From a1c86a656a21d7b55e2363771df53eabe7fc0d38 Mon Sep 17 00:00:00 2001 From: esoteric-ephemera Date: Fri, 27 Oct 2023 16:24:16 -0700 Subject: [PATCH 1/8] Fix issue with using dir_name != ./ in emmet.core.tasks.TaskDoc --- emmet-core/emmet/core/vasp/calculation.py | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/emmet-core/emmet/core/vasp/calculation.py b/emmet-core/emmet/core/vasp/calculation.py index cbda7f8e39..162b048774 100644 --- a/emmet-core/emmet/core/vasp/calculation.py +++ b/emmet-core/emmet/core/vasp/calculation.py @@ -675,9 +675,9 @@ def from_vasp_files( A VASP calculation document. """ dir_name = Path(dir_name) - vasprun_file = dir_name / vasprun_file - outcar_file = dir_name / outcar_file - contcar_file = dir_name / contcar_file + vasprun_file = vasprun_file + outcar_file = outcar_file + contcar_file = contcar_file vasprun_kwargs = vasprun_kwargs if vasprun_kwargs else {} volumetric_files = [] if volumetric_files is None else volumetric_files @@ -688,7 +688,7 @@ def from_vasp_files( output_file_paths = _get_output_file_paths(volumetric_files) vasp_objects: Dict[VaspObject, Any] = _get_volumetric_data( - dir_name, output_file_paths, store_volumetric_data + output_file_paths, store_volumetric_data ) dos = _parse_dos(parse_dos, vasprun) @@ -714,7 +714,7 @@ def from_vasp_files( locpot = vasp_objects[VaspObject.LOCPOT] # type: ignore elif VaspObject.LOCPOT in output_file_paths: locpot_file = output_file_paths[VaspObject.LOCPOT] # type: ignore - locpot = Locpot.from_file(dir_name / locpot_file) + locpot = Locpot.from_file(locpot_file) input_doc = CalculationInput.from_vasprun(vasprun) @@ -856,7 +856,6 @@ def _get_output_file_paths(volumetric_files: List[str]) -> Dict[VaspObject, str] def _get_volumetric_data( - dir_name: Path, output_file_paths: Dict[VaspObject, str], store_volumetric_data: Optional[Tuple[str]], ) -> Dict[VaspObject, VolumetricData]: @@ -896,7 +895,7 @@ def _get_volumetric_data( try: # assume volumetric data is all in CHGCAR format - volumetric_data[file_type] = Chgcar.from_file(dir_name / file) + volumetric_data[file_type] = Chgcar.from_file(file) except Exception: raise ValueError(f"Failed to parse {file_type} at {file}.") return volumetric_data From caead33a63df8d4fb880b6373cfe52c65bfeb447 Mon Sep 17 00:00:00 2001 From: esoteric-ephemera Date: Fri, 27 Oct 2023 16:33:53 -0700 Subject: [PATCH 2/8] Revert previous change - actual fix is using path relative to dir_name of TaskDoc.from_directory --- emmet-core/emmet/core/tasks.py | 11 ++++++----- emmet-core/emmet/core/vasp/calculation.py | 13 +++++++------ 2 files changed, 13 insertions(+), 11 deletions(-) diff --git a/emmet-core/emmet/core/tasks.py b/emmet-core/emmet/core/tasks.py index 7167168052..8bf952300e 100644 --- a/emmet-core/emmet/core/tasks.py +++ b/emmet-core/emmet/core/tasks.py @@ -951,16 +951,17 @@ def _get_task_files(files, suffix=""): vol_files = [] elph_poscars = [] for file in files: + file_no_path = file.relative_to(path) if file.match(f"*vasprun.xml{suffix}*"): - vasp_files["vasprun_file"] = file + vasp_files["vasprun_file"] = file_no_path elif file.match(f"*OUTCAR{suffix}*"): - vasp_files["outcar_file"] = file + vasp_files["outcar_file"] = file_no_path elif file.match(f"*CONTCAR{suffix}*"): - vasp_files["contcar_file"] = file + vasp_files["contcar_file"] = file_no_path elif any(file.match(f"*{f}{suffix}*") for f in volumetric_files): - vol_files.append(file) + vol_files.append(file_no_path) elif file.match(f"*POSCAR.T=*{suffix}*"): - elph_poscars.append(file) + elph_poscars.append(file_no_path) if len(vol_files) > 0: # add volumetric files if some were found or other vasp files were found diff --git a/emmet-core/emmet/core/vasp/calculation.py b/emmet-core/emmet/core/vasp/calculation.py index 162b048774..cbda7f8e39 100644 --- a/emmet-core/emmet/core/vasp/calculation.py +++ b/emmet-core/emmet/core/vasp/calculation.py @@ -675,9 +675,9 @@ def from_vasp_files( A VASP calculation document. """ dir_name = Path(dir_name) - vasprun_file = vasprun_file - outcar_file = outcar_file - contcar_file = contcar_file + vasprun_file = dir_name / vasprun_file + outcar_file = dir_name / outcar_file + contcar_file = dir_name / contcar_file vasprun_kwargs = vasprun_kwargs if vasprun_kwargs else {} volumetric_files = [] if volumetric_files is None else volumetric_files @@ -688,7 +688,7 @@ def from_vasp_files( output_file_paths = _get_output_file_paths(volumetric_files) vasp_objects: Dict[VaspObject, Any] = _get_volumetric_data( - output_file_paths, store_volumetric_data + dir_name, output_file_paths, store_volumetric_data ) dos = _parse_dos(parse_dos, vasprun) @@ -714,7 +714,7 @@ def from_vasp_files( locpot = vasp_objects[VaspObject.LOCPOT] # type: ignore elif VaspObject.LOCPOT in output_file_paths: locpot_file = output_file_paths[VaspObject.LOCPOT] # type: ignore - locpot = Locpot.from_file(locpot_file) + locpot = Locpot.from_file(dir_name / locpot_file) input_doc = CalculationInput.from_vasprun(vasprun) @@ -856,6 +856,7 @@ def _get_output_file_paths(volumetric_files: List[str]) -> Dict[VaspObject, str] def _get_volumetric_data( + dir_name: Path, output_file_paths: Dict[VaspObject, str], store_volumetric_data: Optional[Tuple[str]], ) -> Dict[VaspObject, VolumetricData]: @@ -895,7 +896,7 @@ def _get_volumetric_data( try: # assume volumetric data is all in CHGCAR format - volumetric_data[file_type] = Chgcar.from_file(file) + volumetric_data[file_type] = Chgcar.from_file(dir_name / file) except Exception: raise ValueError(f"Failed to parse {file_type} at {file}.") return volumetric_data From 28ad2b33905ae598771c190036ae392c8987777d Mon Sep 17 00:00:00 2001 From: esoteric-ephemera Date: Thu, 16 Nov 2023 09:42:25 -0800 Subject: [PATCH 3/8] Add new POTCAR summary_stats check for validation, two tests for POTCAR checking/IDing --- emmet-core/emmet/core/vasp/validation.py | 47 ++++++++++++++------ emmet-core/tests/test_calculation.py | 27 ++++++++++++ emmet-core/tests/vasp/test_vasp.py | 56 +++++++++++++++++++++++- 3 files changed, 115 insertions(+), 15 deletions(-) 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..d7f52fa9e9 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: + # missing Pymatgen POTCARs, cannot perform test + return True diff --git a/emmet-core/tests/vasp/test_vasp.py b/emmet-core/tests/vasp/test_vasp.py index c1d3cc69d5..4afe231a90 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 + + except OSError: + # missing Pymatgen POTCARs, cannot perform test + return True + + 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) From 92bbeb0dc702916a1579abba95cedb1a3533c3fc Mon Sep 17 00:00:00 2001 From: esoteric-ephemera Date: Thu, 16 Nov 2023 09:51:13 -0800 Subject: [PATCH 4/8] Adding builder side of commit and test files --- MP_POTCAR_ID.json.gz | Bin 0 -> 33683 bytes .../emmet/builders/vasp/task_validator.py | 2 +- test_files/CoF_TaskDoc.json | 1 + 3 files changed, 2 insertions(+), 1 deletion(-) create mode 100644 MP_POTCAR_ID.json.gz create mode 100644 test_files/CoF_TaskDoc.json diff --git a/MP_POTCAR_ID.json.gz b/MP_POTCAR_ID.json.gz new file mode 100644 index 0000000000000000000000000000000000000000..9b8248f2d4b893689cba4cb143985b7c2ea325d0 GIT binary patch literal 33683 zcmV)tK$pKCiwFo=FjZv&|4mR|P)}4tK~i5yL@sJ`Z*BnWy=#+P$B`xYS77?oW3~$O zw|ne25>1M1i4=`MzqB?c1A!8WZ4%%XfbP+>^?zUYo0*l7ft%EbMzD)e@PR61WahmE zRGs6`bN=&JUwrt{um0}`|M{yAo^Bsr{rS7EUVfXO)&u|7gI_)V^zlc(tKWX{!9V{o 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potcar.md5_header_hash + hashes[calc_type][potcar_symbol] = potcar._summary_stats self.potcar_hashes = potcar_hashes else: diff --git a/test_files/CoF_TaskDoc.json b/test_files/CoF_TaskDoc.json new file mode 100644 index 0000000000..15f7272b0a --- /dev/null +++ b/test_files/CoF_TaskDoc.json @@ -0,0 +1 @@ +{"builder_meta": {"emmet_version": "0.1.dev4174+g0d475e5.d20231116", "pymatgen_version": "2023.11.12", "pull_request": null, "database_version": null, "build_date": "2023-11-16 17:06:45.472172", "license": null}, "nsites": 16, "elements": ["Co", "F"], "nelements": 2, "composition": {"Co": 4.0, "F": 12.0}, "composition_reduced": {"Co": 1.0, "F": 3.0}, "formula_pretty": "CoF3", "formula_anonymous": "AB3", "chemsys": "Co-F", "volume": 221.28952740254556, "density": 3.479670222562854, "density_atomic": 13.830595462659097, "symmetry": {"crystal_system": "Cubic", "symbol": "Pm-3m", "number": 221, "point_group": "4/mmm", "symprec": 0.1, "version": "2.1.0"}, "tags": null, "dir_name": 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zAcN2>`a%y{?3U8UiMNByASrof6jlJ-5+U~&a*{A0&5F)Z$z^KCyFi+VfGMklL|Bf! z4jz?