def run_pyquante(self):
"""Runs the PyQuante calculation.
This method is part of the public interface to allow the user to easily overwrite it in a
subclass to further tailor the behavior to some specific use case.
Raises:
QiskitNatureError: If an invalid HF method type was supplied.
"""
# pylint: disable=import-error
from pyquante2 import rhf, uhf, rohf, basisset
self._bfs = basisset(self._mol, self.basis.value)
if self.method == MethodType.RHF:
self._calc = rhf(self._mol, self._bfs)
elif self.method == MethodType.ROHF:
self._calc = rohf(self._mol, self._bfs)
elif self.method == MethodType.UHF:
self._calc = uhf(self._mol, self._bfs)
else:
raise QiskitNatureError(f"Invalid method type: {self.method}")
self._calc.converge(tol=self.tol, maxiters=self.maxiters)
logger.debug("PyQuante2 processing information:\n%s", self._calc)
def test_oh(self):
bfs = basisset(oh,'sto-3g')
hamiltonian = rohf(bfs)
iterator = ROSCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -74.359151530162, 5)
def test_N8(self):
"""N8"""
N8 = read_xyz('./molfiles/N8.xyz')
bfs = basisset(N8,'cc-pvdz')
hamiltonian = rohf(bfs, twoe_factory=libint_twoe_integrals)
iterator = ROSCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -434.992755329296, 5)
def test_CF3(self):
"""CF3 radical"""
CF3 = read_xyz('./molfiles/CF3.xyz')
bfs = basisset(CF3,'sto-3g')
hamiltonian = rohf(bfs, twoe_factory=libint_twoe_integrals)
iterator = ROSCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -331.479340943449, 5)
def _calculate_integrals(molecule, basis='sto3g', calc_type='rhf'):
"""Function to calculate the one and two electron terms. Perform a Hartree-Fock calculation in
the given basis.
Args:
molecule : A pyquante2 molecular object.
basis : The basis set for the electronic structure computation
calc_type: rhf, uhf, rohf
Returns:
ehf : Hartree-Fock energy
enuke: Nuclear repulsion energy
norbs : Number of orbitals
mohij : One electron terms of the Hamiltonian.
mohijkl : Two electron terms of the Hamiltonian.
orbs: Molecular orbital coefficients
orbs_energy: Orbital energies
"""
bfs = basisset(molecule, basis)
integrals = onee_integrals(bfs, molecule)
hij = integrals.T + integrals.V
hijkl_compressed = twoe_integrals(bfs)
# convert overlap integrals to molecular basis
# calculate the Hartree-Fock solution of the molecule
if calc_type == 'rhf':
solver = rhf(molecule, bfs)
elif calc_type == 'rohf':
solver = rohf(molecule, bfs)
elif calc_type == 'uhf':
solver = uhf(molecule, bfs)
else:
raise QiskitChemistryError('Invalid calc_type: {}'.format(calc_type))
logger.debug('Solver name {}'.format(solver.name))
ehf = solver.converge()
if hasattr(solver, 'orbs'):
orbs = solver.orbs
else:
orbs = solver.orbsa
norbs = len(orbs)
if hasattr(solver, 'orbe'):
orbs_energy = solver.orbe
else:
orbs_energy = solver.orbea
enuke = molecule.nuclear_repulsion()
# Get ints in molecular orbital basis
mohij = simx(hij, orbs)
mohijkl_compressed = transformintegrals(hijkl_compressed, orbs)
mohijkl = np.zeros((norbs, norbs, norbs, norbs))
for i in range(norbs):
for j in range(norbs):
for k in range(norbs):
for l in range(norbs):
mohijkl[i, j, k,
l] = mohijkl_compressed[ijkl2intindex(i, j, k, l)]
return ehf[0], enuke, norbs, mohij, mohijkl, orbs, orbs_energy
def test_CrCO6(self):
# FAIL
"""Cr(CO)6 symmetry Oh
Reference: Whitaker, A.; Jeffery, J. W. Acta Cryst. 1967, 23, 977. DOI: 10.1107/S0365110X67004153
"""
CrCO6 = read_xyz('./molfiles/CrCO6.xyz')
bfs = basisset(CrCO6,'sto-3g')
hamiltonian = rohf(bfs, twoe_factory=libint_twoe_integrals)
iterator = ROSCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -1699.539642257497, 0)
def _calculate_integrals(molecule,
basis="sto3g",
hf_method="rhf",
tol=1e-8,
maxiters=100):
"""Function to calculate the one and two electron terms. Perform a Hartree-Fock calculation in
the given basis.
