KS-DFT average-atom code
Project description
atoMEC: Average-Atom Code for Matter under Extreme Conditions
atoMEC is a python-based average-atom code for simulations of high energy density phenomena such as in warm dense matter. It is designed as an open-source and modular python package.
atoMEC uses Kohn-Sham density functional theory, in combination with an average-atom approximation, to solve the electronic structure problem for single-element materials at finite temperature.
More information on the average-atom methodology and Kohn-Sham density functional theory can be found (for example) in this preprint and references therein.
This repository is structured as follows:
├── atoMEC : source code
├── docs : sphinx documentation
├── examples : useful examples to get you started with the package
└── tests : test scripts used during development, will hold tests for CI in the future
Installation
First, clone the atoMEC repository and cd
into the main directory.
-
Recommended : using pipenv
This route is recommended because
pipenv
automatically creates a virtual environment and manages dependencies.- First, install
pipenv
if it is not already installed, for example viapip install pipenv
(or see pipenv for installation instructions) - Next, install
atoMEC
's dependencies withpipenv install
(use--dev
option to install the test dependencies in the same environment) - Use
pipenv shell
to activate the virtual environment and install atoMEC withpip install atoMEC
(for developers:pip install -e .
) - Now run scripts from inside the
atoMEC
virtual environment, e.g.python examples/simple.py
- First, install
-
Run the tests (see Testing section below) and report any failures (for example by raising an issue)
Please note: atoMEC does not yet support Windows installation. This is due to the dependency on pylibxc
which currently lacks Windows support.
Running
You can familiarize yourself with the usage of this package by running the example scripts in examples/
.
Contributing to atoMEC
We welcome your contributions, please adhere to the following guidelines when contributing to the code:
- In general, contributors should develop on branches based off of
develop
and merge requests should be todevelop
- Please choose a descriptive branch name
- Merges from
develop
tomaster
will be done after prior consultation of the core development team - Merges from
develop
tomaster
are only done for code releases. This way we always have a cleanmaster
that reflects the current release - Code should be formatted using black style
Testing
- First, install the test requirements (if not already installed in the virtual env with
pipenv install --dev
):
# activate environment first (optional)
$ pipenv shell
# install atoMEC as editable project in current directory (for developers)
$ pip install -e .[tests]
# alternatively install package from PyPI with test dependencies
$ pip install atoMEC[tests]
- To run the tests:
$ pytest --cov=atoMEC --random-order tests/
Build documentation locally (for developers)
Install the prerequisites:
$ pip install -r docs/requirements.txt
- Change into
docs/
folder. - Run
make apidocs
. - Run
make html
. This creates a_build
folder insidedocs
. You may also want to usemake html SPHINXOPTS="-W"
sometimes. This treats warnings as errors and stops the output at first occurrence of an error (useful for debugging rST syntax). - Open
docs/_build/html/index.html
. make clean
if required (e.g. after fixing errors) and building again.
Developers
Scientific Supervision
- Attila Cangi (Center for Advanced Systems Understanding)
- Eli Kraisler (Hebrew University of Jerusalem)
Core Developers and Maintainers
- Tim Callow (Center for Advanced Systems Understanding)
- Daniel Kotik (Center for Advanced Systems Understanding)
Contributions (alphabetical)
- Nathan Rahat (Hebrew University of Jerusalem)
- Ekaterina Tsvetoslavova Stankulova (Center for Advanced Systems Understanding)
Citing atoMEC
If you use code from this repository in a published work, please cite
- T. J. Callow, D. Kotik, E. Kraisler, and A. Cangi, "atoMEC: An open-source average-atom Python code", Proceedings of the 21st Python in Science Conference, edited by Meghann Agarwal, Chris Calloway, Dillon Niederhut, and David Shupe (2022), pp. 31 – 39
- The DOI corresponding to the specific version of atoMEC that you used (DOIs are listed at Zenodo.org)
Project details
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