Features#

Parse

Extract structured tables and ASE structures from engine outputs.

Units

pint quantities end-to-end — no silent eV/kcal mix-ups.

Surfaces

Gradient-enhanced GPs via rgpycrumbs.surfaces, optional SurfaceFitConfig.

CLI suite

Call from rgpycrumbs eon plt-* with TOML --config for dense option sets.

Data flow#

        flowchart LR
  OUT[Engine outputs] --> PARSE[chemparseplot.parse]
  PARSE --> COORDS[RMSD / energy arrays]
  COORDS --> FIT{SurfaceFitConfig auto_thin?}
  FIT -->|default off| FULL[Full cloud fit]
  FIT -->|opt-in| THIN[Even subsample + endpoints]
  FULL --> GP[rgpycrumbs.surfaces]
  THIN --> GP
  GP --> FIG[Publication figure]

Important

auto_thin defaults to false. Enable via SurfaceFitConfig or the matching keys in rgpycrumbs plot TOML when dense force-eval movies make grad_imq non-finite.

  • Parsing computational chemistry output files into structured data

  • Plotting with scientific color maps (camera-ready)

  • Unit preserving throughout via pint

  • Computation delegated to rgpycrumbs for surface fitting, interpolation, and structure analysis

  • Concurrent RMSD landscape calculations via ThreadPoolExecutor

Supported Engines#

ORCA (5.x)#

  • Geometry scan (OPT) energy profiles

  • Nudged elastic band (NEB) path visualization over the linearized reaction coordinate

eOn#

  • Saddle search parsing (Dimer, GPRD, LBFGS methods) with status tracking

  • NEB path energy profiles with RMSD landscape projections

Sella#

  • Saddle point optimization result parsing

ChemGP#

GP-based optimization visualization from HDF5 output (chemparseplot.plot.chemgp):

  • 1D plotnine charts: convergence curves, RFF quality sweeps, NEB energy profiles, FPS subset scatter (PCA projection)

  • 2D matplotlib surfaces: PES contour with NEB path overlay, GP surrogate progression panels, MAP-NLL landscape, variance overlay with hatching, trust region illustration, hyperparameter sensitivity grid

Trajectory Formats#

  • HDF5 trajectories from ChemGP output (pre-computed forces and reaction coordinates)

  • Generic ASE-readable formats (extxyz, .traj) for NEB analysis with tangent force computation and RMSD landscape coordinates

  • eOn ConFrame series (parse.eon.frame_series): energies and trajectory DTOs from stamped frames for object-plot adapters.