def plot_h2_lineplot():
bfs = basisset(h2,'6-31G')
solver = rhf(h2,bfs)
solver.converge()
points = [(0,0,z) for z in np.linspace(-5,5)]
lineplot_orbs(points,solver.orbs[:,:2],bfs,True)
return
def test_h2o_averaging(self):
from pyquante2.scf.iterators import AveragingIterator
bfs = basisset(h2o, 'sto3g')
solver = rhf(h2o, bfs)
ens = solver.converge(AveragingIterator)
self.assertAlmostEqual(solver.energy, -74.959847457272502,
match_digits)
def test_lih_averaging(self):
from pyquante2.scf.iterators import AveragingIterator
bfs = basisset(lih, 'sto3g')
solver = rhf(lih, bfs)
ens = solver.converge(AveragingIterator)
self.assertAlmostEqual(solver.energy, -7.8607375733271088,
match_digits)
def test_lih_averaging(self):
bfs = basisset(lih,'sto-3g')
hamiltonian = rhf(bfs)
iterator = AveragingIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -7.860746149768, 6)
def test_h2_631(self):
bfs = basisset(h2,'6-31gss')
hamiltonian = rhf(bfs)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -1.131333590574, 7)
def test_h2(self):
bfs = basisset(h2,'sto-3g')
hamiltonian = rhf(bfs)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -1.117099435262, 7)
def test_h2o_averaging(self):
bfs = basisset(h2o,'sto-3g')
hamiltonian = rhf(bfs)
iterator = AveragingIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -74.959857776754, 5)
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_h2(self):
bfs = basisset(h2,'6-31g**')
solver=rhf(h2,bfs)
solver.converge()
nvirt = len(bfs)-h2.nocc()
emp2 = mp2(solver.i2,solver.orbs,solver.orbe,h2.nocc(),len(bfs)-h2.nocc())
self.assertAlmostEqual(emp2,-0.02632654197486595)
return
def test_CH4(self):
"""CH4 symmetry Td"""
bfs = basisset(ch4,'sto-3g')
hamiltonian = rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -39.726862723517, 6)
def test_CH4(self):
"""CH4 symmetry Td"""
bfs = basisset(CH4, "sto-3g")
solver = rhf(CH4, bfs, libint=True)
ens = solver.converge()
hp5("Ham.h5", solver.i1.V + solver.i1.T)
hp5("TwoS.h5", solver.i2._2e_ints)
self.assertPrecisionEqual(solver.energy, -39.72591203477140)
def test_H2(self):
bfs = basisset(h2,'cc-pvdz')
hamiltonian = rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
nvirt = len(bfs)-h2.nocc()
eccsd = ccsd(hamiltonian, iterator.orbs, iterator.orbe, h2.nocc(), nvirt)
self.assertAlmostEqual(eccsd, -0.034544318453406, 8)
def test_CH4(self):
bfs = basisset(ch4,'cc-pvdz')
hamiltonian = rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
nvirt = len(bfs)-ch4.nocc()
eccsd = ccsd(hamiltonian, iterator.orbs, iterator.orbe, ch4.nocc(), nvirt)
self.assertAlmostEqual(eccsd, -0.189626419684193, 7)
def test_LiH(self):
bfs = basisset(lih,'cc-pvdz')
hamiltonian = rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
nvirt = len(bfs)-lih.nocc()
eccsd = ccsd(hamiltonian, iterator.orbs, iterator.orbe, lih.nocc(), nvirt)
self.assertAlmostEqual(eccsd, -0.032399770519793, 7)
def plot_h2_vtk():
bfs = basisset(h2,'sto3g')
solver = rhf(h2,bfs)
ens = solver.converge()
