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atoMEC-1.2.0
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KS-DFT average-atom code
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | atoMEC-1.2.0 |
| نام | atoMEC |
| نسخه کتابخانه | 1.2.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Tim Callow et al. |
| ایمیل نویسنده | t.callow@hzdr.de |
| آدرس صفحه اصلی | https://github.com/atomec-project/atoMEC |
| آدرس اینترنتی | https://pypi.org/project/atoMEC/ |
| مجوز | BSD 3-Clause License Copyright (c) 2021 (in alphabetical order), Tim Callow, Attila Cangi, Eli Kraisler All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
# atoMEC: Average-Atom Code for Matter under Extreme Conditions
[](https://doi.org/10.5281/zenodo.5205718)
[](https://github.com/atomec-project/atoMEC/actions/workflows/gh-pages.yml)
[](https://opensource.org/licenses/BSD-3-Clause)
[](https://github.com/psf/black)
[](https://badge.fury.io/py/atoMEC)
[](https://www.python.org/downloads/release/python-380/)
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](https://arxiv.org/abs/2103.09928) 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](https://pypi.org/project/pipenv/)
This route is recommended because `pipenv` automatically creates a virtual environment and manages dependencies.
1. First, install `pipenv` if it is not already installed, for example via `pip install pipenv` (or see [pipenv](https://pypi.org/project/pipenv/) for installation instructions)
2. Next, install `atoMEC`'s dependencies with `pipenv install` (use `--dev` option to install the test dependencies in the same environment)
3. Use `pipenv shell` to activate the virtual environment and install atoMEC with `pip install atoMEC` (for developers: `pip install -e .`)
4. Now run scripts from inside the `atoMEC` virtual environment, e.g. `python examples/simple.py`
* 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 to `develop`
* Please choose a descriptive branch name
* Merges from `develop` to `master` will be done after prior consultation of the core development team
* Merges from `develop` to `master` are only done for code releases. This way we always have a clean `master` that reflects the current release
* Code should be formatted using [black](https://pypi.org/project/black/) style
## Testing
* First, install the test requirements (if not already installed in the virtual env with `pipenv install --dev`):
```sh
# 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:
```sh
$ pytest --cov=atoMEC --random-order tests/
```
### Build documentation locally (for developers)
Install the prerequisites:
```sh
$ pip install -r docs/requirements.txt
```
1. Change into `docs/` folder.
2. Run `make apidocs`.
3. Run `make html`. This creates a `_build` folder inside `docs`. You may also want to use `make html SPHINXOPTS="-W"` sometimes. This treats warnings as errors and stops the output at first occurrence of an error (useful for debugging rST syntax).
4. Open `docs/_build/html/index.html`.
5. `make clean` if required (e.g. after fixing errors) and building again.
## Developers
### Scientific Supervision
- Attila Cangi ([Center for Advanced Systems Understanding](https://www.casus.science/))
- Eli Kraisler ([Hebrew University of Jerusalem](https://en.huji.ac.il/en))
### Core Developers and Maintainers
- Tim Callow ([Center for Advanced Systems Understanding](https://www.casus.science/))
- Daniel Kotik ([Center for Advanced Systems Understanding](https://www.casus.science/))
### Contributions (alphabetical)
- Nathan Rahat ([Hebrew University of Jerusalem](https://en.huji.ac.il/en))
- Ekaterina Tsvetoslavova Stankulova ([Center for Advanced Systems Understanding](https://www.casus.science/))
## Citing atoMEC
If you use code from this repository in a published work, please cite
1. 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
2. The DOI corresponding to the specific version of atoMEC that you used (DOIs are listed at [Zenodo.org](https://doi.org/10.5281/zenodo.5205718))
نیازمندی
| مقدار | نام |
|---|---|
| >=1.20.3 | numpy |
| >=1.6.3 | scipy |
| >=0.7.0 | mendeleev |
| >=0.8.9 | tabulate |
| >=6.0.0 | pylibxc2 |
| >=1.0.1 | joblib |
| - | bump2version |
| ==0.16 | docutils |
| ==0.15.1 | myst-parser |
| ==4.0.2 | Sphinx |
| ==0.5.2 | sphinx-rtd-theme |
| ==7.1.3 | pytest |
| ==4.0.0 | pytest-cov |
| ==0.6.3 | pytest-lazy-fixture |
| ==1.0.4 | pytest-random-order |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl atoMEC-1.2.0:
pip install atoMEC-1.2.0.whl
نصب پکیج tar.gz atoMEC-1.2.0:
pip install atoMEC-1.2.0.tar.gz