Phlegethon Documentation

PHLEGETHON is a fully compressible, Eulerian magnetohydrodynamic (MHD) code designed for multidimensional simulations in stellar astrophysics. The code uses a time-explicit, second-order, finite-volume method optimized to model a wide range of dynamical regimes, from very low-Mach-number turbulent convection in the deep interior of stars to supersonic flows in subsurface convection zones. PHLEGETHON runs on CPUs and uses MPI-based parallelization via domain decomposition.

Contents

• Getting Started
  • 1. Clone the git repository
  • 2.1 System dependencies (Debian-based systems)
  • 2.2 System dependencies (MacOS/ Homebrew)
  • 2.3 Containerized setup (Docker, optional)
  • 3. Python environment
  • 4. Download Helmholtz EoS table and JINA REACLIB rates
  • 5. Compile the Fortran EoS modules
  • 6. Set environment variables
  • 7. Choose a build configuration
  • 8. Verify setup
  • Reading HDF5 output in Python
• Troubleshooting FAQ
  • How to use this page
  • FAQ
  • Add a new FAQ entry
• Contributing
  • Who can contribute?
  • Before opening a pull request
  • Suggested local checks
  • How to open a pull request
  • Review and merge process
  • Support policy
  • Questions
• Docker Workflow
  • Install Docker
  • Build and Run (Dockerfile)
  • Build and Run (Docker Compose)
  • Python Post-Processing in Containers
  • JupyterLab
  • Access Output Files
  • Interactive Container Access and Logs
  • Troubleshooting
• Build and Run
  • Setting up a test problem
  • Build workflow
  • Docker workflow (optional)
  • Compile-time configuration
• Compile-Time Flags and Options
  • List of options in Phlegethon
• Generate PIG EoS table
• Phlegethon Overview
  • Key numerical methods:
  • Documentation
  • Authors
  • Citation
  • License
• phloutput (Python post-processing utilities)
  • Minimal requirements
  • Quick start
  • Core concepts
  • Comprehensive overview
• create_input_library Documentation
  • 1. Intended Workflow
  • 2. Notebook Structure
  • 3. Minimal Example (profile10 test case)
  • 4. Toggle and Switch Reference (Section: Toggles and Input Values)
  • 5. Reintegration Methods and Equations
  • 6. Output Files
  • 7. What if the template notebook is not what you are looking for?
• get_rprofs
  • Requirements
  • Input Expectations
  • Run Directly
  • Slurm Workflow (submit_rprofs.py)
  • Output
• get_spectra_plane_parallel
  • Input Expectations
  • Run Directly (Single Process)
  • What extract_spectra.py Computes
  • Slurm Workflow (submit_spectra.py)
  • Output
  • Time-Averaged Spectra (average_spectra.py)
• create_network
  • What the Script Does
  • Typical Workflow
  • Configuration (Edit in Script)
  • Run
  • Generated Fortran Routines & Makefile options
  • Example: tests/nuclear-network