SOF-8043: Gr/Ni(111) registry and separation simulation notebook - #364

Reproduces the registry energetics of graphene on Ni(111) from Dahal &
Batzill, Nanoscale 6, 2548 (2014): which high-symmetry registry is
favourable, and how far the film sits above the surface.

Two tiers. The film is placed at each of top-fcc, top-hcp, bridge-top and
hollow — sites measured from the substrate's own top three Ni layers, and
each registry labelled by where the second carbon sublattice lands — then
scanned in z with MACE-MP + D3. A chemisorbing registry has two minima, so
the comparison reads the chemisorbed branch and compares each registry at
its own minimum; comparing at a shared height misranks them. The platform
tier then computes one Total Energy job per registry at that geometry.

The structure notebook additionally saves the base interface, which the
simulation notebook loads by name: it previously saved only the
empirically optimized variant.

Verified in JupyterLite: top_fcc wins at 2.01 A (article: top-fcc at
2.1 A) and the hollow registry does not chemisorb.

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

The energy-vs-separation figure raised KeyError: 'e_min', a key removed when
the scan was reworked into chemisorbed and dispersion-bound branches. Run
All Cells continues past an error and the assertions were downstream, so it
went unnoticed.

Registries now carry the manuscript's own names and cover all four of its
Fig. 1 configurations — hollow, atop/fcc, atop/hcp, bridge — with the figure
itself embedded. Bridge is defined by its geometry rather than labelled by
nearest site: one of its carbons is equidistant from two sites, so
classifying it returned whichever the dict happened to list first.

Claims match what the evidence supports. The two atop registries differ by a
few meV per carbon, finer than this method resolves, so the check is on the
atop family rather than on one of the two. The hollow registry's
dispersion-bound distance is reported for context, not gated: MACE-MP + D3
places it near 4 A rather than graphite's 3.3 A.

Two same-cell reference jobs (bare slab, free-standing film) now give an
adsorption energy per carbon atom, with the cell, k-grid, cutoffs and
smearing cancelling out of the difference.

Also: the displaced variants are no longer written into uploads/, where
load_material_from_folder's substring match over sorted filenames made them
shadow the base material on a second run; degauss raised to 0.01 Ry for the
metal; the scan-edge guard tests the sampled point rather than the
interpolated minimum; dead label-mapping block removed; stray tildes in the
introduction were rendering as strikethrough.

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

The bridge registry did not match the manuscript's Fig. 1d. The figure puts
a first-layer Ni under the midpoint of a C-C bond — the vertical bonds run
through the centres of the surface atoms — while the code placed a carbon
on the Ni-Ni midpoint, 1.9 A away, which also left that carbon equidistant
from the fcc and hcp sites. The placement is now derived from the bond
midpoint and verified rather than asserted, and it moves the bridge
registry from 95 to 21 meV per carbon above atop/fcc, which is the shallow
saddle it should be.

starting_magnetization is indexed by position in ATOMIC_SPECIES, so the
free-standing graphene reference would have started carbon with nickel's
moment. The patch is now built per material by element, and a reference
whose elements differ from the interface's gets its own workflow.

The adsorption-energy references are off by default: they triple the job
count of a run that is meant to finish one job unattended.

Cutoffs drop to 40 Ry with an 8x density cutoff, per the GBRV guidelines
already followed elsewhere in this repo.

The scan-edge warning fired on every run, including where the minimum was
properly bracketed by the point below it. It now fires only when the lowest
chemisorbed sample is the first in the window, which is the case that
actually means the well may lie outside it.

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

…sion, LDA

The reproduction targets are now the source paper's own numbers — Lahiri et
al., New J. Phys. 13, 025001 (2011), Table 1, reached through the review:
work of adhesion 0.81 / 0.77 / 0.31 J/m^2 for fcc / hcp / hollow at 2.16 /
2.17 / 3.26 A, with the atop carbon buckled outward. (The review's text
quotes the hollow as 0.38; its source's table says 0.31.)

Both tiers relax, because the buckling is one of the published numbers and
no rigid placement can produce one. The fast tier follows the paper's
scheme with MACE — bottom substrate layers fixed, same-cell relaxed
references, registry re-verified after relaxation — and prints its
comparison against Table 1 with an honest per-tier verdict: MACE-MP is
PBE-trained, PBE is the functional the paper rejects for this interface,
and the tier reports "no" with that reason rather than passing invented
criteria. Where torch-dftd is unavailable (the browser), the tier says it
is computing the GGA-level picture the manuscript describes as inadequate,
and a registry with no minimum reports itself unbound instead of raising.

The platform tier now runs the paper's method: LDA (pz, GBRV ultrasoft —
the platform carries the LDA set for C and Ni), spin-polarized, with
relaxation, and no dispersion correction, matching the paper's stated
reason for choosing LDA over GGA. Each selected registry starts from its
MACE-relaxed geometry; the two same-cell references are always submitted
with it, so the work of adhesion is computable; an empty selection skips
the tier, which is what the automated test uses.

The convergence block is unchanged and now evidence-backed: gaussian
smearing at default mixing stops at "convergence NOT achieved after 100
iterations" on this slab, while cold smearing with local-TF mixing
converges the same structure in 62 (both outputs on cluster-001).

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