RMHD_TEs

Thermal Equilibrium states from Radiation MagnetoHydroDynamics simulations of accretion flows at different angular velocities.

Results

Thermal Equilibrium Curves Surface density vs Effective temperature

Alpha Parameter Plot Pressure vs Stress (viscosity analysis)

Overview

This repository compiles results from radiation MHD simulations using the ZEUS code with shearing box approximation. The main script RMHD_TEs.py plots the thermal equilibrium states of accretion flows, showing the relationship between surface density (Σ) and effective temperature (T_eff) for different angular velocities (Ω).

Features

• Compiles multiple simulation results listed in target_config.py
• Generates two types of plots:
  • TE curves: Surface density vs. Effective temperature
  • Alpha plot: Pressure vs. Stress (for viscosity parameter analysis)
• Color-coded by angular velocity Ω for easy comparison
• Supports both special cases (hardcoded values) and full simulation data

Requirements

Python Dependencies

pip3 install numpy matplotlib

• Python 3.7+
• numpy
• matplotlib

Required Python Files

File	Description
RMHD_TEs.py	Main script for generating thermal equilibrium curves
target_config.py	Configuration file listing all simulation targets and their parameters
zeus_param.py	Reads ZEUS simulation parameters from configuration files
readu.py	Binary data reader for ZEUS output files

Simulation Data Structure

The repository includes simulation data in the data/ directory. Each simulation target (e.g., ws0433) has the following file structure:

data/
└── {target_name}/
    ├── h/
    │   ├── resolv.data     # Dimension info (n_t, n_vave) [text]
    │   └── vave.data       # Volume-averaged history data [binary]
    ├── init/               # Parameter files (at least one required)
    │   ├── iparax.data     # Contains omega, h0 [text]
    │   ├── normalize.data  # Alternative parameter file [text]
    │   └── ipara.data      # Alternative parameter file [text]
    ├── src/
    │   └── Makefile        # Determines problem type (isothermal/radiation)
    └── z3dinput            # Simulation input parameters [text]

Data Directory Contents

The data/ directory contains preprocessed simulation data from various ZEUS radiation MHD runs. See target_config.py and Target Configuration and References for details.

File Formats

h/resolv.data

Text file containing:

n_t n_vave

• n_t: Number of time steps
• n_vave: Number of variables

h/vave.data

Binary file (big-endian, float32) with shape [n_t, n_vave] containing:

• Column 3: Density (for Σ calculation)
• Column 4: Energy density (for gas pressure)
• Column 11: Radiation energy density
• Columns 12-13: Shear stress components
• Column 81: Gas pressure (for h2014/h2015/h2016 series)
• Columns 88-89: Maxwell/Reynolds stress (h2016 series)
• Column 79: Self-gravity term (h2016 series)

init/iparax.data (or alternatives)

Text file containing:

omega h0

• omega: Angular frequency Ω
• h0: Scale height

z3dinput

Text file with simulation parameters including:

• gascon line: gamma (column 8), mean molecular weight (column 4)
• ggen1/2/3 lines: Box dimensions in x, y, z directions

Usage

1. Ensure simulation data is properly organized in the directory structure above
2. Configure targets in target_config.py
3. Run the main script:

python3 RMHD_TEs.py

Optional legend toggle:

# Hide legends
python3 RMHD_TEs.py --legend off

# Show legends (default)
python3 RMHD_TEs.py --legend on

Output plots will be saved to:

• outputs/RMHD_TEs.pdf - Thermal equilibrium curves plot
• outputs/RMHD_alphas.pdf - Alpha parameter plot
• outputs/RMHD_TEs.png - PNG version for web display
• outputs/RMHD_alphas.png - PNG version for web display

Target Configuration and References

Simulations are grouped by series in target_config.py:

• h2006 series: Gas-dominated flow around a black hole (https://doi.org/10.1086/519515)
• h2007 series: Gas-radiation-comparable flow around a black hole (https://doi.org/10.1086/519515)
• h2009 series: Radiation-dominated flow around a black hole (https://doi.org/10.1088/0004-637X/691/1/16)
• h2011 series: Outer accretion flow with a dead zone around a young star (https://doi.org/10.1088/2041-8205/732/2/L30)
• h2014 series: Accretion flow around a white dwarf (https://doi.org/10.1088/0004-637X/787/1/1)
• h2015 series: Inner accretion flow around a young star (https://doi.org/10.1093/mnras/stv203)
• h2016 series: Self-gravitating accretion flow around a young star (https://doi.org/10.1093/mnras/stx824)

Each target specifies:

• name: Simulation identifier
• ave: Time averaging window [start, end] in orbital periods
• path: Data volume location
• color_key: Color coding by Ω value

Physical Background

The thermal equilibrium curves represent steady-state solutions of accretion flows where:

• Heating (viscous dissipation) balances cooling (radiative losses)
• Each point represents a converged simulation at fixed (Ω, Σ)
• The S-shaped curves indicate thermal instability regions
• Different colors represent different rotation rates (Ω)

Output Description

TE Curves Plot

• X-axis: Surface density Σ [g cm⁻²]
• Y-axis: Effective temperature T_eff [K]
• Colors: Different angular velocities Ω
• Shows thermal equilibrium states and potential instability regions

Alpha Plot

• X-axis: Pressure [dyn cm⁻²]
• Y-axis: Stress [dyn cm⁻²]
• Reference lines: α = 0.1, 0.01, 0.001
• Used to analyze the effective viscosity parameter

Citation

If you use this code or data in your research, please cite:

@software{rmhd_tes,
  author = {Shigenobu Hirose},
  title = {RMHD_TEs: Thermal Equilibrium states from Radiation MHD simulations},
  year = {2024},
  url = {https://github.com/nombac/RMHD_TEs}
}

Authors

Shigenobu Hirose (shirose@jamstec.go.jp)