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
^^^^^^^^

.. code-block:: console

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

Mac/Linux
^^^^^^^^^^

.. code-block:: console

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

Conda
^^^^^

.. code-block:: console

   $ 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 

.. code-block:: console

   $ pip install -r requirements.txt


Workflow
---------

| The method can be divided into 5 steps:

#. Construction of STGB microstate 
#. Enumeration of disconnection modes
#. Atomistic construction of a disconnection mode
#. Mapping the atomic shuffles
#. Evaluation of the energy barrier and trajectories using NEB.

These steps are discussed in detail in :doc:`Theory <theory>`

Usage
---------

#. Running gridSearch.py script to determine the displacements which need to be applied to as but bicrystal to get to lowest energy microstate.
#. 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 :doc:`Grid Search Example <example_gs>`
and an example run of disconnection image generation is shown in :doc:`GB Kinetics Example<example_gbkinetics>`