def __init__(self, molecule, **kwargs):
if not found:
qtk.exit("horton module not found.")
if 'wf_convergence' not in kwargs:
kwargs['wf_convergence'] = 1e-06
GaussianBasisInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
self.backup()
mol = IOData(coordinates=molecule.R, numbers=molecule.Z)
obasis = get_gobasis(mol.coordinates, mol.numbers,
self.setting['basis_set'])
grid = BeckeMolGrid(mol.coordinates, mol.numbers,
mol.pseudo_numbers)
# Create a linalg factory
lf = DenseLinalgFactory(obasis.nbasis)
# Compute Gaussian integrals
olp = obasis.compute_overlap(lf)
kin = obasis.compute_kinetic(lf)
na = obasis.compute_nuclear_attraction(mol.coordinates,
mol.pseudo_numbers, lf)
er = obasis.compute_electron_repulsion(lf)
# Create alpha orbitals
exp_alpha = lf.create_expansion()
# Initial guess
guess_core_hamiltonian(olp, kin, na, exp_alpha)
external = {'nn': compute_nucnuc(mol.coordinates,
mol.pseudo_numbers)}
libxc_term = RLibXCHybridGGA('xc_b3lyp')
terms = [
#RTwoIndexTerm(kin, 'kin'),
RDirectTerm(er, 'hartree'),
RGridGroup(obasis, grid, [libxc_term]),
RExchangeTerm(er, 'x_hf', libxc_term.get_exx_fraction()),
RTwoIndexTerm(na, 'ne'),
]
ham = REffHam(terms, external)
self.ht_mol = mol
self.ht_grid = grid
self.ht_external = external
self.ht_obasis = obasis
self.ht_lf = lf
self.ht_olp = olp
self.ht_kin = kin
self.ht_na = na
self.ht_er = er
self.ht_exp_alpha = exp_alpha
self.ht_ham = ham
def __init__(self, molecule, **kwargs):
GaussianBasisInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
self.backup()
if 'gaussian_setting' not in self.setting:
gaussian_setting = [
'6d 10f',
'nosymm',
'Scf(maxcycle=1000,verytight)',
'int(grid=ultrafine)',
'IOp(2/12=3)', # allow atoms to be too near
'force',
]
self.setting['gaussian_setting'] = gaussian_setting
def __init__(self, molecule, **kwargs):
GaussianBasisInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
self.backup()
if 'gaussian_setting' not in self.setting:
gaussian_setting = [
'6d 10f',
'nosymm',
'Scf(maxcycle=1000,verytight)',
'int(grid=ultrafine)',
'IOp(2/12=3)', # allow atoms to be too near
'force',
]
self.setting['gaussian_setting'] = gaussian_setting
def __init__(self, molecule, **kwargs):
if not ht_found:
qtk.exit("horton module not found.")
if not ps_found:
qtk.exit("pyscf module not found.")
if not xc_found:
print xcpath
print xc_found
qtk.exit("libxc not found.")
if 'wf_convergence' not in kwargs:
kwargs['wf_convergence'] = 1e-06
if 'kinetic_functional' not in kwargs:
kwargs['kinetic_functional'] = 'LLP'
if 'aufbau' in kwargs and kwargs['aufbau']:
self.aufbau = True
self.orbitals = []
else:
self.aufbau = False
GaussianBasisInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
self.backup()
if 'dft_setting' not in kwargs:
if not self.aufbau:
kf = self.setting['kinetic_functional']
if kf == 'LLP':
self.setting['dft_setting'] = {
'K': {
1.0: 'XC_GGA_K_LLP'
},
}
else:
self.setting['dft_setting'] = {'K': {1.0: 'XC_GGA_K_VW'}}
ss = self.setting['theory']
sdft = self.setting['dft_setting']
if ss == 'pbe':
sdft['X'] = 'XC_GGA_X_PBE'
sdft['C'] = 'XC_GGA_C_PBE'
elif ss == 'blyp':
sdft['X'] = 'XC_GGA_X_B88'
sdft['C'] = 'XC_GGA_C_LYP'
dft = self.setting['dft_setting']
for k, v in dft.iteritems():
if type(dft[k]) is str:
dft[k] = xc_dict[v]
elif type(dft[k]) is dict:
for key, value in dft[k].iteritems():
if type(value) is str:
dft[k][key] = xc_dict[value]
mol_str = []
for i in range(molecule.N):
atm_str = [molecule.type_list[i]]
for j in range(3):
atm_str.append(str(molecule.R[i, j]))
mol_str.append(' '.join(atm_str))
mol_str = '; '.join(mol_str)
mol = gto.Mole()
mol.build(atom=mol_str, basis=self.setting['basis_set'])
ig = ps.scf.hf.get_init_guess(mol, key='atom')
ovl = mol.intor_symmetric("cint1e_ovlp_sph")
kin = mol.intor_symmetric("cint1e_kin_sph")
ext = mol.intor_symmetric("cint1e_nuc_sph")
# 4D array, can be contracted by numpy.tensordot (td)
# nao x nao integrated density Coulomb kernel can be computed via
# int_vee_rho = td(dm, vee, axes=([0,1], [0,1]))
# the final electron-electron cam be computed via
# Vee = 0.5 * trace(dm, int_vee_rho)
nao = mol.nao_nr()
vee = mol.intor(
"cint2e_sph",
comp=1,
hermi=1,
).reshape(nao, nao, nao, nao)
coord = np.array(np.atleast_2d(molecule.R * 1.8897261245650618))
grid = BeckeMolGrid(coord, molecule.Z.astype(int), molecule.Z)
self.molecule = molecule
self.mol = mol
self.ovl = ovl
self.kin = kin
self.ext = ext
self.vee = vee
self.nao = nao
self.dv = self.normalize(sqrt(diag(ig)))
self.initial_guess = copy.deepcopy(self.dv)
self.ig = ig
self.grid = grid
self.update(self.dv)
self.old_deltadv = None
self.new_deltadv = None
self.old_E = None
self.dv_list = []
self.psi_list = []
self.dpsi_list = []
self.optimizers = {
'tnc': opt.fmin_tnc,
'ncg': opt.fmin_ncg,
'cg': opt.fmin_cg,
'bfgs': opt.fmin_bfgs,
'l_bfgs_b': opt.fmin_l_bfgs_b,
'simplex': opt.fmin,
}
self.optimizer_settings = {
'tnc': {
'xtol': 0.0,
'pgtol': 0.0,
'maxfun': 1000
},
'simplex': {
'xtol': 1E-10,
'ftol': 1E-10,
'maxfun': 1000
},
}
self.orbitals = []
def __init__(self, molecule, **kwargs):
inp.ht = ht
if 'theory' not in kwargs:
kwargs['theory'] = 'hf'
if 'save_c_type' not in kwargs:
kwargs['save_c_type'] = True
if not found:
qtk.exit("horton module not found.")
