feat: HOMO/LUMO NB - #351
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📝 WalkthroughWalkthroughAdds defect formation energy, interfacial energy, and HOMO–LUMO/frequency notebooks; introduces shared bulk-material, total-energy, and SCF k-grid utilities; updates surface-energy integration, notebook outputs, documentation links, and link checking. ChangesMaterials Designer workflow expansion
Estimated code review effort: 5 (Critical) | ~120 minutes Sequence Diagram(s)sequenceDiagram
participant Notebook
participant MaterialsAPI
participant WorkflowAPI
participant JobAPI
participant PropertiesAPI
Notebook->>MaterialsAPI: prepare materials and references
Notebook->>WorkflowAPI: configure workflow
Notebook->>JobAPI: create and submit calculation
JobAPI-->>Notebook: completed job
Notebook->>PropertiesAPI: retrieve calculated properties
PropertiesAPI-->>Notebook: visualization data
Possibly related PRs
Suggested reviewers: 🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
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Actionable comments posted: 5
🧹 Nitpick comments (1)
other/materials_designer/workflows/defect_formation_energy.ipynb (1)
458-465: 📐 Maintainability & Code Quality | 🔵 Trivial | ⚡ Quick winReuse
apply_scf_kgridinstead of reimplementing the k-grid patch.This block duplicates the shared
apply_scf_kgridhelper that the surface and interfacial notebooks already call. Reusing it keeps behavior consistent (e.g., thefirst_onlyoption and unit-name handling) and avoids drift.♻️ Suggested change
-# K-grid for the defective-cell SCF. -if SCF_KGRID is not None: - new_context = PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).get_context_item_data() - for subworkflow in defect_workflow.subworkflows: - unit = subworkflow.get_unit_by_name(name="pw_scf") - if unit: - unit.add_context(new_context) - subworkflow.set_unit(unit) +# K-grid for the defective-cell SCF. +defect_workflow = apply_scf_kgrid(defect_workflow, scf_kgrid=SCF_KGRID)This also lets you drop the
PointsGridDataProviderimport and addapply_scf_kgridto the imports in this cell.🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@other/materials_designer/workflows/defect_formation_energy.ipynb` around lines 458 - 465, Replace the inline SCF k-grid patching block with the shared apply_scf_kgrid helper, preserving the defective workflow and SCF_KGRID inputs. Update the cell imports to add apply_scf_kgrid and remove the now-unused PointsGridDataProvider import.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@other/materials_designer/workflows/defect_formation_energy.ipynb`:
- Around line 366-369: Update the RuntimeError message in the defect formation
energy workflow to remove the non-interpolated `{element}` placeholder and
reword the guidance generically for the missing elemental materials, while
preserving the existing missing-material details.
In `@other/materials_designer/workflows/homo_lumo_frequency.ipynb`:
- Around line 514-530: Guard the HOMO/LUMO gap calculation in the
CALCULATE_HOMO_LUMO block after fetching homo_data and lumo_data, checking that
both results are non-empty before indexing their first values. When either
result is empty, emit a clear message and skip the subtraction and formatted gap
output; preserve visualization for any returned data.
- Around line 296-312: Validate the standata lookups and required structure
before composing the workflow in the notebook: ensure the selected base entry
exists and contains the expected HOMO/LUMO configuration, and when both
CALCULATE_HOMO_LUMO and CALCULATE_FREQUENCY are enabled, ensure frequency.json
exists with a valid subworkflows[0] entry. Use specific lookup behavior and
raise clear, actionable errors for missing or malformed entries instead of
allowing KeyError/IndexError or silently omitting frequency calculations;
preserve the existing workflow composition for valid data.
In `@README.md`:
- Line 163: Synchronize the Materials Project API-key guidance by updating the
legacy URL references in README.ipynb and the settings configuration near the
API-key definition to the next-gen Materials Project URL used in README.md. Keep
the guidance consistent across all three locations unless a documented
compatibility reason requires retaining the legacy URL.