# Note: these orbitals are not coming out symmetric. Why not??
print(solver)
print(solver.orbs)
vtk_orbs(h2,solver.orbs,bfs,npts=10)
def test_H2(self):
bfs = basisset(h2,'cc-pvdz')
hamiltonian=rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
nvirt = len(bfs)-h2.nocc()
emp2 = mp2(hamiltonian, iterator.orbs, iterator.orbe, h2.nocc(), nvirt)
self.assertAlmostEqual(emp2, -0.026304104341, 6)
def test_BrF5(self):
"""BrF5 symmetry C4v"""
BrF5 = read_xyz('./molfiles/BrF5.xyz')
bfs = basisset(BrF5,'sto-3g')
hamiltonian = rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -3035.015731331871, 4)
def test_HBr(self):
"""HBr"""
HBr = read_xyz('./molfiles/HBr.xyz')
bfs = basisset(HBr,'sto-3g')
hamiltonian = rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -2545.887434128302, 4)
def test_C2H2Cl2(self):
"""C2H2Cl2 symmetry C2H"""
C2H2Cl2 = read_xyz('./molfiles/C2H2Cl2.xyz')
bfs = basisset(C2H2Cl2,'sto-3g')
hamiltonian = rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -967.533150337277, 4)
def test_H2O_4(self):
"""H2O tethramer symmetry S4"""
H2O4 = read_xyz('./molfiles/H2O_4.xyz')
bfs = basisset(H2O4,'sto-3g')
hamiltonian = rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -299.909789863537, 5)
def test_h2(self):
bfs = basisset(h2, '6-31g**')
solver = rhf(h2, bfs)
solver.converge()
nvirt = len(bfs) - h2.nocc()
emp2 = mp2(solver.i2, solver.orbs, solver.orbe, h2.nocc(),
len(bfs) - h2.nocc())
self.assertAlmostEqual(emp2, -0.02632654197486595)
return
def test_N8(self):
"""N8"""
N8 = read_xyz('./molfiles/N8.xyz')
bfs = basisset(N8,'cc-pvdz')
hamiltonian = rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -434.992755329296, 5)
def test_LiH(self):
bfs = basisset(lih,'cc-pvdz')
hamiltonian=rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
nvirt = len(bfs)-lih.nocc()
emp2 = mp2(hamiltonian, iterator.orbs, iterator.orbe, lih.nocc(), nvirt)
self.assertAlmostEqual(emp2, -0.023948620832, 5)
def test_CH4(self):
bfs = basisset(ch4,'cc-pvdz')
hamiltonian=rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
nvirt = len(bfs)-ch4.nocc()
emp2 = mp2(hamiltonian, iterator.orbs, iterator.orbe, ch4.nocc(), nvirt)
self.assertAlmostEqual(emp2, -0.166640105042, 5)
def test_C8H8(self):
"""C8H8"""
C8H8 = read_xyz('./molfiles/C8H8.xyz')
bfs = basisset(C8H8,'sto-6g')
hamiltonian = rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -306.765545547300, 5)
def test_B12(self):
"""B12 symmetry Ih"""
B12 = read_xyz('./molfiles/B12.xyz')
bfs = basisset(B12,'sto-3g')
hamiltonian = rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -290.579419642829, 0)
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_HBr(self):
HBr = read_xyz('./molfiles/HBr.xyz')
bfs = basisset(HBr,'cc-pvdz')
hamiltonian=rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
nvirt = len(bfs)-HBr.nocc()
emp2 = mp2(hamiltonian, iterator.orbs, iterator.orbe, HBr.nocc(), nvirt)
self.assertAlmostEqual(emp2, -0.153284373119, 6)
def test_C24(self):
# FAIL
"""C24 symmetry Th"""
C24 = read_xyz('./molfiles/C24.xyz')
bfs = basisset(C24,'sto-3g')
hamiltonian = rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -890.071915453874, 0)
def test_N8(self):
# 2.8 Gb memory needed
N8 = read_xyz('./molfiles/N8.xyz')
bfs = basisset(N8,'cc-pvdz')
