Python Organic Crystal Simulation Environment
Project description
Python Organic Crystal Simulation Environment (PYOCSE)
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:
- Automate the geneation of structural model and force field (through
ambertools
oropenff
) - 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 ocse
conda activate osce
pip install .
If you want to update the existing ocse enviroment
conda activate ocse
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 (qzhu8@uncc.edu)
- Shinnosuke Hattori (shinnosuke.hattori@sony.com)
Project details
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