SOF-8043: Gr/Ni(111) registry and separation tutorial - #400
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Companion page for the simulation notebook added in api-examples: what the manuscript (Dahal & Batzill, Nanoscale 6, 2548 (2014)) reports about the high-symmetry registries of graphene on Ni(111), which quantities are comparable across methods and which are not, the two-tier recipe (MACE-MP + D3 survey, then Total Energy jobs per registry), and the computational settings next to the manuscript's. Registered in both navs and linked from the index guide's Dahal row. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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The settings table documented the combination that inverts the result: MACE medium where the notebook uses large, and vdw_corr = "d3_grimme" where the notebook sets "grimme-d3". The medium model at float32 misses the shallow chemisorbed minimum entirely and reports every registry as physisorbed, so the page now says which model is required and why. Covers all four of the review's Fig. 1 registries under its own names, with the figure shown, and states plainly what is not claimed: which of the two atop registries is lowest is below the resolution of either method here. Documents the two same-cell reference jobs and the adsorption energy they produce. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The bridge registry is a C-C bond straddling a first-layer Ni, not a carbon on the Ni-Ni midpoint. Cutoffs follow the notebook at 40/320 Ry. The adsorption-energy references are described as off by default, and what their same-cell arrangement does and does not cancel is stated plainly. Job counts now match the notebook: four registries, and the two reference jobs add to whatever is active rather than being part of a default run. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Cutoffs corrected to the 40 / 200 Ry pair GBRV publishes for its ultrasoft set. The settings section now says, for every value, whether it is a platform default, the pseudopotential set's published value, or something this system's physics requires — including what the SCF defaults did on a first attempt and which three changes address it. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The page now leads with Lahiri et al. Table 1 as the quantitative target, states the published recipe (LDA, spin-polarized, relaxation with the bottom substrate layers fixed) and why relaxation is not optional, explains that the fast tier is expected to fail the energetic targets and why that is the physics working as documented, and lists the divergences from the paper in one place. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Tutorial page for the simulation notebook in mat3ra/api-examples#364 — SOF-8043, epic SOF-7994.
Follows the shape established by the twisted-MoS₂ simulation page: front matter with the M-CODE tag, the manuscript in a
!!!noteblock citing[@Dahal2014](key already present inreferences.bib), the structure tutorial linked as a prerequisite, what is compared and what deliberately is not, a settings table against the manuscript's, step-by-step instructions, and the JupyterLite embed.Registered in
mkdocs.ymlandmkdocs-guide.ymlnext to the structure page, and the index guide's Dahal row now links the simulation page instead of reading "Coming Soon".Two points the page makes explicitly, because both are easy to get wrong:
Draft alongside the api-examples PR, whose DFT tier is blocked on a local messaging fault (see that PR).
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