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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>
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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>
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📝 WalkthroughWalkthroughThe PR adds a graphene/Ni interface simulation notebook with MACE-MP+D3 analysis and optional DFT workflows. It adds cluster selection, saves the base interface material, and links the simulation notebook from the introduction. ChangesGraphene/Ni simulation workflow
Priority: ⬇️ Low Estimated code review effort: 4 (Complex) | ~45 minutes Change: Feature Sequence Diagram(s)sequenceDiagram
participant SimulationNotebook
participant InterfaceParts
participant ASECalculator
participant WorkflowAPI
participant ComputeCluster
SimulationNotebook->>InterfaceParts: extract interface parts and derive registries
SimulationNotebook->>ASECalculator: run MACE-MP+D3 scans and relaxations
ASECalculator-->>SimulationNotebook: return fast-tier energies and structures
SimulationNotebook->>WorkflowAPI: create DFT workflows and jobs
WorkflowAPI->>ComputeCluster: submit registry and reference jobs
ComputeCluster-->>WorkflowAPI: return job status and energies
WorkflowAPI-->>SimulationNotebook: provide DFT results
Merge Risk: 🟠 High · up to This PR adds a substantial new graphene/Ni simulation notebook, but several open issues can cause it to silently report incorrect or misleading energetics: mismatched relaxed geometries can be attributed to the wrong registry, unconverged relaxations can be used as reference energies, some registry scan paths can pick invalid starting points or crash the reporting step, and the DFT tier appears to still run LDA instead of the intended PBE+D3 method. These should be resolved before relying on the notebook's quantitative conclusions. 🚥 Pre-merge checks | ✅ 5✅ Passed checks (5 passed)
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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>
…r a default The density cutoff was 8x the wavefunction cutoff, a ratio taken from a sibling notebook that uses different pseudopotentials for a different system. GBRV publishes its ultrasoft set as a 40 / 200 Ry pair, which is also the platform default, so that is what this uses. Each remaining parameter now states which of the three it rests on. The k-point divisions are a multiple of three because K sits at (1/3, 1/3) and has to lie on the grid, and dense because a metal's Fermi surface needs it. The starting moment is Ni's bulk value. D3 is on because the hollow registry has no chemisorbed minimum at all and is held only by dispersion. The MACE model size is a measurement, not a preference: medium at float32 finds no chemisorbed minimum and inverts the result. The SCF settings are grounded in the failure they fix. A first job stopped at "convergence NOT achieved after 100 iterations" with the total energy oscillating in its fourth decimal — charge sloshing, not divergence. Cold smearing leaves the free energy insensitive to degauss where the gaussian default does not; local-TF mixing is built for the long-wavelength charge oscillation a slab supports; a smaller mixing fraction and more iterations let the magnetic moment settle. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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- Line 434: Update the reference-energy calculation in the plotting cell to skip
registry entries where both chem and phys are None, and fall back to the raw
scan energies when no minimum is available. Preserve the existing minimum-energy
behavior for entries with valid chem or phys results and prevent min() from
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…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>
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`@other/materials_designer/specific_examples/optimization_interface_film_xy_position_graphene_nickel_SIMULATION.ipynb`:
- Around line 854-860: Update the cluster-selection and submission flow around
Compute so empty results from client.clusters.list() and unmatched CLUSTER_NAME
values do not index or dereference a missing cluster. Create Compute and submit
jobs only when a valid cluster is selected, and apply the same guard to the
additional flow around the second affected block.
- Line 668: Update the scan-results persistence loop around the relaxed
assignment to skip a registry when scan_results[label]["relaxed"] is None before
accessing relaxed["material"]. Preserve the existing dft_materials guard so the
DFT tier is also skipped when no valid registry remains.
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534 to 432 code lines, identical physics (verified to the digit), and the 83-line scan+relax cell split into machinery and narrative. Most of what left was generality the notebook itself forbids: it asserts a 1x1 interface up front, so each Ni layer holds one atom — the z-clustering, top-layer averaging and species introspection collapse to a sort, a max, and one assert (Ni is species 1 in the interface and slab, so the magnetization index is fixed; the graphene reference gets the same workflow without the moment, ending the per-element-set dedup machinery). The parabola refinement died with the rigid scan's authority: relaxation supersedes interpolation, so a bracketed minimum is just the lowest non-edge scanned point. The k-grid loops are replaced by notebooks_utils' existing apply_scf_kgrid, which this notebook had re-implemented. The comparison cell drops its checks-dict scaffold for the established style: values beside the paper's, one plain verdict per tier. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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- Around line 279-280: The displacement-labeling logic after site_of must reject
a None result and any site combination outside the expected fcc/hcp hollow pair
or atop pair before deriving the registry name. Validate the computed second
site and pair, then only assign displacements for valid pairs; avoid calling pop
or constructing labels from invalid or ambiguous sets.
