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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.thermo import MoleculeThermoDoc, get_free_energy
@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 sp(test_dir):
data = loadfn((test_dir / "closed_shell_nbo_task.json.gz").as_posix())
task = TaskDocument(**data)
return task
def test_thermo(test_tasks, sp):
# Just energy; no free energy information
doc = MoleculeThermoDoc.from_task(
task=sp,
molecule_id="b9ba54febc77d2a9177accf4605767db-C1Li2O3-1-2",
deprecated=False,
)
assert doc.property_name == "thermo"
assert doc.electronic_energy == sp.output.final_energy * 27.2114
assert doc.free_energy is None
# With all thermodynamic information
task = test_tasks[0]
doc = MoleculeThermoDoc.from_task(
task,
molecule_id="b9ba54febc77d2a9177accf4605767db-C1Li2O3-1-2",
deprecated=False,
)
assert doc.electronic_energy == task.output.final_energy * 27.2114
assert doc.total_enthalpy == task.output.enthalpy * 0.043363
assert doc.total_entropy == task.output.entropy * 0.000043363
assert doc.free_energy == get_free_energy(
task.output.final_energy, task.output.enthalpy, task.output.entropy
)
assert doc.rt == task.calcs_reversed[0]["gas_constant"] * 0.043363
assert doc.vibrational_enthalpy == task.calcs_reversed[0]["vib_enthalpy"] * 0.043363
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