~1}bsb^LKC^M&%fAWy=~p^WnqjnGes=Gko5a={|cCrU}!8X~KN7IW8WQ1Ytxq zw$S?t;oa$Vip!^-0iY9tAN0|a3?osnS1v$v#B^~+VD?41K#ggghLdrUAKW#Q71PiK xY~)+pVM*r=;)GHvsY2e(M<%I)lH75Q(<0{o{onrs009600{~Au|LT{l1^@(Q0j&T4 From 0d71a0ace95c77c9c4fc9620f87449aee6e05a1c Mon Sep 17 00:00:00 2001 From: esoteric-ephemera Date: Thu, 16 Nov 2023 10:00:24 -0800 Subject: [PATCH 6/8] Fix handling of missing POTCAR lib in tests --- emmet-core/tests/test_calculation.py | 2 +- emmet-core/tests/vasp/test_vasp.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/emmet-core/tests/test_calculation.py b/emmet-core/tests/test_calculation.py index d7f52fa9e9..85ee46c521 100644 --- a/emmet-core/tests/test_calculation.py +++ b/emmet-core/tests/test_calculation.py @@ -185,6 +185,6 @@ def test_PotcarSpec(test_dir): assert ps.hash == potcars[ips].md5_header_hash assert ps.summary_stats == potcars[ips]._summary_stats - except OSError: + except (OSError, ValueError): # missing Pymatgen POTCARs, cannot perform test return True diff --git a/emmet-core/tests/vasp/test_vasp.py b/emmet-core/tests/vasp/test_vasp.py index 4afe231a90..013a684fc4 100644 --- a/emmet-core/tests/vasp/test_vasp.py +++ b/emmet-core/tests/vasp/test_vasp.py @@ -119,7 +119,7 @@ def test_potcar_hash_check(test_dir): symbol=symbol, functional="PBE" )._summary_stats - except OSError: + except (OSError, ValueError): # missing Pymatgen POTCARs, cannot perform test return True From 1cc8b01106ee0936765ebab62e0ea32cafa41306 Mon Sep 17 00:00:00 2001 From: esoteric-ephemera Date: Thu, 16 Nov 2023 11:00:36 -0800 Subject: [PATCH 7/8] cleanup tests --- emmet-core/emmet/core/tasks.py | 2 +- emmet-core/tests/test_calculation.py | 2 +- emmet-core/tests/vasp/test_vasp.py | 28 ++++++++++++++-------------- 3 files changed, 16 insertions(+), 16 deletions(-) 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/tests/test_calculation.py b/emmet-core/tests/test_calculation.py index 85ee46c521..30e49d0a17 100644 --- a/emmet-core/tests/test_calculation.py +++ b/emmet-core/tests/test_calculation.py @@ -187,4 +187,4 @@ def test_PotcarSpec(test_dir): except (OSError, ValueError): # missing Pymatgen POTCARs, cannot perform test - return True + assert True diff --git a/emmet-core/tests/vasp/test_vasp.py b/emmet-core/tests/vasp/test_vasp.py index 013a684fc4..60527745c2 100644 --- a/emmet-core/tests/vasp/test_vasp.py +++ b/emmet-core/tests/vasp/test_vasp.py @@ -119,23 +119,23 @@ def test_potcar_hash_check(test_dir): symbol=symbol, functional="PBE" )._summary_stats - except (OSError, ValueError): - # missing Pymatgen POTCARs, cannot perform test - return True + assert not _potcar_hash_check(task_doc, expected_hashes) - assert not _potcar_hash_check(task_doc, expected_hashes) + # Second check: remove POTCAR from expected_hashes, check should fail - # 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) - 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 - # 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 - 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) - assert _potcar_hash_check(task_doc, wrong_hashes) + except (OSError, ValueError): + # missing Pymatgen POTCARs, cannot perform test + assert True From 763e2e892e83848036c2f0a7f1221f8f2c25157a Mon Sep 17 00:00:00 2001 From: esoteric-ephemera Date: Thu, 16 Nov 2023 11:03:05 -0800 Subject: [PATCH 8/8] Hopefully fix weird behavior in failing matcalc tests --- emmet-core/tests/test_ml.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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: