def _rotate_orbitals_in_qmolecule(
qmolecule: QMolecule, orbital_rotation: 'OrbitalRotation') -> None:
"""
Rotates the orbitals by applying a modified a anti-hermitian matrix
(orbital_rotation.matrix_a) onto the MO coefficients matrix and recomputes all the
quantities dependent on the MO coefficients. Be aware that qmolecule is modified
when this executes.
Args:
qmolecule: instance of QMolecule class
orbital_rotation: instance of OrbitalRotation class
"""
# 1 and 2 electron integrals (required) from AO to MO basis
qmolecule.mo_coeff = np.matmul(qmolecule.mo_coeff,
orbital_rotation.matrix_a)
qmolecule.mo_onee_ints = qmolecule.oneeints2mo(qmolecule.hcore,
qmolecule.mo_coeff)
# support for unrestricted spins
if qmolecule.mo_coeff_b is not None:
qmolecule.mo_coeff_b = np.matmul(qmolecule.mo_coeff_b,
orbital_rotation.matrix_b)
qmolecule.mo_onee_ints_b = qmolecule.oneeints2mo(
qmolecule.hcore, qmolecule.mo_coeff)
qmolecule.mo_eri_ints = qmolecule.twoeints2mo(qmolecule.eri,
qmolecule.mo_coeff)
if qmolecule.mo_coeff_b is not None:
mo_eri_b = qmolecule.twoeints2mo(qmolecule.eri,
qmolecule.mo_coeff_b)
norbs = qmolecule.mo_coeff.shape[0]
qmolecule.mo_eri_ints_bb = mo_eri_b.reshape(
norbs, norbs, norbs, norbs)
qmolecule.mo_eri_ints_ba = qmolecule.twoeints2mo_general(
qmolecule.eri, qmolecule.mo_coeff_b, qmolecule.mo_coeff_b,
qmolecule.mo_coeff, qmolecule.mo_coeff)
qmolecule.mo_eri_ints_ba = qmolecule.mo_eri_ints_ba.reshape(
norbs, norbs, norbs, norbs)
# dipole integrals (if available) from AO to MO
if qmolecule.x_dip_ints is not None:
qmolecule.x_dip_mo_ints = qmolecule.oneeints2mo(
qmolecule.x_dip_ints, qmolecule.mo_coeff)
qmolecule.y_dip_mo_ints = qmolecule.oneeints2mo(
qmolecule.y_dip_ints, qmolecule.mo_coeff)
qmolecule.z_dip_mo_ints = qmolecule.oneeints2mo(
qmolecule.z_dip_ints, qmolecule.mo_coeff)
# support for unrestricted spins
if qmolecule.mo_coeff_b is not None and qmolecule.x_dip_ints is not None:
qmolecule.x_dip_mo_ints_b = qmolecule.oneeints2mo(
qmolecule.x_dip_ints, qmolecule.mo_coeff_b)
qmolecule.y_dip_mo_ints_b = qmolecule.oneeints2mo(
qmolecule.y_dip_ints, qmolecule.mo_coeff_b)
qmolecule.z_dip_mo_ints_b = qmolecule.oneeints2mo(
qmolecule.z_dip_ints, qmolecule.mo_coeff_b)
def _parse_matrix_file(self, fname, useAO2E=False):
# get_driver_class is used here because the discovery routine will load all the gaussian
# binary dependencies, if not loaded already. It won't work without it.
try:
# add gauopen to sys.path so that binaries can be loaded
gauopen_directory = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'gauopen')
if gauopen_directory not in sys.path:
sys.path.insert(0, gauopen_directory)
from .gauopen.QCMatEl import MatEl
except ImportError as mnfe:
msg = 'qcmatrixio extension not found. See Gaussian driver readme to build qcmatrixio.F using f2py' \
if mnfe.name == 'qcmatrixio' else str(mnfe)
logger.info(msg)
raise QiskitChemistryError(msg)
mel = MatEl(file=fname)
logger.debug('MatrixElement file:\n{}'.format(mel))
# Create driver level molecule object and populate
_q_ = QMolecule()
# Energies and orbits
_q_.hf_energy = mel.scalar('ETOTAL')
_q_.nuclear_repulsion_energy = mel.scalar('ENUCREP')
_q_.num_orbitals = 0 # updated below from orbital coeffs size
_q_.num_alpha = (mel.ne + mel.multip - 1) // 2
_q_.num_beta = (mel.ne - mel.multip + 1) // 2
_q_.molecular_charge = mel.icharg
# Molecule geometry
_q_.multiplicity = mel.multip
_q_.num_atoms = mel.natoms
_q_.atom_symbol = []
_q_.atom_xyz = np.empty([mel.natoms, 3])
syms = mel.ian
xyz = np.reshape(mel.c, (_q_.num_atoms, 3))
for _n in range(0, _q_.num_atoms):
_q_.atom_symbol.append(QMolecule.symbols[syms[_n]])
for _i in range(xyz.shape[1]):
coord = xyz[_n][_i]
if abs(coord) < 1e-10:
coord = 0
_q_.atom_xyz[_n][_i] = coord
moc = self._getMatrix(mel, 'ALPHA MO COEFFICIENTS')
