PlanckTon

PlanckTon enables exploration of the self-assembly of organic photovoltaic (OPV) compound mixtures under various conditions. Multiple simulation tools are tied together to reproducibly and accurately generate these structures. For managing large parameter spaces and submitting jobs to clusters, we recommend PlanckTon-flow which leverages the Signac framework.

The simulation tools used by PlanckTon are:

• mBuild - builds compounds and initializes simulations

• foyer - manages force-field information

• HOOMD-blue - runs the simulations

How to use

Install

Using a container

PlanckTon provides containers with HOOMD compiled for cpu or gpu. If your system allows, we recommend gpu.

To use PlanckTon in a prebuilt container (using Singularity), run:

singularity pull docker://cmelab/planckton_gpu:latest
singularity exec planckton_gpu_latest.sif bash

Or using Docker, run:

docker pull cmelab/planckton_gpu:latest
docker run -it cmelab/planckton_gpu:latest

Custom install

To create a local environment with conda, run:

conda env create -f environment.yml
conda activate planckton

And to test your installation, run:

pytest

Run simulations

See example in planckton/tests/test_sim.py

How to Contribute

see Contributing guide