pygmol 1.1.2

A plasma global model in python

Introduction to PyGMol

PyGMol (the Python Global Model) is a simple-to-use 0D model of plasma chemistry.

At its current form, the pygmol package defines the system of ordinary differential equations (ODE) which govern the plasma chemistry, and solves them using the scipy.integrate.solve_ivp solver. Quantities resolved presently by the pygmol model are the densities of all the heavy species specified by the chemistry input, electron density, and electron temperature (while heavy-species temperature is treated as a parameter to the model).

The equations being solved for by the model are documented in their full form in the equations document. The package inner workings, structure and some useful examples are discussed in the documentation. For further info, refer to the codebase docstrings.

Installation:

The pygmol package can be installed either from PyPI

python3 -m pip install pygmol

or from the GitHub page

python3 -m pip install git+https://github.com/hanicinecm/pygmol.git

For Developers:

It goes without saying that any development should be done in a clean virtual environment. After cloning or forking the project from its GitHub page, pygmol can be installed into the virtual environment in the editable mode by running

pip install -e .[dev]

The [dev] extra installs (apart from the package dependencies) also several development-related packages, such as pytest, coverage, ipython, or black. The unit tests can then be executed, as well as the suite of run tests and documentation tests, by running (from the project root directory)

pytest [--cov]
pytest run_tests
pytest docs

respectively.

The project does not have the requirements.txt file by design, as all the package dependencies are rather handled by the setup.py. The package therefore needs to be installed locally to run the tests, which grants the testing process another layer of usefulness.

Docstrings in the project adhere to the numpydoc styling. The project code is formatted by black.

For anyone interesting in further development of pygmol, this is where one might start.

A note on version numbering: Following the major.minor.micro versioning convention, the minor version should be increased, if the document describing the maths behind the equations requires an update. The micro version increases are reserved for any other non-breaking changes, such as documentation updates, some minor api tweaks, etc. And the major version? You tell me, I have no plan as where to go with it…