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import json
import datetime
import pytest
from monty.io import zopen
from monty.serialization import loadfn
from emmet.core.qchem.task import TaskDocument
from emmet.core.molecules.atomic import PartialChargesDoc, PartialSpinsDoc
@pytest.fixture(scope="session")
def test_tasks(test_dir):
with zopen(test_dir / "liec_tasks.json.gz") as f:
data = json.load(f)
for d in data:
d["last_updated"] = datetime.datetime.strptime(
d["last_updated"]["string"], "%Y-%m-%d %H:%M:%S.%f"
)
tasks = [TaskDocument(**t) for t in data]
return tasks
@pytest.fixture(scope="session")
def open_shell(test_dir):
task = TaskDocument(**loadfn((test_dir / "open_shell_nbo_task.json.gz")))
return task
def test_partial_charges(test_tasks):
# Test RESP
pcd = PartialChargesDoc.from_task(
test_tasks[0],
molecule_id="b9ba54febc77d2a9177accf4605767db-C1Li2O3-1-2",
preferred_methods=["resp"],
)
assert pcd.property_name == "partial_charges"
assert pcd.method == "resp"
assert pcd.partial_charges == test_tasks[0].output.resp
# Test Mulliken
pcd = PartialChargesDoc.from_task(
test_tasks[0],
molecule_id="b9ba54febc77d2a9177accf4605767db-C1Li2O3-1-2",
preferred_methods=["mulliken"],
)
assert pcd.method == "mulliken"
assert pcd.partial_charges == test_tasks[0].output.mulliken
# Test Critic2
pcd = PartialChargesDoc.from_task(
test_tasks[3],
molecule_id="b9ba54febc77d2a9177accf4605767db-C1Li2O3-1-2",
preferred_methods=["critic2"],
)
assert pcd.method == "critic2"
assert pcd.partial_charges == test_tasks[3].critic2["processed"]["charges"]
# Test NBO
pcd = PartialChargesDoc.from_task(
test_tasks[4],
molecule_id="b9ba54febc77d2a9177accf4605767db-C1Li2O3-1-2",
preferred_methods=["nbo"],
)
assert pcd.method == "nbo"
nbo_charges = [
float(test_tasks[4].output.nbo["natural_populations"][0]["Charge"][str(i)])
for i in range(11)
]
assert pcd.partial_charges == nbo_charges
def test_partial_spins(open_shell):
# Test Mulliken
psd = PartialSpinsDoc.from_task(
open_shell,
molecule_id="b9ba54febc77d2a9177accf4605767db-C1Li2O3-1-2",
preferred_methods=["mulliken"],
)
assert psd.property_name == "partial_spins"
assert psd.method == "mulliken"
assert psd.partial_spins == [m[1] for m in open_shell.output.mulliken]
# Test NBO
psd = PartialSpinsDoc.from_task(
open_shell,
molecule_id="b9ba54febc77d2a9177accf4605767db-C1Li2O3-1-2",
preferred_methods=["nbo"],
)
assert psd.method == "nbo"
spins = [
float(open_shell.output.nbo["natural_populations"][0]["Density"][str(i)])
for i in range(11)
]
assert psd.partial_spins == spins
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