hamiltonian=rhf(bfs, twoe_factory=libint_twoe_integrals)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
nvirt = len(bfs)-N8.nocc()
emp2 = mp2(hamiltonian, iterator.orbs, iterator.orbe, N8.nocc(), nvirt)
self.assertAlmostEqual(emp2, -1.328348475507, 6)
def test_makepyquante(self):
# Test pyquante2 bridge
from pyquante2 import molecule, rhf, h2o, basisset
bfs = basisset(h2o)
# Copied from water_ccsd.log
refmol = molecule(
[(8, 0.0, 0.0, 0.119159), (1, 0, 0.790649, -0.476637),
(1, 0, -0.790649, -0.476637)],
units="Angstroms",
)
refsolver = rhf(refmol, bfs)
refsolver.converge()
pyqmol = cclib2pyquante.makepyquante(self.data)
pyqsolver = rhf(pyqmol, bfs)
pyqsolver.converge()
assert_array_almost_equal(refsolver.energies[-1],
pyqsolver.energies[-1],
decimal=6)
def test_h4(self):
h4 = molecule([
(1, 0.00000000, 0.00000000, 0.36628549),
(1, 0.00000000, 0.00000000, -0.36628549),
(1, 0.00000000, 4.00000000, 0.36628549),
(1, 0.00000000, 4.00000000, -0.36628549),
],
units='Angstrom')
bfs = basisset(h4,'sto3g')
solver = rhf(h4,bfs)
ens = solver.converge()
self.assertAlmostEqual(solver.energy,-2.234185653441159,6)
def test_h4(self):
h4 = molecule([
(1, 0.00000000, 0.00000000, 0.36628549),
(1, 0.00000000, 0.00000000, -0.36628549),
(1, 0.00000000, 4.00000000, 0.36628549),
(1, 0.00000000, 4.00000000, -0.36628549),
],
units='Angstrom')
bfs = basisset(h4, 'sto3g')
solver = rhf(h4, bfs)
ens = solver.converge()
self.assertAlmostEqual(solver.energy, -2.234185653441159, match_digits)
def test_h4(self):
h4 = molecule([
(1, 0.00000000, 0.00000000, 0.36628549),
(1, 0.00000000, 0.00000000, -0.36628549),
(1, 0.00000000, 4.00000000, 0.36628549),
(1, 0.00000000, 4.00000000, -0.36628549),
],
units='Angstrom')
bfs = basisset(h4,'sto-3g')
hamiltonian = rhf(bfs)
iterator = SCFIterator(hamiltonian)
iterator.converge()
self.assertTrue(iterator.converged)
self.assertAlmostEqual(iterator.energy, -2.234185358600, 7)
def test_lih(self):
bfs = basisset(lih, 'sto3g')
solver = rhf(lih, bfs)
ens = solver.converge()
self.assertAlmostEqual(solver.energy, -7.8607437, match_digits)
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_
from pyquante2 import molecule, rhf, uhf, h2, lih, basisset
from pyquante2.graphics.maya import view_mol, view_orb, view_bonds
bfs = basisset(h2)
solver = rhf(h2, bfs)
ens = solver.converge()
orbs = solver.orbs
view_mol(h2, doshow=False)
view_bonds(h2, doshow=False)
view_orb(h2, orbs[:, 1], bfs, planes=[('x', False)])
from pyquante2 import molecule,rhf,uhf,h2,lih,basisset
from pyquante2.graphics.maya import view_mol, view_orb, view_bonds
bfs = basisset(h2)
solver = rhf(h2,bfs)
ens = solver.converge()
orbs = solver.orbs
view_mol(h2,doshow=False)
view_bonds(h2,doshow=False)
view_orb(h2,orbs[:,1],bfs,planes=[('x',False)])
def test_h2o(self):
bfs = basisset(h2o, 'sto3g')
solver = rhf(h2o, bfs)
ens = solver.converge()
self.assertAlmostEqual(solver.energy, -74.959856675848712,
match_digits)
def test_h2o(self):
bfs = basisset(h2o,'sto3g')
solver = rhf(h2o,bfs)
ens = solver.converge()
self.assertAlmostEqual(solver.energy,-74.959856675848712)
def test_h2o_averaging(self):
from pyquante2.scf.iterators import AveragingIterator
bfs = basisset(h2o,'sto3g')
solver = rhf(h2o,bfs)
ens = solver.converge(AveragingIterator)
self.assertAlmostEqual(solver.energy,-74.959847457272502)
def test_h2_631(self):