if 'wf_convergence' not in kwargs:
kwargs['wf_convergence'] = 1e-06
if 'cholesky' not in kwargs:
kwargs['cholesky'] = True
GaussianBasisInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
self.backup()
coord = molecule.R * qtk.setting.a2b
mol = IOData(coordinates=coord, numbers=molecule.Z)
obasis = get_gobasis(mol.coordinates, mol.numbers,
self.setting['basis_set'])
grid = BeckeMolGrid(mol.coordinates, mol.numbers, mol.pseudo_numbers)
olp = obasis.compute_overlap()
kin = obasis.compute_kinetic()
na = obasis.compute_nuclear_attraction(mol.coordinates,
mol.pseudo_numbers)
if self.setting['cholesky']:
er = obasis.compute_electron_repulsion_cholesky()
else:
er = obasis.compute_electron_repulsion()
exp_alpha = orb_alpha = Orbitals(obasis.nbasis)
# Initial guess
guess_core_hamiltonian(olp, kin + na, exp_alpha)
external = {'nn': compute_nucnuc(mol.coordinates, mol.pseudo_numbers)}
theory = self.setting['theory']
if theory in xc_info.xc_map:
self.xc = xc_info.xc_map[theory]
else:
self.xc = None
terms = [
RTwoIndexTerm(kin, 'kin'),
RTwoIndexTerm(na, 'ne'),
RDirectTerm(er, 'hartree'),
]
if self.setting['theory'] == 'hf':
terms.append(RExchangeTerm(er, 'x_hf'))
elif self.setting['theory'] == 'pbe':
libxc_terms = [
RLibXCGGA('x_pbe'),
RLibXCGGA('c_pbe'),
]
terms.append(RGridGroup(obasis, grid, libxc_terms))
elif self.setting['theory'] == 'blyp':
libxc_terms = [
RLibXCGGA('x_b88'),
RLibXCGGA('c_lyp'),
]
terms.append(RGridGroup(obasis, grid, libxc_terms))
elif self.setting['theory'] == 'pbe0':
hyb_term = RLibXCHybridGGA('xc_pbeh')
terms.append(RGridGroup(obasis, grid, [hyb_term]))
terms.append(RExchangeTerm(er, 'x_hf',
hyb_term.get_exx_fraction()))
elif self.setting['theory'] == 'b3lyp':
hyb_term = RLibXCHybridGGA('xc_b3lyp')
terms.append(RGridGroup(obasis, grid, [hyb_term]))
terms.append(RExchangeTerm(er, 'x_hf',
hyb_term.get_exx_fraction()))
elif self.setting['theory'] == 'hse06':
hyb_term = RLibXCHybridGGA('xc_hse06')
terms.append(RGridGroup(obasis, grid, [hyb_term]))
terms.append(RExchangeTerm(er, 'x_hf',
hyb_term.get_exx_fraction()))
elif self.setting['theory'] == 'tpss':
libxc_terms = [
RLibXCMGGA('x_tpss'),
RLibXCMGGA('c_tpss'),
]
terms.append(RGridGroup(obasis, grid, libxc_terms))
elif self.setting['theory'] == 'm05':
hyb_term = RLibXCHybridMGGA('xc_m05')
terms.append(RGridGroup(obasis, grid, [hyb_term]))
terms.append(RExchangeTerm(er, 'x_hf',
hyb_term.get_exx_fraction()))
ham = REffHam(terms, external)
occ_model = AufbauOccModel(
int((sum(self.molecule.Z) - self.molecule.charge) / 2.))
occ_model.assign(orb_alpha)
occ = np.zeros(olp.shape[0])
N = int(sum(self.molecule.Z) - self.molecule.charge)
occ[:N / 2] = 1
C = copy.deepcopy(exp_alpha.coeffs.__array__())
dm = (C * occ).dot(C.T)
if self.setting['save_c_type']:
self.ht_mol = mol
self.ht_grid = grid
self.grid = grid
self.ht_external = external
self.ht_obasis = obasis
self.ht_occ_model = occ_model
self.ht_olp = olp
self.ht_kin = kin
self.ht_na = na
self.ht_er = er
self.ht_exp_alpha = exp_alpha
self.ht_dm_alpha = exp_alpha.to_dm()
self.ht_terms = terms
self.ht_ham = ham
else:
self.grid_points = grid.points
self.grid_weights = grid.weights
self.olp = olp.__array__()
self.S = self.olp
self.kin = kin.__array__()
self.T = self.kin
self.nn = external['nn']
try:
d, U = np.linalg.eigh(self.olp)
self.X = U.dot(np.diag(np.sqrt(1 / d)).dot(U.T))
except Exception as err:
qtk.warning(err)
self.na = na.__array__()
self.er = er.__array__()
self.U = self.er
self.mov = exp_alpha.coeffs.__array__()
self.initial_mov = C
self.initial_dm = dm
self.occ = occ
self.occupation = 2 * occ
self.v_ext = self.na
def __init__(self, molecule, **kwargs):
if 'wf_convergence' not in kwargs:
kwargs['wf_convergence'] = 1e-06
GaussianBasisInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
self.backup()
def __init__(self, molecule, **kwargs):
if 'wf_convergence' not in kwargs:
kwargs['wf_convergence'] = 1e-06
GaussianBasisInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
self.backup()
def __init__(self, molecule, **kwargs):
if not ht_found:
qtk.exit("horton module not found.")
