gemdat

a Generalized Molecular Dynamics Analysis Tool

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What gemdat can do for you

Documentation Status Tests for GEMDAT Coverage PyPI - Python Version PyPI DOI

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GEMDAT

Gemdat is a Python library for the analysis of diffusion in solid-state electrolytes from Molecular Dynamics simulations. Gemdat is built on top of Pymatgen, making it straightforward to integrate it into your Pymatgen-based workflows.

With Gemdat, you can:

  • Explore your MD simulation via an easy-to-use Python API
  • Load and analyze trajectories from VASP and LAMMPS simulation data
  • Find jumps and transitions between sites
  • Effortlessly calculate tracer and jump diffusivity
  • Characterize and visualize diffusion pathways
  • Plot radial distribution functions

To install:

pip install gemdat

The source code is available from Github.

Suggestions, improvements, and edits are most welcome.

Usage

The following snippet to analyze the diffusion trajectory from VASP data.

from gemdat import Trajectory

trajectory = Trajectory.from_vasprun('../example/vasprun.xml')

trajectory.plot_displacement_per_element()

diff_trajectory = trajectory.filter('Li')

diff_trajectory.plot_displacement_per_atom()
diff_trajectory.plot_displacement_histogram()
diff_trajectory.plot_frequency_vs_occurence()
diff_trajectory.plot_vibrational_amplitudes()

Characterize transitions and jumps between sites:

from gemdat.io import load_known_material

sites = load_known_material('argyrodite', supercell=(2, 1, 1))

transitions = trajectory.transitions_between_sites(
    sites=sites,
    floating_specie='Li',
)

jumps = transitions.jumps()

jumps.plot_jumps_vs_distance()
jumps.plot_jumps_vs_time()
jumps.plot_collective_jumps()
jumps.plot_jumps_3d()

jumps.jump_diffusivity(dimensions=3)

To calculate different metrics, such as tracer diffusivity:

from gemdat import TrajectoryMetrics

metrics = TrajectoryMetrics(diff_trajectory)

metrics.tracer_diffusivity(dimensions=3)
metrics.haven_ratio(dimensions=3)
metrics.tracer_conductivity(dimensions=3)
metrics.particle_density()
metrics.vibration_amplitude()

Development

Check out our Contributing Guidelines to get started with development.

How to Cite

Credits

The code in this repository is based on Matlab code to analyse Molecular Dynamics simulations.

For background information on how some of the properties are calculated, check out the accompanying paper:

  • Niek J.J. de Klerk, Eveline van der Maas and Marnix Wagemaker, ACS Applied Energy Materials, (2018), doi: 10.1021/acsaem.8b00457
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  • Python 99%
  • Nix 1%
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Participating organisations

Delft University of Technology
Netherlands eScience Center

Contributors

Stef Smeets
Research Software Engineer
Netherlands eScience Center
AV
Alexandros Vasileiadis
Lead Applicant
Delft University of Technology
TF
Theodosios Famprikis
AL
Anastasiia Lavrinenko
Phd
TU Delft
VA
Victor Azizi
Research Software Engineer
Netherlands eScience Center

Related projects

GEMDAT

Developing a Generalized Molecular Dynamics Analysis Tool

Updated 8 months ago
In progress