Installation

Pre-installed programs

GB Kinetics requires python3, LAMMPS and openmpi installations on the system.
Details on installation of LAMMPS can be found at https://docs.lammps.org/Install.html
Details on installation of openmpi can be found at https://docs.open-mpi.org/en/v5.0.x/installing-open-mpi/quickstart.html

Install GB Kinetics

Create a new python environment for GB Kinetics and activate the new environment:

Windows

$ python -m venv GB_kinetics_env
$ GB_kinetics_env\Scripts\activate

Mac/Linux

$ python3 -m venv GB_kinetics_env
$ source GB_kinetics_env\Scripts\activate

Conda

$ conda create --name GB_kinetics_env
$ conda activate GB_kinetics_env
Necessary packages for python code are listed in requirements.txt and can be installed by
$ pip install -r requirements.txt

Workflow

The method can be divided into 5 steps:

  1. Construction of STGB microstate

  2. Enumeration of disconnection modes

  3. Atomistic construction of a disconnection mode

  4. Mapping the atomic shuffles

  5. Evaluation of the energy barrier and trajectories using NEB.

These steps are discussed in detail in Theory

Usage

  1. Running gridSearch.py script to determine the displacements which need to be applied to as but bicrystal to get to lowest energy microstate.

  2. Inputting the displacements in GB_kinetics.py script and running it to generate disconnection images and neb.

An example run of Grid search procedure is shown in Grid Search Example and an example run of disconnection image generation is shown in GB Kinetics Example