def test_checkpoint_missing():
"""
If the user passes a file with no checkpoint line make sure it is added.
"""
molecule = Molecule(os.path.join(datad, "ethane_no_data.com"))
engine = Gaussian(molecule=molecule, exe="g09", threads=None)
engine.load_gaussian_input(os.path.join(datad, "ethane_no_data.com"))
assert "%Chk=ligand\n" in engine.gauss_temp
def test_setting_threads():
"""
For an input file with threads make sure we can overwrite them to our desired value.
"""
molecule = Molecule(os.path.join(datad, "ethane.com"))
engine = Gaussian(molecule=molecule, exe="g09", threads=30)
engine.load_gaussian_input(os.path.join(datad, "ethane.com"))
assert "%NProcShared=30\n" in engine.gauss_temp
def test_missing_force_input():
"""
Make sure an error is raised if we do not request the force in the input file.
"""
molecule = Molecule(os.path.join(datad, "no_force.com"))
engine = Gaussian(molecule=molecule, exe="g09")
with pytest.raises(RuntimeError):
engine.load_gaussian_input(os.path.join(datad, "no_force.com"))
def test_checkpoint_name():
"""
If the user supplies a file with a different checkpoint name make sure we overwrite it.
"""
molecule = Molecule(os.path.join(datad, "ethane_wrong_name.com"))
engine = Gaussian(molecule=molecule, exe="g09", threads=None)
engine.load_gaussian_input(os.path.join(datad, "ethane_wrong_name.com"))
assert "%Chk=ligand\n" in engine.gauss_temp
def test_adding_threads_none():
"""
If we have an input with no threads and threads is None make sure we write 1.
"""
molecule = Molecule(os.path.join(datad, "ethane_no_data.com"))
engine = Gaussian(molecule=molecule, exe="g09", threads=None)
engine.load_gaussian_input(os.path.join(datad, "ethane_no_data.com"))
assert "%NProcShared=1\n" in engine.gauss_temp
def test_adding_threads_value():
"""
If we read an input file with no threads set but want them make sure they are added.
"""
molecule = Molecule(os.path.join(datad, "ethane_no_data.com"))
engine = Gaussian(molecule=molecule, exe="g09", threads=30)
engine.load_gaussian_input(os.path.join(datad, "ethane_no_data.com"))
assert "%NProcShared=30\n" in engine.gauss_temp
def test_gaussian_template():
"""
Make sure the template is formed properly when reading input files.
"""
molecule = Molecule(os.path.join(datad, "ethane.com"))
engine = Gaussian(molecule=molecule, exe="g09")
engine.load_gaussian_input(os.path.join(datad, "ethane.com"))
assert engine.gauss_temp == [
'%Mem=6GB\n', '%NProcShared=2\n', '%Chk=ligand\n',
'# hf/6-31G(d) Force=NoStep\n', '\n', 'ethane\n', '\n', '0 1\n',
'$!geometry@here', '\n', '\n'
]
def test_gaussian_version_wrong():
"""
Test loading an engine with an incorrect version.
"""
molecule = Molecule(os.path.join(datad, "ethane.com"))
with pytest.raises(ValueError):
_ = Gaussian(molecule=molecule, exe="gaussian09")
def test_gaussian_correct_version(version):
"""
Check that allowed versions do not raise errors.
"""
molecule = Molecule(os.path.join(datad, "ethane.com"))
engine = Gaussian(molecule=molecule, exe=version)
assert engine.gaussian_exe == version.lower()
def test_read_results_gaussian():
"""
Test reading the results from a fchk and log gaussian file.
"""
molecule = Molecule(os.path.join(datad, "ethane.com"))
engine = Gaussian(molecule=molecule, exe="g09")
result = engine.read_result(dirname=datad)
assert result["energy"] == -79.2232076157635
assert np.allclose(
result["gradient"],
np.array([
-0.00656039, -0.00927754, -0.01606933, -0.00169808, 0.01040138,
0.00585666, 0.00044475, -0.00164399, 0.01193617, 0.01037261,
0.00413887, 0.00454436, 0.00656039, 0.00927754, 0.01606933,
-0.00045842, -0.01116123, -0.00453756, 0.00170932, 0.00011823,
-0.01193469, -0.01037017, -0.00185327, -0.00586494
]))
# make sure the gradient array is the same shape ass the coords
assert molecule.xyzs[0].shape == result["gradient"].reshape(-1, 3).shape
def test_calc_new_gaussian():
"""
Test calculating the force using gaussian.
Note this is expected to fail due to gaussian not being installed.
"""
major, minor, _ = platform.python_version_tuple()
if not int(major) >= 3 and int(minor) >= 5:
pytest.skip(
"Python version below 3.5 TemporaryDirectory not available.")
molecule = Molecule(os.path.join(datad, "ethane.com"))
engine = Gaussian(molecule=molecule, exe="g09")
engine.load_gaussian_input(os.path.join(datad, "ethane.com"))
home = os.getcwd()
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
# now we want to run calc new to make sure the file is written correctly
g_version = get_gaussian_version()
if g_version is None:
with pytest.raises(GaussianEngineError):
engine.calc(coords=molecule.xyzs[0] / bohr2ang,
dirname="ethane.tmp")
else:
engine.gaussian_exe = g_version
engine.calc(coords=molecule.xyzs[0] / bohr2ang,
dirname="ethane.tmp")
# now we want to read the file back in to make sure it is correct
molecule_2 = Molecule(os.path.join("ethane.tmp", "gaussian.com"))
# now check over the data
assert molecule.Data["elem"] == molecule_2.Data["elem"]
assert molecule.Data["bonds"] == molecule_2.Data["bonds"]
assert np.allclose(molecule.Data["xyzs"][0],
molecule_2.Data["xyzs"][0])
os.chdir(home)