def test_principal_moments_of_inertia(self):
"""Testing principal moments of inertia and the principal axes for one
logfile where it is printed.
"""
data, logfile = getdatafile(DALTON, "basicDALTON-2015", ["dvb_sp_hf.out"])
nuclear = Nuclear(data)
nuclear.logger.setLevel(logging.ERROR)
ref_pmoi = []
ref_axes = []
with open(logfile.filename) as f:
for line in f:
if line.strip() == "Principal moments of inertia (u*A**2) and principal axes":
next(f)
next(f)
for _ in range(3):
tokens = [float(x) for x in next(f).split()[1:]]
ref_pmoi.append(tokens[0])
ref_axes.append(tokens[1:])
pmoi, axes = nuclear.principal_moments_of_inertia()
np.testing.assert_allclose(pmoi, ref_pmoi, rtol=0, atol=1.0e-4)
# The phases of the eigenvectors may be different, but they
# are still orthonormal within each set.
np.testing.assert_allclose(np.abs(axes), np.abs(ref_axes), rtol=0, atol=1.0e-4)
def test_principal_moments_of_inertia(self):
"""Testing principal moments of inertia and the principal axes for one
logfile where it is printed.
"""
data, logfile = getdatafile(DALTON, "basicDALTON-2015",
["dvb_sp_hf.out"])
nuclear = Nuclear(data)
nuclear.logger.setLevel(logging.ERROR)
ref_pmoi = []
ref_axes = []
with open(logfile.filename) as f:
for line in f:
if line.strip(
) == "Principal moments of inertia (u*A**2) and principal axes":
next(f)
next(f)
for _ in range(3):
tokens = [float(x) for x in next(f).split()[1:]]
ref_pmoi.append(tokens[0])
ref_axes.append(tokens[1:])
pmoi, axes = nuclear.principal_moments_of_inertia()
np.testing.assert_allclose(pmoi, ref_pmoi, rtol=0, atol=1.0e-4)
# The phases of the eigenvectors may be different, but they
# are still orthonormal within each set.
np.testing.assert_allclose(np.abs(axes),
np.abs(ref_axes),
rtol=0,
atol=1.0e-4)
def test_rotational_constants(self):
"""Testing rotational constants for two logfiles where they are
printed.
"""
data, logfile = getdatafile(DALTON, "basicDALTON-2015", ["dvb_sp_hf.out"])
nuclear = Nuclear(data)
nuclear.logger.setLevel(logging.ERROR)
with open(logfile.filename) as f:
for line in f:
if line.strip() == "Rotational constants":
while line.split() != ['A', 'B', 'C']:
line = next(f)
line = next(f)
ref_mhz = [float(x) for x in next(f).split()[:-1]]
ref_invcm = [float(x) for x in next(f).split()[:-1]]
rotconsts_ghz = nuclear.rotational_constants('ghz')
rotconsts_invcm = nuclear.rotational_constants('invcm')
np.testing.assert_allclose(rotconsts_ghz * 1.0e3, ref_mhz, rtol=0, atol=1.0e-4)
np.testing.assert_allclose(rotconsts_invcm, ref_invcm, rtol=0, atol=1.0e-4)
data, logfile = getdatafile(Gaussian, "basicGaussian16", ["dvb_sp.out"])
nuclear = Nuclear(data)
nuclear.logger.setLevel(logging.ERROR)
with open(logfile.filename) as f:
for line in f:
if "Rotational constants (GHZ):" in line:
ref_ghz = [float(x) for x in line.split()[3:]]
rotconsts_ghz = nuclear.rotational_constants('ghz')
np.testing.assert_allclose(rotconsts_ghz, ref_ghz, rtol=0, atol=1.0e-5)
def test_nre(self):
"""Testing nuclear repulsion energy for one logfile where it is printed."""
data, logfile = getdatafile(QChem, "basicQChem4.2", "water_mp4sdq.out")
nuclear = Nuclear(data)
nuclear.logger.setLevel(logging.ERROR)
with open(logfile.filename) as f:
output = f.read()
line = re.search('Nuclear Repulsion Energy = .* hartrees', output).group()
nre = float(line.split()[4])
nre = utils.convertor(nre, 'Angstrom', 'bohr')
self.assertAlmostEqual(nuclear.repulsion_energy(), nre, places=7)
def test_repulsion_energy(self):
"""Testing nuclear repulsion energy for one logfile where it is printed."""
data, logfile = getdatafile(QChem, "basicQChem5.4", ["water_mp4sdq.out"])
nuclear = Nuclear(data)
nuclear.logger.setLevel(logging.ERROR)
with open(logfile.filename) as f:
output = f.read()
line = re.search('Nuclear Repulsion Energy = .* hartrees', output).group()
nre = float(line.split()[4])
nre = utils.convertor(nre, 'Angstrom', 'bohr')
self.assertAlmostEqual(nuclear.repulsion_energy(), nre, places=7)
def test_principal_moments_of_inertia_2(self):
"""Testing principal moments of inertia and the principal axes for one
logfile where it is printed.
This test was added as a follow-up to PR #790.
"""
data, _ = getdatafile(Gaussian, "basicGaussian16", ["dvb_ir.out"])
nuclear = Nuclear(data)
nuclear.logger.setLevel(logging.ERROR)
ref_pmoi = [390.07633792, 2635.01850639, 3025.09484431]
pmoi, _ = nuclear.principal_moments_of_inertia("amu_bohr_2")
np.testing.assert_allclose(pmoi, ref_pmoi, rtol=0, atol=1.0e-4)
def test_rotational_constants(self):
"""Testing rotational constants for two logfiles where they are
printed.
"""
data, logfile = getdatafile(DALTON, "basicDALTON-2015", ["dvb_sp_hf.out"])
nuclear = Nuclear(data)
nuclear.logger.setLevel(logging.ERROR)
with open(logfile.filename) as f:
for line in f:
if line.strip() == "Rotational constants":
while line.split() != ['A', 'B', 'C']:
line = next(f)
line = next(f)
ref_mhz = [float(x) for x in next(f).split()[:-1]]
ref_invcm = [float(x) for x in next(f).split()[:-1]]
rotconsts_ghz = nuclear.rotational_constants('ghz')
rotconsts_invcm = nuclear.rotational_constants('invcm')
np.testing.assert_allclose(rotconsts_ghz * 1.0e3, ref_mhz, rtol=0, atol=1.0e-4)
np.testing.assert_allclose(rotconsts_invcm, ref_invcm, rtol=0, atol=1.0e-4)
data, logfile = getdatafile(Gaussian, "basicGaussian16", ["dvb_sp.out"])
nuclear = Nuclear(data)
nuclear.logger.setLevel(logging.ERROR)
with open(logfile.filename) as f:
for line in f:
if "Rotational constants (GHZ):" in line:
ref_ghz = [float(x) for x in line.split()[3:]]
rotconsts_ghz = nuclear.rotational_constants('ghz')
np.testing.assert_allclose(rotconsts_ghz, ref_ghz, rtol=0, atol=1.0e-5)
def check(atomnos, formula, charge=0):
data.natom = len(atomnos)
data.atomnos = np.array(atomnos)
data.atomcoords = np.zeros((data.natom, 3))
data.charge = charge
self.assertEqual(Nuclear(data).stoichiometry(), formula)