Used By

Author:

Rohit Goswami

The following projects use rgpycrumbs as a dependency or tool.

Libraries

chemparseplot

Parsers and plotting tools for computational chemistry. Uses rgpycrumbs.basetypes, rgpycrumbs.interpolation, rgpycrumbs.surfaces, and rgpycrumbs.parsers as core dependencies.

pychum

Input file generators for computational chemistry. Uses rgpycrumbs for internal helpers and is dispatched via the CLI.

Research Software

eOn

Long-timescale molecular dynamics code. Documentation references rgpycrumbs as the companion diagnostic and visualization suite (docs).

Reproducibility Packages

nebmmf_repro

Reproduction package for NEB machine-learned force field work. Uses rgpycrumbs CLI for NEB plotting and the alignment API.

nebviz_repro

Reproduction package for 2D NEB visualization methods. Imports rgpycrumbs.eon.helpers and runs the CLI for 2D landscape plots.

otgpd_repro

Reproduction package for on-the-fly GP dimer searches. Imports rgpycrumbs._aux, runs CLI for GP trajectory analysis and fragment detection.

gpr_sella_repro

Reproduction package for GP-accelerated Sella saddle point searches (ChemPhysChem, doi: 10.1002/cphc.202500730). Uses rgpycrumbs for auxiliary helpers, parsers, and structure analysis.

brms_idrot_repro

Bayesian reaction mechanism studies reproduction package. Uses both rgpycrumbs and chemparseplot for parsing and analysis.

External Projects

atomistic-cookbook (lab-cosmo)

Community cookbook for atomistic simulations. The eOn PET-NEB example imports rgpycrumbs.eon.helpers and rgpycrumbs.run.jupyter.

metatensor ecosystem-article (metatensor)

Metatensor ecosystem paper. Uses rgpycrumbs for eOn NEB plotting and PLUMED FES reconstruction workflows.

Academic Work

Dissertation

R. Goswami, Efficient Exploration of Chemical Kinetics, Doctoral dissertation, University of Iceland, 2025.

arXiv: 2510.21368

DOI: 10.48550/arXiv.2510.21368

Uses rgpycrumbs.surfaces, rgpycrumbs.geom, rgpycrumbs.interpolation, and the CLI dispatcher throughout for NEB visualization, surface fitting, structure analysis, and fragment detection.

Journal Article

R. Goswami and H. Jonsson, Adaptive Pruning for Increased Robustness and Reduced Computational Overhead in Gaussian Process Accelerated Saddle Point Searches, ChemPhysChem, Nov. 2025.

DOI: 10.1002/cphc.202500730

Reproduction: gpr_sella_repro

python_dissemination_workbench

Teaching materials referencing rgpycrumbs as a helper utility example.