Workflows for getting the carrier mobilities from LAMMPS trajectories. Messy scripts that may or may not work.

To run this workflow, you need to install and build the package MorphCT (https://github.com/cmelab/morphct), along with mBuild and gsd, which you can get by simply using conda-forge.

Dump the relevant snapshot from your LAMMPS trajectory as a LAMMPS data file. Extract the coordinates and bonds and sort them by their index number and save them as "sorted_coords.data" and "sorted_bonds.data" respectively.

Activate a conda environment in which you have mbuild and gsd installed and then run the following command:

python3 gsdwriter.py

This will convert the sorted_coords and sorted_bonds files into a gsd file called "system.gsd". Then you can run any kmc code based off of this. A sample kmc workflow is provided in kmc-script.py. The md-example directory showcases this being used for a system with 10 PEDOT molecules.