def test_isordk_cooo(self):
isordk = one.readisordk(self.aooneint)
C = [0.0000000000, 0.0000000000, -0.8802560791]
O = [0.0000000000, 0.0000000000, 1.0094700459]
H1 = [0.0000000000, 1.8897261250, -2.7699822041]
H2 = [0.0000000000, -1.8897261250, -2.7699822041]
np.testing.assert_almost_equal(isordk["cooo"][0::500], C)
np.testing.assert_almost_equal(isordk["cooo"][1::500], O)
np.testing.assert_almost_equal(isordk["cooo"][2::500], H1)
np.testing.assert_almost_equal(isordk["cooo"][3::500], H2)
def test_isordk_cooo(self):
isordk = one.readisordk(self.aooneint)
C = [-3.0015786160, -1.4563174382, 0.0550080378]
O = [-3.1314330364, 0.8240509816, -0.0184248297]
H1 = [-1.1728925345, -2.4468589606, 0.1025195320]
H2 = [-4.7395143797, -2.6116033945, 0.0761219478]
np.testing.assert_almost_equal(isordk["cooo"][0::120], C)
np.testing.assert_almost_equal(isordk["cooo"][1::120], O)
np.testing.assert_almost_equal(isordk["cooo"][2::120], H1)
np.testing.assert_almost_equal(isordk["cooo"][3::120], H2)
def get_isordk(self):
"""
Get overlap, nuclear charges and coordinates from AOONEINT
"""
#
# Data from the ISORDK section in AOONEINT
#
isordk = one.readisordk(filename=self.aooneint)
#
# Number of nuclei
#
N = isordk["nucdep"]
#
# MXCENT , Fix dimension defined in nuclei.h
#
mxcent = len(isordk["chrn"])
#
# Nuclear charges
#
self.Z = full.matrix((N,))
self.Z[:] = isordk["chrn"][:N]
#
# Nuclear coordinates
#
R = full.matrix((mxcent*3,))
R[:] = isordk["cooo"][:]
self.R = R.reshape((mxcent, 3), order='F')[:N, :]
#
# Bond center matrix and half bond vector
#
noa = self.noa
self.Rab = full.matrix((noa, noa, 3))
self.dRab = full.matrix((noa, noa, 3))
for a in range(noa):
for b in range(noa):
self.Rab[a, b, :] = (self.R[a, :] + self.R[b, :])/2
self.dRab[a, b, :] = (self.R[a, :] - self.R[b, :])/2
def get_molecule_info(self):
"""
` Get overlap, nuclear charges and coordinates from AOONEINT
"""
#
# Data from the ISORDK section in AOONEINT
#
isordk = one.readisordk(filename=self.aooneint)
#
# Number of nuclei
#
N = isordk["nucdep"]
#
# MXCENT , Fix dimension defined in nuclei.h
#
mxcent = len(isordk["chrn"])
#
# Nuclear charges
#
self.Z = full.matrix((N, ))
self.Z[:] = isordk["chrn"][:N]
#
# Nuclear coordinates
#
R = full.matrix((mxcent * 3, ))
R[:] = isordk["cooo"][:]
self.R = R.reshape((mxcent, 3), order="F")[:N, :]
#
# Bond center matrix and half bond vector
#
noa = self.noa
self.Rab = full.matrix((noa, noa, 3))
self.dRab = full.matrix((noa, noa, 3))
for a in range(noa):
for b in range(noa):
self.Rab[a, b, :] = (self.R[a, :] + self.R[b, :]) / 2
self.dRab[a, b, :] = (self.R[a, :] - self.R[b, :]) / 2
def test_isordk_chrn(self):
isordk = one.readisordk(self.aooneint)
assert isordk["chrn"][:3] == (6.0, 8.0, 1.0)
def test_isordk_nucdep(self):
isordk = one.readisordk(self.aooneint)
assert isordk["nucdep"] == 4