- Line 493: Update the loop’s unbound-target reporting to use PAPER.get(label)
instead of direct indexing, and print that no published target is available when
the label has no registry entry, including “bridge”; preserve the existing paper
value output for labels with published targets.
- Around line 434-436: Update the minima selection around i and starts[branch]
to derive the selected point’s position within in_branch, and only accept it
when that branch-local position has both preceding and following neighbors;
compare energies against those same-branch neighbors rather than full-array
neighbors, while preserving the existing starts assignment for valid minima.
- Around line 485-491: Update the MACE verdict and reporting around the rows
built from scan_results so they no longer compare or claim reproduction of
absolute W_adh values from PAPER. Restrict the verdict to supported checks such
as separation, ordering, and qualitative registry behavior, and remove any
“reproduces Table 1” output based on W_adh while preserving the paper reference
data needed for supported comparisons.
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The three stackings are one atop-to-hcp step apart, so the film shifts are 0, one step, two steps — plain computed coordinates, valid for either hex cell convention (a diagonal third is not, and the tie-refusing site check caught that on this 120-degree cell). The site map remains only for what arithmetic cannot give: the fcc/hcp name comes from what lies underneath. Physics verified identical to the digit. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Comments that justified a choice to the reader are gone; the choice stands on its own. The hollow target is Table 1's value with no aside about the review's text; the dispersion note is the runtime print alone; parameter comments are one line each. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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We need a helper function to find coordinates for high-symmetry registries based on lattice types + miller indices
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This is what made#298 became: SurfaceSiteAnalyzer derives the high-symmetry sites (atop, bridge, fcc, hcp, hollow) from the slab's own top layer and the layer beneath it, so it works for any lattice and Miller index whose surface is flat within a tolerance — verified on Ni(111), Cu(001), Cu(110) and MoS2. get_displacement_to_site returns the shift that puts a chosen atom on a chosen site, which is what this notebook uses to build each registry.
…elpers Five modules in notebooks_utils, generic rather than shaped to one notebook, because the specific-examples corpus needs each of them repeatedly: - surface: named high-symmetry adsorption sites — atop, bridge, and the fcc and hcp hollows told apart by which subsurface layer lies beneath, a distinction pymatgen's AdsorbateSiteFinder does not make. Delaunay over the tiled surface layer, so it holds for any lattice and Miller index whose surface is flat within a tolerance, for films and for passivation. - relaxation: relax with the deepest layers held and, optionally, motion along z only, so a structure cannot slide out of its registry. Replaces a to_ase/FixAtoms/BFGS block written by hand in three notebooks already. - energetics: energy from a calculator, in-plane area, and work of adhesion in J/m^2 from same-cell references. - interface: film/substrate split, separation, corrugation. - compute: cluster selection that says what is wrong when none is registered, instead of IndexError from clusters[0] — the pattern in eight merged workflow notebooks. get_site_of returns None when two sites are equidistant rather than resolving by dict order; an ambiguous label is how a structure gets reported under the wrong registry. relax carries build metadata across the ASE round-trip, and get_interface_separation accepts the substrate elements, because the round trip otherwise strips what interface_get_part needs and measuring a relaxed interface raises. The Gr/Ni notebook uses all five: 534 code lines when this review round started, 376 now, with identical results to the digit. Also fixes two CodeRabbit findings on #364 — a registry with no relaxed structure is skipped before persistence, and cluster selection is guarded. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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`@other/materials_designer/specific_examples/optimization_interface_film_xy_position_graphene_nickel_SIMULATION.ipynb`:
- Around line 127-128: Update the notebook’s DFT configuration to use the
intended PBE+D3 workflow: set FUNCTIONAL to pbe, set MODEL_SUBTYPE to gga, and
configure vdw_corr as d3_grimme for both pw_relax and pw_scf.
In `@src/py/mat3ra/notebooks_utils/relaxation.py`:
- Line 58: Update the relaxation flow around BFGS.run so it checks the returned
convergence status and raises an error when max_steps is reached before
satisfying fmax; preserve the existing successful-convergence behavior.
In `@src/py/mat3ra/notebooks_utils/surface.py`:
- Line 18: Update the layer comparison in the relevant surface-layer logic to
use each layer’s seed height—the z value that created the layer—instead of the
input-order-dependent group[0][2]. Preserve the existing tolerance check while
ensuring boundary-near members are compared against the correct seed so
_hollow_name receives the correct subsurface layer.
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surface, relaxation, energetics and interface take a Material and belong in mat3ra.made beside the analyzers, constraints and calculators that already cover the same ground (calculate/ase/constraints.py, analyze/crystal_site/, analyze/interface_material.py, calculate_adhesion_energy). They move there in a made PR; the notebook returns to its inline form until that lands. get_compute takes an API client and stays. The two CodeRabbit fixes are kept inline. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
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- Around line 422-423: Update the relaxation-validation branch around the
carbon_sites registry check so a migrated structure is marked as having no valid
relaxed structure and the current entry skips energy and structure storage.
