Glossary ¶

Author:

Rohit Goswami

Glossary of Computational Chemistry Terms ¶

A ¶

ASE ¶

Atomic Simulation Environment. Python library for atomistic simulations.

Auto-install ¶

Feature that automatically installs optional dependencies. Enabled via RGPYCRUMBS_AUTO_DEPS=1.

B ¶

Batch Command ¶

CLI command that generates multiple plots from TOML configuration with optional parallel processing.

C ¶

chemgp ¶

ChemGP (Chemistry Gaussian Process) tool for plotting GP surrogate model outputs.

D ¶

Diataxis ¶

Documentation framework with four types: tutorials, how-to guides, reference, explanation.

E ¶

eOn ¶

Python framework for automated saddle point searches.

G ¶

GBW ¶

Gaussian Basis Wavefunction. ORCA binary wavefunction file.

H ¶

HDF5 ¶

Hierarchical Data Format version 5. Used by ChemGP for output storage.

I ¶

Image ¶

In NEB context, a replica of the system along reaction path.

J ¶

JAX ¶

High-performance numerical computing library. Used for GP surface fitting.

L ¶

Landscape ¶

2D plot of energy surface in RMSD coordinates.

Lazy Import ¶

Pattern that defers module import until first use via ensure_import().

N ¶

NEB ¶

Nudged Elastic Band. Method for finding minimum energy path.

Nystrom ¶

Approximation method for Gaussian Processes using inducing points.

O ¶

OPI ¶

ORCA Python Interface. Official Python library for ORCA 6.1+.

P ¶

PEP 723 ¶

Python Enhancement Proposal for inline script metadata. Used for CLI dependencies.

R ¶

RMSD ¶

Root Mean Square Deviation. Measure of structural difference.

S ¶

Saddle Point ¶

First-order saddle point on PES. Maximum along reaction coordinate.

T ¶

ThreadPoolExecutor ¶

Python module for parallel execution. Used in batch command.

U ¶

Unit Registry ¶

Pint object for unit-aware calculations.

Opt-in plot TOML key (default false). When true, chemparseplot evenly subsamples dense landscape observations for the GP surface fit only (endpoints kept). Set under [shared] or [min] / [neb]; not a CLI flag.

SurfaceFitConfig ¶

chemparseplot dataclass for TOML-friendly surface-fit knobs (auto_thin, max_surface_points). Built via from_mapping or kwargs; passed as surface_fit= to plot_landscape_surface.

plot.toml ¶

Declarative eOn plot config for plt-neb, plt-min, and plt-saddle (--config). Shared style under [shared]; command inputs under [neb] / [min] / [saddle].