfiler.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/GeometryProfiler.java rename to src/main/java/org/jlab/geom/gui/GeometryProfiler.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/IDetectorComponentSelection.java b/src/main/java/org/jlab/geom/gui/IDetectorComponentSelection.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/IDetectorComponentSelection.java rename to src/main/java/org/jlab/geom/gui/IDetectorComponentSelection.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/IDetectorShapeIntensity.java b/src/main/java/org/jlab/geom/gui/IDetectorShapeIntensity.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/gui/IDetectorShapeIntensity.java rename to src/main/java/org/jlab/geom/gui/IDetectorShapeIntensity.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Arc3D.java b/src/main/java/org/jlab/geom/prim/Arc3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Arc3D.java rename to src/main/java/org/jlab/geom/prim/Arc3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Camera3D.java b/src/main/java/org/jlab/geom/prim/Camera3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Camera3D.java rename to src/main/java/org/jlab/geom/prim/Camera3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Cylindrical3D.java b/src/main/java/org/jlab/geom/prim/Cylindrical3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Cylindrical3D.java rename to src/main/java/org/jlab/geom/prim/Cylindrical3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Face3D.java b/src/main/java/org/jlab/geom/prim/Face3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Face3D.java rename to src/main/java/org/jlab/geom/prim/Face3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Helix3D.java b/src/main/java/org/jlab/geom/prim/Helix3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Helix3D.java rename to src/main/java/org/jlab/geom/prim/Helix3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Line3D.java b/src/main/java/org/jlab/geom/prim/Line3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Line3D.java rename to src/main/java/org/jlab/geom/prim/Line3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Mesh3D.java b/src/main/java/org/jlab/geom/prim/Mesh3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Mesh3D.java rename to src/main/java/org/jlab/geom/prim/Mesh3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Path3D.java b/src/main/java/org/jlab/geom/prim/Path3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Path3D.java rename to src/main/java/org/jlab/geom/prim/Path3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Plane3D.java b/src/main/java/org/jlab/geom/prim/Plane3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Plane3D.java rename to src/main/java/org/jlab/geom/prim/Plane3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Point3D.java b/src/main/java/org/jlab/geom/prim/Point3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Point3D.java rename to src/main/java/org/jlab/geom/prim/Point3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Region3D.java b/src/main/java/org/jlab/geom/prim/Region3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Region3D.java rename to src/main/java/org/jlab/geom/prim/Region3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Sector3D.java b/src/main/java/org/jlab/geom/prim/Sector3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Sector3D.java rename to src/main/java/org/jlab/geom/prim/Sector3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Shape3D.java b/src/main/java/org/jlab/geom/prim/Shape3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Shape3D.java rename to src/main/java/org/jlab/geom/prim/Shape3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Sphere3D.java b/src/main/java/org/jlab/geom/prim/Sphere3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Sphere3D.java rename to src/main/java/org/jlab/geom/prim/Sphere3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Transformable.java b/src/main/java/org/jlab/geom/prim/Transformable.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Transformable.java rename to src/main/java/org/jlab/geom/prim/Transformable.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Transformation3D.java b/src/main/java/org/jlab/geom/prim/Transformation3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Transformation3D.java rename to src/main/java/org/jlab/geom/prim/Transformation3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Trap3D.java b/src/main/java/org/jlab/geom/prim/Trap3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Trap3D.java rename to src/main/java/org/jlab/geom/prim/Trap3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Triangle3D.java b/src/main/java/org/jlab/geom/prim/Triangle3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Triangle3D.java rename to src/main/java/org/jlab/geom/prim/Triangle3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Vector3D.java b/src/main/java/org/jlab/geom/prim/Vector3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/prim/Vector3D.java rename to src/main/java/org/jlab/geom/prim/Vector3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/view/Box3D.java b/src/main/java/org/jlab/geom/view/Box3D.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/view/Box3D.java rename to src/main/java/org/jlab/geom/view/Box3D.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/view/GeometryView.java b/src/main/java/org/jlab/geom/view/GeometryView.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/view/GeometryView.java rename to src/main/java/org/jlab/geom/view/GeometryView.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/view/ShapeObject.java b/src/main/java/org/jlab/geom/view/ShapeObject.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/view/ShapeObject.java rename to src/main/java/org/jlab/geom/view/ShapeObject.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/view/ShapePath.java b/src/main/java/org/jlab/geom/view/ShapePath.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/view/ShapePath.java rename to src/main/java/org/jlab/geom/view/ShapePath.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/view/ShapePoint.java b/src/main/java/org/jlab/geom/view/ShapePoint.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/view/ShapePoint.java rename to src/main/java/org/jlab/geom/view/ShapePoint.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/view/UniverseCoordinateSystem.java b/src/main/java/org/jlab/geom/view/UniverseCoordinateSystem.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/view/UniverseCoordinateSystem.java rename to src/main/java/org/jlab/geom/view/UniverseCoordinateSystem.java diff --git a/common-tools/clas-geometry/src/main/java/org/jlab/geom/view/UniverseScene.java b/src/main/java/org/jlab/geom/view/UniverseScene.java similarity index 100% rename from common-tools/clas-geometry/src/main/java/org/jlab/geom/view/UniverseScene.java rename to src/main/java/org/jlab/geom/view/UniverseScene.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Box.java b/src/main/java/org/jlab/geometry/prim/Box.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Box.java rename to src/main/java/org/jlab/geometry/prim/Box.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Line3d.java b/src/main/java/org/jlab/geometry/prim/Line3d.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Line3d.java rename to src/main/java/org/jlab/geometry/prim/Line3d.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/LineSegment3d.java b/src/main/java/org/jlab/geometry/prim/LineSegment3d.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/LineSegment3d.java rename to src/main/java/org/jlab/geometry/prim/LineSegment3d.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Operation.java b/src/main/java/org/jlab/geometry/prim/Operation.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Operation.java rename to src/main/java/org/jlab/geometry/prim/Operation.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Pgon.java b/src/main/java/org/jlab/geometry/prim/Pgon.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Pgon.java rename to src/main/java/org/jlab/geometry/prim/Pgon.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Ray3d.java b/src/main/java/org/jlab/geometry/prim/Ray3d.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Ray3d.java rename to src/main/java/org/jlab/geometry/prim/Ray3d.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/StlPrim.java b/src/main/java/org/jlab/geometry/prim/StlPrim.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/StlPrim.java rename to src/main/java/org/jlab/geometry/prim/StlPrim.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Straight.java b/src/main/java/org/jlab/geometry/prim/Straight.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Straight.java rename to src/main/java/org/jlab/geometry/prim/Straight.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Trap.java b/src/main/java/org/jlab/geometry/prim/Trap.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Trap.java rename to src/main/java/org/jlab/geometry/prim/Trap.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Trd.java b/src/main/java/org/jlab/geometry/prim/Trd.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Trd.java rename to src/main/java/org/jlab/geometry/prim/Trd.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Triangle3d.java b/src/main/java/org/jlab/geometry/prim/Triangle3d.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Triangle3d.java rename to src/main/java/org/jlab/geometry/prim/Triangle3d.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Tube.java b/src/main/java/org/jlab/geometry/prim/Tube.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/geometry/prim/Tube.java rename to src/main/java/org/jlab/geometry/prim/Tube.java diff --git a/common-tools/clas-jcsg/src/main/java/org/jlab/geometry/utils/SCAD.java b/src/main/java/org/jlab/geometry/utils/SCAD.java similarity index 100% rename from common-tools/clas-jcsg/src/main/java/org/jlab/geometry/utils/SCAD.java rename to src/main/java/org/jlab/geometry/utils/SCAD.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/base/BasicDataBank.java b/src/main/java/org/jlab/io/base/BasicDataBank.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/base/BasicDataBank.java rename to src/main/java/org/jlab/io/base/BasicDataBank.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/base/DataBank.java b/src/main/java/org/jlab/io/base/DataBank.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/base/DataBank.java rename to src/main/java/org/jlab/io/base/DataBank.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/base/DataDescriptor.java b/src/main/java/org/jlab/io/base/DataDescriptor.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/base/DataDescriptor.java rename to src/main/java/org/jlab/io/base/DataDescriptor.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/base/DataDictionary.java b/src/main/java/org/jlab/io/base/DataDictionary.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/base/DataDictionary.java rename to src/main/java/org/jlab/io/base/DataDictionary.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/base/DataEntryType.java b/src/main/java/org/jlab/io/base/DataEntryType.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/base/DataEntryType.java rename to src/main/java/org/jlab/io/base/DataEntryType.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/base/DataEvent.java b/src/main/java/org/jlab/io/base/DataEvent.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/base/DataEvent.java rename to src/main/java/org/jlab/io/base/DataEvent.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/base/DataEventList.java b/src/main/java/org/jlab/io/base/DataEventList.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/base/DataEventList.java rename to src/main/java/org/jlab/io/base/DataEventList.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/base/DataEventType.java b/src/main/java/org/jlab/io/base/DataEventType.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/base/DataEventType.java rename to src/main/java/org/jlab/io/base/DataEventType.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/base/DataSource.java b/src/main/java/org/jlab/io/base/DataSource.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/base/DataSource.java rename to src/main/java/org/jlab/io/base/DataSource.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/base/DataSourceType.java b/src/main/java/org/jlab/io/base/DataSourceType.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/base/DataSourceType.java rename to src/main/java/org/jlab/io/base/DataSourceType.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/base/DataSync.java b/src/main/java/org/jlab/io/base/DataSync.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/base/DataSync.java rename to src/main/java/org/jlab/io/base/DataSync.java diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/Clas12Reader.java b/src/main/java/org/jlab/io/clara/Clas12Reader.java similarity index 100% rename from common-tools/clara-io/src/main/java/org/jlab/io/clara/Clas12Reader.java rename to src/main/java/org/jlab/io/clara/Clas12Reader.java diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/Clas12Types.java b/src/main/java/org/jlab/io/clara/Clas12Types.java similarity index 100% rename from common-tools/clara-io/src/main/java/org/jlab/io/clara/Clas12Types.java rename to src/main/java/org/jlab/io/clara/Clas12Types.java diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/DecoderReader.java b/src/main/java/org/jlab/io/clara/DecoderReader.java similarity index 100% rename from common-tools/clara-io/src/main/java/org/jlab/io/clara/DecoderReader.java rename to src/main/java/org/jlab/io/clara/DecoderReader.java diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/DecoderWriter.java b/src/main/java/org/jlab/io/clara/DecoderWriter.java similarity index 100% rename from common-tools/clara-io/src/main/java/org/jlab/io/clara/DecoderWriter.java rename to src/main/java/org/jlab/io/clara/DecoderWriter.java diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/EvioToEvioReader.java b/src/main/java/org/jlab/io/clara/EvioToEvioReader.java similarity index 100% rename from common-tools/clara-io/src/main/java/org/jlab/io/clara/EvioToEvioReader.java rename to src/main/java/org/jlab/io/clara/EvioToEvioReader.java diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/EvioToEvioSource.java b/src/main/java/org/jlab/io/clara/EvioToEvioSource.java similarity index 100% rename from common-tools/clara-io/src/main/java/org/jlab/io/clara/EvioToEvioSource.java rename to src/main/java/org/jlab/io/clara/EvioToEvioSource.java diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/EvioToEvioWriter.java b/src/main/java/org/jlab/io/clara/EvioToEvioWriter.java similarity index 100% rename from common-tools/clara-io/src/main/java/org/jlab/io/clara/EvioToEvioWriter.java rename to src/main/java/org/jlab/io/clara/EvioToEvioWriter.java diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/HipoFrameReader.java b/src/main/java/org/jlab/io/clara/HipoFrameReader.java similarity index 100% rename from common-tools/clara-io/src/main/java/org/jlab/io/clara/HipoFrameReader.java rename to src/main/java/org/jlab/io/clara/HipoFrameReader.java diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/HipoFrameWriter.java b/src/main/java/org/jlab/io/clara/HipoFrameWriter.java similarity index 100% rename from common-tools/clara-io/src/main/java/org/jlab/io/clara/HipoFrameWriter.java rename to src/main/java/org/jlab/io/clara/HipoFrameWriter.java diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/HipoToHipoReader.java b/src/main/java/org/jlab/io/clara/HipoToHipoReader.java similarity index 100% rename from common-tools/clara-io/src/main/java/org/jlab/io/clara/HipoToHipoReader.java rename to src/main/java/org/jlab/io/clara/HipoToHipoReader.java diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/HipoToHipoWriter.java b/src/main/java/org/jlab/io/clara/HipoToHipoWriter.java similarity index 100% rename from common-tools/clara-io/src/main/java/org/jlab/io/clara/HipoToHipoWriter.java rename to src/main/java/org/jlab/io/clara/HipoToHipoWriter.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataBank.java b/src/main/java/org/jlab/io/evio/EvioDataBank.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataBank.java rename to src/main/java/org/jlab/io/evio/EvioDataBank.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataDescriptor.java b/src/main/java/org/jlab/io/evio/EvioDataDescriptor.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataDescriptor.java rename to src/main/java/org/jlab/io/evio/EvioDataDescriptor.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataDescriptorEntry.java b/src/main/java/org/jlab/io/evio/EvioDataDescriptorEntry.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataDescriptorEntry.java rename to src/main/java/org/jlab/io/evio/EvioDataDescriptorEntry.