Ensure the later result-registration logic does not store the energy or relaxed
structure under the original label when the registry changes.
- Line 365: Check the boolean result returned by each BFGS.run call before
reading energies for E_separated or W_adh. Reject or mark the corresponding
registry unavailable when relaxation does not converge within the step limit,
while preserving energy calculations only for successfully converged structures.
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…ets wrong Review found the platform tier could not have produced a result: - add_relaxation() on the total-energy workflow adds a variable-cell pw_vc-relax unit, and every setting patch named pw_relax/pw_scf, so the geometry step ran unpolarized at default mixing with a relaxing cell — voiding the same-cell cancellation. The tier now uses the platform's fixed_cell_relaxation workflow: one pw_relax unit, calculation='relax', and the rendered input carries nspin=2, starting_magnetization(1)=0.7, cold smearing, local-TF mixing, 12x12x1 and 40/200 Ry. The graphene reference runs nspin=1: it is non-magnetic, and QE needs a starting moment when nspin=2. - properties.get_for_job already returns the data records, so property_data[0]["data"]["value"] would have raised on the first energy. Energies are read with their units; the final structure is read back and separation and buckling compared, not only the work of adhesion. - The verdict is over what was selected, with the ordering check when all three registries are, instead of "no (1 of 3)". The fast tier's prose claimed the structure side as its strength; measured, it buckles the atop carbon toward the surface and sits 0.2 A too close. The notebook now says what it delivers: the registry set, the two-branch landscape and starting geometries, with its numbers beside the paper's. Also: a registry that relaxed onto other sites is dropped, not reported under the requested name; buckling is None where no carbon is atop, so the sign check cannot pass on an unsigned value; bottom layers are frozen by height, not by atom count; references are not uploaded when nothing will run; divergences from the paper are stated in the notebook; the verdict is printed once; get_compute has a unit test; one artifact name. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
The DFT drift check assumed an atop carbon: a correct hollow or bridge result printed "registry may have drifted", and a slide from atop_fcc to atop_hcp passed unnoticed, with the paper's two atop rows close enough that the verdict could read yes for the wrong registry. Both tiers now compare the sites the relaxed carbons occupy against one table of what each named registry is; a drifted row is excluded from the verdict and says so, and buckling is reported only where an atop carbon exists. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
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… uses them The registry, layer and relaxation machinery the Gr/Ni notebook carried inline becomes reusable helpers where helpers belong, organized by what they act on: - material/surface_sites.py — SurfaceSiteAnalyzer: the named sites of a slab's top surface (atop, bridge, fcc/hcp/hollow) from the geometry of the surface layer alone, for any flat surface net; None on a tie or off-site point. Checked on eight nets (fcc 111 at 1x1, 2x2 and a rotated cell; fcc 100 and 110; hcp 0001; rocksalt 100; bcc 100), which caught two bugs the fixture tests had not: atoms on or past the cell boundary were filtered rather than wrapped, and the periodic tiling was not centred on the home cell. Both fixed; a test on a substrate shifted by one whole cell pins them. - material/layers.py — layer grouping independent of basis order, and bottom-layer selection for holding substrate layers fixed. - mlff/relaxation.py — relax_material: ASE relaxation with fixed atoms and z-only motion, returning a copy with only the positions changed, so labels and build metadata survive; raises when not converged. material.py and mlff.py become packages; every existing import keeps working. Energies, interface parts, interlayer distance and area come from mat3ra.made functions that already exist. The notebook calls all of this instead of its own copies — identical results — and cluster selection is five inline lines again rather than a helper. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
A registry on a supercell is a local statement — this film atom over that substrate site, the rest follow — so the anchor has to be something a person can name from what a viewer shows: an element near a coordinate, or an index. material/placement.py provides the pieces separately and one helper that combines them: - get_atom_indices(material, element) and get_atom_index(material, element, near) — "the Mo near (0.25, 0.25, 0.5)" — resolve to indices that describe_atoms lets you check before use. - place_over(interface, film_atom, substrate_atoms) — one film atom over one substrate atom (atop), two (bridge) or three (hollow), by the interface's own indices. Periodic images are chosen as the compact set that forms the site, not each atom's image nearest the first; atoms that are not neighbours of one another are refused against the layer's measured nearest-neighbour distance. - get_film_site_occupation(interface) — which named site each film atom sits on; the diagnostic for incommensurate films, where no single registry exists (Gr/Ni(001): 24 of 30 carbons on no site whichever anchor is moved). Parts are identified by labels, not build metadata, so relaxed and file-loaded structures work. The Gr/Ni notebook names its anchor carbon through the resolver instead of "coordinate 0". Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
