update 29 Jan 2026 at 01:11

Author: VatsalSy

.gitatributes

@@ -0,0 +1 @@
+*.md linguist-detectable=true

.gitattributes

@@ -16862,21 +16862,21 @@
   },
   {
     "title": "Drop Impact Simulations | Drop Impact Simulations: Methods",
-    "content": "Key Features Adaptive Mesh Refinement : Quad/octree-based grids with automatic refinement at interfaces and high-velocity regions Two-Phase Flow : Volume-of-Fluid (VOF) method with surface tension modeling Axisymmetric Formulation : Efficient 2D simulations with cylindrical symmetry Modular Architecture : Separated parameter management, geometry initialization, and diagnostics HPC Ready : MPI parallel execution support for large-scale simulations Case-Based Organization : Automatic folder management with unique case numbers Quick Start Single Simulation # Edit parameters vim default.params # Set CaseNo, We, Oh, etc. # Run simulation (serial) ./runSimulation.sh # Run with MPI (4 cores) ./runSimulation.sh --mpi Parameter Sweep # Configure sweep vim sweep.params # Set CASE_START, CASE_END, sweep variables # Run sweep (serial) ./runParameterSweep.sh # Run sweep with MPI (4 cores per case) ./runParameterSweep.sh --mpi Repository Structure src-local/ - Modular header files params.h - Parameter structures and parsing geometry.h - Drop geometry and initialization diagnostics.h - Statistics and output handling postProcess/ - Post-processing tools and visualization getData-generic.c - Field extraction on structured grids getFacet.c - Interface geometry extraction getFootPrint.c - Footprint height analysis getFootPrint.py - Multi-cutoff footprint time-series plotFootPrint.py - Publication-quality footprint plots Video-generic.py - Frame-by-frame visualization pipeline simulationCases/ - Case-based simulation outputs dropImpact.c - Main simulation case runSimulation.sh - Single case runner runParameterSweep.sh - Parameter sweep runner default.params - Single-case configuration sweep.params - Sweep configuration Key Parameters Weber Number (We) : Ratio of inertial to surface tension forces Ohnesorge Numbers (Ohd, Ohs) : Viscous/surface tension ratios for drop and surrounding phases Reynolds Number : Re = \u221aWe/Oh Maximum Refinement Level : Controls mesh resolution (e.g., level 10 = 1024 cells) Domain Size : Computational domain size in drop radii Requirements Basilisk Framework : Install via the ref-locked script above (upstream docs: basilisk.fr ) MPI (optional): For parallel execution macOS: brew install open-mpi Linux: sudo apt-get install libopenmpi-dev References Key Publications Sanjay, V. & Lohse, D. (2025).",
+    "content": "Key Features Adaptive Mesh Refinement : Quad/octree-based grids with automatic refinement at interfaces and high-velocity regions Two-Phase Flow : Volume-of-Fluid (VOF) method with surface tension modeling Axisymmetric Formulation : Efficient 2D simulations with cylindrical symmetry Modular Architecture : Separated parameter management, geometry initialization, and diagnostics HPC Ready : MPI parallel execution support for large-scale simulations Case-Based Organization : Automatic folder management with unique case numbers Quick Start Single Simulation # Edit parameters vim default.params # Set CaseNo, We, Oh, etc. # Run simulation (serial) ./runSimulation.sh # Run with MPI (4 cores) ./runSimulation.sh --mpi Parameter Sweep # Configure sweep vim sweep.params # Set CASE_START, CASE_END, sweep variables # Run sweep (serial) ./runParameterSweep.sh # Run sweep with MPI (4 cores per case) ./runParameterSweep.sh --mpi Post-processing # Run post-processing on one or more cases ./runPostProcess-Ncases.sh 1000 1001 # Show available options ./runPostProcess-Ncases.sh --help Repository Structure src-local/ - Modular header files params.h - Parameter structures and parsing geometry.h - Drop geometry and initialization diagnostics.h - Statistics and output handling postProcess/ - Post-processing tools and visualization getData-generic.c - Field extraction on structured grids getFacet.c - Interface geometry extraction getFootPrint.c - Footprint height analysis getFootPrint.py - Multi-cutoff footprint time-series plotFootPrint.py - Publication-quality footprint plots Video-generic.py - Frame-by-frame visualization pipeline simulationCases/ - Case-based simulation outputs dropImpact.c - Main simulation case dropImpact_legacy.c - Legacy simulation source runSnellius_legacy.sbatch - Legacy batch script runSimulation.sh - Single case runner runParameterSweep.sh - Parameter sweep runner runPostProcess-Ncases.sh - Post-process multiple cases runSweepHamilton.sbatch - Hamilton batch script runSweepSnellius.sbatch - Snellius batch script default.params - Single-case configuration sweep.params - Sweep configuration Key Parameters Weber Number (We) : Ratio of inertial to surface tension forces Ohnesorge Numbers (Ohd, Ohs) : Viscous/surface tension ratios for drop and surrounding phases Reynolds Number : Re = \u221aWe/Oh Maximum Refinement Level : Controls mesh resolution (e.g., level 10 = 1024 cells) Domain Size : Computational domain size in drop radii Requirements Basilisk Framework : Install via the ref-locked script above (upstream docs: basilisk.fr ) MPI (optional): For parallel execution macOS: brew install open-mpi Linux: sudo apt-get install libopenmpi-dev References Key Publications Sanjay, V. & Lohse, D. (2025).",
     "url": "https://comphy-lab.org/Drop-Impact/index.html",
     "type": "docs_content",
     "priority": 4
   },
   {
     "title": "Drop Impact Simulations | Drop Impact Simulations: Unifying theory of...",
