From ba01dff769eac2bb6204f62acbf21a75513a5b67 Mon Sep 17 00:00:00 2001 From: Aaron Kaplan <33381112+esoteric-ephemera@users.noreply.github.com> Date: Thu, 16 Nov 2023 14:12:06 -0800 Subject: [PATCH] Add new POTCAR validation to VASP validation plus tests (#892) * Fix issue with using dir_name != ./ in emmet.core.tasks.TaskDoc * Revert previous change - actual fix is using path relative to dir_name of TaskDoc.from_directory * Add new POTCAR summary_stats check for validation, two tests for POTCAR checking/IDing * Adding builder side of commit and test files * Remove MP_POTCAR_ID.json.gz test file * Fix handling of missing POTCAR lib in tests * cleanup tests * Hopefully fix weird behavior in failing matcalc tests --------- Co-authored-by: esoteric-ephemera --- .../emmet/builders/vasp/task_validator.py | 2 +- emmet-core/emmet/core/tasks.py | 2 +- emmet-core/emmet/core/vasp/validation.py | 47 +++++++++++----- emmet-core/tests/test_calculation.py | 27 +++++++++ emmet-core/tests/test_ml.py | 2 +- emmet-core/tests/vasp/test_vasp.py | 56 ++++++++++++++++++- test_files/CoF_TaskDoc.json | 1 + 7 files changed, 119 insertions(+), 18 deletions(-) create mode 100644 test_files/CoF_TaskDoc.json diff --git a/emmet-builders/emmet/builders/vasp/task_validator.py b/emmet-builders/emmet/builders/vasp/task_validator.py index 6329918136..a2dc6bc5e0 100644 --- a/emmet-builders/emmet/builders/vasp/task_validator.py +++ b/emmet-builders/emmet/builders/vasp/task_validator.py @@ -52,7 +52,7 @@ def __init__( potcar = PotcarSingle.from_symbol_and_functional( symbol=potcar_symbol, functional=functional ) - hashes[calc_type][potcar_symbol] = potcar.md5_header_hash + hashes[calc_type][potcar_symbol] = potcar._summary_stats self.potcar_hashes = potcar_hashes else: diff --git a/emmet-core/emmet/core/tasks.py b/emmet-core/emmet/core/tasks.py index d55d24f6e5..4f47c23c4b 100644 --- a/emmet-core/emmet/core/tasks.py +++ b/emmet-core/emmet/core/tasks.py @@ -224,7 +224,7 @@ class CustodianDoc(BaseModel): ) job: Optional[Any] = Field( None, - title="Cusotodian Job Data", + title="Custodian Job Data", description="Job data logged by custodian.", ) diff --git a/emmet-core/emmet/core/vasp/validation.py b/emmet-core/emmet/core/vasp/validation.py index 1d278f22b2..28c8648637 100644 --- a/emmet-core/emmet/core/vasp/validation.py +++ b/emmet-core/emmet/core/vasp/validation.py @@ -111,7 +111,7 @@ def from_task_doc( valid_input_set = None if valid_input_set: - # Checking POTCAR hashes if a directory is supplied + # Checking POTCAR summary_stats if a directory is supplied if potcar_hashes: if _potcar_hash_check(task_doc, potcar_hashes): if task_type in [ @@ -313,28 +313,47 @@ def _kspacing_warnings(input_set, inputs, data, warnings, kspacing_tolerance): def _potcar_hash_check(task_doc, potcar_hashes): """ - Checks to make sure the POTCAR hash is equal to the correct value from the - pymatgen input set. + Checks to make sure the POTCAR summary stats is equal to the correct + value from the pymatgen input set. """ + data_tol = 1.0e-6 try: potcar_details = task_doc.calcs_reversed[0]["input"]["potcar_spec"] - all_match = True + except KeyError: + # Assume it is an old calculation without potcar_spec data and treat it as passing POTCAR hash check + return False - for entry in potcar_details: - symbol = entry["titel"].split(" ")[1] - hash = potcar_hashes[str(task_doc.calc_type)].get(symbol, None) + all_match = True + for entry in potcar_details: + symbol = entry["titel"].split(" ")[1] + ref_summ_stats = potcar_hashes[str(task_doc.calc_type)].get(symbol, None) + if not ref_summ_stats: + all_match = False + break + + key_match = all( + set(ref_summ_stats["keywords"][key]) + == set(entry["summary_stats"]["keywords"][key]) + for key in ["header", "data"] + ) - if not hash or hash != entry["hash"]: - all_match = False - break + data_match = all( + abs( + ref_summ_stats["stats"][key][stat] + - entry["summary_stats"]["stats"][key][stat] + ) + < data_tol + for stat in ["MEAN", "ABSMEAN", "VAR", "MIN", "MAX"] + for key in ["header", "data"] + ) - return not all_match + if (not key_match) or (not data_match): + all_match = False + break - except KeyError: - # Assume it is an old calculation without potcar_spec data and treat it as passing POTCAR hash check - return False + return not all_match def _magmom_check(task_doc, chemsys): diff --git a/emmet-core/tests/test_calculation.py b/emmet-core/tests/test_calculation.py index 892ad3a5b2..30e49d0a17 100644 --- a/emmet-core/tests/test_calculation.py +++ b/emmet-core/tests/test_calculation.py @@ -161,3 +161,30 @@ def test_calculation(test_dir, object_name, task_name): # and decoded MontyDecoder().process_decoded(d) + + +def test_PotcarSpec(test_dir): + from emmet.core.vasp.calculation import PotcarSpec + from pymatgen.io.vasp import PotcarSingle, Potcar + + try: + # First test, PotcarSingle object + potcar = PotcarSingle.from_symbol_and_functional(symbol="Si", functional="PBE") + ps_spec = PotcarSpec.from_potcar_single(potcar_single=potcar) + + assert ps_spec.titel == potcar.symbol + assert ps_spec.hash == potcar.md5_header_hash + assert ps_spec.summary_stats == potcar._summary_stats + + # Second test, Potcar object containing mulitple PotcarSingle obejcts + potcars = Potcar(symbols=["Ga_d", "As"], functional="PBE") + ps_spec = PotcarSpec.from_potcar(potcar=potcars) + + for ips, ps in enumerate(ps_spec): + assert ps.titel == potcars[ips].symbol + assert ps.hash == potcars[ips].md5_header_hash + assert ps.summary_stats == potcars[ips]._summary_stats + + except (OSError, ValueError): + # missing Pymatgen POTCARs, cannot perform test + assert True diff --git a/emmet-core/tests/test_ml.py b/emmet-core/tests/test_ml.py index 28ac75c160..ce2d1ade20 100644 --- a/emmet-core/tests/test_ml.py +++ b/emmet-core/tests/test_ml.py @@ -52,7 +52,7 @@ ("calculator", "prop_kwargs"), [ (get_universal_calculator("chgnet"), None), - ("m3gnet", {"ElasticityCalc": {"relax_structure": False}}), + ("M3GNet-MP-2021.2.8-PES", {"ElasticityCalc": {"relax_structure": False}}), ], ) def test_ml_doc(calculator: Union[str, "Calculator"], prop_kwargs: dict) -> None: diff --git a/emmet-core/tests/vasp/test_vasp.py b/emmet-core/tests/vasp/test_vasp.py index c1d3cc69d5..60527745c2 100644 --- a/emmet-core/tests/vasp/test_vasp.py +++ b/emmet-core/tests/vasp/test_vasp.py @@ -5,7 +5,7 @@ from emmet.core.vasp.calc_types import RunType, TaskType, run_type, task_type from emmet.core.vasp.task_valid import TaskDocument -from emmet.core.vasp.validation import ValidationDoc +from emmet.core.vasp.validation import ValidationDoc, _potcar_hash_check def test_task_type(): @@ -85,3 +85,57 @@ def test_ldau_validation(test_dir): valid = ValidationDoc.from_task_doc(task) assert valid.valid + + +def test_potcar_hash_check(test_dir): + from pymatgen.io.vasp import PotcarSingle + + with zopen(test_dir / "CoF_TaskDoc.json") as f: + data = json.load(f) + + """ + NB: seems like TaskDoc is not fully compatible with TaskDocument + excluding all keys but `last_updated` ensures TaskDocument can be built + + Similarly, after a TaskDoc is dumped to a file, using + json.dump( + jsanitize( + < Task Doc >.model_dump() + ), + < filename > ) + I cannot rebuild the TaskDoc without excluding the `orig_inputs` key. + """ + task_doc = TaskDocument(**{key: data[key] for key in data if key != "last_updated"}) + + # First check: generate hashes from POTCARs in TaskDoc, check should pass + calc_type = str(task_doc.calc_type) + expected_hashes = {calc_type: {}} + try: + for spec in task_doc.calcs_reversed[0]["input"]["potcar_spec"]: + symbol = spec["titel"].split(" ")[1] + expected_hashes[calc_type][ + symbol + ] = PotcarSingle.from_symbol_and_functional( + symbol=symbol, functional="PBE" + )._summary_stats + + assert not _potcar_hash_check(task_doc, expected_hashes) + + # Second check: remove POTCAR from expected_hashes, check should fail + + missing_hashes = {calc_type: {**expected_hashes[calc_type]}} + first_element = list(missing_hashes[calc_type])[0] + missing_hashes[calc_type].pop(first_element) + assert _potcar_hash_check(task_doc, missing_hashes) + + # Third check: change data in expected hashes, check should fail + + wrong_hashes = {calc_type: {**expected_hashes[calc_type]}} + for key in wrong_hashes[calc_type][first_element]["stats"]["data"]: + wrong_hashes[calc_type][first_element]["stats"]["data"][key] *= 1.1 + + assert _potcar_hash_check(task_doc, wrong_hashes) + + except (OSError, ValueError): + # missing Pymatgen POTCARs, cannot perform test + assert True diff --git a/test_files/CoF_TaskDoc.json b/test_files/CoF_TaskDoc.json new file mode 100644 index 0000000000..15f7272b0a --- /dev/null +++ b/test_files/CoF_TaskDoc.json @@ -0,0 +1 @@ +{"builder_meta": {"emmet_version": "0.1.dev4174+g0d475e5.d20231116", "pymatgen_version": "2023.11.12", "pull_request": null, "database_version": null, "build_date": "2023-11-16 17:06:45.472172", "license": null}, "nsites": 16, "elements": ["Co", "F"], "nelements": 2, "composition": {"Co": 4.0, "F": 12.0}, "composition_reduced": {"Co": 1.0, "F": 3.0}, "formula_pretty": "CoF3", "formula_anonymous": "AB3", "chemsys": "Co-F", "volume": 221.28952740254556, "density": 3.479670222562854, "density_atomic": 13.830595462659097, "symmetry": {"crystal_system": "Cubic", "symbol": "Pm-3m", "number": 221, "point_group": "4/mmm", "symprec": 0.1, "version": "2.1.0"}, "tags": null, "dir_name": "aarons-mbp.dhcp.lbl.gov:/Users/aaronkaplan/Library/CloudStorage/Dropbox/postdoc_MP/software/temp", "state": "successful", "calcs_reversed": [{"dir_name": ".", "vasp_version": "6.3.2", "has_vasp_completed": "successful", "input": {"incar": {"PREC": "Accurate", "ALGO": "Normal", "ISPIN": 2, "NELM": 200, "EDIFF": 1e-06, "NSW": 0, "ENCUT": 680.0, "ENAUG": 1360.0, "MAGMOM": [-2.94, -2.941, 2.942, 2.94, -0.067, 0.066, -0.066, 0.067, 0.211, -0.0, -0.211, -0.0, -0.066, 0.066, -0.066, 0.066], "LREAL": false, "ISMEAR": -5, "SIGMA": 0.05, "KSPACING": 0.22, 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