get_atom_indices(material, element, coordinate, radius) returns the atoms of an element within a radius of a point — nearest first, periodic images included — and get_atom_index returns the one that qualifies or says how far the nearest actually is. "Nearest, wherever it is" was the wrong contract: a bounded search is what a person means when they point. Distances are made's minimum_image_distances, with the element filter and the bound on top; nothing is re-derived. The notebook names its anchor carbon with a coordinate and a radius. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…ils.mlff The surface-site analyzer, the point-at-an-atom lookups, the film placement and the layer helpers now come from mat3ra.made (made#298), where material geometry belongs; the copies under notebooks_utils/material are removed. The ASE relaxation keeps its place in notebooks_utils/mlff: an optimizer is not part of the structure library. The notebook's registry cell is four statements — the anchor carbon named by coordinate and radius, the site each registry puts it on, the resulting shift, and the occupation check that the other carbon landed where the registry's name says. Results are unchanged to the digit. config.yml's made profile now lists made's own requirements, so a made wheel registered in the JupyterLite bundle resolves them as the PyPI package would. mat3ra-made is pinned to made#298's commit until a release; the one temporary thing here. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…me the anchor from the film's height The git pin would have broken notebooks_utils' own PyPI publish on merge, so mat3ra-made goes back to unversioned; unit tests run against the released made instead of pinning made's own behaviour. The same-cell references now relax under the interface's z-only/fixed-layers constraint, so the work of adhesion subtracts like from like instead of a freely relaxed interface against constrained references. The anchor carbon is named from the film's own measured height rather than a borrowed constant, the registry occupation check is an assertion instead of a print, and the DFT tier's site map is read from the relaxed structure's own Ni rather than the pre-relaxation substrate. Leftovers of the reverted made-extraction design (the empty material/ package, made's own layer-helper tests, the dead SQUARE_NET fixture, the dev-bundle-only config.yml edit) are removed with it. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…ta-driven test_workflow_utils.py's shape — one parametrized test over a module-level CASES list, expected outcomes as data rather than behaviour-narrative test names. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…s, close the vacuous slide-guard sentence The parametrized test passed with the constraint disabled: both fixture rows have no in-plane force to constrain, so along_z_only was unexercised. A second fixture with one carbon nudged off its site gives the test something to hold, and the mutation check (`_constraints` disabled) now fails as it should. The two `slid into a neighbouring registry` sentences (notebook cell 9) claimed a guard that cannot fire under z-only motion; say what actually holds in this tier and where the guard is real. `FixAtoms`/`BFGS`/`from_ase` were left over from the inline optimizer this module replaced. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…cope fix
The four-line "why derived, not pinned" comment in the test and the three-line ANCHOR_SITE
comment in cell 7 both restate what the commit message / dict already say. Cut both.
Lahiri et al. give buckling for the fcc registry only; the DFT-tier verdict was checking it against
PAPER_BUCKLING_FCC for atop_hcp too via a startswith("atop") match. Scoped to atop_fcc, matching the
MACE-tier check it was supposed to mirror. hcp's buckling still prints, just carries no verdict.
Add apply_planewave_cutoffs (workflow.py), get_final_structure_for_job (core/entity/material/api.py) and label_interface_parts (material.py), each with one parametrized test. Removes the Gr/Ni SIMULATION notebook's property_of, total_energy_of, final_structure_of, dft_geometry, buckling_text and the duplicate carbon_sites_and_buckling (kept once, renamed film_sites_and_buckling, shared by both tiers) in favor of these and existing helpers. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
… site map Move label_interface_parts to a leaf core/entity/material/interface.py (material.py re-exports it) so unit tests importing it no longer pull in IPython via material.py's io re-export chain, which was failing CI collection. film_sites_and_buckling now builds its SurfaceSiteAnalyzer from the interface's own labels instead of cell 7's unrelaxed surface, so both tiers read the site map against the relaxed Ni. Restore the one-line buckling_text helper (cell 11), used at its three call sites, in place of the repeated inline ternary. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
The eager re-export pulled mat3ra.made into every import of this module, including set_materials/get_materials/load_material_from_folder consumers that don't need it (e.g. the structure notebook, whose install profile doesn't provision mat3ra-made) -- found by running the browser harness. label_interface_parts is now resolved lazily via a module __getattr__, so only DFT-tier code that actually calls it pays for the made import. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
material.py returns to its state at 910e5ce: no re-export, no __getattr__. The notebook now imports label_interface_parts from its leaf module, mat3ra.notebooks_utils.core.entity.material.interface, the same deep-path style cell 21 already uses for get_or_create_material. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Matches the repo's test-path convention: core/entity/material/api.py -> tests/py/unit/core/entity/test_material_api.py, so the new leaf core/entity/material/interface.py -> test_material_interface.py in the same directory. No content change. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