-    "content": "Unifying theory of scaling in drop impact: forces and maximum spreading diameter . Physical Review Letters, 134(10), 104003. DOI Comprehensive scaling theory for drop impact forces and maximum spreading Josserand, C. & Thoroddsen, S. T. (2016). Drop impact on a solid surface . Annual Review of Fluid Mechanics, 48, 365-391. DOI Comprehensive review of drop impact phenomena Yarin, A. L. (2006). Drop impact dynamics: Splashing, spreading, receding, bouncing\u2026 . Annual Review of Fluid Mechanics, 38, 159-192. DOI Classical review of drop impact dynamics Documentation Comprehensive documentation is available in CLAUDE.md , including: - Coding standards and best practices - Build and compilation instructions - Simulation physics and numerical methods - Parameter descriptions and typical values - Output file formats and visualization License See LICENSE file for details. Contributing This repository follows the CoMPhy Lab coding standards.",
+    "content": "Unifying theory of scaling in drop impact: forces and maximum spreading diameter . Physical Review Letters, 134(10), 104003. DOI Comprehensive scaling theory for drop impact forces and maximum spreading Josserand, C. & Thoroddsen, S. T. (2016). Drop impact on a solid surface . Annual Review of Fluid Mechanics, 48, 365-391. DOI Comprehensive review of drop impact phenomena Yarin, A. L. (2006). Drop impact dynamics: Splashing, spreading, receding, bouncing\u2026 . Annual Review of Fluid Mechanics, 38, 159-192. DOI Classical review of drop impact dynamics Documentation This README provides the user-facing overview and usage. Additional details live in the runnable scripts ( runSimulation.sh , runParameterSweep.sh ) and in the simulation source ( simulationCases/dropImpact.c ) and headers in src-local/ . License See LICENSE file for details. Contributing Follow the existing code style and keep changes consistent with the repository\u2019s structure and scripts.",
     "url": "https://comphy-lab.org/Drop-Impact/index.html",
     "type": "docs_content",
     "priority": 4
   },
   {
-    "title": "Drop Impact Simulations | Drop Impact Simulations: Context",
-    "content": "See CLAUDE.md for detailed guidelines on: - Code style (2-space indentation, 80-character lines) - Naming conventions (snake_case for variables, camelCase for functions) - Documentation requirements - Testing procedures Contact For questions or collaboration inquiries, please contact the CoMPhy Lab . Generated Documentation Root Directory default.params runParameterSweep.sh runPostProcess-Ncases.sh runSimulation.sh runSweepHamilton.sbatch runSweepSnellius.sbatch sweep.params postProcess postProcess/Video-generic.py postProcess/getData-generic.c postProcess/getFacet.c postProcess/getFootPrint.c postProcess/getFootPrint.py postProcess/plotFootPrint.py simulationCases simulationCases/dropImpact.c simulationCases/dropImpact_legacy.c simulationCases/runSnellius_legacy.sbatch src-local src-local/diagnostics.h src-local/geometry.h src-local/params.h src-local/parse_params.sh",
+    "title": "Drop Impact Simulations | Drop Impact Simulations: Contact For questions...",
+    "content": "Contact For questions or collaboration inquiries, please contact the CoMPhy Lab . Generated Documentation Root Directory default.params runParameterSweep.sh runPostProcess-Ncases.sh runSimulation.sh runSweepHamilton.sbatch runSweepSnellius.sbatch sweep.params postProcess postProcess/Video-generic.py postProcess/getData-generic.c postProcess/getFacet.c postProcess/getFootPrint.c postProcess/getFootPrint.py postProcess/plotFootPrint.py simulationCases simulationCases/dropImpact.c simulationCases/dropImpact_legacy.c simulationCases/runSnellius_legacy.sbatch src-local src-local/diagnostics.h src-local/geometry.h src-local/params.h src-local/parse_params.sh",
     "url": "https://comphy-lab.org/Drop-Impact/index.html",
     "type": "docs_content",
     "priority": 4
@@ -16916,6 +16916,20 @@
     "type": "docs_code",
     "priority": 4
   },
+  {
+    "title": "Drop Impact Simulations | Drop Impact Simulations - Code Example",
+    "content": "# Run post-processing on one or more cases./runPostProcess-Ncases.sh1000 1001",
+    "url": "https://comphy-lab.org/Drop-Impact/index.html",
+    "type": "docs_code",
+    "priority": 4
+  },
+  {
+    "title": "Drop Impact Simulations | Drop Impact Simulations - Code Example",
+    "content": "# Show available options./runPostProcess-Ncases.sh--help",
+    "url": "https://comphy-lab.org/Drop-Impact/index.html",
+    "type": "docs_code",
+    "priority": 4
+  },
   {
     "title": "sweep.params | Drop Impact Simulations: Context",
     "content": "sweep.params See raw file sweep.params # # sweep.params # Parameter sweep configuration for batch simulations. # ============================================================ # Base Configuration # ============================================================ # Start from this parameter file and override sweep variables BASE_CONFIG = default.params # ============================================================ # Case Number Range # ============================================================ # Starting case number (4-digit: 1000-9999) # Each parameter combination gets auto-incremented CaseNo CASE_START = 1306 # Ending case number (inclusive) # Number of combinations should equal CASE_END - CASE_START + 1 # For this sweep: 16 We \u00d7 16 Oh = 256 combinations, so CASE_END = 1561 CASE_END = 1561 # ============================================================ # Sweep Variables # ============================================================ # Format: SWEEP_<variable>=value1,value2,value3,... # The sweep will generate all combinations (cartesian product) # Sweep Weber number (vary impact velocity / surface tension) SWEEP_We = 50,60,70,80,90,100,126,158,200,251,316,398,501,631,794,1000 # Sweep Ohnesorge number (vary viscosity) SWEEP_Ohd = 1e-3,3e-3,1e-2,1.7e-2,2.9e-2,4.9e-2,8.4e-2,1.43e-1,2.43e-1,4.13e-1,7.02e-1,1.19,2.03,3.45,5.87,1e1 # Optional: sweep other parameters # SWEEP_MAXlevel=9,10,11 # SWEEP_Ldomain=6.0,8.0,10.0 # ============================================================ # Output Configuration # ============================================================ # Output folders are created in simulationCases/<CaseNo>/ # CaseNo auto-increments from CASE_START for each parameter combination # Cases run sequentially (one at a time)",

