Glossary #

Glossary of Computational Chemistry Terms #

This glossary defines technical terms used throughout chemparseplot documentation.

A #

ASE #

Atomic Simulation Environment. Python library for atomistic simulations. Used for structure handling and RMSD calculations.

See: ASE Documentation

Auto-install #

Feature that automatically installs optional dependencies when first needed. Enabled via RGPYCRUMBS_AUTO_DEPS=1 environment variable.

B #

Barrier #

Energy difference between reactant/product and saddle point. Forward barrier = E_saddle- E_reactant. Reverse barrier = E_saddle- E_product.

C #

CI-NEB #

Climbing Image Nudged Elastic Band. NEB variant where highest energy image climbs to saddle point.

Convergence #

State where optimization algorithm has found stationary point. Typically defined by force threshold (e.g., 0.01 eV/Angstrom).

E #

Energy Profile #

Plot of energy vs reaction coordinate (image index or RMSD). Shows energy changes along reaction path.

eOn #

Python framework for automated saddle point searches using NEB and dimer methods.

See: eOn Website

G #

GBW #

Gaussian Basis Wavefunction. ORCA binary file format containing wavefunction data.

Gradient #

First derivative of energy with respect to coordinates. Points in direction of steepest ascent.

GPRD #

Gaussian Process Regression Dimer. Saddle search method using GP surrogate models.

H #

HDF5 #

Hierarchical Data Format version 5. File format for storing large numerical datasets. Used by ChemGP for output.

Hartree #

Atomic unit of energy. 1 Hartree = 27.211386245988 eV. Symbol: E_h.

I #

Image #

In NEB context, a replica of the system at a point along reaction path. Typical calculations use 5-20 images.

Interpolation #

Estimation of values between known data points. Used for smoothing energy profiles.

J #

JAX #

High-performance numerical computing library. Used for Gaussian Process surface fitting in rgpycrumbs.

See: JAX Documentation

L #

Landscape #

2D plot of energy surface in RMSD coordinates (RMSD from reactant vs RMSD from product).

Lazy Import #

Pattern that defers module import until first use. Reduces startup time and optional dependencies.

N #

NEB #

Nudged Elastic Band. Method for finding minimum energy path between reactant and product.

Nudged #

Projection of spring forces along path and true forces perpendicular to path. Prevents corner-cutting.

Nystrom #

Approximation method for Gaussian Processes using inducing points. Reduces O(n³) to O(m²n) where m << n.

O #

OPI #

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

See: OPI GitHub

ORCA #

Quantum chemistry software package. Supports DFT, wavefunction methods, NEB calculations.

See: ORCA Website

P #

PES #

Potential Energy Surface. Energy as function of nuclear coordinates.

PEP 723 #

Python Enhancement Proposal for inline script metadata. Allows specifying dependencies in script comments.

Profile #

1D plot showing energy or other property along reaction coordinate.

R #

RBF #

Radial Basis Function. Interpolation method using radially symmetric basis functions.

RMSD #

Root Mean Square Deviation. Measure of structural difference. RMSD = sqrt(sum((r1-r2)²)/N).

Reaction Coordinate #

Parameter that describes progress along reaction path. Can be image index, RMSD, or interpolated arc length.

Reactant #

Starting structure of chemical reaction. Local minimum on PES.

RFF #

Random Fourier Features. Approximation method for kernel methods using random feature maps.

S #

Saddle Point #

First-order saddle point on PES. Maximum along reaction coordinate, minimum in all other directions. Also called transition state.

SCF #

Self-Consistent Field. Iterative method for solving Hartree-Fock or Kohn-Sham equations.