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 <[email protected]>

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:

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.",
  )
 

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):

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

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:

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