def zmatrix_tomolecule(zmt):
"Create a pyquante2 molecule from a zmatrix"
from pyquante2.geo.elements import sym2no
from pyquante2.geo.molecule import molecule
atuples = [(sym2atno[sym], x, y, z) for sym, x, y, z in z2xyz(geo)]
return molecule(atuples)
def zmatrix_tomolecule(zmt):
"Create a pyquante2 molecule from a zmatrix"
from pyquante2.geo.elements import sym2no
from pyquante2.geo.molecule import molecule
atuples = [(sym2atno[sym],x,y,z) for sym,x,y,z in z2xyz(geo)]
return molecule(atuples)
"""
A collection of molecules for testing and fun.
>>> h
Stoichiometry = H, Charge = 0, Multiplicity = 2
1 H 0.000000 0.000000 0.000000
"""
from pyquante2.geo.molecule import molecule,read_xyz_lines
h = molecule([(1,0,0,0)],name='Hydrogen')
h2 = molecule([(1, 0.00000000, 0.00000000, 0.36628549),
(1, 0.00000000, 0.00000000, -0.36628549)],
units='Angstrom',
name='Hydrogen')
h2o = molecule([(8, 0.00000000, 0.00000000, 0.04851804),
(1, 0.75300223, 0.00000000, -0.51923377),
(1, -0.75300223, 0.00000000, -0.51923377)],
units='Angstrom',
name='Water')
oh = molecule([(8, 0.00000000, 0.00000000, -0.08687037),
(1, 0.00000000, 0.00000000, 0.86464814)],
units='Angstrom',
multiplicity=2,
name='Hydroxide')
he = molecule(atomlist = [(2,0,0,0)],name='Helium')
he_triplet = molecule(atomlist = [(2,0,0,0)],name='Helium',multiplicity=3)
"""
A collection of molecules for testing and fun.
>>> h
Stoichiometry = H, Charge = 0, Multiplicity = 2
1 H 0.000000 0.000000 0.000000
"""
from pyquante2.geo.molecule import molecule,read_xyz_lines
h = molecule([(1,0,0,0)],name='Hydrogen')
h2 = molecule([(1, 0.00000000, 0.00000000, 0.36628549),
(1, 0.00000000, 0.00000000, -0.36628549)],
units='Angstrom',
name='Hydrogen')
h2o = molecule([(8, 0.00000000, 0.00000000, 0.04851804),
(1, 0.75300223, 0.00000000, -0.51923377),
(1, -0.75300223, 0.00000000, -0.51923377)],
units='Angstrom',
name='Water')
oh = molecule([(8, 0.00000000, 0.00000000, -0.08687037),
(1, 0.00000000, 0.00000000, 0.86464814)],
units='Angstrom',
multiplicity=2,
name='Hydroxide')
he = molecule(atomlist = [(2,0,0,0)],name='Helium')
he_triplet = molecule(atomlist = [(2,0,0,0)],name='Helium',multiplicity=3)
def main(args):
mol = molecule([(1, 0.000, 0.000, 0.000),
(8, 0.000, 0.000, 0.9697)],
units='Angstrom',
charge=0,
multiplicity=2,
name='hydroxyl_radical')
mol_basis = pyquante2.basisset(mol, 'STO-3G'.lower())
solver = pyquante2.uhf(mol, mol_basis)
solver.converge(tol=1e-11, maxiters=1000)
print(solver)
C_alph = solver.orbsa
C_beta = solver.orbsb
NOa = mol.nup()
NOb = mol.ndown()
D_alph = np.dot(C_alph[:, :NOa], C_alph[:, :NOa].transpose())
D_beta = np.dot(C_beta[:, :NOb], C_beta[:, :NOb].transpose())
D = D_alph + D_beta
if args.debug:
print(D_alph)
print(D_beta)