bfs = basisset(h2, '6-31G**')
solver = rhf(h2, bfs)
ens = solver.converge()
self.assertAlmostEqual(solver.energy, -1.1313335790123258,
match_digits)
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_dipole_LiH_H2_HF_STO_3G():
"""Example: LiH--H2, neutral singlet, RHF/STO-3G
"""
# X -4.8174 Y 0.9597 Z -0.0032
# Tot 4.9121
qchem_total_components_debye = np.array([-4.8174, 0.9597, -0.0032])
qchem_total_norm_debye = 4.9121
# DX DY DZ /D/ (DEBYE)
# -4.817430 0.959709 -0.003226 4.912096
gamess_total_components_debye = np.array([-4.817430, 0.959709, -0.003226])
gamess_total_norm_debye = 4.912096
# Dipole moment
# -------------
# au Debye C m (/(10**-30)
# 1.932564 4.912086 16.384956
# Dipole moment components
# ------------------------
# au Debye C m (/(10**-30)
# x -1.89531979 -4.81742209 -16.06919039
# y 0.37757524 0.95970046 3.20121617
# z -0.00126928 -0.00322619 -0.01076141
# Units: 1 a.u. = 2.54175 Debye
# 1 a.u. = 8.47835 (10**-30) C m (SI)
dalton_total_components_debye = np.array(
[-4.81742209, 0.95970046, -0.00322619])
dalton_total_norm_debye = 4.912086
dalton_total_components_au = np.array(
[-1.89531979, 0.37757524, -0.00126928])
dalton_total_norm_au = 1.932564
dalton_center_of_mass_au = np.array(
[-2.468120057069, 2.168586684080, -0.007311931664])
# ORCA uses the center of mass by default.
# Electronic contribution: -4.65190 -3.56492 0.02433
# Nuclear contribution : 2.75658 3.94249 -0.02560
# -----------------------------------------
# Total Dipole Moment : -1.89532 0.37758 -0.00127
# -----------------------------------------
# Magnitude (a.u.) : 1.93256
# Magnitude (Debye) : 4.91219
orca_electronic_components_au = np.array([-4.65190, -3.56492, 0.02433])
orca_nuclear_components_au = np.array([2.75658, 3.94249, -0.02560])
orca_total_components_au = np.array([-1.89532, 0.37758, -0.00127])
assert np.all(
((orca_nuclear_components_au + orca_electronic_components_au) -
orca_total_components_au) < 1.0e-14)
orca_total_norm_au = 1.93256
assert abs(orca_total_norm_au -
npl.norm(orca_total_components_au)) < 1.0e-5
orca_total_norm_debye = 4.91219
# Origin is the Cartesian origin
# Nuclear Dipole Moment: (a.u.)
# X: -12.0198 Y: 17.0002 Z: -0.0698
# Electronic Dipole Moment: (a.u.)
# X: 10.1245 Y: -16.6226 Z: 0.0685
# Dipole Moment: (a.u.)
# X: -1.8953 Y: 0.3776 Z: -0.0013 Total: 1.9326
# Dipole Moment: (Debye)
# X: -4.8174 Y: 0.9597 Z: -0.0032 Total: 4.9121
psi4_nuclear_components_au = np.array([-12.0198, 17.0002, -0.0698])
psi4_electronic_components_au = np.array([10.1245, -16.6226, 0.0685])
psi4_total_components_au = np.array([-1.8953, 0.3776, -0.0013])
assert np.all(
((psi4_nuclear_components_au + psi4_electronic_components_au) -
psi4_total_components_au) < 1.0e-14)
psi4_total_norm_au = 1.9326
assert abs(psi4_total_norm_au -
npl.norm(psi4_total_components_au)) < 1.0e-4
psi4_total_components_debye = np.array([-4.8174, 0.9597, -0.0032])
psi4_total_norm_debye = 4.9121
assert abs(psi4_total_norm_debye -
npl.norm(psi4_total_components_debye)) < 1.0e-4
# pylint: disable=bad-whitespace
mol = molecule([(3, -1.67861, 0.61476, -0.00041),
(1, -0.01729, 0.38654, -0.00063),
(1, -0.84551, 3.08551, -0.00236),
(1, -0.46199, 3.67980, -0.03270)],
units='Angstrom',
charge=0,
multiplicity=1,
name='LiH_H2')
nuccoords = np.array([atom.r for atom in mol.atoms])