In `@src/py/mat3ra/notebooks_utils/core/entity/property/api.py`:
- Around line 96-102: Update find_total_energy_for_material so
source="my_account" filters by the resolved owner account used to create or
resolve the material, rather than always using client.my_account.id. Thread that
account through its callers, including organization accounts selected via
ACCOUNT_ID, while preserving curator ownership handling when the documented
my_account source includes curators.
---
Nitpick comments:
In `@other/materials_designer/workflows/defect_formation_energy.ipynb`:
- Around line 458-465: Replace the inline SCF k-grid patching block with the
shared apply_scf_kgrid helper, preserving the defective workflow and SCF_KGRID
inputs. Update the cell imports to add apply_scf_kgrid and remove the now-unused
PointsGridDataProvider import.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: defaults
Review profile: CHILL
Plan: Pro Plus
Run ID: 5626a0b9-5a13-49d9-903f-cfdec2fad19d
📒 Files selected for processing (16)
.github/workflows/check_links.ymlREADME.mdexamples/assets/README.mdother/materials_designer/workflows/Introduction.ipynbother/materials_designer/workflows/defect_formation_energy.ipynbother/materials_designer/workflows/dielectric_tensor.ipynbother/materials_designer/workflows/homo_lumo_frequency.ipynbother/materials_designer/workflows/interfacial_energy.ipynbother/materials_designer/workflows/phonon_dos_dispersion.ipynbother/materials_designer/workflows/surface_energy.ipynbsrc/py/mat3ra/notebooks_utils/core/entity/material/analysis.pysrc/py/mat3ra/notebooks_utils/core/entity/material/api.pysrc/py/mat3ra/notebooks_utils/core/entity/property/api.pysrc/py/mat3ra/notebooks_utils/workflow.pytests/py/unit/core/entity/test_material_analysis.pytests/py/unit/test_workflow_utils.py
| " raise RuntimeError(\n", | ||
| " f\"Missing elemental reference material(s) for {missing}. \"\n", | ||
| " \"Add elemental material(s) from Standata, or add tag 'elemental' with metadata.element = {element}\"\n", | ||
| " )\n", |
There was a problem hiding this comment.
🎯 Functional Correctness | 🟡 Minor | ⚡ Quick win
{element} won't interpolate in this error message.
Only the first concatenated string is an f-string; the second is a plain literal, so {element} is printed verbatim (and element isn't in scope here anyway). Reword to avoid the misleading placeholder.
🐛 Suggested fix
raise RuntimeError(
f"Missing elemental reference material(s) for {missing}. "
- "Add elemental material(s) from Standata, or add tag 'elemental' with metadata.element = {element}"
+ "Add the elemental material(s) from Standata, or tag existing ones 'elemental' "
+ "with a matching metadata.element."
)📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| " raise RuntimeError(\n", | |
| " f\"Missing elemental reference material(s) for {missing}. \"\n", | |
| " \"Add elemental material(s) from Standata, or add tag 'elemental' with metadata.element = {element}\"\n", | |
| " )\n", | |
| " raise RuntimeError(\n", | |
| " f\"Missing elemental reference material(s) for {missing}. \"\n", | |
| " \"Add the elemental material(s) from Standata, or tag existing ones 'elemental' \"\n", | |
| " \"with a matching metadata.element.\"\n", | |
| " )\n", |
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@other/materials_designer/workflows/defect_formation_energy.ipynb` around
lines 366 - 369, Update the RuntimeError message in the defect formation energy
workflow to remove the non-interpolated `{element}` placeholder and reword the
guidance generically for the missing elemental materials, while preserving the
existing missing-material details.