Args:
molecule (pyQuante2.molecule): A pyquante2 molecular object.
basis (str) : The basis set for the electronic structure computation
hf_method (str): rhf, uhf, rohf
tol (float): tolerance
maxiters (int): max. iterations
Returns:
QMolecule: QMolecule populated with driver integrals etc
Raises:
QiskitNatureError: Invalid hf methods type
"""
bfs = basisset(molecule, basis)
integrals = onee_integrals(bfs, molecule)
hij = integrals.T + integrals.V
hijkl = twoe_integrals(bfs)
# convert overlap integrals to molecular basis
# calculate the Hartree-Fock solution of the molecule
if hf_method == "rhf":
solver = rhf(molecule, bfs)
elif hf_method == "rohf":
solver = rohf(molecule, bfs)
elif hf_method == "uhf":
solver = uhf(molecule, bfs)
else:
raise QiskitNatureError("Invalid hf_method type: {}".format(hf_method))
ehf = solver.converge(tol=tol, maxiters=maxiters)
logger.debug("PyQuante2 processing information:\n%s", solver)
if hasattr(solver, "orbs"):
orbs = solver.orbs
orbs_b = None
else:
orbs = solver.orbsa
orbs_b = solver.orbsb
norbs = len(orbs)
if hasattr(solver, "orbe"):
orbs_energy = solver.orbe
orbs_energy_b = None
else:
orbs_energy = solver.orbea
orbs_energy_b = solver.orbeb
enuke = molecule.nuclear_repulsion()
# Get ints in molecular orbital basis
mohij = simx(hij, orbs)
mohij_b = None
if orbs_b is not None:
mohij_b = simx(hij, orbs_b)
eri = hijkl.transform(np.identity(norbs))
mohijkl = hijkl.transform(orbs)
mohijkl_bb = None
mohijkl_ba = None
if orbs_b is not None:
mohijkl_bb = hijkl.transform(orbs_b)
mohijkl_ba = np.einsum("aI,bJ,cK,dL,abcd->IJKL", orbs_b, orbs_b, orbs,
orbs, hijkl[...])
# Create driver level molecule object and populate
_q_ = QMolecule()
_q_.origin_driver_version = "?" # No version info seems available to access
# Energies and orbits
_q_.hf_energy = ehf[0]
_q_.nuclear_repulsion_energy = enuke
_q_.num_molecular_orbitals = norbs
_q_.num_alpha = molecule.nup()
_q_.num_beta = molecule.ndown()
_q_.mo_coeff = orbs
_q_.mo_coeff_b = orbs_b
_q_.orbital_energies = orbs_energy
_q_.orbital_energies_b = orbs_energy_b
# Molecule geometry
_q_.molecular_charge = molecule.charge
_q_.multiplicity = molecule.multiplicity
_q_.num_atoms = len(molecule)
_q_.atom_symbol = []
_q_.atom_xyz = np.empty([len(molecule), 3])
atoms = molecule.atoms
for n_i in range(0, _q_.num_atoms):
atuple = atoms[n_i].atuple()
_q_.atom_symbol.append(QMolecule.symbols[atuple[0]])
_q_.atom_xyz[n_i][0] = atuple[1]
_q_.atom_xyz[n_i][1] = atuple[2]
_q_.atom_xyz[n_i][2] = atuple[3]
# 1 and 2 electron integrals
_q_.hcore = hij
_q_.hcore_b = None
_q_.kinetic = integrals.T
_q_.overlap = integrals.S
_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
return _q_
def _calculate_integrals(molecule, basis='sto3g', hf_method='rhf', tol=1e-8, maxiters=100):
"""Function to calculate the one and two electron terms. Perform a Hartree-Fock calculation in
the given basis.