QUEUE_NAME=OF, PPN=40, TIME_LIMIT="04:00:00": the Compute model defaults timeLimit to 01:00:00 regardless of queue, and on D with one core the spin-polarized relaxation timed out. On OF/40/04:00:00 all three jobs finished and the fetch path worked on production (W_adh 1.01 J/m^2, d 2.02 A, buckling +0.013 A vs paper 0.81 / 2.16 / 0.03). Cell 28's Compute(...) now passes timeLimit=TIME_LIMIT and prints it alongside the cluster/queue/ppn line. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Human decision: "this makes no sense. just print what we get and what is expected." Cell 14 drops the mace_reproduces boolean block (the MACE-tier print table stays). Cell 34 replaces the two yes/no verdict blocks with one table: paper / MACE / DFT columns for W_adh, separation and buckling, over the paper's three registries plus bridge, "-" wherever a tier did not run or the paper gives nothing. Reuses PAPER, PAPER_BUCKLING_FCC, rows, dft_results and buckling_text; 20 lines. Cell 32 is unchanged -- its drifted-registry print stays, the table just shows the numbers regardless. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
mat3ra.utils.jupyterlite.plot was removed from mat3ra-utils (present in 2025.10.9.post5, absent from every 2026 release) -- those helpers moved into notebooks_utils. plot_2d_heatmap/plot_3d_surface in mat3ra.notebooks_utils.ipython.plot._plotly have byte-identical signatures, and other notebooks on main already import from that path. This was leaving optimized_material undefined and breaking session 1 of the browser harness. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
made 3e229e76 moved get_displacement_to_site/get_site_name to crystal coordinates by default (use_cartesian_coordinates: bool = False, matching the rest of made) and renamed SurfaceSiteEnum -> SurfaceSiteTypesEnum. The registry cell's two get_displacement_to_site calls work in cartesian throughout (film_at adds its z offset in Angstrom), so both now pass use_cartesian_coordinates=True. Nothing else changes; the notebook never referenced SurfaceSiteEnum. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Comparing the branch-boundary candidate against a full-array neighbor from the other branch could accept a chem/phys split point as a bracketed minimum on nothing more than an artifact of where CHEMISORBED_BELOW falls. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
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Do we need this? Should it be in made?
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Agreed — it is in made now as interface_label_parts_by_elements (tools/modify.py, beside interface_get_part/interface_displace_part), with its own test on the repo's existing Gr/Ni fixture. notebooks_utils/core/entity/material/interface.py and its test are deleted; the notebook imports made's function directly. made#298 @ f8dcde7b.
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Done: relax_material moved to top-level notebooks_utils/relaxation.py, test renamed to test_relaxation.py, and mlff.py is back to a single module holding only the calculator helpers.
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I put it top-level rather than in workflow.py: that module is mat3ra.wode platform-job configuration (k-grid, QE input patching), and relax_material takes any ASE calculator and runs locally — putting it there would pull wode into the browser tier. Happy to move it if you meant that module literally.
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How long does this take??
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Measured: 40 ms per relaxation case; the module was 8.9 s, almost all of it the fixture building an interface through the ZSL search at import. That search also returned a different cell under CI's dependency versions (a 25.7 %-strained match that would not converge), so it is gone: the test now builds a plain slab from standata and the module runs in ~4 s.
timurbazhirov
approved these changes
Sep 13, 2026
… labelling from made relax_material and Z_DIRECTION move to a top-level relaxation.py: the function takes any ASE calculator and runs ASE's own BFGS, so it isn't MLFF-specific, and workflow.py is platform QE/k-grid configuration, not local geometry relaxation. Test renamed to match. test_relaxation.py's module-level create_interface_zsl_between_slabs call was 2.85s of its ~8.9s; max_area=100 finds the same 6-atom match as the notebook's 350 (verified byte-identical) an order of magnitude faster, without switching to create_interface_simple_between_slabs (which shears the film across hexagonal settings). label_interface_parts moves to made: the notebook's DFT-tier cell now imports interface_label_parts_by_elements from mat3ra.made.tools.modify (made#298, f8dcde7b), and core/entity/material/interface.py plus its test are deleted. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
…al one 3772d41's max_area=100 changed which candidate create_interface_zsl_ between_slabs' match_id=0 returns under CI's resolved dependency versions -- a 25.7%-strained match instead of the local 6-atom one, and the strained one doesn't relax within fmax in 50 steps. Same defect made's own test suite hit and worked around by dropping the search entirely (see made's "Build the Gr/Ni(111) test fixture deterministically" / "Reuse the repo's ... fixture" commits): a searched cell cannot carry a pinned expectation. relax_material's contract is about constraints (fixed atoms don't move, along_z_only leaves xy untouched, non-convergence raises), not about Gr/Ni physics -- the interface path stays covered by scripts/verify_fast_tier.py and by made's own tests. Test it on a plain create_slab(Nickel) instead: Ni(100)'s own surface-relaxation force already exceeds RELAX's fmax (no ZSL, no artificial strain needed for case 0); one atom displaced in the other two cases gives the in-plane force to test drift vs. along_z_only. Module time is now ~3.8-5s (all import cost), down from the 6.75-8.93s the review measured and the construction-search cost that broke CI. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
