def test_c2pk_md_mock(mocker: MockFixture) -> None:
"""Mock a call to CP2K."""
s = SETTINGS.copy()
s.specific.cp2k += md.specific.cp2k_mm
job = cp2k_mm(s, MOL)
run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_md")
result = run_mocked(job)
assertion.eq(result.status, 'successful')
assertion.isfile(result.results['cp2k-1_1000.restart'])
def test_md() -> None:
"""Test CP2K molecular dynamics calculations with the :class:`CP2K_MM` class."""
mol = Molecule(
PATH_MOLECULES /
'Cd68Cl26Se55__26_acetate.freq.xyz') # Optimized coordinates
s = SETTINGS.copy()
s.specific.cp2k += md.specific.cp2k_mm
s.specific.cp2k.motion.md.steps = 1000
job = cp2k_mm(settings=s, mol=mol, job_name='cp2k_mm_md')
result = run(job, path=PATH)
assertion.eq(result.status, 'successful')
plams_results = result.results
assertion.isfile(plams_results['cp2k-1_1000.restart'])
def test_passes(self, kwargs: Mapping[str, Any]) -> None:
"""Test that whether the code passes as expected."""
# Can't use the pytest `tmp_path` paramater as the (absolute) filename
# becomes too long for COSMO-RS
tmp_path = PATH / "crs"
try:
os.mkdir(tmp_path)
out = run_fast_sigma(SMILES,
SOLVENTS,
output_dir=tmp_path,
**kwargs)
if out is not None:
compare_df(out, REF)
csv_file = tmp_path / "cosmo-rs.csv"
assertion.isfile(csv_file)
df = read_csv(csv_file)
compare_df(df, REF)
finally:
shutil.rmtree(tmp_path)
def test_delete_finally() -> None:
"""Test :exc:`nanoutils.FileNotFoundWarning`."""
assertion.isfile(FILE1, invert=True)
assertion.isdir(DIR1, invert=True)
os.mkdir(DIR1)
with open(FILE1, 'w'):
pass
assertion.isfile(FILE1)
assertion.isdir(DIR1)
@delete_finally(DIR1, FILE1)
def func() -> None:
pass
func()
assertion.isfile(FILE1, invert=True)
assertion.isdir(DIR1, invert=True)
def test_isfile() -> None:
"""Test :meth:`AssertionManager.isfile`."""
assertion.isfile(TEST_FILE)
assertion.isfile(TEST_DIR, invert=True)
assertion.isfile(TEST_DUMMY, invert=True)
assertion.isfile('bob', invert=True)
assertion.isfile(5, 6, 7, 8, exception=TypeError)
assertion.isfile([5], exception=TypeError)