# This is origin used for the multipole analysis.
# origin = np.array([0.0, 0.0, 0.0])
origin = calc_center_of_mass(mol)
print('Origin used: ({}, {}, {})'.format(*origin))
M100_AO = makeM(mol_basis.bfs, origin, [1, 0, 0])
M010_AO = makeM(mol_basis.bfs, origin, [0, 1, 0])
M001_AO = makeM(mol_basis.bfs, origin, [0, 0, 1])
M100_MO = D * M100_AO
M010_MO = D * M010_AO
M001_MO = D * M001_AO
if args.debug:
print('M100_AO')
print(M100_AO)
print('M010_AO')
print(M010_AO)
print('M001_AO')
print(M001_AO)
print('M100_MO')
print(M100_MO)
print('M010_MO')
print(M010_MO)
print('M001_MO')
print(M001_MO)
dipole_electronic_atomic_units = -np.array([np.sum(M100_MO), np.sum(M010_MO), np.sum(M001_MO)])
convfac_au_to_debye = 2.541746230211
dipole_nuclear_atomic_units = nuclear_dipole_contribution(mol, origin)
dipole_total_atomic_units = dipole_nuclear_atomic_units + dipole_electronic_atomic_units
dipole_magnitude_atomic_units = npl.norm(dipole_total_atomic_units)
dipole_magnitude_debye = convfac_au_to_debye * dipole_magnitude_atomic_units
print('=============')
print('Dipole')
print('=============')
print('electronic (a.u.) {:8.5f} {:8.5f} {:8.5f}'.format(*dipole_electronic_atomic_units))
print(' nuclear (a.u.) {:8.5f} {:8.5f} {:8.5f}'.format(*dipole_nuclear_atomic_units))
print(' total (a.u.) {:8.5f} {:8.5f} {:8.5f}'.format(*dipole_total_atomic_units))
print('Dipole moment magnitude')
print(' {:8.5f} a.u'.format(dipole_magnitude_atomic_units))
print(' {:8.5f} D'.format(dipole_magnitude_debye))
print('=============')
print('Origins')
print('=============')
print(' center of mass: {:f} {:f} {:f}'.format(*calc_center_of_mass(mol)))
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_dipole_hydroxyl_radical_HF_STO_3G():
"""Example: OH^{.}, neutral doublet, UHF/STO-3G
"""
qchem_final_energy = -74.3626375184
# Dipole Moment (Debye)
# X 0.0000 Y -0.0000 Z -1.2788
# Tot 1.2788
qchem_total_components_debye = np.array([0.0000, 0.0000, -1.2788])
qchem_total_norm_debye = 1.2788
dalton_final_energy = -74.361530725817
# Dipole moment
# -------------
# au Debye C m (/(10**-30)
# 0.502283 1.276676 4.258534
# Dipole moment components
# ------------------------
# au Debye C m (/(10**-30)
# x -0.00000000 -0.00000000 -0.00000000
# y -0.00000000 -0.00000000 -0.00000000
# z -0.50228316 -1.27667636 -4.25853394
# Units: 1 a.u. = 2.54175 Debye
# 1 a.u. = 8.47835 (10**-30) C m (SI)
dalton_total_components_debye = np.array([0.0, 0.0, -1.27667636])
dalton_total_norm_debye = 1.276676
dalton_total_components_au = np.array([0.0, 0.0, -0.50228316])
dalton_total_norm_au = 0.502283
dalton_center_of_mass_au = np.array([0.0, 0.0, 1.723849254747])
