Repository containing all codes, scripts, and 2D boundary condition files needed to reproduce the results of the sunRunner3D manuscript.
To clone this repository use:
git clone https://github.com/predsci/suRunner3D-manuscript
The sunRunner3D tool is based on the PLUTO code. Hence PLUTO must first be downloaded and installed from here:
If you are not familiar with the PLUTO code, we recommend that you take a moment to read the manual and run the examples. To understand how the boundary conditions (BC) can be defined, please refer to Chapter 5 of the PLUTO manual.
We use the pysunrunner package to visualize the results of sunRunner3D. You will need to clone and install the package using:
git clone https://github.com/predsci/pysunrunner
pip install -e pysunrunner
We recommend that you set up a conda or miniconda environment for the package.
You will start by relaxing the heliospheric domain using the boundary conditions we provide. Start by navigating to your local copy of the relaxation directory
cd relax_dir
The init.c and userdef_output.c in this directory are the only two PLUTO routines we have modified. Together with the definitions.h and pluto.ini files they define your run configuration. The 2D subdirectory includes the boundary files loaded by init.c at each timestep.
Although the relax_dir directory includes the Makefile we use, it is safer to generate a Makefile that is specific to your computer architecture. As explained in Section 1.3 of the PLUTO manual this can be done by invoking the PLUTO setup.py script:
python $PLUTO_DIR/setup.py
Once the Makefile is created PLUTO can be compiled:
make
make clean
We recommend compiling PLUTO with MPI support and running it on multiple threads, e.g.,
mpirun -np 32 ./pluto -no-x3par 1>log 2>err &
The relaxation wall clock time will depend on your platform specifications and the number of threads you use. All output files will be generated in the output subdirectory, which is currently empty.
If you change the name of the output directory, be sure to update the output_dir line in the pluto.ini file.
To track the progression of the relaxation you can use:
tail -f output/pluto.0.log
Once the heliospheric relaxation is complete you can proceed to the CME run step.
Start by navigating to the cme_dir directory
cd cme_dir
here too you see the two PLUTO files we have modified: init.c and userdef_output.c. Note that the init.c in this directory includes the CME and is not the same as the one in the relax_dir
You will need to create your platform-specific Makefile, compile PLUTO, and copy the results of the relaxation to the current directory:
python $PLUTO_DIR/setup.py
make
make clean
cp -r ../relax_dir/output .
The output directory will include all the log files from the relaxation which are not needed and can be deleted:
cd output
/bin/rm -rf pluto*log
cd ..
The CME run is a continuation of the relaxation phase. You will specify this in your command line when starting the run:
mpirun -np 32 ./pluto -no-x3par -restart 1 1>log 2>err &
Here too, all your results will be generated in the output subdirectory and you can track the CME run progression using:
tail -f output/pluto.0.log
The fig_dir directory contains all the scripts needed to reproduce Figures 7-12 from the manuscript. Each figure has its dedicated script. You will need to update each script with the correct path to your PLUTO CME results. The results subdirectory includes a single file orbiter.csv with the Solar Orbiter data needed for Figure 12 (see driver_fig12.py)