.github/assets/js/search_db.json

@@ -429,13 +429,18 @@ def find_source_files(root_dir: Path, source_dirs: List[str]) -> List[Path]:
     """
     valid_exts = {'.c', '.h', '.py', '.sh', '.sbatch', '.ipynb', '.params'}
     valid_names = {'Makefile'}
+    # Exclude 4-digit numeric case folders (e.g., simulationCases/1000/)
+    numeric_case_pattern = re.compile(r'/\d{4}/')
     files = set()
 
     for dir_name in source_dirs:
         src_path = root_dir / dir_name
         if src_path.is_dir():
             for f in src_path.rglob('*'):
                 if f.is_file():
+                    # Skip files in numeric case folders
+                    if numeric_case_pattern.search(str(f)):
+                        continue
                     if f.name in valid_names:
                         files.add(f)
                     elif f.suffix in valid_exts and not f.name.endswith('.dat'):
@@ -478,7 +483,7 @@ def process_params_file(file_path: Path) -> str:
     Reads a parameter configuration file and returns its content as a Markdown-formatted INI code block.
 
     Parameter files (.params) use key=value syntax with # for comments, similar to INI or shell configuration files.
-    This format is used for simulation parameters in the Drop Impact project.
+    This format is used for simulation parameters in CoMPhy Lab Basilisk projects.
     """
     with open(file_path, 'r', encoding='utf-8') as f:
         content = f.read()

.github/scripts/generate_docs.py

@@ -0,0 +1,25 @@
+# AGENTS
+
+## Project Overview
+This repository contains Basilisk CFD simulation cases and post-processing
+tools for lid-driven cavity dye injection, plus generated documentation in
+`docs/`.
+
+## Layout
+- `simulationCases/`: primary `.c` cases and Makefile
+- `src-local/`: project-specific headers
+- `postProcess/`: analysis scripts and notebooks
+- `docs/`: generated documentation site output
+- `.github/`: documentation assets, scripts, and workflows
+- `*.params`, `*.sbatch`: run configurations and cluster scripts
+- `basilisk/`: local Basilisk checkout (ignored; do not commit)
+
+## Documentation workflow
+- Install Python deps: `python3 -m venv .venv && source .venv/bin/activate && pip install -r .github/scripts/requirements.txt`
+- Build docs: `.github/scripts/build.sh`
+- Preview locally: `.github/scripts/deploy.sh`
+
+## Editing guidance
+- Do not commit the `basilisk/` directory or generated outputs outside `docs/`.
+- Keep case output directories untouched unless explicitly requested.
+- C/C++ style: 2-space indent, 80-char lines, use `/**` markdown comments (no leading `*` lines).

