Add NEB schemas#1123
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esoteric-ephemera merged 43 commits intomaterialsproject:mainfrom Jun 27, 2025
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* draft neb task doc and enums * precommit * fix dir_name path/str * precommit * more path / str conversion * add datetime info * minor fixes for optional types and potcar spec handling in neb docs * lint * fix mypy * more mypy * lint * add test for NebTaskDoc * lint * expand NebTaskDoc tests to from_directory * lint * add further directory parsing features to NebTaskDoc + tests * lint * mypy fixes * slight fmt logical * add paths_summary function function that matches unique_hops in migrationgraph to NEB results docs * add classmethod augment_from_mgd_and_npr classmethod to instantiate MigrationGraphDoc using an existing one and augment its fields using calculations data from NebPathwayResult * draft neb task doc and enums * precommit * fix dir_name path/str * precommit * more path / str conversion * add datetime info * minor fixes for optional types and potcar spec handling in neb docs * lint * fix mypy * more mypy * lint * add test for NebTaskDoc * lint * expand NebTaskDoc tests to from_directory * lint * add further directory parsing features to NebTaskDoc + tests * lint * mypy fixes * slight fmt logical * move neb base schemas from atomate2 to emmet-core, change class inheritence * precommit * fix NPR import and temporary fix to ignore metadata * add cathing valueerror in matching * draft neb task doc and enums * precommit * fix dir_name path/str * precommit * more path / str conversion * add datetime info * minor fixes for optional types and potcar spec handling in neb docs * lint * fix mypy * more mypy * lint * add test for NebTaskDoc * lint * expand NebTaskDoc tests to from_directory * lint * add further directory parsing features to NebTaskDoc + tests * lint * mypy fixes * slight fmt logical * move neb base schemas from atomate2 to emmet-core, change class inheritence * precommit * add top-level failure_reasons field and tags for workflow meta * add energy ranges to pathway result * add barrier_type flag add flag in get_paths_summary to specify what kind of barrier is used for cost * avoid original mg contamination * Add identifiers to NEB docs * fix neb doc tests after rewrite * precommit * add gen_sc_scheme method and flag provide option to either generate sc fields with "hops_only" or "complete" (default). old version is what's not considered "complete" * typo * resolve mypy issues in doc schema * add host structure / active site meta to NebPathwayDoc * ensure those new top-levels are uh optional * change gen_sc_schema default * add zero_short_hop_cost option and function * formatting * add successful image index to improve barrier estimates * precommit * max_barrier method update use NPR's native max_barriers field * update test * add tests match mgdoc and npr add tests and test files for get_paths_summary_with_neb_res() and augment_from_mgd_and_npr() --------- Co-authored-by: esoteric-ephemera <aaron.kaplan.physics@gmail.com>
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Thanks @esoteric-ephemera! I think it's ok to merge and put out a release candidate if needed. |
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Adding support for parsing NEB calculations and eventually ApproxNEB calculations. These are still VASP calculations, but have a directory structure which is not parseable by TaskDoc (at least meaningfully). The structure is:
./{INCAR, KPOINTS, POTCAR}
./00/POSCAR
./01/{vasprun.xml, OSZICAR, OUTCAR, CHGCAR, ... }
./02/{vasprun.xml, OSZICAR, OUTCAR, CHGCAR, ... }
...
./0N/POSCAR
Approx / NEB calculations are needed for battery cathode and alloy diffusivity calculations. These schemas will be needed for atomate2 workflows. Once Approx / NEB flows are added to atomate2, we should have full parity with atomate. This will also make it easier to host data from these calculations
Supports parsing NEB calculations (only relaxes images) and NEB + endpoints (three total calculations, two relaxes + one NEB)
Possibly worth adding run / task / calc types? Since this requires a separate doc model, maybe we should avoid this?