…made df3245d's fixed-layer selection used get_atom_indices_by_layer, which only exists in made#298 (the made worktree), not the released mat3ra-made CI installs -- the same "unit tests must not import new made functions" constraint recorded earlier in this task for the same reason. Group the bottom layer and pick the top atom by plain z-coordinate instead, matching the original test's own style (BOTTOM_NI via min z). Verified against released mat3ra-made==2026.9.12.post0 in a scratch venv (agents/workdir/tmp/venv-released-made, not committed): every `from mat3ra.made` import across tests/ (Material, calculate_total_energy, create_slab, CrystalLatticePlanesMaterialAnalyzer) resolves there; `pytest tests/py/unit -q` -> 47 passed. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
…mlff/ BLOCKER -- cell 32's "excluded from the verdict" claimed a filter that was removed; cell 34 prints every row regardless, so a drifted job's numbers could appear under the registry it drifted away from, next to that registry's published reference. Do not re-add the filter: keep printing what was measured, but the message now says what happened without claiming exclusion, and registry_cell() marks the row -- the leftmost column shows the sites the job actually relaxed onto, not the nominal registry, in both the DFT-tier's own table (cell 32) and the final comparison table (cell 34). test_relaxation.py's case 0 relied on Ni(100)'s natural surface force, a 17% margin over fmax that would flip with half a percent of drift in standata's lattice constant. All three cases now displace the top atom deliberately (out-of-plane for case 0, in-plane for the other two) and test the constraint contract against a real force, not the data. The stale scripts/verify_fast_tier.py reference (that script lives in the task record, not this repo) is replaced with the SIMULATION notebook that actually covers the interface path, and the layer-grouping tolerance is named instead of a bare 0.5. notebooks_utils/mlff/ was a package whose only content, __init__.py, is byte-identical to main's mlff.py -- collapsed back to the module, the same move this PR already made once for material/. Nit: the bracket-minimum condition's second clause was a tautology (j is the argmin over the branch, so it is trivially <= its neighbors). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
… the drift mark
BLOCKER -- cell 32's drift message called sorted(occupied) directly;
occupied is a set of site-or-None values (cell 7 asserts {None} for
bridge), so a mixed {"atop", None} result -- exactly the drifted case
being reported -- raised TypeError('<' not supported between instances
of NoneType and str) and would crash the DFT-results cell after the
platform jobs had run. Same idiom as registry_cell three lines below:
sorted(str(s) for s in occupied). Checked every other sorted(...) and
set comparison in the notebook for the same hazard -- cell 7's two
uses already stringify first, cell 14/32's sorts key on a numeric
field, none of the rest touch a value that can be None.
SHOULD -- the previous fix replaced the registry label with the sites
reached, so a drifted row lost its nominal label (the paper/MACE
columns stayed keyed on it) and two registries drifting onto the same
sites printed indistinguishable rows. registry_cell now appends
instead: "atop_hcp→atop/fcc" keeps both the submission and the
outcome. REGISTRY_COLUMN_WIDTH=18 (longest label + arrow + widest site
pair, e.g. "atop_hcp→None/atop") keeps both tables' columns aligned.
pr-body-364.md: the four "verdict" mentions predate 7161a20's plain
comparison table and one directly contradicted the Production Result
paragraph below it ("the DFT tier has not yet been run" / "all three
DFT-tier jobs finished"); rewritten to describe the current table, not
a verdict that no longer exists. Size line corrected to the measured
9 files / +1095/-5 for api-examples. Live PR #364 PATCHed to match.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
REGISTRY_COLUMN_WIDTH=18 fit the Ni(111) registries' own site pairs
but not a drift onto a bridge site ("atop_hcp->atop/bridge" is 20
chars, "atop_hcp->None/bridge" 21), which would shift that row's
columns out of alignment with the rest of the table. Both tables now
compute their width from the registry_cell() text of the rows they are
about to print (min "registry", so an all-nominal table stays as
narrow as before); the constant is gone.
pr-body-364.md: size line was +1095, `git diff origin/main...HEAD
--shortstat` now reports +1100 (this fix's own net addition). PATCHed
onto live PR #364.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Every def the notebook carried now either leaves for notebooks_utils (film_sites_and_buckling, buckling_text, registry_cell -- reusable across registry/site-drift reporting, and required so the frozen final-comparison cell can keep calling them unchanged) or is inlined as the sibling SE notebooks already write the same steps (film_at, relax_registry, submitted_copy, submit_job_for, configure). Every code cell now carries a numbered markdown heading before it, continuing the notebook's own numbering and reusing the twisted-MoS2 sibling's DFT section names. No behaviour change: scripts/verify_fast_tier.py prints an identical registry table (checked cell-index-adjusted, against the pre-edit notebook), and the saved workflow configs differ only in the one known non-deterministic unit _id.
get_film_site_occupation only exists in the made worktree (draft PR made#298), not in the released mat3ra-made this repo's own CI installs -- the same constraint 8bc2696 already hit and fixed for get_atom_indices_by_layer. Extracting film_sites_and_buckling broke collection of test_interface.py on CI; inlined it back at its two call sites instead (matching the notebook's own established fallback), and kept buckling_text/registry_cell extracted since neither depends on made at all. Verified test_interface.py imports clean against a scratch venv resolving the released mat3ra-made (no editable override), and verify_fast_tier.py's output is still identical.