if not ps_found:
qtk.exit("pyscf module not found.")
if not xc_found:
print xcpath
print xc_found
qtk.exit("libxc not found.")
if 'wf_convergence' not in kwargs:
kwargs['wf_convergence'] = 1e-06
if 'kinetic_functional' not in kwargs:
kwargs['kinetic_functional'] = 'LLP'
if 'aufbau' in kwargs and kwargs['aufbau']:
self.aufbau = True
self.orbitals = []
else:
self.aufbau = False
GaussianBasisInput.__init__(self, molecule, **kwargs)
self.setting.update(kwargs)
self.backup()
if 'dft_setting' not in kwargs:
if not self.aufbau:
kf = self.setting['kinetic_functional']
if kf == 'LLP':
self.setting['dft_setting'] = {
'K': {1.0: 'XC_GGA_K_LLP'},
}
else:
self.setting['dft_setting'] = {
'K': {1.0: 'XC_GGA_K_VW'}
}
ss = self.setting['theory']
sdft = self.setting['dft_setting']
if ss == 'pbe':
sdft['X'] = 'XC_GGA_X_PBE'
sdft['C'] = 'XC_GGA_C_PBE'
elif ss == 'blyp':
sdft['X'] = 'XC_GGA_X_B88'
sdft['C'] = 'XC_GGA_C_LYP'
dft = self.setting['dft_setting']
for k, v in dft.iteritems():
if type(dft[k]) is str:
dft[k] = xc_dict[v]
elif type(dft[k]) is dict:
for key, value in dft[k].iteritems():
if type(value) is str:
dft[k][key] = xc_dict[value]
mol_str = []
for i in range(molecule.N):
atm_str = [molecule.type_list[i]]
for j in range(3):
atm_str.append(str(molecule.R[i,j]))
mol_str.append(' '.join(atm_str))
mol_str = '; '.join(mol_str)
mol = gto.Mole()
mol.build(atom=mol_str, basis=self.setting['basis_set'])
ig = ps.scf.hf.get_init_guess(mol, key = 'atom')
ovl = mol.intor_symmetric("cint1e_ovlp_sph")
kin = mol.intor_symmetric("cint1e_kin_sph")
ext = mol.intor_symmetric("cint1e_nuc_sph")
# 4D array, can be contracted by numpy.tensordot (td)
# nao x nao integrated density Coulomb kernel can be computed via
# int_vee_rho = td(dm, vee, axes=([0,1], [0,1]))
# the final electron-electron cam be computed via
# Vee = 0.5 * trace(dm, int_vee_rho)
nao = mol.nao_nr()
vee = mol.intor(
"cint2e_sph", comp=1, hermi=1,
).reshape(nao, nao, nao, nao)
coord = np.array(np.atleast_2d(molecule.R*1.8897261245650618))
grid = BeckeMolGrid(coord, molecule.Z.astype(int), molecule.Z)
self.molecule = molecule
self.mol = mol
self.ovl = ovl
self.kin = kin
self.ext = ext
self.vee = vee
self.nao = nao
self.dv = self.normalize(sqrt(diag(ig)))
self.initial_guess = copy.deepcopy(self.dv)
self.ig = ig
self.grid = grid
self.update(self.dv)
self.old_deltadv = None
self.new_deltadv = None
self.old_E = None
self.dv_list = []
self.psi_list = []
self.dpsi_list = []
self.optimizers = {
'tnc': opt.fmin_tnc,
'ncg': opt.fmin_ncg,
'cg': opt.fmin_cg,
'bfgs': opt.fmin_bfgs,
'l_bfgs_b': opt.fmin_l_bfgs_b,
'simplex': opt.fmin,
}
self.optimizer_settings = {
'tnc': {'xtol': 0.0, 'pgtol': 0.0, 'maxfun': 1000},
'simplex': {'xtol': 1E-10, 'ftol': 1E-10, 'maxfun': 1000},
}
self.orbitals = []