molecular-builder 0.2.0

Package for building moleular systems

Molecular builder

This builder relies heavily on the atomic simulation environment (ase). I particular we use ase to generate crystals from space group descriptions.

This molecular builder is made with LAMMPS in mind. Usually, saving to input files for other simulators will work just fine, but anywhere a choice has to be made, convenience when preparing systems for LAMMPS will be prioritized.

Description

This package facilitates building molecular systems. It has functions for creating bulk crystals and for fetching periodic boxes of non-crystalline systems from the internet. After generating bulk crystals, the user may carve out specific geometries, and combine several elements to create a system.

We also support adding water using packmol. This requires having packmol installed.

Installation

pip install git+https://github.com/henriasv/molecular-builder 

Usage

Simple use case for creating a bulk alpha-quartz crystal.

from molecular_builder import create_bulk_crystal
atoms = create_bulk_crystal("alpha_quartz", [50,100,200])
write(atoms, "alpha_quartz.data)

Please refer to the documentation for more usage examples.