| "from mat3ra.standata.workflows import WorkflowStandata\n", | ||
| "from mat3ra.wode import Workflow, Subworkflow\n", | ||
| "from mat3ra.notebooks_utils.ipython.entity.workflow.visualize import visualize_workflow\n", | ||
| "\n", | ||
| "nwchem_workflows = WorkflowStandata.filter_by_application(app.name)\n", | ||
| "\n", | ||
| "base_search_term = \"total_energy.json\" if CALCULATE_HOMO_LUMO else \"frequency.json\"\n", | ||
| "workflow = Workflow.create(nwchem_workflows.get_by_name_first_match(base_search_term))\n", | ||
| "\n", | ||
| "if CALCULATE_HOMO_LUMO and CALCULATE_FREQUENCY:\n", | ||
| " frequency_config = nwchem_workflows.get_by_name_first_match(\"frequency.json\")\n", | ||
| " workflow.add_subworkflow(Subworkflow(**frequency_config[\"subworkflows\"][0]))\n", | ||
| "\n", | ||
| "workflow.name = MY_WORKFLOW_NAME\n", | ||
| "\n", | ||
| "visualize_workflow(workflow)\n" | ||
| ] |
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🗄️ Data Integrity & Integration | 🟡 Minor | ⚡ Quick win
🧩 Analysis chain
🏁 Script executed:
#!/bin/bash
# Locate the NWChem workflow standata to confirm structure/property outputs
fd -e json total_energy frequency -x cat -n {}Repository: mat3ra/api-examples
Length of output: 254
🏁 Script executed:
#!/bin/bash
set -u
echo "== files matching homo/freq/workflow names =="
git ls-files | rg -n 'homo_lumo|frequency|total_energy|standata|workflow' || true
echo
echo "== target cell context =="
sed -n '260,330p' other/materials_designer/workflows/homo_lumo_frequency.ipynb 2>/dev/null || true
echo
echo "== find JSON files with total_energy or frequency =="
git ls-files | rg -n '(^|/)(total_energy|frequency)\.json$|standata|workflows' || trueRepository: mat3ra/api-examples
Length of output: 6136
Guard the standata workflow composition assumptions.
WorkflowStandata JSON entries are external to this repo, so this notebook assumes total_energy.json has the HOMO/LUMO properties/values and frequency.json["subworkflows"][0] exists. Add fail-safes or explicit checks and use more specific lookup behavior, otherwise the workflow can fail with a confusing KeyError/IndexError or silently skip the requested frequencies.
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@other/materials_designer/workflows/homo_lumo_frequency.ipynb` around lines
296 - 312, Validate the standata lookups and required structure before composing
the workflow in the notebook: ensure the selected base entry exists and contains
the expected HOMO/LUMO configuration, and when both CALCULATE_HOMO_LUMO and
CALCULATE_FREQUENCY are enabled, ensure frequency.json exists with a valid
subworkflows[0] entry. Use specific lookup behavior and raise clear, actionable
errors for missing or malformed entries instead of allowing KeyError/IndexError
or silently omitting frequency calculations; preserve the existing workflow
composition for valid data.
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "40", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from mat3ra.notebooks_utils.ipython.entity.property.visualize import visualize_properties\n", | ||
| "\n", | ||
| "if CALCULATE_HOMO_LUMO:\n", | ||
| " homo_data = client.properties.get_for_job(job_id, property_name=\"homo_energy\")\n", | ||
| " lumo_data = client.properties.get_for_job(job_id, property_name=\"lumo_energy\")\n", | ||
| " visualize_properties(homo_data, title=\"HOMO Energy\")\n", | ||
| " visualize_properties(lumo_data, title=\"LUMO Energy\")\n", | ||
| " homo_lumo_gap = lumo_data[0][\"value\"] - homo_data[0][\"value\"]\n", | ||
| " print(f\"HOMO-LUMO gap: {homo_lumo_gap:.4f} eV\")\n" | ||
| ] |
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🩺 Stability & Availability | 🟡 Minor | ⚡ Quick win
Guard against empty HOMO/LUMO property results before indexing.
homo_data[0]["value"] / lumo_data[0]["value"] will raise an unguarded IndexError if get_for_job returns an empty list (e.g., the property wasn't produced for this job). Since this runs unconditionally right after fetching the data, a partial failure here crashes the notebook with a low-signal traceback instead of a clear message.
