Running RH 1.5D¶
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
run, there are already some input files and directories. You can do a test run of RH by doing:
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.
run directory go through the different tasks:
- Run the different binaries:
- What happens if you run
- Explore the output files in the command line with
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¶
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:
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.