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataDictionary.java b/src/main/java/org/jlab/io/evio/EvioDataDictionary.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataDictionary.java rename to src/main/java/org/jlab/io/evio/EvioDataDictionary.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataEvent.java b/src/main/java/org/jlab/io/evio/EvioDataEvent.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataEvent.java rename to src/main/java/org/jlab/io/evio/EvioDataEvent.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataEventHandler.java b/src/main/java/org/jlab/io/evio/EvioDataEventHandler.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataEventHandler.java rename to src/main/java/org/jlab/io/evio/EvioDataEventHandler.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataSync.java b/src/main/java/org/jlab/io/evio/EvioDataSync.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDataSync.java rename to src/main/java/org/jlab/io/evio/EvioDataSync.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDescriptor.java b/src/main/java/org/jlab/io/evio/EvioDescriptor.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDescriptor.java rename to src/main/java/org/jlab/io/evio/EvioDescriptor.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDictionary.java b/src/main/java/org/jlab/io/evio/EvioDictionary.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioDictionary.java rename to src/main/java/org/jlab/io/evio/EvioDictionary.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioETSource.java b/src/main/java/org/jlab/io/evio/EvioETSource.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioETSource.java rename to src/main/java/org/jlab/io/evio/EvioETSource.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioETSync.java b/src/main/java/org/jlab/io/evio/EvioETSync.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioETSync.java rename to src/main/java/org/jlab/io/evio/EvioETSync.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioFactory.java b/src/main/java/org/jlab/io/evio/EvioFactory.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioFactory.java rename to src/main/java/org/jlab/io/evio/EvioFactory.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioRingSource.java b/src/main/java/org/jlab/io/evio/EvioRingSource.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioRingSource.java rename to src/main/java/org/jlab/io/evio/EvioRingSource.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioSource.java b/src/main/java/org/jlab/io/evio/EvioSource.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioSource.java rename to src/main/java/org/jlab/io/evio/EvioSource.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioTreeBranch.java b/src/main/java/org/jlab/io/evio/EvioTreeBranch.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/evio/EvioTreeBranch.java rename to src/main/java/org/jlab/io/evio/EvioTreeBranch.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/hipo/HipoDataBank.java b/src/main/java/org/jlab/io/hipo/HipoDataBank.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/hipo/HipoDataBank.java rename to src/main/java/org/jlab/io/hipo/HipoDataBank.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/hipo/HipoDataDescriptor.java b/src/main/java/org/jlab/io/hipo/HipoDataDescriptor.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/hipo/HipoDataDescriptor.java rename to src/main/java/org/jlab/io/hipo/HipoDataDescriptor.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/hipo/HipoDataDictionary.java b/src/main/java/org/jlab/io/hipo/HipoDataDictionary.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/hipo/HipoDataDictionary.java rename to src/main/java/org/jlab/io/hipo/HipoDataDictionary.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/hipo/HipoDataEvent.java b/src/main/java/org/jlab/io/hipo/HipoDataEvent.java similarity index 100% rename from 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common-tools/clas-io/src/main/java/org/jlab/io/hipo/HipoDataSync.java rename to src/main/java/org/jlab/io/hipo/HipoDataSync.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/hipo/HipoRingSource.java b/src/main/java/org/jlab/io/hipo/HipoRingSource.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/hipo/HipoRingSource.java rename to src/main/java/org/jlab/io/hipo/HipoRingSource.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/hipo/HipoUtilities.java b/src/main/java/org/jlab/io/hipo/HipoUtilities.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/hipo/HipoUtilities.java rename to src/main/java/org/jlab/io/hipo/HipoUtilities.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/ring/DataDistributionRing.java b/src/main/java/org/jlab/io/ring/DataDistributionRing.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/ring/DataDistributionRing.java rename to src/main/java/org/jlab/io/ring/DataDistributionRing.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/ring/DataRingProducer.java b/src/main/java/org/jlab/io/ring/DataRingProducer.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/ring/DataRingProducer.java rename to src/main/java/org/jlab/io/ring/DataRingProducer.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/stream/EvioInputStream.java b/src/main/java/org/jlab/io/stream/EvioInputStream.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/stream/EvioInputStream.java rename to src/main/java/org/jlab/io/stream/EvioInputStream.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/stream/EvioOutputStream.java b/src/main/java/org/jlab/io/stream/EvioOutputStream.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/stream/EvioOutputStream.java rename to src/main/java/org/jlab/io/stream/EvioOutputStream.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/stream/EvioStreamObject.java b/src/main/java/org/jlab/io/stream/EvioStreamObject.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/stream/EvioStreamObject.java rename to src/main/java/org/jlab/io/stream/EvioStreamObject.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/task/DataSourceProcessor.java b/src/main/java/org/jlab/io/task/DataSourceProcessor.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/task/DataSourceProcessor.java rename to src/main/java/org/jlab/io/task/DataSourceProcessor.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/task/DataSourceProcessorPane.java b/src/main/java/org/jlab/io/task/DataSourceProcessorPane.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/task/DataSourceProcessorPane.java rename to 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a/common-tools/clas-io/src/main/java/org/jlab/io/ui/ConnectionDialogHipo.java b/src/main/java/org/jlab/io/ui/ConnectionDialogHipo.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/ui/ConnectionDialogHipo.java rename to src/main/java/org/jlab/io/ui/ConnectionDialogHipo.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/ui/DialogUtilities.java b/src/main/java/org/jlab/io/ui/DialogUtilities.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/ui/DialogUtilities.java rename to src/main/java/org/jlab/io/ui/DialogUtilities.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/utils/CompositeFormatReader.java b/src/main/java/org/jlab/io/utils/CompositeFormatReader.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/utils/CompositeFormatReader.java rename to src/main/java/org/jlab/io/utils/CompositeFormatReader.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/utils/DictionaryLoader.java b/src/main/java/org/jlab/io/utils/DictionaryLoader.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/utils/DictionaryLoader.java rename to src/main/java/org/jlab/io/utils/DictionaryLoader.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/utils/DstMaker.java b/src/main/java/org/jlab/io/utils/DstMaker.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/utils/DstMaker.java rename to src/main/java/org/jlab/io/utils/DstMaker.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/utils/EvioCure.java b/src/main/java/org/jlab/io/utils/EvioCure.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/utils/EvioCure.java rename to src/main/java/org/jlab/io/utils/EvioCure.java diff --git a/common-tools/clas-io/src/main/java/org/jlab/io/utils/EvioFileRecover.java b/src/main/java/org/jlab/io/utils/EvioFileRecover.java similarity index 100% rename from common-tools/clas-io/src/main/java/org/jlab/io/utils/EvioFileRecover.java rename to src/main/java/org/jlab/io/utils/EvioFileRecover.java diff --git a/common-tools/clas-logging/src/main/java/org/jlab/logging/SplitLogManager.java b/src/main/java/org/jlab/logging/SplitLogManager.java similarity index 100% rename from common-tools/clas-logging/src/main/java/org/jlab/logging/SplitLogManager.java rename to src/main/java/org/jlab/logging/SplitLogManager.java diff --git a/common-tools/clas-logging/src/main/java/org/jlab/logging/SplitLogManagerConfig.java b/src/main/java/org/jlab/logging/SplitLogManagerConfig.java similarity index 100% rename from common-tools/clas-logging/src/main/java/org/jlab/logging/SplitLogManagerConfig.java rename to src/main/java/org/jlab/logging/SplitLogManagerConfig.java diff --git a/common-tools/clas-logging/src/main/java/org/jlab/logging/TestLogManager.java b/src/main/java/org/jlab/logging/TestLogManager.java similarity index 100% rename from common-tools/clas-logging/src/main/java/org/jlab/logging/TestLogManager.java rename to src/main/java/org/jlab/logging/TestLogManager.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/analysis/EventOperator.java b/src/main/java/org/jlab/physics/analysis/EventOperator.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/analysis/EventOperator.java rename to src/main/java/org/jlab/physics/analysis/EventOperator.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/analysis/GenericEventOperator.java b/src/main/java/org/jlab/physics/analysis/GenericEventOperator.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/analysis/GenericEventOperator.java rename to src/main/java/org/jlab/physics/analysis/GenericEventOperator.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/analysis/PhysicsAnalysis.java b/src/main/java/org/jlab/physics/analysis/PhysicsAnalysis.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/analysis/PhysicsAnalysis.java rename to src/main/java/org/jlab/physics/analysis/PhysicsAnalysis.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/analysis/PhysicsDataObject.java b/src/main/java/org/jlab/physics/analysis/PhysicsDataObject.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/analysis/PhysicsDataObject.java rename to src/main/java/org/jlab/physics/analysis/PhysicsDataObject.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/base/DimensionSpace.java b/src/main/java/org/jlab/physics/base/DimensionSpace.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/base/DimensionSpace.java rename to src/main/java/org/jlab/physics/base/DimensionSpace.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/base/EventOperation.java b/src/main/java/org/jlab/physics/base/EventOperation.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/base/EventOperation.java rename to src/main/java/org/jlab/physics/base/EventOperation.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/base/EventSelector.java b/src/main/java/org/jlab/physics/base/EventSelector.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/base/EventSelector.java rename to src/main/java/org/jlab/physics/base/EventSelector.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/base/IEventFilter.java b/src/main/java/org/jlab/physics/base/IEventFilter.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/base/IEventFilter.java rename to src/main/java/org/jlab/physics/base/IEventFilter.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/base/IPhysicsCut.java b/src/main/java/org/jlab/physics/base/IPhysicsCut.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/base/IPhysicsCut.java rename to src/main/java/org/jlab/physics/base/IPhysicsCut.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/base/ParameterSpace.java b/src/main/java/org/jlab/physics/base/ParameterSpace.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/base/ParameterSpace.java rename to src/main/java/org/jlab/physics/base/ParameterSpace.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/base/ParticleSelector.java b/src/main/java/org/jlab/physics/base/ParticleSelector.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/base/ParticleSelector.java rename to src/main/java/org/jlab/physics/base/ParticleSelector.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/base/ParticleStringParser.java b/src/main/java/org/jlab/physics/base/ParticleStringParser.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/base/ParticleStringParser.java rename to src/main/java/org/jlab/physics/base/ParticleStringParser.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/base/PhaseSpace.java b/src/main/java/org/jlab/physics/base/PhaseSpace.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/base/PhaseSpace.java rename to src/main/java/org/jlab/physics/base/PhaseSpace.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/io/LundReader.java b/src/main/java/org/jlab/physics/io/LundReader.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/io/LundReader.java rename to src/main/java/org/jlab/physics/io/LundReader.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/oper/PhysicsCutDescriptor.java b/src/main/java/org/jlab/physics/oper/PhysicsCutDescriptor.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/oper/PhysicsCutDescriptor.java rename to src/main/java/org/jlab/physics/oper/PhysicsCutDescriptor.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/oper/PhysicsEventOperator.java b/src/main/java/org/jlab/physics/oper/PhysicsEventOperator.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/oper/PhysicsEventOperator.java rename to src/main/java/org/jlab/physics/oper/PhysicsEventOperator.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/oper/PhysicsEventProcessor.java b/src/main/java/org/jlab/physics/oper/PhysicsEventProcessor.java similarity index 100% rename from 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a/common-tools/clas-physics/src/main/java/org/jlab/physics/process/DVCSProcess.java b/src/main/java/org/jlab/physics/process/DVCSProcess.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/process/DVCSProcess.java rename to src/main/java/org/jlab/physics/process/DVCSProcess.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/process/IPhysicsProcess.java b/src/main/java/org/jlab/physics/process/IPhysicsProcess.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/process/IPhysicsProcess.java rename to src/main/java/org/jlab/physics/process/IPhysicsProcess.java diff --git a/common-tools/clas-physics/src/main/java/org/jlab/physics/process/KinematicsFactory.java b/src/main/java/org/jlab/physics/process/KinematicsFactory.java similarity index 100% rename from common-tools/clas-physics/src/main/java/org/jlab/physics/process/KinematicsFactory.java rename to src/main/java/org/jlab/physics/process/KinematicsFactory.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/AI/AIPrediction.java b/src/main/java/org/jlab/rec/ahdc/AI/AIPrediction.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/AI/AIPrediction.java rename to src/main/java/org/jlab/rec/ahdc/AI/AIPrediction.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/AI/InterCluster.java b/src/main/java/org/jlab/rec/ahdc/AI/InterCluster.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/AI/InterCluster.java rename to src/main/java/org/jlab/rec/ahdc/AI/InterCluster.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/AI/ModelTrackFinding.java b/src/main/java/org/jlab/rec/ahdc/AI/ModelTrackFinding.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/AI/ModelTrackFinding.java rename to src/main/java/org/jlab/rec/ahdc/AI/ModelTrackFinding.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/AI/PreClustering.java b/src/main/java/org/jlab/rec/ahdc/AI/PreClustering.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/AI/PreClustering.java rename to src/main/java/org/jlab/rec/ahdc/AI/PreClustering.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/AI/TrackCandidatesGenerator.java b/src/main/java/org/jlab/rec/ahdc/AI/TrackCandidatesGenerator.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/AI/TrackCandidatesGenerator.java rename to src/main/java/org/jlab/rec/ahdc/AI/TrackCandidatesGenerator.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/AI/TrackPrediction.java b/src/main/java/org/jlab/rec/ahdc/AI/TrackPrediction.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/AI/TrackPrediction.java rename to src/main/java/org/jlab/rec/ahdc/AI/TrackPrediction.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Banks/RecoBankWriter.java b/src/main/java/org/jlab/rec/ahdc/Banks/RecoBankWriter.