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:

pip install .[develop]

The source code is available from Github.

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.

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:

import gemdat
gemdat.analyse_md('<path to data>', 'Li', 'argyrodite')

Development

Check out our Contributing Guidelines 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