pyocse 0.1.0

Python Organic Crystal Simulation Environment

Organic Simulation Toolkit (OST)

This is a public repository that aims to automate the simulation of organic crystals with a primary emphasis on the mechanical properties of organic crystals. Currently, we focus on two components:

1. Automate the geneation of structural model and force field (through ambertools or openff)
2. Design different workflows to simulate the properties of organic crystals under mechanical loads (powered by lammps)

Python Setup

git clone this repository and then go to the root directory

conda install -c conda-forge mamba
mamba env create -n ost 
conda activate ost
pip install .

If you want to update the existing ost enviroment

conda activate ost
mamba env update --file environment.yml

LAMMPS Setup:

make yes-MOLECULE
make yes-EXTRA-MOLECULE 
make yes-KSPACE 
make mpi -j 12

Examples

3D periodic boundary condictions (shearing/tensile/compression)

check the uniaxial.py

2D PBC bending

check the 3pf.py

no PBC free bending (to add)

Contacts:

• Qiang Zhu ([e-mail])
• Shinnosuke Hattori ([e-mail])