feature/SOF-8044 Feature: add the h-BN boron-vacancy formation-energy tutorial page - #404
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Reproduces QPOD's neutral V_B formation energy (10.18 eV, standard states) for the h-BN vacancy tutorial pair, mirroring the graphene substitution simulation page's structure. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Review blockers: correct n_i to the signed atom-count change (the page had E_f short by 2*mu_B), stop promising the four Total Energy jobs always share one model (the notebook reuses an existing job per material instead), state the 0.02 eV finite-size offset without implying it bounds the tolerance, and register the page in mkdocs-guide.yml (Tutorials site), which was missing it entirely. Should-fix: numeric cutoff/k-grid in the settings table, npj (not Nature) Computational Materials in the body, reconcile the nitrogen reference job with its zero coefficient, $$...$$ for the equation, and name the compute defaults in what the default run does. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
The notebook's model is GBRV ultrasoft PBE at 40 Ry / 200 Ry, not PAW PseudoDojo JTH -- ultrasoft PBE sets for B and N do exist. Update the settings table and the surrounding sentence, and keep the pseudopotential family as one of the differences the 0.5 eV tolerance covers. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Round-2 review: the "clean project" sentence described a project selector the notebook doesn't have -- replace it with the actual consistency check the results cell runs (recompute E_f from three owned total energies, warn on mismatch). Note that PAW and ultrasoft cutoffs aren't comparable numbers, and fold cutoff into the tolerance's unestimated differences. Correct "jobs already finished are reused" -- only the three reference jobs are; the defect job always runs. Fix the references.bib journal to npj Computational Materials (was Nature). Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Round-3 review: the reference-reuse and cluster-fallback paragraphs described notebook behaviour 64b562aa changed away from. Reuse is now keyed to a per-material, per-model job name, so a cutoff change can't silently reuse a stale reference -- the residual hazard is the workflow's own elemental-energy resolution, which the results cell's consistency check catches; a missing cluster now raises and lists the available ones instead of falling back silently. Also: fix the inverted "skipped otherwise" for reference jobs, add the third verdict line form (reference mismatch), add k-point density to the unestimated differences, and make the atom counts (pristine -> defective) explicit in the settings table. Prerequisite page: journal name and a line noting both materials (h-BN supercell, B-vacancy h-BN) are saved by name, matching its own notebook's cell 15. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
api-examples 144f2c2f lets CLUSTER_NAME be None to use the first listed cluster; a name that is set but not found still raises and lists the available ones. State both in the compute paragraph. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Round-4 blocker: the prerequisite page's generic create_nanoribbon / create_point_defect route does not save two named materials -- only the combined notebook embedded in its own section 6 does. Say so on both pages, so the new page's prerequisite step names the right notebook. Should-fix: CLUSTER_NAME's shipped default is "cluster-001", not unset; match cell 44's verdict suffix byte for byte (ASCII "--", not an em dash); expand QPOD, GPAW, PBE, PAW at first use; state once that the elemental references are the platform's own seeded materials (why mu_B is alpha-boron specifically) and that an unseeded account stops the notebook at that step. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
… ref QPOD expands to "Quantum Point Defect database" (singular, lowercase "database") per the manuscript itself, not "Quantum Point Defects Database". Reflow that paragraph to the surrounding line width. The prerequisite notebook lives in its section 6, not "its last section" (References). Expand GBRV once (Garrity-Bennett-Rabe-Vanderbilt). Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
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Tutorial page for the h-BN boron-vacancy formation-energy Specific Example (api-examples PR: mat3ra/api-examples#367), Jira SOF-8044, epic SOF-7994.
What changed
tutorials/materials/specific/defect-point-vacancy-boron-nitride-simulation.md: what is reproduced (QPOD1BN-1.2d.v_B.0.1, 10.18 eV, standard states; only q = 0), the formation-energy definition, settings and where they differ from QPOD (GBRV ultrasoft vs PAW, 48- vs 84-atom cell, SCF vs relaxed — the two estimated offsets are 0.02 and 0.04 eV), theory vs experiment, what the default run submits, the JupyterLite embed.mkdocs.ymlandmkdocs-guide.yml: one nav line each, next to the structure page.references.bib:Bertoldo2022journal corrected to npj Computational Materials.Verified
scripts/serve-all.sh --build+scripts/links/check-links.py: no broken internal links (332 664 checked); the page appears in the Guide nav next to its prerequisite; the citation renders.Manual checks (merging accepts anything unticked)
jupyterlite_embedopensspecific_examples/defect_point_vacancy_boron_nitride_SIMULATION.ipynbon the preview — requires the api-examples PR merged and the JupyterLite build refreshed first.Merge after mat3ra/api-examples#367.