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QCflow

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

A typical workflow involves:

Generating a series of input molecules as SMILES - optionally, by combining different fragments into larger molecules/oligomers
For each molecule:

a. write .com Gaussian input files, .sh SLURM submission files

b. submit a job (assuming you are working within a HPC)

c. parse output file to submit further calculations or retrieve descriptors
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/qcflow-0.3.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 and Advice

The run_calc function within run_gaussian.py is an example workflow that submit gaussian calculations to the KCL CREATE HPC.

Users external to Kings College London will need to alter the slurm.py file to match their HPC submission requirements.

Altering the loaded modules found on line 55 within slurm.py file will allow you to submit jobs to your HPC.

file.write(f'module load gaussian_sse4/16-C-gcc-13.2.0 \n') ### KCL CREATE HPC

file.write(f'module load your_gaussian_module \n') ### Your HPC

Once the alteration has been made, just pip install . again and the package will update for your HPC.

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
Single point calculation neutral charge, cationic geometry → n_c_geo
Single point calculation neutral charge, anioinc geometry → n_a_geo
Geometry optimisation, neutral -> opt
Torsional scan, neutral → tor
Optimisation anion → opt_a
Optimisation cation → opt_c
Optimisation neutral + Population analysis → pop_opt_n
Single point Hirshfeld calculation → sp_hirsh

Files

├── build
│   ├── bdist.macosx-10.13-x86_64
│   └── lib
│       └── QCflow
│           ├── energy_calculations.py
│           ├── find_torsion.py
│           ├── fragments.py
│           ├── __init__.py
│           ├── load_gaussian.py
│           ├── run_gaussian.py
│           ├── slurm.py
│           ├── testing_data.py
│           ├── torsion_parser.py
│           └── write_gaussian.py
├── LICENSE
├── QCflow
│   ├── energy_calculations.py
│   ├── find_torsion.py
│   ├── fragments.py
│   ├── future_functions
│   │   └── orbital_parse.py
│   ├── __init__.py
│   ├── load_gaussian.py
│   ├── __pycache__
│   │   ├── find_torsion.cpython-311.pyc
│   │   ├── find_torsion.cpython-39.pyc
│   │   ├── fragments.cpython-311.pyc
│   │   ├── fragments.cpython-38.pyc
│   │   ├── fragments.cpython-39.pyc
│   │   ├── __init__.cpython-311.pyc
│   │   ├── __init__.cpython-38.pyc
│   │   ├── __init__.cpython-39.pyc
│   │   ├── load_gaussian.cpython-311.pyc
│   │   ├── load_gaussian.cpython-39.pyc
│   │   ├── run_opt_neutral.cpython-311.pyc
│   │   ├── run_opt_neutral.cpython-39.pyc
│   │   ├── run_opt_set_dihedral.cpython-311.pyc
│   │   ├── slurm.cpython-311.pyc
│   │   ├── slurm.cpython-39.pyc
│   │   ├── torsion_parser.cpython-311.pyc
│   │   ├── torsion_parser.cpython-39.pyc
│   │   ├── torsion_run.cpython-311.pyc
│   │   ├── torsion_run.cpython-39.pyc
│   │   ├── write_gaussian.cpython-311.pyc
│   │   └── write_gaussian.cpython-39.pyc
│   ├── run_gaussian.py
│   ├── slurm.py
│   ├── testing_data.py
│   ├── torsion_parser.py
│   └── write_gaussian.py
├── qcflow.egg-info
│   ├── dependency_links.txt
│   ├── PKG-INFO
│   ├── SOURCES.txt
│   └── top_level.txt
├── QCflow_logo_narrow.jpg
├── QCflow.yml
├── README.md
├── setup.py
└── tests
    ├── b_18_v2
    │   ├── b_18_v2_n_a_geo.log
    │   ├── b_18_v2_n_c_geo.log
    │   ├── b_18_v2_opt_a.log
    │   ├── b_18_v2_opt_c.log
    │   ├── b_18_v2_opt.com
    │   ├── b_18_v2_opt.log
    │   ├── b_18_v2_opt.sh
    │   ├── b_18_v2_sp_a.log
    │   ├── b_18_v2_sp_c.log
    │   ├── b_18_v2_sp_hirsh.log
    │   └── b_18_v2_tor.log
    ├── example_dic.json
    ├── fake_dict.json
    ├── __pycache__
    │   ├── tests.cpython-312.pyc
    │   └── tests.cpython-312-pytest-7.4.4.pyc
    ├── test_dict.json
    ├── test.py
    └── torsion_1
        └── torsion_1_tor.log

matta-research-group / QCflow

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