_q_.num_orbitals = moc.shape[0]
_q_.mo_coeff = moc
orbs_energy = self._getMatrix(mel, 'ALPHA ORBITAL ENERGIES')
_q_.orbital_energies = orbs_energy
# 1 and 2 electron integrals
hcore = self._getMatrix(mel, 'CORE HAMILTONIAN ALPHA')
logger.debug('CORE HAMILTONIAN ALPHA {}'.format(hcore.shape))
mohij = QMolecule.oneeints2mo(hcore, moc)
if useAO2E:
# These are 2-body in AO. We can convert to MO via the QMolecule
# method but using ints in MO already, as in the else here, is better
eri = self._getMatrix(mel, 'REGULAR 2E INTEGRALS')
logger.debug('REGULAR 2E INTEGRALS {}'.format(eri.shape))
mohijkl = QMolecule.twoeints2mo(eri, moc)
else:
# These are in MO basis but by default will be reduced in size by
# frozen core default so to use them we need to add Window=Full
# above when we augment the config
mohijkl = self._getMatrix(mel, 'AA MO 2E INTEGRALS')
logger.debug('AA MO 2E INTEGRALS {}'.format(mohijkl.shape))
_q_.mo_onee_ints = mohij
_q_.mo_eri_ints = mohijkl
# dipole moment
dipints = self._getMatrix(mel, 'DIPOLE INTEGRALS')
dipints = np.einsum('ijk->kji', dipints)
_q_.x_dip_mo_ints = QMolecule.oneeints2mo(dipints[0], moc)
_q_.y_dip_mo_ints = QMolecule.oneeints2mo(dipints[1], moc)
_q_.z_dip_mo_ints = QMolecule.oneeints2mo(dipints[2], moc)
nucl_dip = np.einsum('i,ix->x', syms, xyz)
nucl_dip = np.round(nucl_dip, decimals=8)
_q_.nuclear_dipole_moment = nucl_dip
_q_.reverse_dipole_sign = True
return _q_
def _parse_matrix_file(self, fname, useao2e=False):
# get_driver_class is used here because the discovery routine will load all the gaussian
# binary dependencies, if not loaded already. It won't work without it.
try:
# add gauopen to sys.path so that binaries can be loaded
gauopen_directory = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'gauopen')
if gauopen_directory not in sys.path:
sys.path.insert(0, gauopen_directory)
# pylint: disable=import-outside-toplevel
from .gauopen.QCMatEl import MatEl
except ImportError as mnfe:
msg = ('qcmatrixio extension not found. '
'See Gaussian driver readme to build qcmatrixio.F using f2py') \
if mnfe.name == 'qcmatrixio' else str(mnfe)
logger.info(msg)
raise QiskitChemistryError(msg) from mnfe
mel = MatEl(file=fname)
logger.debug('MatrixElement file:\n%s', mel)
# Create driver level molecule object and populate
_q_ = QMolecule()
_q_.origin_driver_version = mel.gversion
# Energies and orbits
_q_.hf_energy = mel.scalar('ETOTAL')
_q_.nuclear_repulsion_energy = mel.scalar('ENUCREP')
_q_.num_orbitals = 0 # updated below from orbital coeffs size
_q_.num_alpha = (mel.ne + mel.multip - 1) // 2
_q_.num_beta = (mel.ne - mel.multip + 1) // 2
moc = self._get_matrix(mel, 'ALPHA MO COEFFICIENTS')
moc_b = self._get_matrix(mel, 'BETA MO COEFFICIENTS')
if np.array_equal(moc, moc_b):
logger.debug('ALPHA and BETA MO COEFFS identical, keeping only ALPHA')
moc_b = None
_q_.num_orbitals = moc.shape[0]
_q_.mo_coeff = moc
_q_.mo_coeff_b = moc_b
orbs_energy = self._get_matrix(mel, 'ALPHA ORBITAL ENERGIES')
_q_.orbital_energies = orbs_energy
orbs_energy_b = self._get_matrix(mel, 'BETA ORBITAL ENERGIES')
_q_.orbital_energies_b = orbs_energy_b if moc_b is not None else None
# Molecule geometry
_q_.molecular_charge = mel.icharg
_q_.multiplicity = mel.multip
_q_.num_atoms = mel.natoms
_q_.atom_symbol = []
_q_.atom_xyz = np.empty([mel.natoms, 3])
syms = mel.ian
xyz = np.reshape(mel.c, (_q_.num_atoms, 3))
for n_i in range(0, _q_.num_atoms):
_q_.atom_symbol.append(QMolecule.symbols[syms[n_i]])
for idx in range(xyz.shape[1]):
coord = xyz[n_i][idx]
if abs(coord) < 1e-10:
coord = 0
_q_.atom_xyz[n_i][idx] = coord
# 1 and 2 electron integrals
hcore = self._get_matrix(mel, 'CORE HAMILTONIAN ALPHA')
logger.debug('CORE HAMILTONIAN ALPHA %s', hcore.shape)
hcore_b = self._get_matrix(mel, 'CORE HAMILTONIAN BETA')
if np.array_equal(hcore, hcore_b):
# From Gaussian interfacing documentation: "The two
# core Hamiltonians are identical unless
# a Fermi contact perturbation has been applied."
logger.debug('CORE HAMILTONIAN ALPHA and BETA identical, keeping only ALPHA')
hcore_b = None
logger.debug('CORE HAMILTONIAN BETA %s',
'- Not present' if hcore_b is None else hcore_b.shape)
kinetic = self._get_matrix(mel, 'KINETIC ENERGY')
logger.debug('KINETIC ENERGY %s', kinetic.shape)
overlap = self._get_matrix(mel, 'OVERLAP')
logger.debug('OVERLAP %s', overlap.shape)
mohij = QMolecule.oneeints2mo(hcore, moc)
mohij_b = None
if moc_b is not None:
mohij_b = QMolecule.oneeints2mo(hcore if hcore_b is None else hcore_b, moc_b)
eri = self._get_matrix(mel, 'REGULAR 2E INTEGRALS')
logger.debug('REGULAR 2E INTEGRALS %s', eri.shape)
if moc_b is None and mel.matlist.get('BB MO 2E INTEGRALS') is not None:
# It seems that when using ROHF, where alpha and beta coeffs are
# the same, that integrals
# for BB and BA are included in the output, as well as just AA
# that would have been expected
# Using these fails to give the right answer (is ok for UHF).
# So in this case we revert to
# using 2 electron ints in atomic basis from the output and
# converting them ourselves.
useao2e = True
logger.info(
'Identical A and B coeffs but BB ints are present - using regular 2E ints instead')
if useao2e:
# eri are 2-body in AO. We can convert to MO via the QMolecule
# method but using ints in MO already, as in the else here, is better
mohijkl = QMolecule.twoeints2mo(eri, moc)
mohijkl_bb = None
mohijkl_ba = None
if moc_b is not None:
mohijkl_bb = QMolecule.twoeints2mo(eri, moc_b)
mohijkl_ba = QMolecule.twoeints2mo_general(eri, moc_b, moc_b, moc, moc)
else:
# These are in MO basis but by default will be reduced in size by
# frozen core default so to use them we need to add Window=Full
# above when we augment the config
mohijkl = self._get_matrix(mel, 'AA MO 2E INTEGRALS')
logger.debug('AA MO 2E INTEGRALS %s', mohijkl.shape)
mohijkl_bb = self._get_matrix(mel, 'BB MO 2E INTEGRALS')
logger.debug('BB MO 2E INTEGRALS %s',
'- Not present' if mohijkl_bb is None else mohijkl_bb.shape)
mohijkl_ba = self._get_matrix(mel, 'BA MO 2E INTEGRALS')
logger.debug('BA MO 2E INTEGRALS %s',
'- Not present' if mohijkl_ba is None else mohijkl_ba.shape)
_q_.hcore = hcore
_q_.hcore_b = hcore_b
_q_.kinetic = kinetic
_q_.overlap = overlap
_q_.eri = eri
_q_.mo_onee_ints = mohij
_q_.mo_onee_ints_b = mohij_b
_q_.mo_eri_ints = mohijkl
_q_.mo_eri_ints_bb = mohijkl_bb
_q_.mo_eri_ints_ba = mohijkl_ba
# dipole moment
dipints = self._get_matrix(mel, 'DIPOLE INTEGRALS')
dipints = np.einsum('ijk->kji', dipints)
_q_.x_dip_ints = dipints[0]
_q_.y_dip_ints = dipints[1]
_q_.z_dip_ints = dipints[2]
_q_.x_dip_mo_ints = QMolecule.oneeints2mo(dipints[0], moc)
_q_.x_dip_mo_ints_b = None
_q_.y_dip_mo_ints = QMolecule.oneeints2mo(dipints[1], moc)
_q_.y_dip_mo_ints_b = None
_q_.z_dip_mo_ints = QMolecule.oneeints2mo(dipints[2], moc)
_q_.z_dip_mo_ints_b = None
if moc_b is not None:
_q_.x_dip_mo_ints_b = QMolecule.oneeints2mo(dipints[0], moc_b)
_q_.y_dip_mo_ints_b = QMolecule.oneeints2mo(dipints[1], moc_b)
_q_.z_dip_mo_ints_b = QMolecule.oneeints2mo(dipints[2], moc_b)
nucl_dip = np.einsum('i,ix->x', syms, xyz)
nucl_dip = np.round(nucl_dip, decimals=8)
_q_.nuclear_dipole_moment = nucl_dip
_q_.reverse_dipole_sign = True
return _q_