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feature/SOF-8072 Feature: tutorials for a Ti adatom on a 5×5 TiN island, descent energetics of Fig. 6 (MACE and DFT) - #415

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feature/SOF-8072

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@VsevolodX VsevolodX commented Oct 9, 2026 •

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Adds the two tutorial pages for the Ti adatom on a 5×5 TiN island (D-2D-ADA): the structure page for the new notebook and the simulation page, which covers both methods the notebook runs — MACE in the notebook and DFT on the platform — and lists what each gives beside Sangiovanni et al. 2018. The manuscript's Fig. 1(b) is on the structure page and its Fig. 6 on the simulation page. The island structure page is unchanged.

SOF-8072. Notebooks: mat3ra/api-examples#385.

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Merging accepts anything unticked.

  • jupyterlite_embed on each page points at the literal notebook filename in api-examples.
  • Quoted cells match the notebooks at the PR head.
  • Deploy preview: the figures, the two gifs and the results table render.

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VsevolodX and others added 2 commits October 8, 2026 17:53
…ect the island structure page to build the paper's 458-atom cell.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…the paper's protocol for c in its own words, and match the browser and run-time statements to the notebook.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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VsevolodX and others added 4 commits October 8, 2026 19:48
…atom pages

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…om notebook

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@VsevolodX VsevolodX changed the title feature/SOF-8072 Feature: tutorial for a Ti adatom on a 5×5 TiN island, descent energetics of Fig. 6 (MACE) feature/SOF-8072 Feature: tutorials for a Ti adatom on a 5×5 TiN island, descent energetics of Fig. 6 (MACE) Oct 9, 2026
VsevolodX and others added 10 commits October 9, 2026 09:45
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…e SE tutorials

Removed the measured notebook wall time and the per-step BFGS time.
Pages: Ti adatom on the TiN island (simulation).
Why: a tutorial teaches the platform; it does not record one run.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
@VsevolodX VsevolodX changed the title feature/SOF-8072 Feature: tutorials for a Ti adatom on a 5×5 TiN island, descent energetics of Fig. 6 (MACE) feature/SOF-8072 Feature: tutorials for a Ti adatom on a 5×5 TiN island, descent energetics of Fig. 6 (MACE and DFT) Nov 6, 2026
VsevolodX and others added 2 commits November 6, 2026 06:04
… default

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
…bes the DFT jobs

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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