FlashSync

Scripts to generate synchrotron maps from the customized FLASH simulation.

How to use

0. You will need:

1. FLASH plot and particle files
   • XXX_plt_cnt_####
   • XXX_part_####
2. Software and library
   • python, including h5py and astropy
   • my (slightly modified) version of yt
   • MPI and HDF5
3. The scripts in this repository

Everything should be setup on cetus. You can use my Anaconda environment on the cetus cluster.

source /home/ychen/anaconda3/etc/profile.d/conda.sh

Then you need to make symlinks of the three scripts to the directory where the FLASH outputs are located yt_write_synchrotron_hdf5.py, yt_plot_synchrotron_fits.py, and yt_plot_synchrotron_from_fits.py.

1. Calculate and write the synchrotron emissivity in each cell to an HDF5 file

Set the frequencies nus, projection axis proj_axis (could be x, y, z, or a vector specifying the normal direction, e.g. [0,1,2] in the script yt_write_synchrotron_hdf5.py.

python yt_write_synchrotron_hdf5.py [file#]

This step will take the longest time. So it would be a good idea to run it in parallel. This also take a lot of memory for each process.

For example:

mpirun -hostfile ~/hostfile/hostfile -np 32 python yt_write_synchrotron_hdf5.py 2200

This will generate a hdf5 file XXX_plt_cnt_####_synchrotron_peak_gc8.

2. Make a projection plot to a fits file

Set the same frequencies nus and projection axis proj_axis as in the previous step in yt_plot_synchrotron_fits.py. Additionally, set the resolution res and res_obs of the output image and a zoom-in factor zoom_fac. For mock observation fits, set the distance dist_obj and the coordinate coord [RA, Dec] to the object.

python yt_plot_synchrotron_fits.py [file#]

This will generate fits file in synchortron_lobe/fits and the mock observation fits file in synchrotron_lobe/fits_obs.

3. Make images from the fits file

Set the same frequencies nus and projection axis proj_axis as in the previous step in yt_plot_synchrotron_fits.py. You can also fine-tune the output figures in the code, e.g. field of view, colormap, or range of the emissivity. There is also option to do a convolved image.

python yt_plot_synchrotron_from_its.py [file#]

This can generate emissivity, polarization, and spectral index figures.