🛡️ Proposed fix
if CALCULATE_HOMO_LUMO:
homo_data = client.properties.get_for_job(job_id, property_name="homo_energy")
lumo_data = client.properties.get_for_job(job_id, property_name="lumo_energy")
visualize_properties(homo_data, title="HOMO Energy")
visualize_properties(lumo_data, title="LUMO Energy")
- homo_lumo_gap = lumo_data[0]["value"] - homo_data[0]["value"]
- print(f"HOMO-LUMO gap: {homo_lumo_gap:.4f} eV")
+ if homo_data and lumo_data:
+ homo_lumo_gap = lumo_data[0]["value"] - homo_data[0]["value"]
+ print(f"HOMO-LUMO gap: {homo_lumo_gap:.4f} eV")
+ else:
+ print("⚠️ HOMO/LUMO data not available for this job")📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "id": "40", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "from mat3ra.notebooks_utils.ipython.entity.property.visualize import visualize_properties\n", | |
| "\n", | |
| "if CALCULATE_HOMO_LUMO:\n", | |
| " homo_data = client.properties.get_for_job(job_id, property_name=\"homo_energy\")\n", | |
| " lumo_data = client.properties.get_for_job(job_id, property_name=\"lumo_energy\")\n", | |
| " visualize_properties(homo_data, title=\"HOMO Energy\")\n", | |
| " visualize_properties(lumo_data, title=\"LUMO Energy\")\n", | |
| " homo_lumo_gap = lumo_data[0][\"value\"] - homo_data[0][\"value\"]\n", | |
| " print(f\"HOMO-LUMO gap: {homo_lumo_gap:.4f} eV\")\n" | |
| ] | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "id": "40", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "from mat3ra.notebooks_utils.ipython.entity.property.visualize import visualize_properties\n", | |
| "\n", | |
| "if CALCULATE_HOMO_LUMO:\n", | |
| " homo_data = client.properties.get_for_job(job_id, property_name=\"homo_energy\")\n", | |
| " lumo_data = client.properties.get_for_job(job_id, property_name=\"lumo_energy\")\n", | |
| " visualize_properties(homo_data, title=\"HOMO Energy\")\n", | |
| " visualize_properties(lumo_data, title=\"LUMO Energy\")\n", | |
| " if homo_data and lumo_data:\n", | |
| " homo_lumo_gap = lumo_data[0][\"value\"] - homo_data[0][\"value\"]\n", | |
| " print(f\"HOMO-LUMO gap: {homo_lumo_gap:.4f} eV\")\n", | |
| " else:\n", | |
| " print(\"⚠️ HOMO/LUMO data not available for this job\")\n" | |
| ] |
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@other/materials_designer/workflows/homo_lumo_frequency.ipynb` around lines
514 - 530, Guard the HOMO/LUMO gap calculation in the CALCULATE_HOMO_LUMO block
after fetching homo_data and lumo_data, checking that both results are non-empty
before indexing their first values. When either result is empty, emit a clear
message and skip the subtraction and formatted gap output; preserve
visualization for any returned data.
| 3. Optionally, for local Jupyter without OIDC, set legacy API token values in [settings.json](src/py/mat3ra/notebooks_utils/core/api/settings.json). See [Get Authentication Params](examples/system/get_authentication_params.ipynb) for details. API tokens can also be generated in [Account Preferences](https://docs.mat3ra.com/accounts/ui/preferences/api/) on the platform. | ||
|
|
||
| NOTE: The Materials Project API key should be set in `settings.json` and obtained from [https://legacy.materialsproject.org/open](https://legacy.materialsproject.org/open). | ||
| NOTE: The Materials Project API key should be set in `settings.json` and obtained from [https://next-gen.materialsproject.org/api](https://next-gen.materialsproject.org/api). |
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📐 Maintainability & Code Quality | 🟡 Minor | ⚡ Quick win
Synchronize the remaining Materials Project API-key references.
README.ipynb (Lines 83-91) and src/py/mat3ra/notebooks_utils/core/api/settings.py (Lines 9-18) still point to the legacy URL, so repository guidance is now inconsistent. Update those references or explicitly document why they must remain legacy.