nuccharges = np.array([atom.Z for atom in mol.atoms])[..., np.newaxis]
masses = get_isotopic_masses(nuccharges[:, 0])
mol_basis = pyquante2.basisset(mol, 'STO-3G'.lower())
solver = pyquante2.rhf(mol, mol_basis)
solver.converge(tol=1e-11, maxiters=1000)
C = solver.orbs
NOa = mol.nup()
NOb = mol.ndown()
assert NOa == NOb
D = 2 * np.dot(C[:, :NOa], C[:, :NOa].T)
origin_zero = np.array([0.0, 0.0, 0.0])
ref = psi4_nuclear_components_au
res = nuclear_dipole_contribution(nuccoords, nuccharges, origin_zero)
abs_diff = np.absolute(ref - res)
assert np.all(abs_diff < 1.0e-4)
ref = psi4_electronic_components_au
res = electronic_dipole_contribution_pyquante(D, mol_basis, origin_zero)
abs_diff = np.absolute(ref - res)
assert np.all(abs_diff < 1.0e-4)
res1 = nuclear_dipole_contribution(nuccoords, nuccharges, origin_zero)
res2 = nuclear_dipole_contribution_pyquante(mol, origin_zero)
assert np.all((res1 - res2) < 1.0e-15)
ref = dalton_center_of_mass_au
res = calc_center_of_mass_pyquante(mol)
abs_diff = np.absolute(ref - res)
assert np.all(abs_diff < 1.0e-6)
com = res
assert np.all(np.equal(np.sign(com), np.sign(ref)))
res1 = calc_center_of_mass_pyquante(mol)
res2 = calc_center_of_mass(nuccoords, masses)
assert np.all((res1 - res2) < 1.0e-15)
ncc = calc_center_of_nuclear_charge(nuccoords, nuccharges)
assert np.all(
(ncc - np.array([-2.00330482, 2.83337011, -0.01162811])) < 1.0e-8)
ecc = calc_center_of_electronic_charge_pyquante(D, mol_basis)
assert np.all(
(ecc - np.array([-1.68741793, 2.77044101, -0.01141657])) < 1.0e-8)
origin_zero = calculate_origin_pyquante('zero',
nuccoords,
nuccharges,
D,
mol_basis,
do_print=True)
dipole_zero = calculate_dipole_pyquante(nuccoords,
nuccharges,
origin_zero,
D,
mol_basis,
do_print=True)
origin_com = calculate_origin_pyquante('com',
nuccoords,
nuccharges,
D,
mol_basis,
do_print=True)
dipole_com = calculate_dipole_pyquante(nuccoords,
nuccharges,
origin_com,
D,
mol_basis,
do_print=True)
origin_ncc = calculate_origin_pyquante('ncc',
nuccoords,
nuccharges,
D,
mol_basis,
do_print=True)
dipole_ncc = calculate_dipole_pyquante(nuccoords,
nuccharges,
origin_ncc,
D,
mol_basis,
do_print=True)
origin_ecc = calculate_origin_pyquante('ecc',
nuccoords,
nuccharges,
D,
mol_basis,
do_print=True)
dipole_ecc = calculate_dipole_pyquante(nuccoords,
nuccharges,
origin_ecc,
D,
mol_basis,
do_print=True)
# ORCA: center of mass; TODO why is the answer so different?
n_dipole_com_au = nuclear_dipole_contribution(nuccoords, nuccharges,
origin_com)
assert np.all(
np.equal(np.sign(n_dipole_com_au),
np.sign(orca_nuclear_components_au)))
print(np.absolute(orca_nuclear_components_au - n_dipole_com_au))
e_dipole_com_au = electronic_dipole_contribution_pyquante(
D, mol_basis, origin_com)
assert np.all(
np.equal(np.sign(e_dipole_com_au),
np.sign(orca_electronic_components_au)))
print(np.absolute(orca_electronic_components_au - e_dipole_com_au))
# For an uncharged system, these should all be identical.
my_ref = np.array([-1.89532134e+00, 3.77574623e-01, -1.26926571e-03])
for res in (dipole_zero, dipole_com, dipole_ncc, dipole_ecc):
assert np.all(np.absolute(my_ref - res) < 1.0e-8)
return
def test_h2(self):
bfs = basisset(h2, 'sto3g')
solver = rhf(h2, bfs)
ens = solver.converge()
self.assertAlmostEqual(solver.energy, -1.117099582955609, match_digits)
