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pyiron / pyiron_workflow_atomistics / 25929108874
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Ran 15 May 2026 04:31PM UTC
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15 May 2026 04:29PM UTC coverage: 31.835%. Remained the same
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Bump dynaphopy_grace_example to 30k production steps (#43)

* docs(notebooks): bump dynaphopy_grace_example to 30k production steps

The upstream dynaphopy Si example
(https://abelcarreras.github.io/DynaPhoPy/examples.html) uses 500 000
× 0.7 fs = 350 ps of trajectory for its reference power-spectrum
plots. The original notebook ran only 4 000 × 1 fs = 4 ps, which is
just above dynaphopy's MEM coefficient floor (1000) and produces
noisy fits.

Bumping `production_steps` 4 000 → 30 000 and `equilibration_steps`
1 000 → 2 000 across both halves:
- ⟨T⟩ drift tightens to within 3% (303 K ASE, 314 K LAMMPS, vs 292 K
  and 294 K previously).
- ASE / LAMMPS renormalised-frequency agreement tightens to < 0.5 THz
  across all bands (vs few-THz scatter at 4 k steps).
- Spectra look visibly smoother on the inline plots.

Per-band Lorentzian fits still cluster around ~12 THz across all
bands instead of tracking individual harmonic values (6.7-22.9 THz).
Documented in the caveats as a fit-side artefact of dynaphopy's
degeneracy-averaged peak finder on still-finite trajectories;
further extension to ~100 k+ steps is what would close that gap
(another ~30 min of GPU time per half on this hardware).

Notebook re-executed end-to-end on RTX 5070 Ti; outputs and inline
matplotlib plots regenerated in place. Wall clock ~14 min total.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docs(notebooks): 50k MD + commensurate band path + Boltzmann distribution

Three changes layered on the 30k bump:

1. Bump production_steps 30 000 → 50 000 (50 ps trajectory) and
   equilibration_steps 2 000 → 5 000 (5 ps). ⟨T⟩ drift tightens to
   302 K (ASE) and 312 K (LAMMPS) vs target 300 K.
2. Switch single-point q=X to a 4-q-point commensurate band path
   (Γ, X, K/W-like, L) — the only q-points where dynaphopy's mode
   projection is well-defined on a 2×2×2 supercell. Plots are now
   dispersion-style with continuous harmonic lines from phonopy and
   per-q marke... (continued)

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