3D MHD simulations of kink waves cutoff through the solar transition region with PLUTO.

This repository contains the setups and analysis code used for the paper Pelouze et al. 2023, A&A 672, A105.

This features files to simulate the propagation of kink waves through the transition region, and study their cutoff.

Directories description

setups/: PLUTO setup files (see their respective README):
- open_chromos_relax_2D: 2D flux tube relaxation
- open_chromos_3D: 3D kink wave propagation
conversion/relax_2D_to_3D.py: converts the output of the 2D relaxation runs to input files for the 3D simulations.
mock/: Python scripts that replicate some C functions from the PLUTO setup.
viz/: Python scripts to analyze simulation output and make plots:
- viz/paper_kink_cutoff.py and viz/paper_vrw_av.py: makes the plots shown in the paper
- viz/amplitude_altitude_cut_3D.py computes the wave amplitude (ampl_alt_data.npz)
- viz/phase_altitude_3D.py computes the phase phase_amplitude_data.npz files
- remaining files are dependencies of the above.

Install Python dependencies in requirement.txt
Edit simulation parameters by editing setups/open_chromos_relax_2D/pluto.ini.j2 and setups/open_chromos_3D/pluto.ini. Do not change values in double curly braces ({{ }}) in pluto.ini.j2. Edit setup_config.yml if you need to change them.
Run the 2D relaxation with PLUTO:
- Initialize the simulation with field-aligned hydrostatic equilibrium:
```
cd setups/open_chromos_relax_2D
python setup_init.py
```
- Run the relaxation with mpirun -np <cpu count> ./pluto (see e.g. genius.pbs)
Convert the output of the 2D simulation to 3D with conversion/relax_2D_to_2D.py and place the output in setups/open_chromos_3D/initial_state.
Run the 3D simulation with PLUTO. Unlike the 2D relaxation, it is a standard PLUTO setup.