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Banks/RecoBankWriter.java rename to src/main/java/org/jlab/rec/ahdc/Banks/RecoBankWriter.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Cluster/Cluster.java b/src/main/java/org/jlab/rec/ahdc/Cluster/Cluster.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Cluster/Cluster.java rename to src/main/java/org/jlab/rec/ahdc/Cluster/Cluster.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Cluster/ClusterFinder.java b/src/main/java/org/jlab/rec/ahdc/Cluster/ClusterFinder.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Cluster/ClusterFinder.java rename to src/main/java/org/jlab/rec/ahdc/Cluster/ClusterFinder.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Distance/CircleFitPars.java b/src/main/java/org/jlab/rec/ahdc/Distance/CircleFitPars.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Distance/CircleFitPars.java rename to src/main/java/org/jlab/rec/ahdc/Distance/CircleFitPars.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Distance/CircleFitter.java b/src/main/java/org/jlab/rec/ahdc/Distance/CircleFitter.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Distance/CircleFitter.java rename to src/main/java/org/jlab/rec/ahdc/Distance/CircleFitter.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Distance/Distance.java b/src/main/java/org/jlab/rec/ahdc/Distance/Distance.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Distance/Distance.java rename to src/main/java/org/jlab/rec/ahdc/Distance/Distance.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/DocaCluster/DocaCluster.java b/src/main/java/org/jlab/rec/ahdc/DocaCluster/DocaCluster.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/DocaCluster/DocaCluster.java rename to src/main/java/org/jlab/rec/ahdc/DocaCluster/DocaCluster.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/DocaCluster/DocaClusterRefiner.java b/src/main/java/org/jlab/rec/ahdc/DocaCluster/DocaClusterRefiner.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/DocaCluster/DocaClusterRefiner.java rename to src/main/java/org/jlab/rec/ahdc/DocaCluster/DocaClusterRefiner.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/HelixFit/HelixFitJava.java b/src/main/java/org/jlab/rec/ahdc/HelixFit/HelixFitJava.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/HelixFit/HelixFitJava.java rename to src/main/java/org/jlab/rec/ahdc/HelixFit/HelixFitJava.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/HelixFit/HelixFitObject.java b/src/main/java/org/jlab/rec/ahdc/HelixFit/HelixFitObject.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/HelixFit/HelixFitObject.java rename to src/main/java/org/jlab/rec/ahdc/HelixFit/HelixFitObject.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Hit/Hit.java b/src/main/java/org/jlab/rec/ahdc/Hit/Hit.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Hit/Hit.java rename to src/main/java/org/jlab/rec/ahdc/Hit/Hit.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Hit/HitReader.java b/src/main/java/org/jlab/rec/ahdc/Hit/HitReader.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Hit/HitReader.java rename to src/main/java/org/jlab/rec/ahdc/Hit/HitReader.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Hit/TrueHit.java b/src/main/java/org/jlab/rec/ahdc/Hit/TrueHit.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Hit/TrueHit.java rename to src/main/java/org/jlab/rec/ahdc/Hit/TrueHit.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/HoughTransform/HoughTransform.java b/src/main/java/org/jlab/rec/ahdc/HoughTransform/HoughTransform.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/HoughTransform/HoughTransform.java rename to src/main/java/org/jlab/rec/ahdc/HoughTransform/HoughTransform.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/Hit_beam.java b/src/main/java/org/jlab/rec/ahdc/KalmanFilter/Hit_beam.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/Hit_beam.java rename to src/main/java/org/jlab/rec/ahdc/KalmanFilter/Hit_beam.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/KFitter.java b/src/main/java/org/jlab/rec/ahdc/KalmanFilter/KFitter.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/KFitter.java rename to src/main/java/org/jlab/rec/ahdc/KalmanFilter/KFitter.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/KalmanFilter.java b/src/main/java/org/jlab/rec/ahdc/KalmanFilter/KalmanFilter.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/KalmanFilter.java rename to src/main/java/org/jlab/rec/ahdc/KalmanFilter/KalmanFilter.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/MaterialMap.java b/src/main/java/org/jlab/rec/ahdc/KalmanFilter/MaterialMap.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/MaterialMap.java rename to src/main/java/org/jlab/rec/ahdc/KalmanFilter/MaterialMap.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/Propagator.java b/src/main/java/org/jlab/rec/ahdc/KalmanFilter/Propagator.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/Propagator.java rename to src/main/java/org/jlab/rec/ahdc/KalmanFilter/Propagator.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/RungeKutta4.java b/src/main/java/org/jlab/rec/ahdc/KalmanFilter/RungeKutta4.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/RungeKutta4.java rename to src/main/java/org/jlab/rec/ahdc/KalmanFilter/RungeKutta4.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/Stepper.java b/src/main/java/org/jlab/rec/ahdc/KalmanFilter/Stepper.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/KalmanFilter/Stepper.java rename to src/main/java/org/jlab/rec/ahdc/KalmanFilter/Stepper.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/ModeTrackFinding.java b/src/main/java/org/jlab/rec/ahdc/ModeTrackFinding.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/ModeTrackFinding.java rename to src/main/java/org/jlab/rec/ahdc/ModeTrackFinding.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/PreCluster/PreCluster.java b/src/main/java/org/jlab/rec/ahdc/PreCluster/PreCluster.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/PreCluster/PreCluster.java rename to src/main/java/org/jlab/rec/ahdc/PreCluster/PreCluster.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/PreCluster/PreClusterFinder.java b/src/main/java/org/jlab/rec/ahdc/PreCluster/PreClusterFinder.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/PreCluster/PreClusterFinder.java rename to src/main/java/org/jlab/rec/ahdc/PreCluster/PreClusterFinder.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Track/Track.java b/src/main/java/org/jlab/rec/ahdc/Track/Track.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/ahdc/Track/Track.java rename to src/main/java/org/jlab/rec/ahdc/Track/Track.java diff --git a/reconstruction/ai/src/main/java/org/jlab/rec/ai/dcCluster/DCCluster.java b/src/main/java/org/jlab/rec/ai/dcCluster/DCCluster.java similarity index 100% rename from reconstruction/ai/src/main/java/org/jlab/rec/ai/dcCluster/DCCluster.java rename to src/main/java/org/jlab/rec/ai/dcCluster/DCCluster.java diff --git a/reconstruction/ai/src/main/java/org/jlab/rec/ai/dcCluster/DCClusterCombo.java b/src/main/java/org/jlab/rec/ai/dcCluster/DCClusterCombo.java similarity index 100% rename from reconstruction/ai/src/main/java/org/jlab/rec/ai/dcCluster/DCClusterCombo.java rename to src/main/java/org/jlab/rec/ai/dcCluster/DCClusterCombo.java diff --git a/reconstruction/ai/src/main/java/org/jlab/rec/ai/dcHBTrackState/HBTrackStateEstimator.java b/src/main/java/org/jlab/rec/ai/dcHBTrackState/HBTrackStateEstimator.java similarity index 100% rename from reconstruction/ai/src/main/java/org/jlab/rec/ai/dcHBTrackState/HBTrackStateEstimator.java rename to src/main/java/org/jlab/rec/ai/dcHBTrackState/HBTrackStateEstimator.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/alert/AIPID/ModelPrePID.java b/src/main/java/org/jlab/rec/alert/AIPID/ModelPrePID.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/alert/AIPID/ModelPrePID.java rename to src/main/java/org/jlab/rec/alert/AIPID/ModelPrePID.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/alert/AIPID/PrePIDResult.java b/src/main/java/org/jlab/rec/alert/AIPID/PrePIDResult.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/alert/AIPID/PrePIDResult.java rename to src/main/java/org/jlab/rec/alert/AIPID/PrePIDResult.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/alert/TrackMatchingAI/ModelTrackMatching.java b/src/main/java/org/jlab/rec/alert/TrackMatchingAI/ModelTrackMatching.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/alert/TrackMatchingAI/ModelTrackMatching.java rename to src/main/java/org/jlab/rec/alert/TrackMatchingAI/ModelTrackMatching.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/alert/banks/RecoBankWriter.java b/src/main/java/org/jlab/rec/alert/banks/RecoBankWriter.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/alert/banks/RecoBankWriter.java rename to src/main/java/org/jlab/rec/alert/banks/RecoBankWriter.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/alert/projections/TrackProjection.java b/src/main/java/org/jlab/rec/alert/projections/TrackProjection.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/alert/projections/TrackProjection.java rename to src/main/java/org/jlab/rec/alert/projections/TrackProjection.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/alert/projections/TrackProjector.java b/src/main/java/org/jlab/rec/alert/projections/TrackProjector.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/alert/projections/TrackProjector.java rename to src/main/java/org/jlab/rec/alert/projections/TrackProjector.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/atof/banks/RecoBankWriter.java b/src/main/java/org/jlab/rec/atof/banks/RecoBankWriter.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/atof/banks/RecoBankWriter.java rename to src/main/java/org/jlab/rec/atof/banks/RecoBankWriter.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/atof/cluster/ATOFCluster.java b/src/main/java/org/jlab/rec/atof/cluster/ATOFCluster.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/atof/cluster/ATOFCluster.java rename to src/main/java/org/jlab/rec/atof/cluster/ATOFCluster.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/atof/cluster/ClusterFinder.java b/src/main/java/org/jlab/rec/atof/cluster/ClusterFinder.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/atof/cluster/ClusterFinder.java rename to src/main/java/org/jlab/rec/atof/cluster/ClusterFinder.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/atof/constants/Parameters.java b/src/main/java/org/jlab/rec/atof/constants/Parameters.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/atof/constants/Parameters.java rename to src/main/java/org/jlab/rec/atof/constants/Parameters.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/atof/hit/ATOFHit.java b/src/main/java/org/jlab/rec/atof/hit/ATOFHit.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/atof/hit/ATOFHit.java rename to src/main/java/org/jlab/rec/atof/hit/ATOFHit.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/atof/hit/BarHit.java b/src/main/java/org/jlab/rec/atof/hit/BarHit.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/atof/hit/BarHit.java rename to src/main/java/org/jlab/rec/atof/hit/BarHit.java diff --git a/reconstruction/alert/src/main/java/org/jlab/rec/atof/hit/HitFinder.java b/src/main/java/org/jlab/rec/atof/hit/HitFinder.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/rec/atof/hit/HitFinder.java rename to src/main/java/org/jlab/rec/atof/hit/HitFinder.java diff --git a/reconstruction/band/src/main/java/org/jlab/rec/band/banks/HitReader.java b/src/main/java/org/jlab/rec/band/banks/HitReader.java similarity index 100% rename from reconstruction/band/src/main/java/org/jlab/rec/band/banks/HitReader.java rename to src/main/java/org/jlab/rec/band/banks/HitReader.java diff --git a/reconstruction/band/src/main/java/org/jlab/rec/band/banks/RecoBankWriter.java b/src/main/java/org/jlab/rec/band/banks/RecoBankWriter.java similarity index 100% rename from reconstruction/band/src/main/java/org/jlab/rec/band/banks/RecoBankWriter.java rename to src/main/java/org/jlab/rec/band/banks/RecoBankWriter.java diff --git a/reconstruction/band/src/main/java/org/jlab/rec/band/constants/CalibrationConstantsLoader.java b/src/main/java/org/jlab/rec/band/constants/CalibrationConstantsLoader.java similarity index 100% rename from reconstruction/band/src/main/java/org/jlab/rec/band/constants/CalibrationConstantsLoader.java rename to src/main/java/org/jlab/rec/band/constants/CalibrationConstantsLoader.java diff --git a/reconstruction/band/src/main/java/org/jlab/rec/band/constants/Parameters.java b/src/main/java/org/jlab/rec/band/constants/Parameters.java similarity index 100% rename from reconstruction/band/src/main/java/org/jlab/rec/band/constants/Parameters.java rename to src/main/java/org/jlab/rec/band/constants/Parameters.java diff --git a/reconstruction/band/src/main/java/org/jlab/rec/band/hit/BandHit.java b/src/main/java/org/jlab/rec/band/hit/BandHit.java similarity index 100% rename from reconstruction/band/src/main/java/org/jlab/rec/band/hit/BandHit.java rename to src/main/java/org/jlab/rec/band/hit/BandHit.java diff --git a/reconstruction/band/src/main/java/org/jlab/rec/band/hit/BandHitCandidate.java b/src/main/java/org/jlab/rec/band/hit/BandHitCandidate.java similarity index 100% rename from reconstruction/band/src/main/java/org/jlab/rec/band/hit/BandHitCandidate.java rename to src/main/java/org/jlab/rec/band/hit/BandHitCandidate.java diff --git a/reconstruction/band/src/main/java/org/jlab/rec/band/hit/BandHitFinder.java b/src/main/java/org/jlab/rec/band/hit/BandHitFinder.java similarity index 100% rename from reconstruction/band/src/main/java/org/jlab/rec/band/hit/BandHitFinder.java rename to src/main/java/org/jlab/rec/band/hit/BandHitFinder.java diff --git a/reconstruction/cnd/src/main/java/org/jlab/rec/cnd/banks/HitReader.java b/src/main/java/org/jlab/rec/cnd/banks/HitReader.java similarity index 100% rename from reconstruction/cnd/src/main/java/org/jlab/rec/cnd/banks/HitReader.java rename to src/main/java/org/jlab/rec/cnd/banks/HitReader.java diff --git a/reconstruction/cnd/src/main/java/org/jlab/rec/cnd/banks/RecoBankWriter.java b/src/main/java/org/jlab/rec/cnd/banks/RecoBankWriter.java similarity index 100% rename from reconstruction/cnd/src/main/java/org/jlab/rec/cnd/banks/RecoBankWriter.java rename to src/main/java/org/jlab/rec/cnd/banks/RecoBankWriter.java diff --git a/reconstruction/cnd/src/main/java/org/jlab/rec/cnd/cluster/CNDCluster.java b/src/main/java/org/jlab/rec/cnd/cluster/CNDCluster.java similarity index 100% rename from reconstruction/cnd/src/main/java/org/jlab/rec/cnd/cluster/CNDCluster.java rename to src/main/java/org/jlab/rec/cnd/cluster/CNDCluster.java diff --git a/reconstruction/cnd/src/main/java/org/jlab/rec/cnd/cluster/CNDClusterFinder.java b/src/main/java/org/jlab/rec/cnd/cluster/CNDClusterFinder.java similarity index 100% rename from reconstruction/cnd/src/main/java/org/jlab/rec/cnd/cluster/CNDClusterFinder.java rename to src/main/java/org/jlab/rec/cnd/cluster/CNDClusterFinder.java diff --git a/reconstruction/cnd/src/main/java/org/jlab/rec/cnd/constants/CalibrationConstantsLoader.java b/src/main/java/org/jlab/rec/cnd/constants/CalibrationConstantsLoader.java similarity index 100% rename from reconstruction/cnd/src/main/java/org/jlab/rec/cnd/constants/CalibrationConstantsLoader.java rename to src/main/java/org/jlab/rec/cnd/constants/CalibrationConstantsLoader.java diff --git a/reconstruction/cnd/src/main/java/org/jlab/rec/cnd/constants/Parameters.java b/src/main/java/org/jlab/rec/cnd/constants/Parameters.java similarity index 100% rename from reconstruction/cnd/src/main/java/org/jlab/rec/cnd/constants/Parameters.java rename to src/main/java/org/jlab/rec/cnd/constants/Parameters.java diff --git a/reconstruction/cnd/src/main/java/org/jlab/rec/cnd/hit/CndHit.java b/src/main/java/org/jlab/rec/cnd/hit/CndHit.java similarity index 100% rename from reconstruction/cnd/src/main/java/org/jlab/rec/cnd/hit/CndHit.java rename to src/main/java/org/jlab/rec/cnd/hit/CndHit.java diff --git a/reconstruction/cnd/src/main/java/org/jlab/rec/cnd/hit/CndHitFinder.java b/src/main/java/org/jlab/rec/cnd/hit/CndHitFinder.java similarity index 100% rename from reconstruction/cnd/src/main/java/org/jlab/rec/cnd/hit/CndHitFinder.java rename to src/main/java/org/jlab/rec/cnd/hit/CndHitFinder.java diff --git a/reconstruction/cnd/src/main/java/org/jlab/rec/cnd/hit/CvtGetHTrack.java b/src/main/java/org/jlab/rec/cnd/hit/CvtGetHTrack.java similarity index 100% rename from reconstruction/cnd/src/main/java/org/jlab/rec/cnd/hit/CvtGetHTrack.java rename to src/main/java/org/jlab/rec/cnd/hit/CvtGetHTrack.java diff --git a/reconstruction/cnd/src/main/java/org/jlab/rec/cnd/hit/HalfHit.java b/src/main/java/org/jlab/rec/cnd/hit/HalfHit.java similarity index 100% rename from reconstruction/cnd/src/main/java/org/jlab/rec/cnd/hit/HalfHit.java rename to src/main/java/org/jlab/rec/cnd/hit/HalfHit.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/ctof/Constants.java b/src/main/java/org/jlab/rec/ctof/Constants.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/ctof/Constants.java rename to src/main/java/org/jlab/rec/ctof/Constants.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/ctof/package-info.java b/src/main/java/org/jlab/rec/ctof/package-info.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/ctof/package-info.java rename to src/main/java/org/jlab/rec/ctof/package-info.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/Constants.java b/src/main/java/org/jlab/rec/cvt/Constants.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/Constants.java rename to src/main/java/org/jlab/rec/cvt/Constants.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/Geometry.java b/src/main/java/org/jlab/rec/cvt/Geometry.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/Geometry.java rename to src/main/java/org/jlab/rec/cvt/Geometry.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/banks/HitReader.java b/src/main/java/org/jlab/rec/cvt/banks/HitReader.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/banks/HitReader.java rename to src/main/java/org/jlab/rec/cvt/banks/HitReader.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/banks/RecoBankReader.java b/src/main/java/org/jlab/rec/cvt/banks/RecoBankReader.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/banks/RecoBankReader.java rename to src/main/java/org/jlab/rec/cvt/banks/RecoBankReader.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/banks/RecoBankWriter.java b/src/main/java/org/jlab/rec/cvt/banks/RecoBankWriter.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/banks/RecoBankWriter.java rename to src/main/java/org/jlab/rec/cvt/banks/RecoBankWriter.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/bmt/BMTConstants.java b/src/main/java/org/jlab/rec/cvt/bmt/BMTConstants.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/bmt/BMTConstants.java rename to src/main/java/org/jlab/rec/cvt/bmt/BMTConstants.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/bmt/BMTGeometry.java b/src/main/java/org/jlab/rec/cvt/bmt/BMTGeometry.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/bmt/BMTGeometry.java rename to src/main/java/org/jlab/rec/cvt/bmt/BMTGeometry.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/bmt/BMTType.java b/src/main/java/org/jlab/rec/cvt/bmt/BMTType.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/bmt/BMTType.java rename to src/main/java/org/jlab/rec/cvt/bmt/BMTType.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/bmt/CCDBConstantsLoader.java b/src/main/java/org/jlab/rec/cvt/bmt/CCDBConstantsLoader.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/bmt/CCDBConstantsLoader.java rename to src/main/java/org/jlab/rec/cvt/bmt/CCDBConstantsLoader.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/bmt/Lorentz.java b/src/main/java/org/jlab/rec/cvt/bmt/Lorentz.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/bmt/Lorentz.java rename to src/main/java/org/jlab/rec/cvt/bmt/Lorentz.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cluster/Cluster.java b/src/main/java/org/jlab/rec/cvt/cluster/Cluster.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cluster/Cluster.java rename to src/main/java/org/jlab/rec/cvt/cluster/Cluster.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cluster/ClusterFinder.java b/src/main/java/org/jlab/rec/cvt/cluster/ClusterFinder.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cluster/ClusterFinder.java rename to src/main/java/org/jlab/rec/cvt/cluster/ClusterFinder.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cross/Cross.java b/src/main/java/org/jlab/rec/cvt/cross/Cross.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cross/Cross.java rename to src/main/java/org/jlab/rec/cvt/cross/Cross.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cross/CrossList.java b/src/main/java/org/jlab/rec/cvt/cross/CrossList.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cross/CrossList.java rename to src/main/java/org/jlab/rec/cvt/cross/CrossList.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cross/CrossMaker.java b/src/main/java/org/jlab/rec/cvt/cross/CrossMaker.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cross/CrossMaker.java rename to src/main/java/org/jlab/rec/cvt/cross/CrossMaker.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cross/HelixCrossListFinder.java b/src/main/java/org/jlab/rec/cvt/cross/HelixCrossListFinder.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cross/HelixCrossListFinder.java rename to src/main/java/org/jlab/rec/cvt/cross/HelixCrossListFinder.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cross/StraightTrackCrossListFinder.java b/src/main/java/org/jlab/rec/cvt/cross/StraightTrackCrossListFinder.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/cross/StraightTrackCrossListFinder.java rename to src/main/java/org/jlab/rec/cvt/cross/StraightTrackCrossListFinder.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/CircleCalcPars.java b/src/main/java/org/jlab/rec/cvt/fit/CircleCalcPars.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/CircleCalcPars.java rename to src/main/java/org/jlab/rec/cvt/fit/CircleCalcPars.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/CircleCalculator.java b/src/main/java/org/jlab/rec/cvt/fit/CircleCalculator.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/CircleCalculator.java rename to src/main/java/org/jlab/rec/cvt/fit/CircleCalculator.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/CircleFitPars.java b/src/main/java/org/jlab/rec/cvt/fit/CircleFitPars.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/CircleFitPars.java rename to src/main/java/org/jlab/rec/cvt/fit/CircleFitPars.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/CircleFitter.java b/src/main/java/org/jlab/rec/cvt/fit/CircleFitter.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/CircleFitter.java rename to src/main/java/org/jlab/rec/cvt/fit/CircleFitter.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/CosmicFitPars.java b/src/main/java/org/jlab/rec/cvt/fit/CosmicFitPars.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/CosmicFitPars.java rename to src/main/java/org/jlab/rec/cvt/fit/CosmicFitPars.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/CosmicFitter.java b/src/main/java/org/jlab/rec/cvt/fit/CosmicFitter.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/CosmicFitter.java rename to src/main/java/org/jlab/rec/cvt/fit/CosmicFitter.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/HelicalTrackFitPars.java b/src/main/java/org/jlab/rec/cvt/fit/HelicalTrackFitPars.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/HelicalTrackFitPars.java rename to src/main/java/org/jlab/rec/cvt/fit/HelicalTrackFitPars.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/HelicalTrackFitter.java b/src/main/java/org/jlab/rec/cvt/fit/HelicalTrackFitter.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/HelicalTrackFitter.java rename to src/main/java/org/jlab/rec/cvt/fit/HelicalTrackFitter.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/LineFitPars.java b/src/main/java/org/jlab/rec/cvt/fit/LineFitPars.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/LineFitPars.java rename to src/main/java/org/jlab/rec/cvt/fit/LineFitPars.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/LineFitter.java b/src/main/java/org/jlab/rec/cvt/fit/LineFitter.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/LineFitter.java rename to src/main/java/org/jlab/rec/cvt/fit/LineFitter.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/StraightTrackFitter.java b/src/main/java/org/jlab/rec/cvt/fit/StraightTrackFitter.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/fit/StraightTrackFitter.java rename to src/main/java/org/jlab/rec/cvt/fit/StraightTrackFitter.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/hit/ADCConvertor.java b/src/main/java/org/jlab/rec/cvt/hit/ADCConvertor.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/hit/ADCConvertor.java rename to src/main/java/org/jlab/rec/cvt/hit/ADCConvertor.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/hit/Hit.java b/src/main/java/org/jlab/rec/cvt/hit/Hit.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/hit/Hit.java rename to src/main/java/org/jlab/rec/cvt/hit/Hit.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/hit/Strip.java b/src/main/java/org/jlab/rec/cvt/hit/Strip.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/hit/Strip.java rename to src/main/java/org/jlab/rec/cvt/hit/Strip.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/measurement/MLayer.java b/src/main/java/org/jlab/rec/cvt/measurement/MLayer.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/measurement/MLayer.java rename to src/main/java/org/jlab/rec/cvt/measurement/MLayer.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/measurement/Measurements.java b/src/main/java/org/jlab/rec/cvt/measurement/Measurements.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/measurement/Measurements.java rename to src/main/java/org/jlab/rec/cvt/measurement/Measurements.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/services/CVTEngine.java b/src/main/java/org/jlab/rec/cvt/services/CVTEngine.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/services/CVTEngine.java rename to src/main/java/org/jlab/rec/cvt/services/CVTEngine.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/services/CVTReconstruction.java b/src/main/java/org/jlab/rec/cvt/services/CVTReconstruction.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/services/CVTReconstruction.java rename to src/main/java/org/jlab/rec/cvt/services/CVTReconstruction.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/services/CVTSecondPassEngine.java b/src/main/java/org/jlab/rec/cvt/services/CVTSecondPassEngine.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/services/CVTSecondPassEngine.java rename to src/main/java/org/jlab/rec/cvt/services/CVTSecondPassEngine.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/services/CosmicTracksRec.java b/src/main/java/org/jlab/rec/cvt/services/CosmicTracksRec.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/services/CosmicTracksRec.java rename to src/main/java/org/jlab/rec/cvt/services/CosmicTracksRec.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/services/RecUtilities.java b/src/main/java/org/jlab/rec/cvt/services/RecUtilities.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/services/RecUtilities.java rename to src/main/java/org/jlab/rec/cvt/services/RecUtilities.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/services/TracksFromTargetRec.java b/src/main/java/org/jlab/rec/cvt/services/TracksFromTargetRec.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/services/TracksFromTargetRec.java rename to src/main/java/org/jlab/rec/cvt/services/TracksFromTargetRec.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/svt/SVTGeometry.java b/src/main/java/org/jlab/rec/cvt/svt/SVTGeometry.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/svt/SVTGeometry.java rename to src/main/java/org/jlab/rec/cvt/svt/SVTGeometry.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/svt/SVTParameters.java b/src/main/java/org/jlab/rec/cvt/svt/SVTParameters.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/svt/SVTParameters.java rename to src/main/java/org/jlab/rec/cvt/svt/SVTParameters.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/Cell.java b/src/main/java/org/jlab/rec/cvt/track/Cell.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/Cell.java rename to src/main/java/org/jlab/rec/cvt/track/Cell.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/MakerCA.java b/src/main/java/org/jlab/rec/cvt/track/MakerCA.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/MakerCA.java rename to src/main/java/org/jlab/rec/cvt/track/MakerCA.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/Seed.java b/src/main/java/org/jlab/rec/cvt/track/Seed.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/Seed.java rename to src/main/java/org/jlab/rec/cvt/track/Seed.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/StraightTrack.java b/src/main/java/org/jlab/rec/cvt/track/StraightTrack.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/StraightTrack.java rename to src/main/java/org/jlab/rec/cvt/track/StraightTrack.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/StraightTrackCandListFinder.java b/src/main/java/org/jlab/rec/cvt/track/StraightTrackCandListFinder.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/StraightTrackCandListFinder.java rename to src/main/java/org/jlab/rec/cvt/track/StraightTrackCandListFinder.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/StraightTrackSeeder.java b/src/main/java/org/jlab/rec/cvt/track/StraightTrackSeeder.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/StraightTrackSeeder.java rename to src/main/java/org/jlab/rec/cvt/track/StraightTrackSeeder.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/Track.java b/src/main/java/org/jlab/rec/cvt/track/Track.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/Track.java rename to src/main/java/org/jlab/rec/cvt/track/Track.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/TrackSeeder.java b/src/main/java/org/jlab/rec/cvt/track/TrackSeeder.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/TrackSeeder.java rename to src/main/java/org/jlab/rec/cvt/track/TrackSeeder.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/TrackSeederCA.java b/src/main/java/org/jlab/rec/cvt/track/TrackSeederCA.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/TrackSeederCA.java rename to src/main/java/org/jlab/rec/cvt/track/TrackSeederCA.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/TrackSeederRZ.java b/src/main/java/org/jlab/rec/cvt/track/TrackSeederRZ.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/TrackSeederRZ.java rename to src/main/java/org/jlab/rec/cvt/track/TrackSeederRZ.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/TrackSeederSVTLinker.java b/src/main/java/org/jlab/rec/cvt/track/TrackSeederSVTLinker.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/TrackSeederSVTLinker.java rename to src/main/java/org/jlab/rec/cvt/track/TrackSeederSVTLinker.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/TrackSeederXY.java b/src/main/java/org/jlab/rec/cvt/track/TrackSeederXY.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/TrackSeederXY.java rename to src/main/java/org/jlab/rec/cvt/track/TrackSeederXY.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/trajectory/Helix.java b/src/main/java/org/jlab/rec/cvt/trajectory/Helix.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/trajectory/Helix.java rename to src/main/java/org/jlab/rec/cvt/trajectory/Helix.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/trajectory/Ray.java b/src/main/java/org/jlab/rec/cvt/trajectory/Ray.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/trajectory/Ray.java rename to src/main/java/org/jlab/rec/cvt/trajectory/Ray.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/trajectory/StateVec.java b/src/main/java/org/jlab/rec/cvt/trajectory/StateVec.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/trajectory/StateVec.java rename to src/main/java/org/jlab/rec/cvt/trajectory/StateVec.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/trajectory/Trajectory.java b/src/main/java/org/jlab/rec/cvt/trajectory/Trajectory.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/trajectory/Trajectory.java rename to src/main/java/org/jlab/rec/cvt/trajectory/Trajectory.java diff --git a/reconstruction/cvt/src/main/java/org/jlab/rec/cvt/trajectory/TrajectoryFinder.java b/src/main/java/org/jlab/rec/cvt/trajectory/TrajectoryFinder.java similarity index 100% rename from reconstruction/cvt/src/main/java/org/jlab/rec/cvt/trajectory/TrajectoryFinder.java rename to src/main/java/org/jlab/rec/cvt/trajectory/TrajectoryFinder.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/Constants.java b/src/main/java/org/jlab/rec/dc/Constants.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/Constants.java rename to src/main/java/org/jlab/rec/dc/Constants.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/DCTranslationTable.java b/src/main/java/org/jlab/rec/dc/DCTranslationTable.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/DCTranslationTable.java rename to src/main/java/org/jlab/rec/dc/DCTranslationTable.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/banks/Banks.java b/src/main/java/org/jlab/rec/dc/banks/Banks.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/banks/Banks.java rename to src/main/java/org/jlab/rec/dc/banks/Banks.