Args:
molecule : A pyquante2 molecular object.
basis : The basis set for the electronic structure computation
hf_method: rhf, uhf, rohf
Returns:
QMolecule: QMolecule populated with driver integrals etc
"""
bfs = basisset(molecule, basis)
integrals = onee_integrals(bfs, molecule)
hij = integrals.T + integrals.V
hijkl = twoe_integrals(bfs)
# convert overlap integrals to molecular basis
# calculate the Hartree-Fock solution of the molecule
if hf_method == 'rhf':
solver = rhf(molecule, bfs)
elif hf_method == 'rohf':
solver = rohf(molecule, bfs)
elif hf_method == 'uhf':
solver = uhf(molecule, bfs)
else:
raise QiskitChemistryError('Invalid hf_method type: {}'.format(hf_method))
ehf = solver.converge(tol=tol, maxiters=maxiters)
logger.debug('PyQuante2 processing information:\n{}'.format(solver))
if hasattr(solver, 'orbs'):
orbs = solver.orbs
orbs_B = None
else:
orbs = solver.orbsa
orbs_B = solver.orbsb
norbs = len(orbs)
if hasattr(solver, 'orbe'):
orbs_energy = solver.orbe
orbs_energy_B = None
else:
orbs_energy = solver.orbea
orbs_energy_B = solver.orbeb
enuke = molecule.nuclear_repulsion()
# Get ints in molecular orbital basis
mohij = simx(hij, orbs)
mohij_B = None
if orbs_B is not None:
mohij_B = simx(hij, orbs_B)
eri = hijkl.transform(np.identity(norbs))
mohijkl = hijkl.transform(orbs)
mohijkl_BB = None
mohijkl_BA = None
if orbs_B is not None:
mohijkl_BB = hijkl.transform(orbs_B)
mohijkl_BA = np.einsum('aI,bJ,cK,dL,abcd->IJKL', orbs_B, orbs_B, orbs, orbs, hijkl[...])
# Create driver level molecule object and populate
_q_ = QMolecule()
_q_.origin_driver_version = '?' # No version info seems available to access
# Energies and orbits
_q_.hf_energy = ehf[0]
_q_.nuclear_repulsion_energy = enuke
_q_.num_orbitals = norbs
_q_.num_alpha = molecule.nup()
_q_.num_beta = molecule.ndown()
_q_.mo_coeff = orbs
_q_.mo_coeff_B = orbs_B
_q_.orbital_energies = orbs_energy
_q_.orbital_energies_B = orbs_energy_B
# Molecule geometry
_q_.molecular_charge = molecule.charge
_q_.multiplicity = molecule.multiplicity
_q_.num_atoms = len(molecule)
_q_.atom_symbol = []
_q_.atom_xyz = np.empty([len(molecule), 3])
atoms = molecule.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_.hcore = hij
_q_.hcore_B = None
_q_.kinetic = integrals.T
_q_.overlap = integrals.S
_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
return _q_
def test_li_rohf(self):
from pyquante2 import li
bfs = basisset(li, 'sto3g')
solver = rohf(li, bfs)
Es = solver.converge()
self.assertAlmostEqual(solver.energy, -7.31552591799, match_digits)
def test_oh_rohf(self):
from pyquante2 import oh
bfs = basisset(oh, 'sto3g')
solver = rohf(oh, bfs)
Es = solver.converge()
self.assertAlmostEqual(solver.energy, -74.3591663559, match_digits)
