densityNEB

Code for calculating the path of least resistance between two points in a scalar field using nudged elastic band (NEB).

The method is described in our paper Accelerated Autonomous Workflow For Antiperovskite-based Solid State Electrolytes.

Parts of the code is based on Pytorch-AutoNEB.

The two main components of the software is a module for linear interpolation on a grid interpolate_grid.py and a module for running NEB torchneb.py.

Installation

Clone the repository and install the code as a python package by running the following in the cloned directory:

pip install .

If you want to be able to run the examples with an interactive window showing the path on the charge density, install it with pip install .[viewer]. This will install mayavi and PyQt5. If using these with an X-server, make sure not to use Xming, since it's generally unsupported by PyQt5.

Only numpy and torch are strictly needed. The rest of the dependencies are only for running the examples.

Running

You can run a simple toy example by running torchneb.py as a script:

python src/densityNEB/torchneb.py

Another example script will visualize the NEB path finding between two Li atoms in a charge density file from VASP:

python examples/chgcar_neb_animation.py examples/calculations/Li3SeF_Pm-3m/charge_density/CHGCAR

The chgcar_neb.py file is included as an example on how to process multiple CHGCARs in a batch job.

Acknowledgements

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 957189.