matta-research-group / QCflow

Workflow tools for high-throughput QC calculations

QCflow

A cheminformatics -> quantum chemistry workflow toolkit leveraging rdkit and cclib.

A typical workflow involves:

1. Generating a series of input molecules as SMILES - optionally, by combining different fragments into larger molecules/oligomers

2. For each molecule: a. write .com Gaussian input files, .sh SLURM submission files b. submit job (assuming you are working within a HPC) c. parse output file to submit further calculations or retrieve descriptors

3. Combine descriptors and results in a pandas dataframe format or similar for plotting / further analysis

Supported QC codes

Only Gaussian is supported at the moment, but we plan to add support for Psi4.

Installation

git clone https://github.com/matta-research-group/QCflow.git
cd QCflow
# install requirements into new environment
conda env create -f QCflow.yml
conda activate QCflow
# install the QCflow package
pip install .

Usage Examples

The run_torsion and run_opt_neutral functions contain example workflows that read in molecules from .smi files and submit quantum chemistry jobs for each molecule.

Calculation settings

QCflow can prepare and submit input files for the following jobs:

• Single point calculation, neutral -> sp
• Single point calculation, anion → sp_a
• Single point calculation, cation → sp_c
• Geometry optimisation, neutral -> opt
• Torsional scan, neutral → tor
• Optimisation anion → opt_a
• Optimisation cation → opt_c
• Optimisation neutral + Population analysis → pop_opt_n