AGENTS.md

@@ -13,16 +13,18 @@ The codebase implements a classical lid driven cavity flow problem with dye inje
 ## Repository Structure
 
 ```
-├── basilisk/src/               Core Basilisk CFD library (reference only, do not modify)
+├── basilisk/                   Local Basilisk checkout (ignored; do not commit)
 ├── simulationCases/            Test cases for simulation
 │   └── LidDrivenCavity-Newtonian-dyeInjection.c    Lid-driven cavity with dye injection
 ├── src-local/                  Custom header files extending Basilisk functionality
 │   └── dye-injection.h         Dye injection for flow visualization
 ├── postProcess/                Project-specific post-processing tools
 │   ├── LidDrivenCavity-Newtonian-dyeInjection.ipynb  Jupyter notebook for analysis
 │   ├── LidDrivenCavity-Newtonian-dyeInjection.py     Python script for post-processing
-│   ├── Visualization3D.ipynb   Jupyter notebook for 3D visualization
+│   ├── Visulization3D.ipynb    Jupyter notebook for 3D visualization
 │   └── getData-LidDriven.c     Data extraction utility
+├── docs/                       Generated documentation site output
+├── .github/                    Documentation assets, scripts, workflows
 ├── runSweepHamilton.sbatch     HPC batch script for Durham Hamilton cluster
 └── runSweepSnellius.sbatch     HPC batch script for Snellius cluster
 ```
@@ -52,6 +54,8 @@ The [`postProcess/`](postProcess) directory provides tools for analyzing and vis
   - Adds streamlines to visualize flow patterns
   - Uses 'getData-LidDriven' utility to extract field data
 
+- [Visulization3D.ipynb](postProcess/Visulization3D.ipynb): Jupyter notebook for 3D visualization
+
 - [getData-LidDriven.c](postProcess/getData-LidDriven.c): C utility that extracts and processes numerical data from simulation output files
 
 ### simulationCases/ Directory
@@ -82,8 +86,8 @@ These scripts run Stage 2 (MPI simulation) of parameter sweeps. Stage 1 (restart
 - Basilisk C installed ([Installation instructions](http://basilisk.fr/src/INSTALL))
 - C compiler (gcc recommended)
 - Make build system
-- Python 3 with pip for documentation generation
-- BeautifulSoup4 for HTML processing (included in requirements.txt)
+- Python 3 with pip for documentation generation (see `.github/scripts/requirements.txt`)
+- Pandoc for HTML generation used by `.github/scripts/generate_docs.py`
 - Scientific visualization tools (optional: ParaView, Gnuplot, etc.)
 
 ### Installation
@@ -96,14 +100,11 @@ These scripts run Stage 2 (MPI simulation) of parameter sweeps. Stage 1 (restart
 
 2. Make sure Basilisk is properly installed and the BASILISK environment variable is set.
 
-3. Install Python dependencies (uses a virtual environment):
+3. Install Python dependencies for documentation generation:
    ```bash
-   # This will automatically set up a virtual environment and install dependencies
-   # like BeautifulSoup4 for HTML processing
-   ./reset_install_requirements.sh
-
-   # To activate the virtual environment for manual commands:
+   python3 -m venv .venv
    source .venv/bin/activate
+   pip install -r .github/scripts/requirements.txt
    ```
 
 4. Compile a test case to verify the setup:
@@ -281,16 +282,9 @@ Please include:
 - Additional functionality in the codebase
 - Improvements to existing materials
 
-#### Example Request:
-[Report here](https://github.com/comphy-lab/documentationWeb/issues/new?template=example_request.md)
-- For requesting specific examples that demonstrate:
-- Particular Basilisk features
-- Solutions to common problems
-- Implementation of specific physics or numerical methods
-
-#### General Question:
-[Report here](https://github.com/comphy-lab/documentationWeb/issues/new?template=general_question.md)
-- For any other questions
+#### Question/Discussion:
+[Report here](https://github.com/comphy-lab/documentationWeb/issues/new?template=question.md)
+- For any other questions or discussions
 
 ### How to Create an Issue
 
@@ -307,4 +301,4 @@ This project is licensed under the [GNU General Public License v3.0](LICENSE) -
 
 ## Acknowledgments
 
-- S. Popinet & collaborators, Basilisk C, [http://basilisk.fr](http://basilisk.fr) (Last accessed: June 2025) (2013-2025)
+- S. Popinet & collaborators, Basilisk C, [http://basilisk.fr](http://basilisk.fr) (Last accessed: June 2025) (2013-2025)