Refactor: Replace RapidJSON with nlohmann-json

[Growl1234]

RapidJSON seems to be discontinued and has been no release for 10 years, and its CMake configuration is confusing (latest release vs main branch).

This PR replaces it with nlohmann-json for ABACUS JSON output, which is actively maintained, provides a simpler modern C++ interface, and offers well-supported CMake package integration through nlohmann_jsonConfig.cmake and nlohmann_json::nlohmann_json target. This also makes downstream integration more straightforward: its distro packages such as Ubuntu's nlohmann-json3-dev or Fedora's json-devel already ship the completed CMake config and exported target, avoiding the compatibility concerns around RapidJSON's decade-old upstream release.

Test shows that semantic JSON behavior is unchanged, but textual floating-point formatting has difference (0.0000121 with RapidJSON vs 1.21e-05 with nlohmann-json).

What's left for future PR: Further refactor and simplify JSON workflow, e.g. remove jsonKeyNode.

[Copilot]

🟡 Changes recommended

Critical installer and cache-handling defects, plus unresolved code-quality and dependency issues, block approval.

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Pull request overview

This pull request replaces RapidJSON with nlohmann-json for ABACUS JSON output and updates build, toolchain, container, CI, and testing integration. It also adds a code-quality scoring utility.

Changes:

• Migrates JSON serialization and tests to nlohmann::ordered_json.
• Updates CMake, installers, toolchains, Dockerfiles, CI, and build metadata.
• Adds code-quality analysis functionality.

File summaries

File	Review summary
tools/03_code_analysis/code_quality_score.py	Final comments cover directory skipping, duplicate caps, literal-aware parsing, ownership heuristics, call-expression rejection, comment boundaries, and focused tests.
toolchain/toolchain_intel.sh	Updates toolchain JSON configuration; no final comments.
toolchain/toolchain_gnu.sh	Updates toolchain JSON configuration; no final comments.
toolchain/toolchain_gcc-mkl.sh	Updates toolchain JSON configuration; no final comments.
toolchain/toolchain_gcc-aocl.sh	Updates toolchain JSON configuration; no final comments.
toolchain/toolchain_aocc-aocl.sh	Updates toolchain JSON configuration; no final comments.
toolchain/tests/test_rapidjson_cmake.sh	Removes the RapidJSON test; replacement nlohmann-json integration coverage is requested.
toolchain/scripts/tool_kit.sh	Updates dependency tooling; no final comments.
toolchain/scripts/stage4/install_stage4.sh	Integrates JSON installation; no final comments.
toolchain/scripts/stage4/install_rapidjson.sh	Removes the RapidJSON installer; no final comments.
toolchain/scripts/stage4/install_json.sh	Final comments identify incorrect extraction-directory handling and masked installation failures.
toolchain/scripts/package_versions.sh	Pins the nlohmann-json version and checksum; no final comments.
toolchain/scripts/lib/user_interface.sh	Updates package interface text; no final comments.
toolchain/scripts/lib/package_manager.sh	Updates package management; no final comments.
toolchain/scripts/lib/config_manager.sh	Renames package configuration; no final comments.
toolchain/README.md	Documents nlohmann-json usage; no final comments.
toolchain/build_abacus_intel.sh	Enables the new JSON option; no final comments.
toolchain/build_abacus_gnu.sh	Enables the new JSON option; no final comments.
toolchain/build_abacus_gcc-mkl.sh	Enables the new JSON option; no final comments.
toolchain/build_abacus_gcc-aocl.sh	Enables the new JSON option; no final comments.
toolchain/build_abacus_aocc-aocl.sh	Enables the new JSON option; no final comments.
source/source_relax/relax_driver.cpp	Renames the JSON feature guard; no final comments.
source/source_main/driver_run.cpp	Renames the JSON feature guard; no final comments.
source/source_io/parse_args.cpp	Updates JSON build metadata handling; no final comments.
source/source_io/module_json/test/para_json_test.cpp	Final comment identifies new global-state reads and writes in the fixture.
source/source_io/module_json/readin_info.h	Updates JSON declarations; no final comments.
source/source_io/module_json/readin_info.cpp	Updates JSON input handling; no final comments.
source/source_io/module_json/para_json.cpp	Updates JSON orchestration; no final comments.
source/source_io/module_json/output_info.h	Updates output declarations; no final comments.
source/source_io/module_json/output_info.cpp	Final comments identify new PARAM flag dependencies that should be explicit inputs.
source/source_io/module_json/json_node.h	Defines JSON path nodes; no final comments.
source/source_io/module_json/init_info.h	Updates initialization declarations; no final comments.
source/source_io/module_json/init_info.cpp	Final comment requests splitting a comma-separated declaration.
source/source_io/module_json/general_info.h	Updates general-info declarations; no final comments.
source/source_io/module_json/general_info.cpp	Updates general JSON output; no final comments.
source/source_io/module_json/abacusjson.h	Defines the nlohmann-json interface; no final comments.
source/source_io/module_json/abacusjson.cpp	Implements nlohmann-json serialization; no final comments.
source/source_io/CMakeLists.txt	Gates the JSON module on the new option; no final comments.
source/source_io/build_info.h.in	Renames JSON build metadata; no final comments.
source/source_esolver/esolver_ks.cpp	Renames the JSON feature guard; no final comments.
source/CMakeLists.txt	Updates JSON definitions and linking; no final comments.
Dockerfile.intel	Installs nlohmann-json; no final comments.
Dockerfile.gnu	Installs nlohmann-json; no final comments.
Dockerfile.cuda	Installs nlohmann-json; no final comments.
CMakeLists.txt	Final comments identify stale documentation, legacy-cache failure handling, and missing nlohmann-json integration coverage.
cmake/CollectBuildInfoVars.cmake	Reports the JSON dependency version; no final comments.
.github/workflows/test.yml	Updates CI JSON configuration; no final comments.
.github/workflows/coverage.yml	Updates coverage JSON configuration; no final comments.
.github/workflows/build_test_cmake.yml	Enables nlohmann-json builds; no final comments.