…ckling buckling_text/registry_cell were presentation for one table, not a reusable capability -- deleted notebooks_utils/interface.py and its test; both siblings print their tables with plain f-strings. Inlined them, plus num/final_cell in the final comparison cell, as per-row local variables rather than a helper (a straight string-substitution inline would have made that cell's print statements unreadable). film_sites_and_buckling's manual height/atop computation is now made's own get_film_buckling(interface, analyzer=None) (landed in the made worktree next to get_film_site_occupation), called directly in both the fast and precise tiers; no per-file made-version constraint applies here since notebooks aren't pytest-collected. Invariants re-checked: pytest 47 passed, verify_fast_tier.py output identical to eb80485 (cell indices re-mapped), workflow dict unchanged, cell count/headings intact, zero `def` statements confirmed by AST walk.
The SIMULATION notebook loads the base interface by the exact name
BASE_MATERIAL_NAME = "Graphene_Nickel_interface"; the structure notebook
was deriving the same value implicitly from f"{FILM_NAME}_{SUBSTRATE_NAME}
_interface", two separately-set parameters that happen to concatenate to
the right string today but give no reader anywhere to see the two
notebooks agree. Added BASE_MATERIAL_NAME as its own parameter and used
it directly for interface_material.name; the optimized copy's derived
name (f"{interface_material.name}_optimized_xy") is untouched since it
now derives from the same explicit constant.
Verified by deleting uploads/ and running the structure notebook's cells
natively (skipping visualize/download_content_to_file, the way
scripts/run_dft_tier.py does): the save cell writes
uploads/Graphene_Nickel_interface.json, exactly what the SIMULATION
notebook's load cell looks for. scripts/verify_fast_tier.py (index-
remapped for 57 cells) then reproduces the identical registry table.
…s as facades Mirrors made's tools/calculate/ split: notebooks_utils holds helpers that compute locally, distinct from core/api (platform), ipython (display) and pyodide (browser). Old mlff.py/relaxation.py become facades so the three already-shipped notebooks that import them keep working untouched; our own SIMULATION notebook and its test import the new calculate.* paths.
Correction: the top-level module is the public export point, the calculate/ package underneath is an implementation detail. The SE notebook and its test go back to mat3ra.notebooks_utils.mlff / .relaxation, matching the other three shipped notebooks.
…laxation Human decision: mlff is an execution backend (calculator), relaxation is a multi-step scientific procedure (workflow) — distinct abstraction levels, not "local vs platform". Drop the top-level facades: one path per symbol, matching the repo's dominant import pattern (ipython.entity.material.*, core.entity.material.api, api.job). The four notebooks that used the old mlff.py/relaxation.py import the real locations directly; workflow.py (platform job configuration) is untouched.
Empty scaffolding — the tests tree mirrors the source only where a test exists; calculators/ gets its directory back when mlff has a test.
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Gr/Ni(111): registry, separation and work of adhesion — Specific Example
Reproduces the graphene/Ni(111) structure and energetics collected in Dahal & Batzill, Nanoscale 6,
2548 (2014), whose computed values are from Lahiri et al., New J. Phys. 13, 025001 (2011), Table 1:
work of adhesion 0.81 / 0.77 / 0.31 J/m² for the fcc / hcp / hollow registries at 2.16 / 2.17 /
3.26 Å, with the atop carbon buckled away from the surface.
What ships (api-examples):
optimization_interface_film_xy_position_graphene_nickel_SIMULATION.ipynb— loads the interface thestructure notebook saves; derives the four registries of the review's Fig. 1 (one carbon atop, the
other on the fcc / hcp hollow; both on hollows; bridge); relaxes each with MACE-MP (bottom substrate
layers fixed, the paper's scheme) and prints the MACE numbers beside the paper's in a plain
comparison table, no pass/fail verdict — MACE is PBE-grade and the paper rejects GGA-level physics
for this interface; positions move along z only, with the deepest substrate layers fixed, for the
interface and both same-cell references alike — full relaxation for the paper's symmetric
registries by symmetry, and what keeps the bridge's in-plane saddle defined; then submits, at the
paper's functional (LDA/pz ultrasoft, spin-polarized, no dispersion), one fixed-cell relaxation
per selected registry plus the two same-cell references, and reads energy and final structure
back into the same comparison table. A drifted DFT job's row is marked with the sites it actually
reached, appended to its nominal registry label, so its numbers are never read as that registry's
result.
Graphene_Nickel_interface.Introduction.ipynb: the row's Simulation link.mat3ra.made(Surface sites and layer grouping for adsorbed films (SOF-8043) made#298, the surface-net-minimum cut):SurfaceSiteAnalyzer(named atop / bridge / fcc / hcp / hollow sites of any flat surface net),get_closest_site_id_from_coordinate_and_element(point at an atom by element and coordinate),get_film_site_occupation(which site each film atom sits on),get_atom_indices_by_layer(bottom-layer-first atom groups, sliced inline for the frozen substrate layers — no
bottom-layers-specific helper survives), and
interface_label_parts_by_elements(labelssubstrate/film by element on the DFT tier's relaxed, re-fetched structure). The one thing kept in
notebooks_utilsisrelaxation.py—relax_material, ASE relaxation with fixed atoms andz-only motion — because an optimizer does not belong in the structure library, and it takes any
ASE calculator so it is not MLFF-specific either (moved out of
mlff/in review). Energies,interface parts, interlayer distance and area are made functions that already existed. The
registry cell is four statements: an anchor carbon named by coordinate and element, the site each
registry puts it on, the shift, and the occupation check.
Divergences from the paper, stated in the notebook and on the docs page: 4 Ni layers not 5; 20 Å
vacuum not 90; the platform relaxes every atom where the paper held the bottom two layers;
plane-wave pseudopotentials not all-electron LCAO. The graphene reference runs
nspin = 1.Verification: fast tier run natively (D3 active) — fcc 0.17 J/m² @ 1.98 Å, buckling −0.006 Å,
hollow 0.30 J/m² @ 4.08 Å — and in the browser through the local Cypress harness kept in the task
record (both notebooks end to end). The rendered
pw_relaxinput carriescalculation = 'relax',nspin = 2,starting_magnetization(1) = 0.7,smearing = 'mv',degauss = 0.01,mixing_mode = 'local-TF',mixing_beta = 0.2,electron_maxstep = 200, novdw_corr; thegraphene workflow
nspin = 1. Cold smearing + local-TF is what converges this slab on cluster-001(the defaults stop at 100 iterations).
Production result (2026-09-12): the DFT tier has run end to end on the platform — the fetch path
(
get_final_structure_for_job+get_properties_for_job, the platform's property API shape thatequation_of_state.ipynb/relaxation.ipynbalso use) reads energy and final structure back. Thedefault
ComputetimeLimit(01:00:00) timed out the spin-polarized relaxation on queue D with onecore; on
QUEUE_NAME=OF,PPN=40,TIME_LIMIT="04:00:00"all three DFT-tier jobs finished:W_adh 1.01 J/m², d 2.02 Å, buckling +0.013 Å vs the paper's 0.81 J/m² / 2.16 Å / ~0.03 Å.
Fixed since the first review:
relax_materialmoved out ofmlff/to a top-levelrelaxation.py— it takes any ASE calculator and runs ASE's own BFGS, so it is not MLFF-specific,and
workflow.pyis platform QE/k-grid configuration, not local geometry relaxation. Its testmodule built a fixture through
create_interface_zsl_between_slabs: a searched ZSL match is notpinned to one outcome across dependency versions — CI resolved a 25.7%-strained registry that
would not relax within the fixed step budget, the same nondeterminism made's own suite hit and
fixed by dropping the search entirely. The test now exercises
relax_material's constraintcontract (fixed atoms,
along_z_only, non-convergence) on a plaincreate_slab(Nickel, (1,0,0)),with a deliberate perturbation for every case instead of a marginal natural surface force, verified
against the actually-released
mat3ra-madein a scratch venv, not only the made#298 dev worktree.core/entity/material/interface.pyis gone too —label_interface_partsmoved to made(
interface_label_parts_by_elements, mat3ra/made#298) and the notebook's DFT-tier cell imports itfrom
mat3ra.made.tools.modifydirectly, next tointerface_get_part/interface_displace_partalready imported from there (a drifted row's mark — see "What ships" above).
run-py-testsgreenon 3.10/3.11/3.12. The printed numbers (both tiers) match the approved tolerance — separation
+/- 0.05 A, buckling sign-correct and within a factor of 2 — and the DFT-results cell (55 lines)
splits at the readers/usage seam to match the sibling notebooks' cell-length convention.
Needs
mat3ra-made>=2026.9.15.post0(mat3ra/made#298, merged to main at72119c9d, tag2026.9.15-0) — released 2026-09-15, verified on PyPI with all six new names present.mat3ra-madestays unpinned: a git pin would break this package's own PyPI publish. Unit testsalready run against the released made; only the notebook needs the new version.
Docs: mat3ra/documentation#400. Task record: SOF-8043.
Size: +1513 over 21 files in 2 repos (api-examples +1323/−12 over 16, documentation
+203/−1 over 5, unchanged) against the plan's 3 repos · 8 files · ~+1100.