def test_orbital_based_from_molecule_orbital_expression_ch4_uhf_ccpvdz():
# load data computed with Fortran code
with path("chemtools.data", "data_fortran_ch4_uhf_ccpvdz.npz") as fname:
data = np.load(str(fname))
# test from_molecule initialization with exp_beta & check against Fortran code
with path("chemtools.data", "ch4_uhf_ccpvdz.fchk") as fname:
molecule = Molecule.from_file(fname)
tool = DFTBasedTool(molecule, data["points"])
check_orbital_expression(tool, data)
# test from_molecule initialization without exp_beta & check against Fortran code
del molecule._exp_beta
with path("chemtools.data", "ch4_uhf_ccpvdz.fchk") as fname:
molecule = Molecule.from_file(fname)
tool = DFTBasedTool(molecule, data["points"])
check_orbital_expression(tool, data)
def test_orbital_based_raises():
# check file name
assert_raises(ValueError, DFTBasedTool.from_file, "gibberish",
np.array([0.0, 1.0]))
with path("chemtools.data", "h2o_dimer_pbe_sto3g.wfn") as fname:
assert_raises(ValueError, DFTBasedTool.from_file, fname,
np.array([0.0, 1.0]))
assert_raises(ValueError, DFTBasedTool.from_file, fname,
np.array([0.0, 1.0]))
with path("chemtools.data", "h2o_dimer_pbe_sto3g.wfn") as fname:
assert_raises(ValueError, DFTBasedTool.from_file, fname,
np.array([0.0, 1.0]))
assert_raises(ValueError, DFTBasedTool.from_file, fname,
np.array([0.0, 1.0, 0.0]))
assert_raises(ValueError, DFTBasedTool.from_file, fname,
np.array([[0, 1], [1, 0.]]))
# check spin argument
tool = DFTBasedTool.from_file(fname, np.array([[0., 0., 0.]]))
assert_raises(KeyError,
tool._compute_orbital_expression,
np.array([9]),
spin="error")
assert_raises(KeyError,
tool._compute_orbital_expression,
np.array([9]),
spin="alph")
assert_raises(KeyError,
tool._compute_orbital_expression,
np.array([9]),
spin="bet")
def test_orbital_based_h2o_b3lyp_sto3g():
# points array
points = np.array([[-3., -3., -3.], [-3., -3., 0.], [-3., -3., 3.],
[-3., 0., -3.], [-3., 0., 0.], [-3., 0., 3.],
[-3., 3., -3.], [-3., 3., 0.], [-3., 3., 3.],
[0., -3., -3.], [0., -3., 0.], [0., -3., 3.],
[0., 0., -3.], [0., 0., 0.],
[0., 0., 3.], [0., 3., -3.], [0., 3., 0.], [0., 3., 3.],
[3., -3., -3.], [3., -3., 0.], [3., -3., 3.],
[3., 0., -3.], [3., 0., 0.], [3., 0.,
3.], [3., 3., -3.],
[3., 3., 0.], [3., 3., 3.]])
# initialize OrbitalLocalTool from_file
with path("chemtools.data", "water_b3lyp_sto3g.fchk") as fname:
tool = DFTBasedTool.from_file(fname, points)
# check mep against Fortran code
expected = np.array([
-0.01239766, -0.02982537, -0.02201149, -0.01787292, -0.05682143,
-0.02503563, -0.00405942, -0.00818772, -0.00502268, 0.00321181,
-0.03320573, -0.02788605, 0.02741914, 1290.21135500, -0.03319778,
0.01428660, 0.10127092, 0.01518299, 0.01530548, 0.00197975,
-0.00894206, 0.04330806, 0.03441681, -0.00203017, 0.02272626,
0.03730846, 0.01463959
])
assert_array_almost_equal(tool.electrostatic_potential,
expected,
decimal=6)
# check spin chemical potential against manual calculation
result = tool.compute_spin_chemical_potential(25000.0)
assert_array_almost_equal(result, [0.10821228040, 0.10821228040],
decimal=6)
def test_orbital_based_from_file_ch4_uhf_ccpvdz():
# load data computed with Fortran code
with path("chemtools.data", "data_fortran_ch4_uhf_ccpvdz.npz") as fname:
data = np.load(str(fname))
# test from_file initialization & check against Fortran code
with path("chemtools.data", "ch4_uhf_ccpvdz.fchk") as fname:
tool = DFTBasedTool.from_file(fname, data["points"])
check_orbital_based_properties(tool, data)