Getting started¶

Requirements¶

Python 3.10 or newer
LAMMPS for running generated workflows
ReaxFF parameter file for your target chemistry (or the provided default Si/O/H file)

Installation¶

Direct installation from github:

python -m pip install git+https://github.com/ProkopK/PoreReax.git

Core concepts¶

Simulate: Builds simulation files from a GROMACS .gro structure.
Sample: Loads trajectory/bond data and runs one or more analysis samplers.
plot(...): Visualizes sampled results.

Typical workflow¶

Create simulation files with Simulate and run LAMMPS.
Load generated outputs with Sample.
Add desired samplers (charge, density, angle, bond, reaction, RDF, etc.).
Run sampling and visualize the results.