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[](https://pypi.org/project/gemdat/)
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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](https://pymatgen.org/), 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 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:
```console
pip install gemdat
```
The source code is available from [Github](https://github.com/GEMDAT-repos/GEMDAT).
Suggestions, improvements, and edits are most welcome.
## Usage
The following snippet to analyze the diffusion trajectory from VASP data.
```python
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:
```python
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:
```python
from gemdat import SimulationMetrics
metrics = SimulationMetrics(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](CONTRIBUTING.md#Getting-started-with-development) to get started with development.
## References
The code in this repository is based on [Matlab code to analyse Molecular Dynamics simulations](https://bitbucket.org/niekdeklerk/md-analysis-with-matlab/src/master/).
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](https://doi.org/10.1021/acsaem.8b00457)
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