Ssot

_quarto.yml

@@ -11,26 +11,75 @@ book:
   repo-branch: main
   repo-actions: [edit, issue]
   favicon: figures/ippl-logo.png
+  sidebar:
+    collapse-level: 1
   chapters:
     - index.qmd
-    - sections/overview/index.qmd
-    - sections/theory/index.qmd
-    - sections/getting-started/index.qmd
-    - sections/examples/alpine-manager-hierarchy.qmd
-    - sections/core-concepts/index.qmd
-    - sections/fields/index.qmd
-    - sections/particles/index.qmd
-    - sections/particle-mesh/index.qmd
-    - sections/fft/index.qmd
-    - sections/poisson-solvers/index.qmd
-    - sections/maxwell-solvers/index.qmd
-    - sections/fem/index.qmd
-    - sections/communication/index.qmd
-    - sections/performance-portability/index.qmd
-    - sections/examples/index.qmd
-    - sections/developer-guide/index.qmd
-    - sections/api-reference/index.qmd
-    - sections/literature/index.qmd
+
+    - part: sections/introduction/index.qmd
+      chapters:
+        - sections/introduction/theory/index.qmd
+        - sections/introduction/overview/index.qmd
+
+    # - part: "Getting Started"
+    - part: sections/getting-started/index.qmd
+      chapters:
+        - sections/getting-started/installation/index.qmd
+        - sections/getting-started/hello-ippl/index.qmd
+        - sections/getting-started/slurm/index.qmd
+
+    - part: sections/ippl-core/index.qmd
+      chapters:
+        - sections/ippl-core/core-concepts/index.qmd
+        - sections/ippl-core/fields/index.qmd
+        - sections/ippl-core/particles/index.qmd
+        - sections/ippl-core/communication/index.qmd
+
+    - part: sections/methods-operators/index.qmd
+      chapters:
+        - sections/methods-operators/particle-mesh-interpolation/index.qmd
+        - sections/methods-operators/differential-operators/index.qmd
+        - sections/methods-operators/cg/index.qmd
+        - sections/methods-operators/fft/index.qmd
+        - file: sections/methods-operators/nufft/index.qmd
+          text: "NUFFT"
+        - sections/methods-operators/fem/index.qmd
+
+    - part: sections/field-solvers/index.qmd
+      chapters:
+        - sections/field-solvers/poisson-solvers/index.qmd
+        - sections/field-solvers/maxwell-solvers/index.qmd
+
+    - part: sections/analysis-performance/index.qmd
+      chapters:
+        - sections/analysis-performance/profiling/index.qmd
+        - sections/analysis-performance/in-situ/index.qmd
+
+    - part: sections/tests/index.qmd
+      chapters:
+        - sections/tests/integration-tests/index.qmd
+        - sections/tests/unit-tests/index.qmd
+
+    - part: sections/demos/index.qmd
+      chapters:
+        - sections/demos/alpine/index.qmd
+        - sections/demos/alpine-pif/index.qmd
+        - sections/demos/cosmology/index.qmd
+        - sections/demos/collisions/index.qmd
+        - sections/demos/fel/index.qmd
+
+    - part: sections/for-developers/index.qmd
+      chapters:
+        - sections/for-developers/developer-guide/index.qmd
+        - sections/for-developers/workflow/index.qmd
+        - sections/for-developers/writing-unit-tests/index.qmd
+        - sections/for-developers/performance-portability/index.qmd
+        - sections/for-developers/api-reference/index.qmd
+
+    - part: sections/appendix/index.qmd
+      chapters: 
+        - sections/appendix/literature/index.qmd
+        - sections/appendix/playground/index.qmd
 
 number-sections: true
 number-depth: 3
@@ -39,6 +88,7 @@ format:
   html:
     toc: true
     toc-depth: 3
+    # toc-location: right
     number-sections: true
     html-math-method: mathjax
     code-fold: false

index.qmd

@@ -1,8 +1,9 @@
 ---
-title: "IPPL Manual"
+unnumbered: true
 number-sections: false
 ---
 
+# Welcome {.unnumbered}
 ::: {.hero}
 ::: {}
 IPPL, the Independent Parallel Particle Layer, is a C++20 library for performance-portable particle, field, and particle-mesh simulations. It provides dimension-independent building blocks for Eulerian, Lagrangian, and hybrid methods on CPUs and GPUs.
@@ -19,10 +20,11 @@ IPPL uses Kokkos for performance portability, MPI for distributed memory communi
 
 For users:
 
-1. Start with @sec-overview and @sec-getting-started.
+1. Start with @sec-overview and @sec-hello-ippl.
 2. Read @sec-core-concepts, then the data model chapters on fields and particles.
 3. Move to FFT, Poisson, Maxwell, or FEM depending on the application.
-4. Use @sec-examples as executable documentation.
+4. Use @sec-tests and @sec-demos as executable documentation.
+
 
 For developers:
 

sections/analysis-performance/in-situ/index.qmd

@@ -0,0 +1,12 @@
+---
+subtitle: "In situ analysis and visualization with ParaView Catalyst."
+---
+
+# In Situ {#sec-in-situ}
+
+coming soon!
+
+## Visualization
+
+
+## Steering

sections/analysis-performance/index.qmd

@@ -0,0 +1,14 @@
+---
+title: "Analysis & Performance"
+subtitle: "Performance evaluation and in-situ analysis"
+---
+
+# Analysis & Performance {#sec-analysis-performance}
+<style>
+#sec-analysis-performance > h1 { display: none; }
+</style>
+
+This chapter covers tools and techniques for analyzing the performance of IPPL applications and visualizing data in situ.
+
+- @sec-profiling: Profiling tools and memory events tracking.
+- @sec-in-situ: In situ analysis and visualization with ParaView Catalyst.