Real systems for documentation

These tutorials ship self-contained geometries and configs that use only built-in eOn potentials (no Hugging Face download, no external DFT). They are the recommended path for:

  • learning client jobs end-to-end (eonclient + outputs)

  • exercising the current rgpycrumbs / chemparseplot visualization stack (plt-neb, plt-min)

  • CI-stable MyST-NB execution (docs build does not depend on metatomic models)

For a metatomic / PET-MAD walkthrough (oxadiazole, vinyl alcohol), see the atomistic-cookbook eon-pet-neb recipe and the in-tree Visualizing Optimization Trajectories tutorial.

Systems

System

Potential

Job

Docs page

Data under systems/data/

Pt adatom / surface hop (few-atom Morse)

morse_pt

NEB

Morse Pt NEB (built-in potential)

morse_pt_neb/

Lennard-Jones cluster

ljcluster

minimization

LJ cluster minimization (built-in potential)

lj_min/

Pt saddle (dimer)

morse_pt

saddle search

Morse Pt saddle search (built-in potential)

pt_saddle/

Geometries are copied from the in-repo benchmarks/data/ and examples/ trees so the same inputs power unit/ASV benchmarks and the docs.

Plotting conventions (current stack)

These conventions match the production rgpycrumbs / chemparseplot tools:

NEB (plt-neb)

  • Prefer full history: --landscape-path all, --show-pts, --highlight-last

  • Structure strip: --plot-structures all (every band image) or crit_points (R / SP / P only for a lighter figure)

  • Landscape: --project-path so the panel is true 1:1 Å in reaction-valley coordinates (Δs = Δd); colorbar and strip sit under a content-sized figure

  • SP marker: gold star on the 1D profile (and landscape) when the final band and/or sp.con are present

Minimization (plt-min)

  • Require movies: [Debug] write_movies = true (and optionally write_deprecated_outs = true for legacy .dat sidecars)

  • One 2D landscape per endpoint — do not overlay reactant and product on a shared (s, d) frame; each trajectory defines its own RMSD basis

  • Use --label reactant / --label product so titles read Reactant minimization / Product minimization with initial / minimized endpoint captions

  • Relative energy on the colorbar (readable tick labels)

Systems