def compute_integrals(config):
# Get config from input parameters
# Molecule is in this format:
# atoms=H .0 .0 .0; H .0 .0 0.2
# units=Angstrom
# charge=0
# multiplicity=1
# where we support symbol for atom as well as number
if 'atoms' not in config:
raise AquaChemistryError('Atoms is missing')
val = config['atoms']
if val is None:
raise AquaChemistryError('Atoms value is missing')
charge = int(config.get('charge', '0'))
multiplicity = int(config.get('multiplicity', '1'))
units = __checkUnits(config.get('units', 'Angstrom'))
mol = __parseMolecule(val, units, charge, multiplicity)
basis = config.get('basis', 'sto3g')
calc_type = config.get('calc_type', 'rhf').lower()
try:
ehf, enuke, norbs, mohij, mohijkl, orbs, orbs_energy = _calculate_integrals(
mol, basis, calc_type)
except Exception as exc:
raise AquaChemistryError(
'Failed electronic structure computation') from exc
# Create driver level molecule object and populate
_q_ = QMolecule()
# Energies and orbits
_q_._hf_energy = ehf
_q_._nuclear_repulsion_energy = enuke
_q_._num_orbitals = norbs
_q_._num_alpha = mol.nup()
_q_._num_beta = mol.ndown()
_q_._mo_coeff = orbs
_q_._orbital_energies = orbs_energy
# Molecule geometry
_q_._molecular_charge = mol.charge
_q_._multiplicity = mol.multiplicity
_q_._num_atoms = len(mol)
_q_._atom_symbol = []
_q_._atom_xyz = np.empty([len(mol), 3])
atoms = mol.atoms
for _n in range(0, _q_._num_atoms):
atuple = atoms[_n].atuple()
_q_._atom_symbol.append(QMolecule.symbols[atuple[0]])
_q_._atom_xyz[_n][0] = atuple[1]
_q_._atom_xyz[_n][1] = atuple[2]
_q_._atom_xyz[_n][2] = atuple[3]
# 1 and 2 electron integrals
_q_._mo_onee_ints = mohij
_q_._mo_eri_ints = mohijkl
return _q_
def compute_integrals(config):
# Get config from input parameters
# molecule is in PySCF atom string format e.g. "H .0 .0 .0; H .0 .0 0.2"
# other parameters are as per PySCF got.Mole format
if 'atom' not in config:
raise AquaChemistryError('Atom is missing')
val = config['atom']
if val is None:
raise AquaChemistryError('Atom value is missing')
atom = val
basis = config.get('basis', 'sto3g')
unit = config.get('unit', 'Angstrom')
charge = int(config.get('charge', '0'))
spin = int(config.get('spin', '0'))
max_memory = config.get('max_memory')
if max_memory is None:
max_memory = param.MAX_MEMORY
calc_type = config.get('calc_type', 'rhf').lower()
try:
mol = gto.Mole(atom=atom, unit=unit, basis=basis, max_memory=max_memory, verbose=pylogger.QUIET)
mol.symmetry = False
mol.charge = charge
mol.spin = spin
mol.build(parse_arg=False)
ehf, enuke, norbs, mohij, mohijkl, mo_coeff, orbs_energy, x_dip, y_dip, z_dip, nucl_dip = _calculate_integrals(mol, calc_type)
except Exception as exc:
raise AquaChemistryError('Failed electronic structure computation') from exc
# Create driver level molecule object and populate
_q_ = QMolecule()
# Energies and orbits
_q_._hf_energy = ehf
_q_._nuclear_repulsion_energy = enuke
_q_._num_orbitals = norbs
_q_._num_alpha = mol.nelec[0]
_q_._num_beta = mol.nelec[1]
_q_._mo_coeff = mo_coeff
_q_._orbital_energies = orbs_energy
# Molecule geometry
_q_._molecular_charge = mol.charge
_q_._multiplicity = mol.spin + 1
_q_._num_atoms = mol.natm
_q_._atom_symbol = []
_q_._atom_xyz = np.empty([mol.natm, 3])
atoms = mol.atom_coords()
for _n in range(0, _q_._num_atoms):
xyz = mol.atom_coord(_n)
_q_._atom_symbol.append(mol.atom_pure_symbol(_n))
_q_._atom_xyz[_n][0] = xyz[0]
_q_._atom_xyz[_n][1] = xyz[1]
_q_._atom_xyz[_n][2] = xyz[2]
# 1 and 2 electron integrals. h1 & h2 are ready to pass to FermionicOperator
_q_._mo_onee_ints = mohij
_q_._mo_eri_ints = mohijkl
# dipole integrals
_q_._x_dip_mo_ints = x_dip
_q_._y_dip_mo_ints = y_dip
_q_._z_dip_mo_ints = z_dip
# dipole moment
_q_._nuclear_dipole_moment = nucl_dip
_q_._reverse_dipole_sign = True
return _q_
def _parse_matrix_file(self, fname, useAO2E=False):
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_