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import pytest
from tests.conftest import assert_schemas_equal, get_test_object
@pytest.mark.parametrize(
"object_name",
[
pytest.param("SiOptimizeDouble", id="SiOptimizeDouble"),
pytest.param("SiStatic", id="SiStatic"),
pytest.param("SiNonSCFUniform", id="SiNonSCFUniform"),
],
)
def test_analysis_summary(test_dir, object_name):
from monty.json import MontyDecoder, jsanitize
from emmet.core.tasks import AnalysisDoc
from emmet.core.vasp.calculation import Calculation
test_object = get_test_object(object_name)
dir_name = test_dir / "vasp" / test_object.folder
calcs_reversed = []
for task_name, files in test_object.task_files.items():
doc, _ = Calculation.from_vasp_files(dir_name, task_name, **files)
calcs_reversed.append(doc)
# The 2 tasks of double-relaxation have been reversed in
# "/atomate2/tests/vasp/schemas/conftest.py" for "SiOptimizeDouble"
# task_files are in the order of {"relax2","relax1"}
test_doc = AnalysisDoc.from_vasp_calc_docs(calcs_reversed)
valid_doc = test_object.task_doc["analysis"]
assert_schemas_equal(test_doc, valid_doc)
# test document can be jsanitized
d = jsanitize(test_doc, strict=True, enum_values=True, allow_bson=True)
# and decoded
MontyDecoder().process_decoded(d)
@pytest.mark.parametrize(
("object_name", "task_name"),
[
pytest.param("SiOptimizeDouble", "relax1", id="SiOptimizeDouble"),
pytest.param("SiStatic", "standard", id="SiStatic"),
pytest.param("SiNonSCFUniform", "standard", id="SiNonSCFUniform"),
],
)
def test_input_summary(test_dir, object_name, task_name):
from monty.json import MontyDecoder, jsanitize
from emmet.core.tasks import InputDoc
from emmet.core.vasp.calculation import Calculation
test_object = get_test_object(object_name)
dir_name = test_dir / "vasp" / test_object.folder
files = test_object.task_files[task_name]
calc_doc, _ = Calculation.from_vasp_files(dir_name, task_name, **files)
test_doc = InputDoc.from_vasp_calc_doc(calc_doc)
valid_doc = test_object.task_doc["input"]
assert_schemas_equal(test_doc, valid_doc)
# test document can be jsanitized
d = jsanitize(test_doc, strict=True, enum_values=True, allow_bson=True)
# and decoded
MontyDecoder().process_decoded(d)
@pytest.mark.parametrize(
("object_name", "task_name"),
[
pytest.param("SiOptimizeDouble", "relax2", id="SiOptimizeDouble"),
pytest.param("SiStatic", "standard", id="SiStatic"),
pytest.param("SiNonSCFUniform", "standard", id="SiNonSCFUniform"),
],
)
def test_output_summary(test_dir, object_name, task_name):
from monty.json import MontyDecoder, jsanitize
from emmet.core.tasks import OutputDoc
from emmet.core.vasp.calculation import Calculation
test_object = get_test_object(object_name)
dir_name = test_dir / "vasp" / test_object.folder
files = test_object.task_files[task_name]
calc_doc, _ = Calculation.from_vasp_files(dir_name, task_name, **files)
test_doc = OutputDoc.from_vasp_calc_doc(calc_doc)
valid_doc = test_object.task_doc["output"]
assert_schemas_equal(test_doc, valid_doc)
# test document can be jsanitized
d = jsanitize(test_doc, strict=True, enum_values=True, allow_bson=True)
# and decoded
MontyDecoder().process_decoded(d)
@pytest.mark.parametrize(
"object_name",
[
pytest.param("SiOptimizeDouble", id="SiOptimizeDouble"),
pytest.param("SiStatic", id="SiStatic"),
pytest.param("SiNonSCFUniform", id="SiNonSCFUniform"),
],
)
def test_task_doc(test_dir, object_name, tmpdir):
from monty.json import jsanitize
from monty.serialization import dumpfn
import os
from pymatgen.alchemy.materials import TransformedStructure
from pymatgen.entries.computed_entries import ComputedEntry
from pymatgen.transformations.standard_transformations import (
DeformStructureTransformation,
)
import shutil
from emmet.core.tasks import TaskDoc
test_object = get_test_object(object_name)
dir_name = test_dir / "vasp" / test_object.folder
test_doc = TaskDoc.from_directory(dir_name)
assert_schemas_equal(test_doc, test_object.task_doc)
# test document can be jsanitized
jsanitize(test_doc, strict=True, enum_values=True, allow_bson=True)
# This is currently an issue as older versions of dumped custodian VaspJob objects are in the
# test files. This needs to be updated to properly test decoding.
# MontyDecoder().process_decoded(dct)
# Test that additional_fields works
test_doc = TaskDoc.from_directory(dir_name, additional_fields={"foo": "bar"})
assert test_doc.model_dump()["foo"] == "bar"
assert len(test_doc.calcs_reversed) == len(test_object.task_files)
# ensure that number of electronic steps are correctly populated
for cr in test_doc.calcs_reversed:
assert len(cr.output.ionic_steps) == len(cr.output.num_electronic_steps)
assert cr.output.num_electronic_steps == [
len(ionic_step.electronic_steps) for ionic_step in cr.output.ionic_steps
]
# ensure that run stats are not all identically zero (i.e., they are parsed correctly)
for run_stats in test_doc.run_stats.values():
assert any(abs(time) > 1e-6 for time in run_stats.model_dump().values())
# Check that entry is populated when calcs_reversed is not None
if test_doc.calcs_reversed:
assert isinstance(
test_doc.entry, ComputedEntry
), f"Unexpected entry {test_doc.entry} for {object_name}"
# Test that transformations field works, using hydrostatic compression as example
ts = TransformedStructure(
test_doc.output.structure,
transformations=[
DeformStructureTransformation(
deformation=[
[0.9 if i == j else 0.0 for j in range(3)] for i in range(3)
]
)
],
)
ts_json = jsanitize(ts.as_dict())
dumpfn(ts, f"{tmpdir}/transformations.json")
for f in os.listdir(dir_name):
if os.path.isfile(os.path.join(dir_name, f)):
shutil.copy(os.path.join(dir_name, f), tmpdir)
test_doc = TaskDoc.from_directory(tmpdir)
# if other_parameters == {}, this is popped from the TaskDoc.transformations field
# seems like @version is added by monty serialization
# jsanitize needed because pymatgen.core.Structure.pbc is a tuple
assert all(
test_doc.transformations[k] == v
for k, v in ts_json.items()
if k
not in (
"other_parameters",
"@version",
"last_modified",
)
)
assert isinstance(test_doc.transformations, dict)
# now test case when transformations are serialized, relevant for atomate2
test_doc = TaskDoc(
**{
"transformations": ts,
**{
k: v for k, v in test_doc.model_dump().items() if k != "transformations"
},
}
)
assert test_doc.transformations == ts
|
