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pyiron / pyiron_workflow_atomistics / 25933357740
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Ran 15 May 2026 06:06PM UTC
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15 May 2026 06:02PM UTC coverage: 89.094%. Remained the same
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docs(notebooks): add 0.7 fs sibling notebook (50k × 0.7 fs = 35 ps) (#45)

Adds notebooks/dynaphopy_grace_example_long.ipynb — a sibling of
dynaphopy_grace_example.ipynb with the MD integrator step dropped from
1.0 fs to 0.7 fs (matches the dynaphopy upstream Tersoff Si example,
which uses `-ts 0.0007`). All other knobs unchanged: same 50 000
production steps, same 5 000-step equilibration, same 4-q-point
commensurate band path (Γ, X, K/W, L), same Boltzmann analysis cell.

The 0.7 fs step gives 35 ps of trajectory vs the 1.0 fs sibling's
50 ps, but with a higher Nyquist limit and somewhat better integrator
accuracy. Results:

- ASE ⟨T⟩ = 294.5 K (drift 1.8%)
- LAMMPS ⟨T⟩ = 319.8 K (drift 6.6%, above the 3% auto-warn tolerance)
- Boltzmann analysis T from ⟨|v|²⟩ = 299.3 K  (target 300, <1%)
- Renormalised dispersion: same ~13.5 THz cluster at the zone-folded
  optical bands as in the 1.0 fs run — the fit-collapse pattern is
  step-size-invariant, consistent with it being a dynaphopy
  peak-finder behaviour rather than an integration-accuracy issue.

Both notebooks use disjoint working directories
(`./_dynaphopy_grace/...` and `./_dynaphopy_grace_0p7fs/...`) so
they can run in the same checkout without clobbering each other.

Added to `.ci_support/exclude` because, like the 1 fs sibling, it
needs `tensorpotential` + a `pair_style grace`-capable LAMMPS that
the CI standard notebook environment doesn't provide.

Co-authored-by: Han Mai <ligerzerof@gmail.com>
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

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