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/banks/HitReader.java b/src/main/java/org/jlab/rec/dc/banks/HitReader.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/banks/HitReader.java rename to src/main/java/org/jlab/rec/dc/banks/HitReader.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/banks/RecoBankWriter.java b/src/main/java/org/jlab/rec/dc/banks/RecoBankWriter.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/banks/RecoBankWriter.java rename to src/main/java/org/jlab/rec/dc/banks/RecoBankWriter.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/Cluster.java b/src/main/java/org/jlab/rec/dc/cluster/Cluster.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/Cluster.java rename to src/main/java/org/jlab/rec/dc/cluster/Cluster.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterCleanerUtilities.java b/src/main/java/org/jlab/rec/dc/cluster/ClusterCleanerUtilities.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterCleanerUtilities.java rename to src/main/java/org/jlab/rec/dc/cluster/ClusterCleanerUtilities.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFinder.java b/src/main/java/org/jlab/rec/dc/cluster/ClusterFinder.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/cluster/ClusterFinder.java rename to 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a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cross/CrossList.java b/src/main/java/org/jlab/rec/dc/cross/CrossList.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/cross/CrossList.java rename to src/main/java/org/jlab/rec/dc/cross/CrossList.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cross/CrossListFinder.java b/src/main/java/org/jlab/rec/dc/cross/CrossListFinder.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/cross/CrossListFinder.java rename to src/main/java/org/jlab/rec/dc/cross/CrossListFinder.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/cross/CrossMaker.java b/src/main/java/org/jlab/rec/dc/cross/CrossMaker.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/cross/CrossMaker.java rename to src/main/java/org/jlab/rec/dc/cross/CrossMaker.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/hit/FittedHit.java b/src/main/java/org/jlab/rec/dc/hit/FittedHit.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/hit/FittedHit.java rename to src/main/java/org/jlab/rec/dc/hit/FittedHit.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/hit/Hit.java b/src/main/java/org/jlab/rec/dc/hit/Hit.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/hit/Hit.java rename to src/main/java/org/jlab/rec/dc/hit/Hit.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/nn/PatternRec.java b/src/main/java/org/jlab/rec/dc/nn/PatternRec.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/nn/PatternRec.java rename to src/main/java/org/jlab/rec/dc/nn/PatternRec.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/segment/Segment.java b/src/main/java/org/jlab/rec/dc/segment/Segment.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/segment/Segment.java rename to src/main/java/org/jlab/rec/dc/segment/Segment.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/segment/SegmentFinder.java b/src/main/java/org/jlab/rec/dc/segment/SegmentFinder.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/segment/SegmentFinder.java rename to src/main/java/org/jlab/rec/dc/segment/SegmentFinder.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/timetodistance/T2DFunctions.java b/src/main/java/org/jlab/rec/dc/timetodistance/T2DFunctions.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/timetodistance/T2DFunctions.java rename to src/main/java/org/jlab/rec/dc/timetodistance/T2DFunctions.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/timetodistance/TableLoader.java b/src/main/java/org/jlab/rec/dc/timetodistance/TableLoader.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/timetodistance/TableLoader.java rename to src/main/java/org/jlab/rec/dc/timetodistance/TableLoader.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/timetodistance/TimeToDistanceEstimator.java b/src/main/java/org/jlab/rec/dc/timetodistance/TimeToDistanceEstimator.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/timetodistance/TimeToDistanceEstimator.java rename to src/main/java/org/jlab/rec/dc/timetodistance/TimeToDistanceEstimator.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/track/Track.java b/src/main/java/org/jlab/rec/dc/track/Track.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/track/Track.java rename to src/main/java/org/jlab/rec/dc/track/Track.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/track/TrackCandListFinder.java b/src/main/java/org/jlab/rec/dc/track/TrackCandListFinder.java similarity index 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reconstruction/dc/src/main/java/org/jlab/rec/dc/track/fit/MeasVecsDoca.java rename to src/main/java/org/jlab/rec/dc/track/fit/MeasVecsDoca.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/track/fit/RungeKuttaDoca.java b/src/main/java/org/jlab/rec/dc/track/fit/RungeKuttaDoca.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/track/fit/RungeKuttaDoca.java rename to src/main/java/org/jlab/rec/dc/track/fit/RungeKuttaDoca.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/track/fit/StateVecsDoca.java b/src/main/java/org/jlab/rec/dc/track/fit/StateVecsDoca.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/track/fit/StateVecsDoca.java rename to src/main/java/org/jlab/rec/dc/track/fit/StateVecsDoca.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/track/fit/basefit/LineFitPars.java b/src/main/java/org/jlab/rec/dc/track/fit/basefit/LineFitPars.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/track/fit/basefit/LineFitPars.java rename to src/main/java/org/jlab/rec/dc/track/fit/basefit/LineFitPars.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/track/fit/basefit/LineFitter.java b/src/main/java/org/jlab/rec/dc/track/fit/basefit/LineFitter.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/track/fit/basefit/LineFitter.java rename to src/main/java/org/jlab/rec/dc/track/fit/basefit/LineFitter.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/Road.java b/src/main/java/org/jlab/rec/dc/trajectory/Road.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/Road.java rename to src/main/java/org/jlab/rec/dc/trajectory/Road.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/RoadFinder.java b/src/main/java/org/jlab/rec/dc/trajectory/RoadFinder.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/RoadFinder.java rename to src/main/java/org/jlab/rec/dc/trajectory/RoadFinder.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/SegmentTrajectory.java b/src/main/java/org/jlab/rec/dc/trajectory/SegmentTrajectory.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/SegmentTrajectory.java rename to src/main/java/org/jlab/rec/dc/trajectory/SegmentTrajectory.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/StateVec.java b/src/main/java/org/jlab/rec/dc/trajectory/StateVec.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/StateVec.java rename to src/main/java/org/jlab/rec/dc/trajectory/StateVec.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/Surface.java b/src/main/java/org/jlab/rec/dc/trajectory/Surface.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/Surface.java rename to src/main/java/org/jlab/rec/dc/trajectory/Surface.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/TrackVec.java b/src/main/java/org/jlab/rec/dc/trajectory/TrackVec.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/TrackVec.java rename to src/main/java/org/jlab/rec/dc/trajectory/TrackVec.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/Trajectory.java b/src/main/java/org/jlab/rec/dc/trajectory/Trajectory.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/Trajectory.java rename to src/main/java/org/jlab/rec/dc/trajectory/Trajectory.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/TrajectoryFinder.java b/src/main/java/org/jlab/rec/dc/trajectory/TrajectoryFinder.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/TrajectoryFinder.java rename to src/main/java/org/jlab/rec/dc/trajectory/TrajectoryFinder.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/TrajectorySurfaces.java b/src/main/java/org/jlab/rec/dc/trajectory/TrajectorySurfaces.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/TrajectorySurfaces.java rename to src/main/java/org/jlab/rec/dc/trajectory/TrajectorySurfaces.java diff --git a/reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/Vertex.java b/src/main/java/org/jlab/rec/dc/trajectory/Vertex.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/rec/dc/trajectory/Vertex.java rename to src/main/java/org/jlab/rec/dc/trajectory/Vertex.java diff --git a/reconstruction/eb/src/main/java/org/jlab/rec/eb/EBCCDBConstants.java b/src/main/java/org/jlab/rec/eb/EBCCDBConstants.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/rec/eb/EBCCDBConstants.java rename to src/main/java/org/jlab/rec/eb/EBCCDBConstants.java diff --git a/reconstruction/eb/src/main/java/org/jlab/rec/eb/EBCCDBEnum.java b/src/main/java/org/jlab/rec/eb/EBCCDBEnum.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/rec/eb/EBCCDBEnum.java rename to src/main/java/org/jlab/rec/eb/EBCCDBEnum.java diff --git a/reconstruction/eb/src/main/java/org/jlab/rec/eb/EBConstants.java b/src/main/java/org/jlab/rec/eb/EBConstants.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/rec/eb/EBConstants.java rename to src/main/java/org/jlab/rec/eb/EBConstants.java diff --git a/reconstruction/eb/src/main/java/org/jlab/rec/eb/EBRadioFrequency.java b/src/main/java/org/jlab/rec/eb/EBRadioFrequency.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/rec/eb/EBRadioFrequency.java rename to src/main/java/org/jlab/rec/eb/EBRadioFrequency.java diff --git a/reconstruction/eb/src/main/java/org/jlab/rec/eb/EBScalers.java b/src/main/java/org/jlab/rec/eb/EBScalers.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/rec/eb/EBScalers.java rename to src/main/java/org/jlab/rec/eb/EBScalers.java diff --git a/reconstruction/eb/src/main/java/org/jlab/rec/eb/EBUtil.java b/src/main/java/org/jlab/rec/eb/EBUtil.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/rec/eb/EBUtil.java rename to src/main/java/org/jlab/rec/eb/EBUtil.java diff --git a/reconstruction/eb/src/main/java/org/jlab/rec/eb/SamplingFractions.java b/src/main/java/org/jlab/rec/eb/SamplingFractions.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/rec/eb/SamplingFractions.java rename to src/main/java/org/jlab/rec/eb/SamplingFractions.java diff --git a/reconstruction/eb/src/main/java/org/jlab/rec/eb/Versions.java b/src/main/java/org/jlab/rec/eb/Versions.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/rec/eb/Versions.java rename to src/main/java/org/jlab/rec/eb/Versions.java diff --git a/reconstruction/fmt/src/main/java/org/jlab/rec/fmt/Constants.java b/src/main/java/org/jlab/rec/fmt/Constants.java similarity index 100% rename from reconstruction/fmt/src/main/java/org/jlab/rec/fmt/Constants.java rename to src/main/java/org/jlab/rec/fmt/Constants.java diff --git a/reconstruction/fmt/src/main/java/org/jlab/rec/fmt/banks/RecoBankWriter.java b/src/main/java/org/jlab/rec/fmt/banks/RecoBankWriter.java similarity index 100% rename from reconstruction/fmt/src/main/java/org/jlab/rec/fmt/banks/RecoBankWriter.java rename to src/main/java/org/jlab/rec/fmt/banks/RecoBankWriter.java diff --git a/reconstruction/fmt/src/main/java/org/jlab/rec/fmt/cluster/Cluster.java b/src/main/java/org/jlab/rec/fmt/cluster/Cluster.java similarity index 100% rename from reconstruction/fmt/src/main/java/org/jlab/rec/fmt/cluster/Cluster.java rename to src/main/java/org/jlab/rec/fmt/cluster/Cluster.java diff --git a/reconstruction/fmt/src/main/java/org/jlab/rec/fmt/cross/Cross.java b/src/main/java/org/jlab/rec/fmt/cross/Cross.java similarity index 100% rename from reconstruction/fmt/src/main/java/org/jlab/rec/fmt/cross/Cross.java rename to src/main/java/org/jlab/rec/fmt/cross/Cross.java diff --git a/reconstruction/fmt/src/main/java/org/jlab/rec/fmt/hit/Hit.java b/src/main/java/org/jlab/rec/fmt/hit/Hit.java similarity index 100% rename from reconstruction/fmt/src/main/java/org/jlab/rec/fmt/hit/Hit.java rename to src/main/java/org/jlab/rec/fmt/hit/Hit.java diff --git a/reconstruction/fmt/src/main/java/org/jlab/rec/fmt/track/Track.java b/src/main/java/org/jlab/rec/fmt/track/Track.java similarity index 100% rename from reconstruction/fmt/src/main/java/org/jlab/rec/fmt/track/Track.java rename to src/main/java/org/jlab/rec/fmt/track/Track.java diff --git a/reconstruction/fmt/src/main/java/org/jlab/rec/fmt/track/Trajectory.java b/src/main/java/org/jlab/rec/fmt/track/Trajectory.java similarity index 100% rename from reconstruction/fmt/src/main/java/org/jlab/rec/fmt/track/Trajectory.java rename to src/main/java/org/jlab/rec/fmt/track/Trajectory.java diff --git a/reconstruction/fmt/src/main/java/org/jlab/rec/fmt/track/fit/KFitter.java b/src/main/java/org/jlab/rec/fmt/track/fit/KFitter.java similarity index 100% rename from reconstruction/fmt/src/main/java/org/jlab/rec/fmt/track/fit/KFitter.java rename to src/main/java/org/jlab/rec/fmt/track/fit/KFitter.java diff --git a/reconstruction/fmt/src/main/java/org/jlab/rec/fmt/track/fit/MeasVecs.java b/src/main/java/org/jlab/rec/fmt/track/fit/MeasVecs.java similarity index 100% rename from reconstruction/fmt/src/main/java/org/jlab/rec/fmt/track/fit/MeasVecs.java rename to src/main/java/org/jlab/rec/fmt/track/fit/MeasVecs.java diff --git a/reconstruction/fmt/src/main/java/org/jlab/rec/fmt/track/fit/RungeKutta.java b/src/main/java/org/jlab/rec/fmt/track/fit/RungeKutta.java similarity index 100% rename from reconstruction/fmt/src/main/java/org/jlab/rec/fmt/track/fit/RungeKutta.java rename to src/main/java/org/jlab/rec/fmt/track/fit/RungeKutta.java diff --git a/reconstruction/fmt/src/main/java/org/jlab/rec/fmt/track/fit/StateVecs.java b/src/main/java/org/jlab/rec/fmt/track/fit/StateVecs.java similarity index 100% rename from reconstruction/fmt/src/main/java/org/jlab/rec/fmt/track/fit/StateVecs.java rename to src/main/java/org/jlab/rec/fmt/track/fit/StateVecs.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/FTConstants.java b/src/main/java/org/jlab/rec/ft/FTConstants.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/FTConstants.java rename to src/main/java/org/jlab/rec/ft/FTConstants.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/FTEBEngine.java b/src/main/java/org/jlab/rec/ft/FTEBEngine.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/FTEBEngine.java rename to src/main/java/org/jlab/rec/ft/FTEBEngine.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/FTEventBuilder.java b/src/main/java/org/jlab/rec/ft/FTEventBuilder.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/FTEventBuilder.java rename to src/main/java/org/jlab/rec/ft/FTEventBuilder.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/FTParticle.java b/src/main/java/org/jlab/rec/ft/FTParticle.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/FTParticle.java rename to src/main/java/org/jlab/rec/ft/FTParticle.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/FTResponse.java b/src/main/java/org/jlab/rec/ft/FTResponse.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/FTResponse.java rename to src/main/java/org/jlab/rec/ft/FTResponse.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/cal/FTCALCluster.java b/src/main/java/org/jlab/rec/ft/cal/FTCALCluster.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/cal/FTCALCluster.java rename to src/main/java/org/jlab/rec/ft/cal/FTCALCluster.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/cal/FTCALConstantsLoader.java b/src/main/java/org/jlab/rec/ft/cal/FTCALConstantsLoader.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/cal/FTCALConstantsLoader.java rename to src/main/java/org/jlab/rec/ft/cal/FTCALConstantsLoader.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/cal/FTCALEngine.java b/src/main/java/org/jlab/rec/ft/cal/FTCALEngine.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/cal/FTCALEngine.java rename to src/main/java/org/jlab/rec/ft/cal/FTCALEngine.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/cal/FTCALHit.java b/src/main/java/org/jlab/rec/ft/cal/FTCALHit.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/cal/FTCALHit.java rename to src/main/java/org/jlab/rec/ft/cal/FTCALHit.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/cal/FTCALReconstruction.java b/src/main/java/org/jlab/rec/ft/cal/FTCALReconstruction.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/cal/FTCALReconstruction.java rename to src/main/java/org/jlab/rec/ft/cal/FTCALReconstruction.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/hodo/FTHODOCluster.java b/src/main/java/org/jlab/rec/ft/hodo/FTHODOCluster.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/hodo/FTHODOCluster.java rename to src/main/java/org/jlab/rec/ft/hodo/FTHODOCluster.