Running RH 1.5D

Auxiliary files

The RH 1.5D distribution that you obtained from Github does not contain all the files necessary for this course. Please download an additional archive and unpack it in the RH main folder:

$ tar jxvf rh_ast5210.tar.bz2

This will place all files in their correct directories.

Quickstart: running and looking at output

You should run the code in a run directory. When you get the source, there should be a directory under rh/rh15d/run_example. You can copy this directory to your own so you can make your changes:

$ cp -rp run_example run
$ cd run

Once inside run, there are already some input files and directories. You can do a test run of RH by doing:

../rh15d_ray

By default this will run with only one processor, and an example calculation with a Ca atom. You can read a lot more detail into the input files and running options in the documentation.

Inside your run directory go through the different tasks:

• Run the different binaries: rh15d_ray, rh15d_ray_pool, rh15d_lteray.
• What happens if you run rh15d_ray_pool without calling mpiexec or mpirun?
• Explore the output files in the command line with ncdump -h or h5dump -H.

Using Jupyter notebooks

You can have a look at the RH 1.5D sample notebooks under rh/doc/notebooks/. For the work in these exercises, it is recommend it that you run jupyter from a directory of your chosing, ideally where you have output files from RH (e.g. the directory output/ inside your run directory). The notebook source files (*.ipynb) will be saved there.

Once in the jupyter starting page, select "New" and then "Python 3". In the first cell, add the boilerplate code mentioned earlier:

%matplotlib widget
import numpy as np
import matplotlib.pyplot as plt
from helita.sim import rh15d, rh15d_vis

And now you are ready to start playing with RH.

Exploring input atmospheres

Your default keyword.input file uses the FALC_82_5x5.hdf5 atmosphere file, which is a FAL C atmosphere converted to HDF5 format and replicated to 5x5 columns in 3D. All columns have the same information. Under the directory rh/Atmos you will also find a file called bifrost_cb24bih_s385_cut.hdf5, which is a cut from a 3D simulation from Bifrost. You can explore both with the rh15d_vis.InputAtmosphere procedure. You need to pass the filename of an atmosphere file as argument:

rh15d_vis.InputAtmosphere('MY_ATMOS_DIR/Atmos/FALC_82_5x5.hdf5');

Replace MY_ATMOS_DIR with the directory where you have the RH atmospheres (typically in rh/Atmos). You can give relative or absolute paths.

Exploring the output

If you are in a directory with the output files of RH, you can simply enter the following to load the data:

data = rh15d.Rh15dout()

If your output files are in a different directory, pass that directory as an argument to Rh15dout(). Once you have the output loaded, a simple inspection of the intensity can be made with:

fig, ax = plt.subplots()
data.ray.intensity.plot()

By default this will show all calculated wavelengths, but you can zoom in to a line of interest with matplotlib's interactive figure.