Review details

Suppressed comments (4)

CMakeLists.txt:152

• Rule: Focused tests
  Severity: warning
  Location: CMakeLists.txt:151
  Reason: The RapidJSON CMake integration test was removed, but there is no equivalent nlohmann-json configure/link check for nlohmann_jsonConfig.cmake and nlohmann_json::nlohmann_json; a broken package-prefix or imported-target integration can therefore go undetected.
  Suggested action: Replace the deleted test with a focused nlohmann-json CMake integration test that configures with the toolchain prefix and links a minimal target through the imported target.
  Exception: not allowed

# enable json support
if(ENABLE_JSON)
  find_package(nlohmann_json REQUIRED)
endif()

source/source_io/module_json/init_info.cpp:24

• Rule: One variable per declaration
  Severity: error
  Location: source/source_io/module_json/init_info.cpp:24
  Reason: This newly added comma-separated declaration violates ABACUS baseline rule 8 and is rejected by the governance check.
  Suggested action: Split the two declarations into separate statements.
  Exception: not allowed

    int ntype = ucell->ntype, nelec_total = 0;

source/source_io/module_json/output_info.cpp:35

• Rule: Global dependencies must not increase
  Severity: error
  Location: source/source_io/module_json/output_info.cpp:35
  Reason: This backend rewrite adds a direct PARAM.inp.cal_force read in the JSON output path; the governance check reports it as part of a net increase of seven GlobalV/GlobalC/PARAM references in the PR. The JSON helper now couples output serialization to mutable global configuration instead of receiving the flag it needs.
  Suggested action: Pass cal_force explicitly from the caller (and keep the JSON helper independent of PARAM) so the PR's global-dependency budget is non-increasing.
  Exception: not allowed

    if (PARAM.inp.cal_force)

source/source_io/module_json/output_info.cpp:53

• Rule: Global dependencies must not increase
  Severity: error
  Location: source/source_io/module_json/output_info.cpp:53
  Reason: This rewrite adds a direct PARAM.inp.cal_stress read in the JSON output path; the governance check reports it as part of a net increase of seven GlobalV/GlobalC/PARAM references in the PR. This makes the serializer depend on mutable global state rather than an explicit input.
  Suggested action: Pass cal_stress explicitly from the caller (or pass a narrow output-options object) and remove the new PARAM dependency from this helper.
  Exception: not allowed

    if (PARAM.inp.cal_stress)

• Files reviewed: 48/49 changed files
• Comments generated: 5
• Review effort level: Lite

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[Growl1234]

The re-integration exposed a bug that had previously been silently hidden by the RapidJSON-based implementation: the MD path could append SCF data before initializing an output record, producing an invalid JSON structure instead of failing. The stricter nlohmann-json path handling now catches this explicitly. I'll add a fix that initializes one output record at the beginning of each UnitCell-backed MD step.

[ZhouXY-PKU]

Nice job!