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import pytest
from tests.conftest import assert_schemas_equal, get_test_object
def test_init():
from emmet.core.vasp.calculation import (
Calculation,
CalculationInput,
CalculationOutput,
RunStatistics,
)
calc_input = CalculationInput()
assert calc_input is not None
calc_input = CalculationOutput()
assert calc_input is not None
calc_input = RunStatistics()
assert calc_input is not None
calc_input = Calculation()
assert calc_input is not None
@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_calculation_input(test_dir, object_name, task_name):
from monty.json import MontyDecoder, jsanitize
from pymatgen.io.vasp import Vasprun
from emmet.core.vasp.calculation import CalculationInput
test_object = get_test_object(object_name)
vasprun_file = test_dir / "vasp" / test_object.folder
vasprun_file /= test_object.task_files[task_name]["vasprun_file"]
test_doc = CalculationInput.from_vasprun(Vasprun(vasprun_file))
valid_doc = test_object.task_doc["calcs_reversed"][0]["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_calculation_output(test_dir, object_name, task_name):
from monty.json import MontyDecoder, jsanitize
from pymatgen.io.vasp import Outcar, Poscar, Vasprun
from emmet.core.vasp.calculation import CalculationOutput
test_object = get_test_object(object_name)
folder = test_dir / "vasp" / test_object.folder
vasprun_file = folder / test_object.task_files[task_name]["vasprun_file"]
outcar_file = folder / test_object.task_files[task_name]["outcar_file"]
contcar_file = folder / test_object.task_files[task_name]["contcar_file"]
vasprun = Vasprun(vasprun_file)
outcar = Outcar(outcar_file)
contcar = Poscar.from_file(contcar_file)
test_doc = CalculationOutput.from_vasp_outputs(vasprun, outcar, contcar)
valid_doc = test_object.task_doc["calcs_reversed"][0]["output"]
assert_schemas_equal(test_doc, valid_doc)
assert test_doc.efermi == vasprun.get_band_structure(efermi="smart").efermi
# test document can be jsanitized
d = jsanitize(test_doc, strict=True, enum_values=True, allow_bson=True)
# and decoded
MontyDecoder().process_decoded(d)
def test_mag_calculation_output(test_dir):
from pymatgen.io.vasp import Outcar, Poscar, Vasprun
from emmet.core.vasp.calculation import CalculationOutput
# Test magnetic properties
dir_name = test_dir / "vasp" / "magnetic_run"
d = CalculationOutput.from_vasp_outputs(
Vasprun(dir_name / "vasprun.xml.gz"),
Outcar(dir_name / "OUTCAR.gz"),
Poscar.from_file(dir_name / "CONTCAR.gz"),
)
assert d.model_dump()["mag_density"] == pytest.approx(0.19384725901794095)
@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_run_statistics(test_dir, object_name, task_name):
from monty.json import MontyDecoder, jsanitize
from pymatgen.io.vasp import Outcar
from emmet.core.vasp.calculation import RunStatistics
test_object = get_test_object(object_name)
folder = test_dir / "vasp" / test_object.folder
outcar_file = folder / test_object.task_files[task_name]["outcar_file"]
outcar = Outcar(outcar_file)
test_doc = RunStatistics.from_outcar(outcar)
valid_doc = test_object.task_doc["calcs_reversed"][0]["output"]["run_stats"]
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_calculation(test_dir, object_name, task_name):
from monty.json import MontyDecoder, jsanitize
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]
test_doc, objects = Calculation.from_vasp_files(dir_name, task_name, **files)
valid_doc = test_object.task_doc["calcs_reversed"][0]
assert_schemas_equal(test_doc, valid_doc)
assert set(objects.keys()) == set(test_object.objects[task_name])
# check bader and ddec6 keys exist
assert test_doc.bader is None
assert test_doc.ddec6 is None
# test document can be jsanitized
d = jsanitize(test_doc, strict=True, enum_values=True, allow_bson=True)
# and decoded
MontyDecoder().process_decoded(d)
def test_calculation_run_type_metagga(test_dir):
# Test to ensure that meta-GGA calculations are correctly identified
# The VASP files were kindly provided by @Andrew-S-Rosen in issue #960
from emmet.core.vasp.calculation import Calculation
calc_input, _ = Calculation.from_vasp_files(
dir_name=test_dir / "vasp" / "r2scan_relax",
task_name="relax",
vasprun_file="vasprun.xml.gz",
outcar_file="OUTCAR.gz",
contcar_file="CONTCAR.gz",
)
assert "r2SCAN" in repr(calc_input.run_type)
assert "r2SCAN" in repr(calc_input.calc_type)
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
|