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/hodo/FTHODOConstantsLoader.java b/src/main/java/org/jlab/rec/ft/hodo/FTHODOConstantsLoader.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/hodo/FTHODOConstantsLoader.java rename to src/main/java/org/jlab/rec/ft/hodo/FTHODOConstantsLoader.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/hodo/FTHODOEngine.java b/src/main/java/org/jlab/rec/ft/hodo/FTHODOEngine.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/hodo/FTHODOEngine.java rename to src/main/java/org/jlab/rec/ft/hodo/FTHODOEngine.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/hodo/FTHODOHit.java b/src/main/java/org/jlab/rec/ft/hodo/FTHODOHit.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/hodo/FTHODOHit.java rename to src/main/java/org/jlab/rec/ft/hodo/FTHODOHit.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/hodo/FTHODOReconstruction.java b/src/main/java/org/jlab/rec/ft/hodo/FTHODOReconstruction.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/hodo/FTHODOReconstruction.java rename to src/main/java/org/jlab/rec/ft/hodo/FTHODOReconstruction.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/trk/FTTRKCluster.java b/src/main/java/org/jlab/rec/ft/trk/FTTRKCluster.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/trk/FTTRKCluster.java rename to src/main/java/org/jlab/rec/ft/trk/FTTRKCluster.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/trk/FTTRKConstantsLoader.java b/src/main/java/org/jlab/rec/ft/trk/FTTRKConstantsLoader.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/trk/FTTRKConstantsLoader.java rename to src/main/java/org/jlab/rec/ft/trk/FTTRKConstantsLoader.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/trk/FTTRKCross.java b/src/main/java/org/jlab/rec/ft/trk/FTTRKCross.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/trk/FTTRKCross.java rename to src/main/java/org/jlab/rec/ft/trk/FTTRKCross.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/trk/FTTRKEngine.java b/src/main/java/org/jlab/rec/ft/trk/FTTRKEngine.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/trk/FTTRKEngine.java rename to src/main/java/org/jlab/rec/ft/trk/FTTRKEngine.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/trk/FTTRKHit.java b/src/main/java/org/jlab/rec/ft/trk/FTTRKHit.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/trk/FTTRKHit.java rename to src/main/java/org/jlab/rec/ft/trk/FTTRKHit.java diff --git a/reconstruction/ft/src/main/java/org/jlab/rec/ft/trk/FTTRKReconstruction.java b/src/main/java/org/jlab/rec/ft/trk/FTTRKReconstruction.java similarity index 100% rename from reconstruction/ft/src/main/java/org/jlab/rec/ft/trk/FTTRKReconstruction.java rename to src/main/java/org/jlab/rec/ft/trk/FTTRKReconstruction.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/ftof/Constants.java b/src/main/java/org/jlab/rec/ftof/Constants.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/ftof/Constants.java rename to src/main/java/org/jlab/rec/ftof/Constants.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/ftof/package-info.java b/src/main/java/org/jlab/rec/ftof/package-info.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/ftof/package-info.java rename to src/main/java/org/jlab/rec/ftof/package-info.java diff --git a/reconstruction/htcc/src/main/java/org/jlab/rec/htcc/Geom.java b/src/main/java/org/jlab/rec/htcc/Geom.java similarity index 100% rename from reconstruction/htcc/src/main/java/org/jlab/rec/htcc/Geom.java rename to src/main/java/org/jlab/rec/htcc/Geom.java diff --git a/reconstruction/htcc/src/main/java/org/jlab/rec/htcc/HTCCCluster.java b/src/main/java/org/jlab/rec/htcc/HTCCCluster.java similarity index 100% rename from reconstruction/htcc/src/main/java/org/jlab/rec/htcc/HTCCCluster.java rename to src/main/java/org/jlab/rec/htcc/HTCCCluster.java diff --git a/reconstruction/htcc/src/main/java/org/jlab/rec/htcc/HTCCReconstruction.java b/src/main/java/org/jlab/rec/htcc/HTCCReconstruction.java similarity index 100% rename from reconstruction/htcc/src/main/java/org/jlab/rec/htcc/HTCCReconstruction.java rename to src/main/java/org/jlab/rec/htcc/HTCCReconstruction.java diff --git a/reconstruction/htcc/src/main/java/org/jlab/rec/htcc/package-info.java b/src/main/java/org/jlab/rec/htcc/package-info.java similarity index 100% rename from reconstruction/htcc/src/main/java/org/jlab/rec/htcc/package-info.java rename to src/main/java/org/jlab/rec/htcc/package-info.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/mucal/MUCALCluster.java b/src/main/java/org/jlab/rec/mucal/MUCALCluster.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/mucal/MUCALCluster.java rename to src/main/java/org/jlab/rec/mucal/MUCALCluster.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/mucal/MUCALConstants.java b/src/main/java/org/jlab/rec/mucal/MUCALConstants.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/mucal/MUCALConstants.java rename to src/main/java/org/jlab/rec/mucal/MUCALConstants.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/mucal/MUCALEngine.java b/src/main/java/org/jlab/rec/mucal/MUCALEngine.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/mucal/MUCALEngine.java rename to src/main/java/org/jlab/rec/mucal/MUCALEngine.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/mucal/MUCALHit.java b/src/main/java/org/jlab/rec/mucal/MUCALHit.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/mucal/MUCALHit.java rename to src/main/java/org/jlab/rec/mucal/MUCALHit.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/mucal/MUCALReconstruction.java b/src/main/java/org/jlab/rec/mucal/MUCALReconstruction.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/mucal/MUCALReconstruction.java rename to src/main/java/org/jlab/rec/mucal/MUCALReconstruction.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muhd/MUHDCluster.java b/src/main/java/org/jlab/rec/muhd/MUHDCluster.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muhd/MUHDCluster.java rename to src/main/java/org/jlab/rec/muhd/MUHDCluster.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muhd/MUHDConstants.java b/src/main/java/org/jlab/rec/muhd/MUHDConstants.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muhd/MUHDConstants.java rename to src/main/java/org/jlab/rec/muhd/MUHDConstants.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muhd/MUHDEngine.java b/src/main/java/org/jlab/rec/muhd/MUHDEngine.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muhd/MUHDEngine.java rename to src/main/java/org/jlab/rec/muhd/MUHDEngine.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muhd/MUHDHit.java b/src/main/java/org/jlab/rec/muhd/MUHDHit.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muhd/MUHDHit.java rename to src/main/java/org/jlab/rec/muhd/MUHDHit.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muhd/MUHDReconstruction.java b/src/main/java/org/jlab/rec/muhd/MUHDReconstruction.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muhd/MUHDReconstruction.java rename to src/main/java/org/jlab/rec/muhd/MUHDReconstruction.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTCluster.java b/src/main/java/org/jlab/rec/muvt/MUVTCluster.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTCluster.java rename to src/main/java/org/jlab/rec/muvt/MUVTCluster.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTConstants.java b/src/main/java/org/jlab/rec/muvt/MUVTConstants.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTConstants.java rename to src/main/java/org/jlab/rec/muvt/MUVTConstants.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTCross.java b/src/main/java/org/jlab/rec/muvt/MUVTCross.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTCross.java rename to src/main/java/org/jlab/rec/muvt/MUVTCross.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTEngine.java b/src/main/java/org/jlab/rec/muvt/MUVTEngine.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTEngine.java rename to src/main/java/org/jlab/rec/muvt/MUVTEngine.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTStrip.java b/src/main/java/org/jlab/rec/muvt/MUVTStrip.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTStrip.java rename to src/main/java/org/jlab/rec/muvt/MUVTStrip.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTTrack.java b/src/main/java/org/jlab/rec/muvt/MUVTTrack.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTTrack.java rename to src/main/java/org/jlab/rec/muvt/MUVTTrack.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTTrajectory.java b/src/main/java/org/jlab/rec/muvt/MUVTTrajectory.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muvt/MUVTTrajectory.java rename to src/main/java/org/jlab/rec/muvt/MUVTTrajectory.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muvt/track/fit/KFitter.java b/src/main/java/org/jlab/rec/muvt/track/fit/KFitter.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muvt/track/fit/KFitter.java rename to src/main/java/org/jlab/rec/muvt/track/fit/KFitter.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muvt/track/fit/MeasVecs.java b/src/main/java/org/jlab/rec/muvt/track/fit/MeasVecs.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muvt/track/fit/MeasVecs.java rename to src/main/java/org/jlab/rec/muvt/track/fit/MeasVecs.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muvt/track/fit/RungeKutta.java b/src/main/java/org/jlab/rec/muvt/track/fit/RungeKutta.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muvt/track/fit/RungeKutta.java rename to src/main/java/org/jlab/rec/muvt/track/fit/RungeKutta.java diff --git a/reconstruction/mu/src/main/java/org/jlab/rec/muvt/track/fit/StateVecs.java b/src/main/java/org/jlab/rec/muvt/track/fit/StateVecs.java similarity index 100% rename from reconstruction/mu/src/main/java/org/jlab/rec/muvt/track/fit/StateVecs.java rename to src/main/java/org/jlab/rec/muvt/track/fit/StateVecs.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/Quaternion.java b/src/main/java/org/jlab/rec/rich/Quaternion.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/Quaternion.java rename to src/main/java/org/jlab/rec/rich/Quaternion.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHCalibration.java b/src/main/java/org/jlab/rec/rich/RICHCalibration.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHCalibration.java rename to src/main/java/org/jlab/rec/rich/RICHCalibration.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHCluster.java b/src/main/java/org/jlab/rec/rich/RICHCluster.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHCluster.java rename to src/main/java/org/jlab/rec/rich/RICHCluster.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHConstants.java b/src/main/java/org/jlab/rec/rich/RICHConstants.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHConstants.java rename to src/main/java/org/jlab/rec/rich/RICHConstants.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHEBEngine.java b/src/main/java/org/jlab/rec/rich/RICHEBEngine.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHEBEngine.java rename to src/main/java/org/jlab/rec/rich/RICHEBEngine.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHEdge.java b/src/main/java/org/jlab/rec/rich/RICHEdge.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHEdge.java rename to src/main/java/org/jlab/rec/rich/RICHEdge.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHEvent.java b/src/main/java/org/jlab/rec/rich/RICHEvent.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHEvent.java rename to src/main/java/org/jlab/rec/rich/RICHEvent.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHEventBuilder.java b/src/main/java/org/jlab/rec/rich/RICHEventBuilder.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHEventBuilder.java rename to 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a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHParticle.java b/src/main/java/org/jlab/rec/rich/RICHParticle.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHParticle.java rename to src/main/java/org/jlab/rec/rich/RICHParticle.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHRayTrace.java b/src/main/java/org/jlab/rec/rich/RICHRayTrace.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHRayTrace.java rename to src/main/java/org/jlab/rec/rich/RICHRayTrace.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHRecoType.java b/src/main/java/org/jlab/rec/rich/RICHRecoType.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHRecoType.java rename to src/main/java/org/jlab/rec/rich/RICHRecoType.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHSolution.java b/src/main/java/org/jlab/rec/rich/RICHSolution.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHSolution.java rename to src/main/java/org/jlab/rec/rich/RICHSolution.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHTime.java b/src/main/java/org/jlab/rec/rich/RICHTime.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHTime.java rename to src/main/java/org/jlab/rec/rich/RICHTime.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHUtil.java b/src/main/java/org/jlab/rec/rich/RICHUtil.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHUtil.java rename to src/main/java/org/jlab/rec/rich/RICHUtil.java diff --git a/reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHio.java b/src/main/java/org/jlab/rec/rich/RICHio.java similarity index 100% rename from reconstruction/rich/src/main/java/org/jlab/rec/rich/RICHio.java rename to src/main/java/org/jlab/rec/rich/RICHio.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/Geometry.java b/src/main/java/org/jlab/rec/rtpc/Geometry.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/Geometry.java rename to src/main/java/org/jlab/rec/rtpc/Geometry.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/KalmanFilter/Hit.java b/src/main/java/org/jlab/rec/rtpc/KalmanFilter/Hit.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/KalmanFilter/Hit.java rename to src/main/java/org/jlab/rec/rtpc/KalmanFilter/Hit.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/KalmanFilter/Indicator.java b/src/main/java/org/jlab/rec/rtpc/KalmanFilter/Indicator.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/KalmanFilter/Indicator.java rename to src/main/java/org/jlab/rec/rtpc/KalmanFilter/Indicator.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/KalmanFilter/KFitter.java b/src/main/java/org/jlab/rec/rtpc/KalmanFilter/KFitter.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/KalmanFilter/KFitter.java rename to src/main/java/org/jlab/rec/rtpc/KalmanFilter/KFitter.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/KalmanFilter/KalmanFitter.java b/src/main/java/org/jlab/rec/rtpc/KalmanFilter/KalmanFitter.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/KalmanFilter/KalmanFitter.java rename to src/main/java/org/jlab/rec/rtpc/KalmanFilter/KalmanFitter.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/KalmanFilter/KalmanFitterInfo.java b/src/main/java/org/jlab/rec/rtpc/KalmanFilter/KalmanFitterInfo.java similarity index 100% rename from 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rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/HelixFitJava.java rename to src/main/java/org/jlab/rec/rtpc/hit/HelixFitJava.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/HelixFitObject.java b/src/main/java/org/jlab/rec/rtpc/hit/HelixFitObject.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/HelixFitObject.java rename to src/main/java/org/jlab/rec/rtpc/hit/HelixFitObject.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/HelixFitTest.java b/src/main/java/org/jlab/rec/rtpc/hit/HelixFitTest.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/HelixFitTest.java rename to src/main/java/org/jlab/rec/rtpc/hit/HelixFitTest.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/Hit.java b/src/main/java/org/jlab/rec/rtpc/hit/Hit.java similarity index 100% rename from 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reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/HitReconstruction.java rename to src/main/java/org/jlab/rec/rtpc/hit/HitReconstruction.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/HitVector.java b/src/main/java/org/jlab/rec/rtpc/hit/HitVector.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/HitVector.java rename to src/main/java/org/jlab/rec/rtpc/hit/HitVector.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/PadVector.java b/src/main/java/org/jlab/rec/rtpc/hit/PadVector.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/PadVector.java rename to src/main/java/org/jlab/rec/rtpc/hit/PadVector.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/RecoHitVector.java b/src/main/java/org/jlab/rec/rtpc/hit/RecoHitVector.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/RecoHitVector.java rename to src/main/java/org/jlab/rec/rtpc/hit/RecoHitVector.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/ReducedTrack.java b/src/main/java/org/jlab/rec/rtpc/hit/ReducedTrack.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/ReducedTrack.java rename to src/main/java/org/jlab/rec/rtpc/hit/ReducedTrack.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/ReducedTrackMap.java b/src/main/java/org/jlab/rec/rtpc/hit/ReducedTrackMap.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/ReducedTrackMap.java rename to src/main/java/org/jlab/rec/rtpc/hit/ReducedTrackMap.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/SignalSimulation.java b/src/main/java/org/jlab/rec/rtpc/hit/SignalSimulation.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/SignalSimulation.java rename to src/main/java/org/jlab/rec/rtpc/hit/SignalSimulation.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/TimeAverage.java b/src/main/java/org/jlab/rec/rtpc/hit/TimeAverage.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/TimeAverage.java rename to src/main/java/org/jlab/rec/rtpc/hit/TimeAverage.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/Track.java b/src/main/java/org/jlab/rec/rtpc/hit/Track.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/Track.java rename to src/main/java/org/jlab/rec/rtpc/hit/Track.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/TrackDisentangler.java b/src/main/java/org/jlab/rec/rtpc/hit/TrackDisentangler.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/TrackDisentangler.java rename to src/main/java/org/jlab/rec/rtpc/hit/TrackDisentangler.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/TrackFinder.java b/src/main/java/org/jlab/rec/rtpc/hit/TrackFinder.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/TrackFinder.java rename to src/main/java/org/jlab/rec/rtpc/hit/TrackFinder.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/TrackHitReco.java b/src/main/java/org/jlab/rec/rtpc/hit/TrackHitReco.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/TrackHitReco.java rename to src/main/java/org/jlab/rec/rtpc/hit/TrackHitReco.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/rec/rtpc/hit/TrackMap.java b/src/main/java/org/jlab/rec/rtpc/hit/TrackMap.java similarity index 100% rename from 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a/reconstruction/tof/src/main/java/org/jlab/rec/tof/banks/FTOFMatch.java b/src/main/java/org/jlab/rec/tof/banks/FTOFMatch.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/banks/FTOFMatch.java rename to src/main/java/org/jlab/rec/tof/banks/FTOFMatch.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/tof/banks/IBaseHit.java b/src/main/java/org/jlab/rec/tof/banks/IBaseHit.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/banks/IBaseHit.java rename to src/main/java/org/jlab/rec/tof/banks/IBaseHit.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/tof/banks/IMatchedHit.java b/src/main/java/org/jlab/rec/tof/banks/IMatchedHit.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/banks/IMatchedHit.java rename to src/main/java/org/jlab/rec/tof/banks/IMatchedHit.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/tof/banks/ctof/HitReader.java 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a/reconstruction/tof/src/main/java/org/jlab/rec/tof/banks/ctof/package-info.java b/src/main/java/org/jlab/rec/tof/banks/ctof/package-info.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/banks/ctof/package-info.java rename to src/main/java/org/jlab/rec/tof/banks/ctof/package-info.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/tof/banks/ftof/HitReader.java b/src/main/java/org/jlab/rec/tof/banks/ftof/HitReader.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/banks/ftof/HitReader.java rename to src/main/java/org/jlab/rec/tof/banks/ftof/HitReader.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/tof/banks/ftof/RecoBankWriter.java b/src/main/java/org/jlab/rec/tof/banks/ftof/RecoBankWriter.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/banks/ftof/RecoBankWriter.java rename to src/main/java/org/jlab/rec/tof/banks/ftof/RecoBankWriter.java diff 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a/reconstruction/tof/src/main/java/org/jlab/rec/tof/cluster/ftof/package-info.java b/src/main/java/org/jlab/rec/tof/cluster/ftof/package-info.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/cluster/ftof/package-info.java rename to src/main/java/org/jlab/rec/tof/cluster/ftof/package-info.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/tof/cluster/package-info.java b/src/main/java/org/jlab/rec/tof/cluster/package-info.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/cluster/package-info.java rename to src/main/java/org/jlab/rec/tof/cluster/package-info.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/tof/hit/AHit.java b/src/main/java/org/jlab/rec/tof/hit/AHit.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/hit/AHit.java rename to src/main/java/org/jlab/rec/tof/hit/AHit.java diff --git 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a/reconstruction/tof/src/main/java/org/jlab/rec/tof/hit/ctof/package-info.java b/src/main/java/org/jlab/rec/tof/hit/ctof/package-info.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/hit/ctof/package-info.java rename to src/main/java/org/jlab/rec/tof/hit/ctof/package-info.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/tof/hit/ftof/Hit.java b/src/main/java/org/jlab/rec/tof/hit/ftof/Hit.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/hit/ftof/Hit.java rename to src/main/java/org/jlab/rec/tof/hit/ftof/Hit.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/tof/hit/ftof/package-info.java b/src/main/java/org/jlab/rec/tof/hit/ftof/package-info.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/hit/ftof/package-info.java rename to src/main/java/org/jlab/rec/tof/hit/ftof/package-info.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/tof/hit/package-info.java b/src/main/java/org/jlab/rec/tof/hit/package-info.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/hit/package-info.java rename to src/main/java/org/jlab/rec/tof/hit/package-info.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/tof/package-info.java b/src/main/java/org/jlab/rec/tof/package-info.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/package-info.java rename to src/main/java/org/jlab/rec/tof/package-info.java diff --git a/reconstruction/tof/src/main/java/org/jlab/rec/tof/track/Track.java b/src/main/java/org/jlab/rec/tof/track/Track.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/rec/tof/track/Track.java rename to src/main/java/org/jlab/rec/tof/track/Track.java diff --git a/reconstruction/vtx/src/main/java/org/jlab/rec/vtx/Constants.java 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a/reconstruction/vtx/src/main/java/org/jlab/rec/vtx/banks/package.html b/src/main/java/org/jlab/rec/vtx/banks/package.html similarity index 100% rename from reconstruction/vtx/src/main/java/org/jlab/rec/vtx/banks/package.html rename to src/main/java/org/jlab/rec/vtx/banks/package.html diff --git a/reconstruction/alert/src/main/java/org/jlab/service/ahdc/AHDCEngine.java b/src/main/java/org/jlab/service/ahdc/AHDCEngine.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/service/ahdc/AHDCEngine.java rename to src/main/java/org/jlab/service/ahdc/AHDCEngine.java diff --git a/reconstruction/ai/src/main/java/org/jlab/service/ai/DCClsComboEngine.java b/src/main/java/org/jlab/service/ai/DCClsComboEngine.java similarity index 100% rename from reconstruction/ai/src/main/java/org/jlab/service/ai/DCClsComboEngine.java rename to src/main/java/org/jlab/service/ai/DCClsComboEngine.java diff --git a/reconstruction/ai/src/main/java/org/jlab/service/ai/DCDenoiseEngine.java b/src/main/java/org/jlab/service/ai/DCDenoiseEngine.java similarity index 100% rename from reconstruction/ai/src/main/java/org/jlab/service/ai/DCDenoiseEngine.java rename to src/main/java/org/jlab/service/ai/DCDenoiseEngine.java diff --git a/reconstruction/ai/src/main/java/org/jlab/service/ai/PredictorPool.java b/src/main/java/org/jlab/service/ai/PredictorPool.java similarity index 100% rename from reconstruction/ai/src/main/java/org/jlab/service/ai/PredictorPool.java rename to src/main/java/org/jlab/service/ai/PredictorPool.java diff --git a/reconstruction/alert/src/main/java/org/jlab/service/alert/ALERTEngine.java b/src/main/java/org/jlab/service/alert/ALERTEngine.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/service/alert/ALERTEngine.java rename to src/main/java/org/jlab/service/alert/ALERTEngine.java diff --git a/reconstruction/alert/src/main/java/org/jlab/service/atof/ATOFEngine.java b/src/main/java/org/jlab/service/atof/ATOFEngine.java similarity index 100% rename from reconstruction/alert/src/main/java/org/jlab/service/atof/ATOFEngine.java rename to src/main/java/org/jlab/service/atof/ATOFEngine.java diff --git a/reconstruction/band/src/main/java/org/jlab/service/band/BANDEngine.java b/src/main/java/org/jlab/service/band/BANDEngine.java similarity index 100% rename from reconstruction/band/src/main/java/org/jlab/service/band/BANDEngine.java rename to src/main/java/org/jlab/service/band/BANDEngine.java diff --git a/reconstruction/bg/src/main/java/org/jlab/service/bg/BackgroundEngine.java b/src/main/java/org/jlab/service/bg/BackgroundEngine.java similarity index 100% rename from reconstruction/bg/src/main/java/org/jlab/service/bg/BackgroundEngine.java rename to src/main/java/org/jlab/service/bg/BackgroundEngine.java diff --git a/reconstruction/cnd/src/main/java/org/jlab/service/cnd/CNDCalibrationEngine.java b/src/main/java/org/jlab/service/cnd/CNDCalibrationEngine.java similarity index 100% rename from reconstruction/cnd/src/main/java/org/jlab/service/cnd/CNDCalibrationEngine.java rename to src/main/java/org/jlab/service/cnd/CNDCalibrationEngine.java diff --git a/reconstruction/tof/src/main/java/org/jlab/service/ctof/CTOFEngine.java b/src/main/java/org/jlab/service/ctof/CTOFEngine.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/service/ctof/CTOFEngine.java rename to src/main/java/org/jlab/service/ctof/CTOFEngine.java diff --git a/reconstruction/tof/src/main/java/org/jlab/service/ctof/package-info.java b/src/main/java/org/jlab/service/ctof/package-info.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/service/ctof/package-info.java rename to src/main/java/org/jlab/service/ctof/package-info.java diff --git a/reconstruction/dc/src/main/java/org/jlab/service/dc/DCEngine.java b/src/main/java/org/jlab/service/dc/DCEngine.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/service/dc/DCEngine.java rename to src/main/java/org/jlab/service/dc/DCEngine.java diff --git a/reconstruction/dc/src/main/java/org/jlab/service/dc/DCHBClustering.java b/src/main/java/org/jlab/service/dc/DCHBClustering.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/service/dc/DCHBClustering.java rename to src/main/java/org/jlab/service/dc/DCHBClustering.java diff --git a/reconstruction/dc/src/main/java/org/jlab/service/dc/DCHBEngine.java b/src/main/java/org/jlab/service/dc/DCHBEngine.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/service/dc/DCHBEngine.java rename to src/main/java/org/jlab/service/dc/DCHBEngine.java diff --git a/reconstruction/dc/src/main/java/org/jlab/service/dc/DCHBPostClusterAI.java b/src/main/java/org/jlab/service/dc/DCHBPostClusterAI.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/service/dc/DCHBPostClusterAI.java rename to src/main/java/org/jlab/service/dc/DCHBPostClusterAI.java diff --git a/reconstruction/dc/src/main/java/org/jlab/service/dc/DCHBPostClusterConv.java b/src/main/java/org/jlab/service/dc/DCHBPostClusterConv.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/service/dc/DCHBPostClusterConv.java rename to src/main/java/org/jlab/service/dc/DCHBPostClusterConv.java diff --git a/reconstruction/dc/src/main/java/org/jlab/service/dc/DCHBTrackingAI.java b/src/main/java/org/jlab/service/dc/DCHBTrackingAI.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/service/dc/DCHBTrackingAI.java rename to src/main/java/org/jlab/service/dc/DCHBTrackingAI.java diff --git a/reconstruction/dc/src/main/java/org/jlab/service/dc/DCTBEngine.java b/src/main/java/org/jlab/service/dc/DCTBEngine.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/service/dc/DCTBEngine.java rename to src/main/java/org/jlab/service/dc/DCTBEngine.java diff --git a/reconstruction/dc/src/main/java/org/jlab/service/dc/DCTBEngineAI.java b/src/main/java/org/jlab/service/dc/DCTBEngineAI.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/service/dc/DCTBEngineAI.java rename to src/main/java/org/jlab/service/dc/DCTBEngineAI.java diff --git a/reconstruction/dc/src/main/java/org/jlab/service/dc/LayerEfficiencyAnalyzer.java b/src/main/java/org/jlab/service/dc/LayerEfficiencyAnalyzer.java similarity index 100% rename from reconstruction/dc/src/main/java/org/jlab/service/dc/LayerEfficiencyAnalyzer.java rename to src/main/java/org/jlab/service/dc/LayerEfficiencyAnalyzer.java diff --git a/reconstruction/eb/src/main/java/org/jlab/service/eb/EBAnalyzer.java b/src/main/java/org/jlab/service/eb/EBAnalyzer.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/service/eb/EBAnalyzer.java rename to src/main/java/org/jlab/service/eb/EBAnalyzer.java diff --git a/reconstruction/eb/src/main/java/org/jlab/service/eb/EBEngine.java b/src/main/java/org/jlab/service/eb/EBEngine.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/service/eb/EBEngine.java rename to src/main/java/org/jlab/service/eb/EBEngine.java diff --git a/reconstruction/eb/src/main/java/org/jlab/service/eb/EBHBAIEngine.java b/src/main/java/org/jlab/service/eb/EBHBAIEngine.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/service/eb/EBHBAIEngine.java rename to src/main/java/org/jlab/service/eb/EBHBAIEngine.java diff --git a/reconstruction/eb/src/main/java/org/jlab/service/eb/EBHBEngine.java b/src/main/java/org/jlab/service/eb/EBHBEngine.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/service/eb/EBHBEngine.java rename to src/main/java/org/jlab/service/eb/EBHBEngine.java diff --git a/reconstruction/eb/src/main/java/org/jlab/service/eb/EBMatching.java b/src/main/java/org/jlab/service/eb/EBMatching.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/service/eb/EBMatching.java rename to src/main/java/org/jlab/service/eb/EBMatching.java diff --git a/reconstruction/eb/src/main/java/org/jlab/service/eb/EBTBAIEngine.java b/src/main/java/org/jlab/service/eb/EBTBAIEngine.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/service/eb/EBTBAIEngine.java rename to src/main/java/org/jlab/service/eb/EBTBAIEngine.java diff --git a/reconstruction/eb/src/main/java/org/jlab/service/eb/EBTBEngine.java b/src/main/java/org/jlab/service/eb/EBTBEngine.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/service/eb/EBTBEngine.java rename to src/main/java/org/jlab/service/eb/EBTBEngine.java diff --git a/reconstruction/eb/src/main/java/org/jlab/service/eb/EBio.java b/src/main/java/org/jlab/service/eb/EBio.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/service/eb/EBio.java rename to src/main/java/org/jlab/service/eb/EBio.java diff --git a/reconstruction/eb/src/main/java/org/jlab/service/eb/EventBuilder.java b/src/main/java/org/jlab/service/eb/EventBuilder.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/service/eb/EventBuilder.java rename to src/main/java/org/jlab/service/eb/EventBuilder.java diff --git a/reconstruction/eb/src/main/java/org/jlab/service/eb/VersionEngine.java b/src/main/java/org/jlab/service/eb/VersionEngine.java similarity index 100% rename from reconstruction/eb/src/main/java/org/jlab/service/eb/VersionEngine.java rename to src/main/java/org/jlab/service/eb/VersionEngine.java diff --git a/reconstruction/ec/src/main/java/org/jlab/service/ec/ECCluster.java b/src/main/java/org/jlab/service/ec/ECCluster.java similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/service/ec/ECCluster.java rename to src/main/java/org/jlab/service/ec/ECCluster.java diff --git a/reconstruction/ec/src/main/java/org/jlab/service/ec/ECCommon.java b/src/main/java/org/jlab/service/ec/ECCommon.java similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/service/ec/ECCommon.java rename to src/main/java/org/jlab/service/ec/ECCommon.java diff --git a/reconstruction/ec/src/main/java/org/jlab/service/ec/ECEngine.java b/src/main/java/org/jlab/service/ec/ECEngine.java similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/service/ec/ECEngine.java rename to src/main/java/org/jlab/service/ec/ECEngine.java diff --git a/reconstruction/ec/src/main/java/org/jlab/service/ec/ECPeak.java b/src/main/java/org/jlab/service/ec/ECPeak.java similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/service/ec/ECPeak.java rename to src/main/java/org/jlab/service/ec/ECPeak.java diff --git a/reconstruction/ec/src/main/java/org/jlab/service/ec/ECPeakAnalysis.java b/src/main/java/org/jlab/service/ec/ECPeakAnalysis.java similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/service/ec/ECPeakAnalysis.java rename to src/main/java/org/jlab/service/ec/ECPeakAnalysis.java diff --git a/reconstruction/ec/src/main/java/org/jlab/service/ec/ECPeakSplitter.java b/src/main/java/org/jlab/service/ec/ECPeakSplitter.java similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/service/ec/ECPeakSplitter.java rename to src/main/java/org/jlab/service/ec/ECPeakSplitter.java diff --git a/reconstruction/ec/src/main/java/org/jlab/service/ec/ECStrip.java b/src/main/java/org/jlab/service/ec/ECStrip.java similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/service/ec/ECStrip.java rename to src/main/java/org/jlab/service/ec/ECStrip.java diff --git a/reconstruction/fmt/src/main/java/org/jlab/service/fmt/FMTEngine.java b/src/main/java/org/jlab/service/fmt/FMTEngine.java similarity index 100% rename from reconstruction/fmt/src/main/java/org/jlab/service/fmt/FMTEngine.java rename to src/main/java/org/jlab/service/fmt/FMTEngine.java diff --git a/reconstruction/tof/src/main/java/org/jlab/service/ftof/FTOFEngine.java b/src/main/java/org/jlab/service/ftof/FTOFEngine.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/service/ftof/FTOFEngine.java rename to src/main/java/org/jlab/service/ftof/FTOFEngine.java diff --git a/reconstruction/tof/src/main/java/org/jlab/service/ftof/FTOFHBEngine.java b/src/main/java/org/jlab/service/ftof/FTOFHBEngine.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/service/ftof/FTOFHBEngine.java rename to src/main/java/org/jlab/service/ftof/FTOFHBEngine.java diff --git a/reconstruction/tof/src/main/java/org/jlab/service/ftof/FTOFTBEngine.java b/src/main/java/org/jlab/service/ftof/FTOFTBEngine.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/service/ftof/FTOFTBEngine.java rename to src/main/java/org/jlab/service/ftof/FTOFTBEngine.java diff --git a/reconstruction/tof/src/main/java/org/jlab/service/ftof/package-info.java b/src/main/java/org/jlab/service/ftof/package-info.java similarity index 100% rename from reconstruction/tof/src/main/java/org/jlab/service/ftof/package-info.java rename to src/main/java/org/jlab/service/ftof/package-info.java diff --git a/reconstruction/htcc/src/main/java/org/jlab/service/htcc/HTCCReconstructionService.java b/src/main/java/org/jlab/service/htcc/HTCCReconstructionService.java similarity index 100% rename from reconstruction/htcc/src/main/java/org/jlab/service/htcc/HTCCReconstructionService.java rename to src/main/java/org/jlab/service/htcc/HTCCReconstructionService.java diff --git a/reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/LTCCCluster.java b/src/main/java/org/jlab/service/ltcc/LTCCCluster.java similarity index 100% rename from reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/LTCCCluster.java rename to src/main/java/org/jlab/service/ltcc/LTCCCluster.java diff --git a/reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/LTCCClusterCorrection.java b/src/main/java/org/jlab/service/ltcc/LTCCClusterCorrection.java similarity index 100% rename from reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/LTCCClusterCorrection.java rename to src/main/java/org/jlab/service/ltcc/LTCCClusterCorrection.java diff --git a/reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/LTCCClusterFinder.java b/src/main/java/org/jlab/service/ltcc/LTCCClusterFinder.java similarity index 100% rename from reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/LTCCClusterFinder.java rename to src/main/java/org/jlab/service/ltcc/LTCCClusterFinder.java diff --git a/reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/LTCCEngine.java b/src/main/java/org/jlab/service/ltcc/LTCCEngine.java similarity index 100% rename from reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/LTCCEngine.java rename to src/main/java/org/jlab/service/ltcc/LTCCEngine.java diff --git a/reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/LTCCHit.java b/src/main/java/org/jlab/service/ltcc/LTCCHit.java similarity index 100% rename from reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/LTCCHit.java rename to src/main/java/org/jlab/service/ltcc/LTCCHit.java diff --git a/reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/viewer/LTCCClusterHistos.java b/src/main/java/org/jlab/service/ltcc/viewer/LTCCClusterHistos.java similarity index 100% rename from reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/viewer/LTCCClusterHistos.java rename to src/main/java/org/jlab/service/ltcc/viewer/LTCCClusterHistos.java diff --git a/reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/viewer/LTCCHistogrammer.java b/src/main/java/org/jlab/service/ltcc/viewer/LTCCHistogrammer.java similarity index 100% rename from reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/viewer/LTCCHistogrammer.java rename to src/main/java/org/jlab/service/ltcc/viewer/LTCCHistogrammer.java diff --git a/reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/viewer/LTCCHitHistos.java b/src/main/java/org/jlab/service/ltcc/viewer/LTCCHitHistos.java similarity index 100% rename from reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/viewer/LTCCHitHistos.java rename to src/main/java/org/jlab/service/ltcc/viewer/LTCCHitHistos.java diff --git a/reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/viewer/LTCCViewer.java b/src/main/java/org/jlab/service/ltcc/viewer/LTCCViewer.java similarity index 100% rename from reconstruction/ltcc/src/main/java/org/jlab/service/ltcc/viewer/LTCCViewer.java rename to src/main/java/org/jlab/service/ltcc/viewer/LTCCViewer.java diff --git a/reconstruction/mc/src/main/java/org/jlab/service/mc/Figs/ClustersInRecParticle.png b/src/main/java/org/jlab/service/mc/Figs/ClustersInRecParticle.png similarity index 100% rename from reconstruction/mc/src/main/java/org/jlab/service/mc/Figs/ClustersInRecParticle.png rename to src/main/java/org/jlab/service/mc/Figs/ClustersInRecParticle.png diff --git a/reconstruction/mc/src/main/java/org/jlab/service/mc/Figs/ExampleStatWord.png b/src/main/java/org/jlab/service/mc/Figs/ExampleStatWord.png similarity index 100% rename from reconstruction/mc/src/main/java/org/jlab/service/mc/Figs/ExampleStatWord.png rename to src/main/java/org/jlab/service/mc/Figs/ExampleStatWord.png diff --git a/reconstruction/mc/src/main/java/org/jlab/service/mc/Figs/HitsInCluster.png b/src/main/java/org/jlab/service/mc/Figs/HitsInCluster.png similarity index 100% rename from reconstruction/mc/src/main/java/org/jlab/service/mc/Figs/HitsInCluster.png rename to src/main/java/org/jlab/service/mc/Figs/HitsInCluster.png diff --git a/reconstruction/mc/src/main/java/org/jlab/service/mc/Figs/Layer_Bits.png b/src/main/java/org/jlab/service/mc/Figs/Layer_Bits.png similarity index 100% rename from reconstruction/mc/src/main/java/org/jlab/service/mc/Figs/Layer_Bits.png rename to src/main/java/org/jlab/service/mc/Figs/Layer_Bits.png diff --git a/reconstruction/mc/src/main/java/org/jlab/service/mc/README.md b/src/main/java/org/jlab/service/mc/README.md similarity index 100% rename from reconstruction/mc/src/main/java/org/jlab/service/mc/README.md rename to src/main/java/org/jlab/service/mc/README.md diff --git a/reconstruction/mc/src/main/java/org/jlab/service/mc/TruthMatch.java b/src/main/java/org/jlab/service/mc/TruthMatch.java similarity index 100% rename from reconstruction/mc/src/main/java/org/jlab/service/mc/TruthMatch.java rename to src/main/java/org/jlab/service/mc/TruthMatch.java diff --git a/reconstruction/mltn/src/main/java/org/jlab/service/mltn/MLTDEngine.java b/src/main/java/org/jlab/service/mltn/MLTDEngine.java similarity index 100% rename from reconstruction/mltn/src/main/java/org/jlab/service/mltn/MLTDEngine.java rename to src/main/java/org/jlab/service/mltn/MLTDEngine.java diff --git a/reconstruction/mltn/src/main/java/org/jlab/service/mltn/MLTNEngine.java b/src/main/java/org/jlab/service/mltn/MLTNEngine.java similarity index 100% rename from reconstruction/mltn/src/main/java/org/jlab/service/mltn/MLTNEngine.java rename to src/main/java/org/jlab/service/mltn/MLTNEngine.java diff --git a/reconstruction/postproc/src/main/java/org/jlab/service/postproc/PostprocEngine.java b/src/main/java/org/jlab/service/postproc/PostprocEngine.java similarity index 100% rename from reconstruction/postproc/src/main/java/org/jlab/service/postproc/PostprocEngine.java rename to src/main/java/org/jlab/service/postproc/PostprocEngine.java diff --git a/reconstruction/raster/src/main/java/org/jlab/service/raster/RasterEngine.java b/src/main/java/org/jlab/service/raster/RasterEngine.java similarity index 100% rename from reconstruction/raster/src/main/java/org/jlab/service/raster/RasterEngine.java rename to src/main/java/org/jlab/service/raster/RasterEngine.java diff --git a/reconstruction/recoil/src/main/java/org/jlab/service/recoil/RecoilCluster.java b/src/main/java/org/jlab/service/recoil/RecoilCluster.java similarity index 100% rename from reconstruction/recoil/src/main/java/org/jlab/service/recoil/RecoilCluster.java rename to src/main/java/org/jlab/service/recoil/RecoilCluster.java diff --git a/reconstruction/recoil/src/main/java/org/jlab/service/recoil/RecoilConstants.java b/src/main/java/org/jlab/service/recoil/RecoilConstants.java similarity index 100% rename from reconstruction/recoil/src/main/java/org/jlab/service/recoil/RecoilConstants.java rename to src/main/java/org/jlab/service/recoil/RecoilConstants.java diff --git a/reconstruction/recoil/src/main/java/org/jlab/service/recoil/RecoilCross.java b/src/main/java/org/jlab/service/recoil/RecoilCross.java similarity index 100% rename from reconstruction/recoil/src/main/java/org/jlab/service/recoil/RecoilCross.java rename to src/main/java/org/jlab/service/recoil/RecoilCross.java diff --git a/reconstruction/recoil/src/main/java/org/jlab/service/recoil/RecoilEngine.java b/src/main/java/org/jlab/service/recoil/RecoilEngine.java similarity index 100% rename from reconstruction/recoil/src/main/java/org/jlab/service/recoil/RecoilEngine.java rename to src/main/java/org/jlab/service/recoil/RecoilEngine.java diff --git a/reconstruction/recoil/src/main/java/org/jlab/service/recoil/RecoilStrip.java b/src/main/java/org/jlab/service/recoil/RecoilStrip.java similarity index 100% rename from reconstruction/recoil/src/main/java/org/jlab/service/recoil/RecoilStrip.java rename to src/main/java/org/jlab/service/recoil/RecoilStrip.java diff --git a/reconstruction/rtpc/src/main/java/org/jlab/service/rtpc/RTPCEngine.java b/src/main/java/org/jlab/service/rtpc/RTPCEngine.java similarity index 100% rename from reconstruction/rtpc/src/main/java/org/jlab/service/rtpc/RTPCEngine.java rename to 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--git a/reconstruction/ec/src/main/java/org/jlab/service/swim/MagF.java b/src/main/java/org/jlab/service/swim/MagF.java similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/service/swim/MagF.java rename to src/main/java/org/jlab/service/swim/MagF.java diff --git a/reconstruction/ec/src/main/java/org/jlab/service/swim/SwimEngine.java.old b/src/main/java/org/jlab/service/swim/SwimEngine.java.old similarity index 100% rename from reconstruction/ec/src/main/java/org/jlab/service/swim/SwimEngine.java.old rename to src/main/java/org/jlab/service/swim/SwimEngine.java.old diff --git a/reconstruction/uber/src/main/java/org/jlab/service/uber/Uber.java b/src/main/java/org/jlab/service/uber/Uber.java similarity index 100% rename from reconstruction/uber/src/main/java/org/jlab/service/uber/Uber.java rename to src/main/java/org/jlab/service/uber/Uber.java diff --git a/reconstruction/urwt/src/main/java/org/jlab/service/urwt/URWRStrip.java b/src/main/java/org/jlab/service/urwt/URWRStrip.java similarity index 100% rename from reconstruction/urwt/src/main/java/org/jlab/service/urwt/URWRStrip.java rename to src/main/java/org/jlab/service/urwt/URWRStrip.java diff --git a/reconstruction/urwt/src/main/java/org/jlab/service/urwt/URWTCluster.java b/src/main/java/org/jlab/service/urwt/URWTCluster.java similarity index 100% rename from reconstruction/urwt/src/main/java/org/jlab/service/urwt/URWTCluster.java rename to src/main/java/org/jlab/service/urwt/URWTCluster.java diff --git a/reconstruction/urwt/src/main/java/org/jlab/service/urwt/URWTConstants.java b/src/main/java/org/jlab/service/urwt/URWTConstants.java similarity index 100% rename from reconstruction/urwt/src/main/java/org/jlab/service/urwt/URWTConstants.java rename to src/main/java/org/jlab/service/urwt/URWTConstants.java diff --git a/reconstruction/urwt/src/main/java/org/jlab/service/urwt/URWTCross.java b/src/main/java/org/jlab/service/urwt/URWTCross.java similarity 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reconstruction/cvt/src/test/java/org/jlab/rec/cvt/services/CVTReconstructionTest.java rename to src/test/java/org/jlab/rec/cvt/services/CVTReconstructionTest.java diff --git a/reconstruction/alert/src/test/java/org/jlab/service/alert/AHDCTest.java b/src/test/java/org/jlab/service/alert/AHDCTest.java similarity index 100% rename from reconstruction/alert/src/test/java/org/jlab/service/alert/AHDCTest.java rename to src/test/java/org/jlab/service/alert/AHDCTest.java diff --git a/reconstruction/alert/src/test/java/org/jlab/service/alert/ATOFTest.java b/src/test/java/org/jlab/service/alert/ATOFTest.java similarity index 100% rename from reconstruction/alert/src/test/java/org/jlab/service/alert/ATOFTest.java rename to src/test/java/org/jlab/service/alert/ATOFTest.java diff --git a/reconstruction/dc/src/test/java/org/jlab/service/dc/DCReconstructionTest.java b/src/test/java/org/jlab/service/dc/DCReconstructionTest.java similarity index 100% rename from reconstruction/dc/src/test/java/org/jlab/service/dc/DCReconstructionTest.java rename to src/test/java/org/jlab/service/dc/DCReconstructionTest.java diff --git a/reconstruction/eb/src/test/java/org/jlab/service/eb/EBReconstructionTest.java b/src/test/java/org/jlab/service/eb/EBReconstructionTest.java similarity index 100% rename from reconstruction/eb/src/test/java/org/jlab/service/eb/EBReconstructionTest.java rename to src/test/java/org/jlab/service/eb/EBReconstructionTest.java diff --git a/reconstruction/ec/src/test/java/org/jlab/service/ec/ECReconstructionTest.java b/src/test/java/org/jlab/service/ec/ECReconstructionTest.java similarity index 100% rename from reconstruction/ec/src/test/java/org/jlab/service/ec/ECReconstructionTest.java rename to src/test/java/org/jlab/service/ec/ECReconstructionTest.java diff --git a/reconstruction/ft/src/test/java/org/jlab/service/ft/FTEBEngineTest.java b/src/test/java/org/jlab/service/ft/FTEBEngineTest.java similarity index 100% rename from reconstruction/ft/src/test/java/org/jlab/service/ft/FTEBEngineTest.java rename to src/test/java/org/jlab/service/ft/FTEBEngineTest.java diff --git a/reconstruction/ft/src/test/java/org/jlab/service/ft/FTTRKEngineTest.java b/src/test/java/org/jlab/service/ft/FTTRKEngineTest.java similarity index 100% rename from reconstruction/ft/src/test/java/org/jlab/service/ft/FTTRKEngineTest.java rename to src/test/java/org/jlab/service/ft/FTTRKEngineTest.java diff --git a/validation/advanced-tests/data b/validation/advanced-tests/data index b9f2abe1ff..198e15dca3 160000 --- a/validation/advanced-tests/data +++ b/validation/advanced-tests/data @@ -1 +1 @@ -Subproject commit b9f2abe1ff7ee7698ff57a276bba8e0866660f8d +Subproject commit 198e15dca3b5a661e57a401312e14a0a88a002ea diff --git a/validation/jacoco-aggregate.sh b/validation/jacoco-aggregate.sh index 07dafd5abc..340debffc8 100755 --- a/validation/jacoco-aggregate.sh +++ b/validation/jacoco-aggregate.sh @@ -1,14 +1,22 @@ #!/bin/bash -# simple script to aggregate jacoco results, until we figure out a better way +# Prepare JaCoCo report for docs site CI. +# With single-module Maven layout, target/site/jacoco/ is produced directly. +# This script copies the single report to publish/ for CI artifact ingestion. + +set -e mkdir -p publish -rm -r publish +rm -rf publish mkdir -p publish -for d in $(find -type d -name 'jacoco'); do - target=publish/$(echo $d | sed 's;^\./;;') - mkdir -p $target - cp -r $d/* $target/ -done + +# Single module: copy root target/site/jacoco directly +if [ -d "target/site/jacoco" ]; then + cp -r target/site/jacoco publish/ + echo "Copied target/site/jacoco to publish/jacoco" +else + echo "ERROR: target/site/jacoco not found (build may not have run)" >&2 + exit 1 +fi pushd publish @@ -20,19 +28,8 @@ cat << EOF > index.html

JaCoCo Coverage Summary

    -EOF - -indexPages=$(find . -name "index.html" | grep 'jacoco/index') -[ -z "$indexPages" ] && echo "ERROR: no jacoco HTML pages found" >&2 && exit 1 -for indexPage in $indexPages; do - link=$(echo $indexPage | sed 's;^./;;') - name=$(echo $link | sed 's;/target/site/.*;;') - cat << EOF >> index.html -
  • $name
    • -EOF -done - -cat << EOF >> index.html +
  • JaCoCo Coverage Report
    • +
EOF