Metadata-Version: 2.1
Name: GEMDAT
Version: 0.0.1
Summary: Generalized Molecular Dynamics Analysis Tool
Author-email: Victor Azizi <v.azizi@esciencecenter.nl>, Stef Smeets <s.smeets@esciencecenter.nl>
License: Apache 2.0 License
Project-URL: homepage, https://github.com/GEMDAT-repos/GEMDAT
Project-URL: issues, https://github.com/GEMDAT-repos/GEMDAT/issues
Project-URL: documentation, https://gemdat.readthedocs.io
Project-URL: changelog, https://github.com/GEMDAT-repos/GEMDAT/releases
Keywords: analysis,molecular dynamics,plastic crystals,batteries
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.10
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# GEMDAT

This repository contains Python code to analyse Molecular Dynamics simulations.

The code in this repository is based on:
https://bitbucket.org/niekdeklerk/md-analysis-with-matlab/src/master/

## Installation

To install:

```console
pip install .[develop]
```

The source code is available from [Github](https://github.com/GEMDAT-repos/GEMDAT).

Suggestions, improvements, and edits are most welcome.

## Usage

The following snippet can be used to test the code (provided that you have some VASP data or intermediate `.mat` files.

```python
from gemdat import SimulationData, plot_all, plot

data = SimulationData.from_vasprun(Path('../example/vasprun.xml'), cache=Path('cache'))
extra = data.calculate_all(equilibration_steps=1250, diffusing_element='Li')

plot_all(data = data, **extra)
```

**not yet available:**
```python
import gemdat
gemdat.analyse_md('<path to data>', 'Li', 'argyrodite')
```

## Development

Check out our [Contributing Guidelines](CONTRIBUTING.md#Getting-started-with-development) to get started with development.

## References

- Niek J.J. de Klerk, Eveline van der Maas and Marnix Wagemaker, ACS Applied Energy Materials, (2018), doi: [10.1021/acsaem.8b00457](https://doi.org/10.1021/acsaem.8b00457)