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@README.md` at line 163, Synchronize the Materials Project API-key guidance by
updating the legacy URL references in README.ipynb and the settings
configuration near the API-key definition to the next-gen Materials Project URL
used in README.md. Keep the guidance consistent across all three locations
unless a documented compatibility reason requires retaining the legacy URL.
| query = {"exabyteId": exabyte_id, "slug": "total_energy"} | ||
| if source == "curators": | ||
| query["owner.slug"] = "curators" | ||
| elif source == "my_account": | ||
| query["owner._id"] = client.my_account.id | ||
| elif source != "public": | ||
| raise ValueError(f"Invalid source: {source!r}. Expected 'public', 'curators', or 'my_account'.") |
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🎯 Functional Correctness | 🟠 Major | ⚡ Quick win
🧩 Analysis chain
🏁 Script executed:
#!/bin/bash
# Confirm callers pass ACCOUNT_ID (possibly org) while this fn uses my_account.id
rg -nP --type=py -C2 'find_total_energy_for_material\s*\('
rg -nP --glob '*.ipynb' -C2 'find_total_energy_for_material'
# Inspect the my_account attribute source
rg -nP --type=py -C3 'my_account' src/py/mat3ra/notebooks_utilsRepository: mat3ra/api-examples
Length of output: 157
🏁 Script executed:
#!/bin/bash
set -u
echo "Repo files matching api.py / notebooks_utils:"
git ls-files | grep -E '(^|/)api\.py$|notebooks_utils|\.ipynb$' | sed -n '1,200p'
echo
echo "Find target file:"
fd -ap 'api.py' . | sed -n '1,120p'
echo
echo "Search exact function name all files:"
rg -n -C3 'find_total_energy_for_material' . || true
echo
echo "Search total_energy related:"
rg -n -C2 'total_energy|TotalEnergy|Total Energy|TOTAL' . | sed -n '1,240p' || trueRepository: mat3ra/api-examples
Length of output: 38750
🏁 Script executed:
#!/bin/bash
set -u
echo "Target function:"
sed -n '60,130p' src/py/mat3ra/notebooks_utils/core/entity/property/api.py
echo
echo "Auth/client/account-related definitions and selected account setup:"
rg -n -C3 'selected_account|client =|APIClient|ACCOUNT_ID|ORGANIZATION_NAME|my_account|owner_id' src/py/mat3ra/notebooks_utils core src/py examples other -g '*.py' -g '*.ipynb' | sed -n '1,260p'
echo
echo "Bulk material functions:"
rg -n -C3 'def get_bulk_material|def get_bulk_material_by_crystal' src/py/mat3ra/notebooks_utils
sed -n '1,140p' src/py/mat3ra/notebooks_utils/core/entity/material/api.pyRepository: mat3ra/api-examples
Length of output: 28047
🏁 Script executed:
#!/bin/bash
set -u
python3 - <<'PY'
import json
from pathlib import Path
targets = [
"other/materials_designer/workflows/interfacial_energy.ipynb",
"other/materials_designer/workflows/surface_energy.ipynb",
"other/materials_designer/workflows/defect_formation_energy.ipynb",
"other/materials_designer/workflows/total_energy.ipynb",
]
for path in targets:
p = Path(path)
print(f"\n--- {path} ---")
data = json.loads(p.read_text())
cells = data.get("cells", [])
for i, cell in enumerate(cells):
source = "".join(cell.get("source", []))
if "ACCOUNT_ID" in source or "BULK_TOTAL_ENERGY_SOURCE" in source or "PRISTINE_TOTAL_ENERGY_SOURCE" in source:
print(f"[cell {i}]")
print(source)
PYRepository: mat3ra/api-examples
Length of output: 14219
Route source="my_account" through the resolved account selector.
The notebooks resolve and create materials under ACCOUNT_ID, which can be an organization account when ORGANIZATION_NAME is set, but find_total_energy_for_material(..., source="my_account") queries only client.my_account.id. This makes total-energy lookups fail even though the matching bulk/material was resolved under a different owner, breaking surface, interfacial, and defect formation energy notebooks. Thread the requested owner account into this lookup, including curators when the source documentation says my_account is “curators' or your own”.
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@src/py/mat3ra/notebooks_utils/core/entity/property/api.py` around lines 96 -
102, Update find_total_energy_for_material so source="my_account" filters by the
resolved owner account used to create or resolve the material, rather than
always using client.my_account.id. Thread that account through its callers,
including organization accounts selected via ACCOUNT_ID, while preserving
curator ownership handling when the documented my_account source includes
curators.
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