# ORCA uses the center of mass by default.
orca_final_energy = -74.362637379044
# Electronic contribution: 0.00000 -0.00000 0.35185
# Nuclear contribution : 0.00000 0.00000 -0.85498
# -----------------------------------------
# Total Dipole Moment : 0.00000 -0.00000 -0.50312
# -----------------------------------------
# Magnitude (a.u.) : 0.50312
# Magnitude (Debye) : 1.27884
orca_electronic_components_au = np.array([0.0, 0.0, 0.35185])
orca_nuclear_components_au = np.array([0.0, 0.0, -0.85498])
orca_total_components_au = np.array([0.0, 0.0, -0.50312])
assert np.all(
((orca_nuclear_components_au + orca_electronic_components_au) -
orca_total_components_au) < 1.0e-14)
orca_total_norm_au = 0.50312
assert abs(orca_total_norm_au -
npl.norm(orca_total_components_au)) < 1.0e-5
orca_total_norm_debye = 1.27884
# prop_orca_coe.out
# 505:Coordinates of the origin ... 0.00000000 -0.00000000 1.68476265 (bohrs)
# prop_orca_com.out
# 505:Coordinates of the origin ... 0.00000000 0.00000000 1.72385761 (bohrs)
# prop_orca_con.out
# 505:Coordinates of the origin ... 0.00000000 0.00000000 1.62885994 (bohrs)
orca_center_of_electronic_charge_au = np.array(
[0.00000000, 0.00000000, 1.68476265])
orca_center_of_mass_au = np.array([0.00000000, 0.00000000, 1.72385761])
orca_center_of_nuclear_charge_au = np.array(
[0.00000000, 0.00000000, 1.62885994])
psi4_final_energy = -74.3626375190713986
# Origin is the Cartesian origin
# Nuclear Dipole Moment: (a.u.)
# X: 0.0000 Y: 0.0000 Z: 14.6597
# Electronic Dipole Moment: (a.u.)
# X: -0.0000 Y: 0.0000 Z: -15.1629
# Dipole Moment: (a.u.)
# X: -0.0000 Y: 0.0000 Z: -0.5031 Total: 0.5031
# Dipole Moment: (Debye)
# X: -0.0000 Y: 0.0000 Z: -1.2788 Total: 1.2788
psi4_nuclear_components_au = np.array([0.0, 0.0, 14.6597])
psi4_electronic_components_au = np.array([0.0, 0.0, -15.1629])
psi4_total_components_au = np.array([0.0, 0.0, -0.5031])
assert np.all(
((psi4_nuclear_components_au + psi4_electronic_components_au) -
psi4_total_components_au) < 1.0e-14)
psi4_total_norm_au = 0.5031
assert abs(psi4_total_norm_au -
npl.norm(psi4_total_components_au)) < 1.0e-4
psi4_total_components_debye = np.array([0.0, 0.0, -1.2788])
psi4_total_norm_debye = 1.2788
assert abs(psi4_total_norm_debye -
npl.norm(psi4_total_components_debye)) < 1.0e-4
mol = molecule([(1, 0.000, 0.000, 0.000), (8, 0.000, 0.000, 0.9697)],
units='Angstrom',
charge=0,
multiplicity=2,
name='hydroxyl_radical')
mol_basis = pyquante2.basisset(mol, 'STO-3G'.lower())
solver = pyquante2.uhf(mol, mol_basis)
solver.converge(tol=1e-11, maxiters=1000)
C_alph = solver.orbsa
C_beta = solver.orbsb
NOa = mol.nup()
NOb = mol.ndown()
D_alph = np.dot(C_alph[:, :NOa], C_alph[:, :NOa].T)
D_beta = np.dot(C_beta[:, :NOb], C_beta[:, :NOb].T)
D = D_alph + D_beta
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])
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(orca_center_of_mass_au)))
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(
np.equal(np.sign(ncc), np.sign(orca_center_of_nuclear_charge_au)))
assert np.all((ncc - orca_center_of_nuclear_charge_au) < 1.0e-8)
ecc = screen(calc_center_of_electronic_charge_pyquante(D, mol_basis))
assert np.all(
np.equal(np.sign(ecc), np.sign(orca_center_of_electronic_charge_au)))
assert np.all((ecc - orca_center_of_electronic_charge_au) < 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)
# For an uncharged system, these should all be identical.
my_ref = np.array([0.0, 0.0, -0.5031245309396919])
for res in (dipole_zero, dipole_com, dipole_ncc, dipole_ecc):
assert (np.absolute(my_ref - res) < 1.0e-8).all()
return