scripts/README.md

Pipeline

Run in order, each with the work directory as the first argument (build_fixed.py WORK OUT). Paths to the upstream HF snapshot and the MP S3 manifests are hard-coded at the top of the scripts. mpclient.py reads MP_API_KEY from a .env file.

1. load_meta.py: per-row metadata from upstream compatible_pbe.
2. join.py: joins in the MLIP energies of LeMat-Bulk-MLIP-Hull-All.
3. dl_collections.py: the MP thermo GGA_GGA+U collection. Its unsorted core pull is superseded by step 4.
4. dl_core.py: MP material docs for the LeMat MP ids.
5. dl_tasks.py: task metadata for every GGA/GGA+U static and relaxation.
6. dl_aliases.py: LeMat ids MP has merged into other materials, mapped to their parent material.
7. identify.py: the upstream source task per row, MP's current task, and the provenance group.
8. s3_extract.py: candidate tasks' full outputs from s3://materialsproject-parsed.
9. review_rows.py: full upstream rows under review.
10. decide.py: geometry matching and the replace/keep rules.
11. label_geo.py: StructureMatcher labels for whole-structure replacements.
12. check_contacts.py: shortest-bond sanity check on every replacement.
13. s3_steps.py: last-ionic-step forces/stress for replacement tasks whose output fields are empty. Reads need_steps.txt, the new task ids of replaced rows with empty forces.
14. build_fixed.py: writes the shards and audit/changes.parquet. It also fills upstream-empty forces/stress from scripts/recover_mp_forces.py's cache/mp_forces_recovery/runs/full/results.parquet. Removals come only from removal_causes.py, each with its evidence, plus MP-deprecated materials with measured non-standard-POTCAR offsets.

The evidence for the calculation defects comes from two scripts:

• traj_find.py: Alexandria relaxation trajectories from LeMaterial/LeMat-Traj.
• siblings.py: identical-structure duplicates across MP, Alexandria and OQMD.

Alexandria's Bader charges come from its OPTIMADE API, and the MP task documents from S3.