Version 2.0

Release Date: June 20, 2025

🚀 Major Highlights

This release represents a significant evolution of the Jumping Bubbles framework, featuring a complete documentation overhaul, improved code organization, enhanced visualization capabilities, and numerous quality-of-life improvements.

📚 Documentation Overhaul

• New Documentation Website

  • Comprehensive GitHub Pages documentation with modern, responsive design
  • Interactive search functionality with command palette
  • Dark/light theme toggle support
  • Mobile-friendly interface with custom styling
  • Full HTML documentation for all source files

• Enhanced Content

  • Detailed inline documentation added to all source files
  • Comprehensive installation and usage guides
  • Added contribution guidelines and issue templates
  • Improved code examples and tutorials

🏗️ Project Restructuring

• Reorganized Directory Structure
  • Simulation files moved to simulationCases/ directory
  • Post-processing tools consolidated in postProcess/ folder
  • Clear separation between core simulation code and utilities
  • Better naming conventions throughout the project

✨ New Features

• Enhanced Contact Angle Support

  • Extended implementation for arbitrary contact angles
  • Improved boundary condition handling for contact lines
  • Added Bond number variable for better physical modeling

• Hydrophilic Surface Modeling

  • New JumpingBubbles-hydrophilic.c variant
  • Enables comparative studies between different wetting conditions

• Advanced Visualization

  • Updated Visualization3D.ipynb Jupyter notebook
  • Enhanced 2D/3D video generation capabilities
  • PNG image support for documentation

🐛 Bug Fixes

• Fixed boolean parsing in data extraction utilities (getDataXSlice.c, getDataZSlice.c)
• Resolved NameError in Video3D.py subprocess exception handling
• Fixed subprocess import alias in Video2DSlice.py
• Corrected unescaped dash in regex patterns
• Fixed YAML indentation in GitHub workflows
• Added localStorage error handling for theme toggle
• Added guard checks for window.searchHelper

🔧 Improvements

• Code Quality

  • Standardized naming conventions across postProcess folder
  • Improved error handling in Python visualization scripts
  • Enhanced .gitignore patterns for better repository management
  • Consistent code formatting and documentation style

• Build System

  • GitHub Actions workflows for automated documentation deployment
  • Search index generation workflow
  • Improved installation script with better Basilisk handling

• HPC Support

  • Updated SLURM batch scripts
  • Better handling of distributed computing scenarios
  • Maintained OpenMP/MPI compatibility

📊 Known Issues

• Basilisk's distance.h remains incompatible with MPI (unchanged from v1.0)
• Some HPC environments still require manual compiler configuration

🔮 Future Directions

• Automated regression testing framework implementation
• Further optimization of parallel computing performance
• Enhanced interface tracking algorithms
• Additional test cases for validation

📝 Citation

@software{jumping_bubbles_2025,
  author       = {Sanjay, V. and Yang, R.},
  title        = {Jumping Bubbles: A Computational Framework for Studying Bubble Coalescence},
  year         = {2025},
  publisher    = {Zenodo},
  version      = {v2.0},
  doi          = {10.5281/zenodo.14602623},
  url          = {https://comphy-lab.org/JumpingBubbles/}
}

Release Notes:

Release Date: January 5, 2025

Highlights

1. Expanded Two-Phase Flow Capabilities

   • VOF-based interface tracking with an option for the conservative momentum advection module.
   • Added the reduced gravity approach for precise control over effective body forces.

2. Improved HPC Support

   • MPI integration for large-scale parallel runs on HPC clusters.
   • Refined instructions and Slurm scripts for streamlined deployment on typical HPC infrastructures.

3. Enhanced Post-Processing Tools

   • New Python scripts for 2D and 3D visualization (Video2DSlice.py, Video3D.py).
   • Jupyter notebook (Visualization3D.ipynb) for interactive exploration of simulation data.
   • getFacets3D.c for interface extraction and geometric analysis.

4. Robust Initialization Workflow

   • Option to generate initial conditions in a single-threaded (OpenMP) run before migrating to MPI.
   • Automatic environment configuration via .project_config to minimize setup inconsistencies.

Bug Fixes

• Resolved mesh refinement edge cases when using distance.h.
• Corrected velocity boundary conditions on domain walls for axisymmetric setups.
• Addressed race conditions in OpenMP runs by clarifying memory allocation routines.

Known Issues

• Basilisk’s distance.h remains incompatible with MPI, necessitating local initialization before parallel runs.
• Some HPC environments require manual customization of compiler and library paths in .project_config.

Future Directions

• Addition of automated regression tests in testCases/ for routine CI checks.
• Enhancements to post-processing scripts for slice-by-slice interface tracking.
• Further optimization of load balancing in MPI runs.

Citation

@software{jumping_bubbles_2024,
  author       = {Sanjay, V. and Yang, R.},
  title        = {Jumping Bubbles: A Computational Framework for Studying Bubble Coalescence},
  year         = {2024},
  publisher    = {Zenodo},
  version      = {v1.0},
  doi          = {10.5281/zenodo.14602622},
  url          = {https://doi.org/10.5281/zenodo.14602622}
}