pychumpchem 0.0.1

Input file generators for computational chemistry

Table of Contents

• About
  • Features
    • Supported Engines
  • Rationale
• Usage
• Development
  • Adding ORCA blocks
  • Documentation
    • Readme
• License

About

A pure-python project to generate input files for various common computational chemistry workflows. This means:

• Generating input structures for jobflow / Fireworks
  • From unified toml inputs

This is a spin-off from wailord (here) which is meant to handle aggregated runs in a specific workflow, while pychum is meant to generate single runs. It is also a companion to chemparseplot (here) which is meant to provide uniform visualizations for the outputs of various computational chemistry programs.

Features

• Jobflow support
  • Along with Fireworks
• Unit aware conversions
  • Via pint

Supported Engines

• NEB calculations
  • ORCA
  • EON
• Single point calculations
  • ORCA
  • EON

Rationale

I needed to run a bunch of systems. jobflow / Fireworks / AiiDA were ideal, until I realized only VASP is really well supported by them.

Usage

The simplest usage is via the CLI:

python -m pychum.cli

Development

Before writing tests and incorporating the functions into the CLI it is helpful to often visualize the intermediate steps. For this we can setup a complete development environment including the notebook server.

pixi shell
pdm sync
pdm run $SHELL
jupyter lab --ServerApp.allow_remote_access=1 \
    --ServerApp.open_browser=False --port=8889

Then go through the nb folder notebooks.

Adding ORCA blocks

Changes are to be made in the following files under the pychum/engine/orca/ folder:

• The relevant .jinja file in the _blocks directory
• The configuration loading mechanism in config_loader.py
• The dataclasses folder
• A sample test .toml file under tests/test_orca

While working on this, it may be instructive to use the nb folder notebooks. Also all PRs must include a full test suite for the new blocks.

Documentation

Readme

The readme can be constructed via:

./scripts/org_to_md.sh readme_src.org readme.md

License

MIT. However, this is an academic resource, so please cite as much as possible via:

• The Zenodo DOI for general use.
• The wailord paper for ORCA usage