cfe316 / atomic

Simple atomic processes, coronal equilibrium, rate equations, radiation. Now for python 3!

Atomic

Atomic is a set of tools to calculate fractional abundance and radiation of different elements in hot plasmas.

Requirements

• python3
• scipy, numpy, matplotlib
• f2py
• a Fortran compiler. For me, f2py appears to use gfortran:f77.

Installation and running the code

Required data files and code from OPEN-ADAS:

$ ./fetch_adas_data # fetch the atomic data and reading routines
$ python3 setup.py build_ext --inplace # to compile the extension module

See below for details.

Try one of the examples:

$ python3 examples/radiation.py

Or launch jupyter notebook (with a python3 kernel):

>>> %run examples/radiation.py

Fetching the atomic data

Atomic needs atomic data ionisation/recombination etc. coefficients, as well as the routines to read them. These are fetched from the OpenADAS [1] website. In order to download your own dataset and reading routines run the python script:

$ ./fetch_adas_data

It will download files to a folder called adas_data.

For description of these so called iso-nuclear master files see [2].

The routines to download are

http://open.adas.ac.uk/codes/xxdata_11.tar.gz and http://open.adas.ac.uk/codes/xxdata_15.tar.gz

and should be put in the src folder and unzipped to

src/xxdata_11
src/xxdata_15.

Compiling python extension module

The extension module is compiled using numpy.distutils:

$ python3 setup.py build_ext --inplace

Testing

Have nose2 installed.

$ nose2

Test boilerplate was first produced automatedly with pythoscope, so at time of writing (20160916) many tests are skipped. (S)

Cleaning

These clean up the effects of source file downloads and Fortran compliation from the above setup.py command. Recompiling is necessary after these commands.

$ rm -r build/ src/xxdata_11 src/xxdata_15
$ rm atomic/_xxdata_* src/*.gz src/*.c

References

[1] http://open.adas.ac.uk [2] http://www.adas.ac.uk/man/chap4-04.pdf