rgpycrumbs

Author:

Rohit Goswami

_images/pycrumbs_logo.webp

Overview

rgpycrumbs functions as a unified dispatcher for research scripts and computational utilities, tailored for computational chemistry.

rgpycrumbs employs PEP 723 metadata to isolate dependencies for each tool individually. This architecture ensures:

Conflict-Free Execution

Scripts with incompatible requirements like different numpy versions run side-by-side without issue.

On-Demand Retrieval

The core package remains lightweight. The system fetches heavy libraries (like ase or matplotlib) via uv only when executing a script that requires them.

Strict Reproducibility

Every script explicitly declares its necessary environment, preventing “works on my machine” errors.

Broadly speaking, the tooling here assists with computational methods to find reaction pathways, along with packaging helpers.

Advanced NEB Visualization

The plt-neb tool offers novel visualization capabilities for Nudged Elastic Band calculations:

Force-Corrected Interpolation

Uses Hermite splines incorporating force projections to produce physically consistent energy profiles.

2D Energy Landscapes

Projects reaction paths onto Reactant/Product RMSD coordinates to reveal path complexity often hidden in 1D profiles.

Structural Context

Automatically renders and embeds atomic structure insets for critical points or all images directly onto the plots.

Simulation Setup & Analysis

EON

NEB initial path generation

con-splitter simplifies the generation of initial paths enabling for instance IDPP initialization through ase by processing multi-image trajectories into EON-compatible input lists.

Defect Identification

ptmdisp employs Polyhedral Template Matching via OVITO to algorithmically identify and index interstitial defects in crystalline systems.

NWChem Input Generation

generate-nwchem-input generates complete input files compatible with EON’s SocketNWChemPot, merging geometry data with calculation settings.

PLUMED

Free Energy Reconstruction

Pure-python implementations for reconstructing bias potentials from PLUMED hills files.

Infrastructure & Maintenance

Prefix.dev Management

delete_packages helps maintain custom Conda/Pixi channels by automating the cleanup of old or specific package versions on prefix.dev.

Utility Functions

Beyond the command line tools, the package includes pure-python helpers for parsing logs like those from bless and managing data structures in Jupyter notebooks.

Tool Categories

Developer Reference

For details on the dispatcher architecture or internal API: