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SOF-8067: convex hull takes total energies from jobs on a chosen k-grid; fix the Material ID column [AI-written] - #379
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… from its job on SCF_KGRID when set, and the results table reads Material ID from the phase-diagram entry: `precision.value` is not a k-grid measure (monoclinic HfO2 carries a Gamma-only energy at precision 2000 and a 4x4x4 one at 768), so selecting by highest precision mixed grids; `find_job_for_material_with_property(..., kgrid=SCF_KGRID)` picks the job whose pw_scf unit ran on that grid, searched over every account material with the same exabyteId because the job may sit on a saved copy ("final structure") rather than the material found, and its total_energy is read with `properties.get_for_job`, while SCF_KGRID = None keeps the highest-precision rule; `get_results_table` indexed `entries_data` by position in `phase_diagram.all_entries`, which pymatgen sorts by reduced composition, so IDs were shifted against formulas (HfO2 showed the ZrO2 id, ZrO2 the O2 id); each entry already carries its `material_id` as `entry_id`.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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Included review availability: This review used your included allowance. Your plan provides up to 1 included review per hour; 0 remain after this review. 📝 WalkthroughWalkthroughThe convex hull notebook can optionally retrieve total energy from a matching job when an SCF k-grid is configured. Analysis helpers now read material IDs from phase-diagram entries and provide chemical-potential tables for stable-compound stability-region corners. ChangesConvex Hull Analysis
Priority: ⬇️ Low Estimated code review effort: 3 (Moderate) | ~20 minutes Change: Feature Suggested reviewers: Merge Risk: 🟡 Moderate · up to With SCF_KGRID enabled, a matching job from another property group can produce an inconsistent convex hull. Restore the configured group constraint before merging. Security Architecture ReviewSecurity architecture risk: 🔵 Low · up to The new lookup retains the chosen account’s ownership filters and reads existing job data. No authorization bypass or additional privileges were established, but server-side access enforcement could not be verified from this repository. Retained concerns Security review detailsSecurity Blast Radius
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Review comments at
@other/materials_designer/workflows/analyze_convex_hull.ipynb:
- Line 275: Update the job lookup in the materials_with_exabyte_id flow so jobs
are accepted only when they match the configured GROUP, including when SCF_KGRID
is set; do not rely on find_job_for_material_with_property alone to enforce this
filter.
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other/materials_designer/workflows/analyze_convex_hull.ipynbsrc/py/mat3ra/notebooks_utils/core/entity/property/analysis.py
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| " property_holder = properties_by_exabyte_id.get(exabyte_id)\n", | ||
| " if SCF_KGRID:\n", | ||
| " materials_with_exabyte_id = client.materials.list({\"exabyteId\": exabyte_id, \"owner._id\": ACCOUNT_ID})\n", | ||
| " jobs = (find_job_for_material_with_property(client, candidate[\"_id\"], \"total_energy\", ACCOUNT_ID, kgrid=SCF_KGRID) for candidate in materials_with_exabyte_id)\n", |
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🎯 Functional Correctness | 🟠 Major | 🏗️ Heavy lift
Preserve the configured GROUP filter in the job lookup.
When SCF_KGRID is set, this lookup can select any matching-grid total_energy job. The helper in src/py/mat3ra/notebooks_utils/core/entity/job/api.py, Lines 189–219, does not filter by GROUP, unlike the existing property query at Line 251. If the account has a matching-grid job from another functional or application, the notebook uses its energy in the hull. Apply the configured GROUP constraint before accepting a job.
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only still-valid issues, skip the rest with a brief reason, keep changes
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Review comment at @other/materials_designer/workflows/analyze_convex_hull.ipynb
at line 275:
Update the job lookup in the materials_with_exabyte_id flow so jobs are accepted
only when they match the configured GROUP, including when SCF_KGRID is set; do
not rely on find_job_for_material_with_property alone to enforce this filter.
After applying the fix, consider running `coderabbit review --agent` for local
review. Visit https://docs.coderabbit.ai/cli?utm_source=ghpr
…e defect formation energy notebooks take `get_chemical_potentials_table` lists, for every stable compound, the corners of its stability region as pymatgen's `get_all_chempots` returns them (named by the phases in equilibrium there, e.g. "ZrO2-O2-HfO2"), with each element's chemical potential minus its elemental reference energy per atom: Δμ ≤ 0 in eV, the flat dict `CHEMICAL_POTENTIALS` takes in the defect formation energy notebooks. Until now these were worked out by hand from the formation energies. The notebook shows the table as section 6.2 after the results table. The test checks the five corners of the Hf-Zr-O fixture against values computed by hand, and that Σ nᵢΔμᵢ equals the compound's formation energy per formula unit on every row. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
… the identity check that held by construction `stable_entries` is a set, so the compounds came out in a different order per session; they are now sorted by formula. The Σ nᵢΔμᵢ = ΔH_f assertion added in 8f26dbc could not fail on its own — the expected Δμ satisfy it by construction — so the test keeps only the comparison with the hand-computed corners. The notebook says the Δμ apply in the defect notebook only when its elemental references are the same calculations as the hull's. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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analyze_convex_hull.ipynbpicked each material's total energy by highestprecision. On production, monoclinic HfO₂ carries a Γ-only energy at precision 2000 next to a 4×4×4 one at 768, so the hull used the Γ-only value and ΔH_f(HfO₂) came out 0.4 eV/f.u. too high — the same reference trap #378 fixed in the defect notebooks.SCF_KGRID = Noneparameter: when set, the energy comes from the Total Energy job whosepw_scfk-grid equals it (looked up across every copy of the material in the account);Nonekeeps the old highest-precision rule.get_results_tableread ids by list position after pymatgen re-sorted the entries. It now reads the id stored on each entry.+13/−6, notebook +11/−3 and
property/analysis.py+2/−3; cell count unchanged. Offline stub:[4,4,4]picks the 768 job even when it sits on a copy of the material;Noneunchanged; ids align.🤖 Generated with Claude Code
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