def _fix_molden_from_buggy_codes(result, filename):
'''Detect errors in the data loaded from a molden/mkl/... file and correct.
**Argument:**
result
A dictionary with the data loaded in the ``load_molden`` function.
This function can recognize erroneous files created by PSI4 and ORCA. The
data in the obasis and signs fields will be updated accordingly.
'''
obasis = result['obasis']
permutation = result.get('permutation', None)
if _is_normalized_properly(result['lf'], obasis, permutation,
result['exp_alpha'], result.get('exp_beta')):
# The file is good. No need to change data.
return
if log.do_medium:
log('Detected incorrect normalization of orbitals loaded from a file.')
# Try to fix it as if it was a file generated by ORCA.
orca_signs = _get_orca_signs(obasis)
orca_con_coeffs = _get_fixed_con_coeffs(obasis, 'orca')
orca_obasis = GOBasis(obasis.centers, obasis.shell_map, obasis.nprims,
obasis.shell_types, obasis.alphas, orca_con_coeffs)
if _is_normalized_properly(result['lf'], orca_obasis,
permutation, result['exp_alpha'],
result.get('exp_beta'), orca_signs):
if log.do_medium:
log('Detected typical ORCA errors in file. Fixing them...')
result['obasis'] = orca_obasis
result['signs'] = orca_signs
return
# Try to fix it as if it was a file generated by PSI4.
psi4_con_coeffs = _get_fixed_con_coeffs(obasis, 'psi4')
psi4_obasis = GOBasis(obasis.centers, obasis.shell_map, obasis.nprims,
obasis.shell_types, obasis.alphas, psi4_con_coeffs)
if _is_normalized_properly(result['lf'], psi4_obasis, permutation,
result['exp_alpha'], result.get('exp_beta')):
if log.do_medium:
log('Detected typical PSI4 errors in file. Fixing them...')
result['obasis'] = psi4_obasis
return
raise IOError(('Could not correct the data read from %s. The molden or '
'mkl file you are trying to load contains errors. Please '
'report this problem to [email protected], so he '
'can fix it.') % filename)
def helper_obasis(f, coordinates):
from horton.gbasis.io import str_to_shell_types
from horton.gbasis.gobasis import GOBasis
shell_types = []
shell_map = []
nprims = []
alphas = []
con_coeffs = []
center_counter = 0
in_shell = False
nprim = None
while True:
line = f.readline()
lstrip = line.strip()
if len(line) == 0 or lstrip == '$END':
break
if len(lstrip) == 0:
continue
if lstrip == '$$':
center_counter += 1
in_shell = False
else:
words = line.split()
if len(words) == 2:
assert in_shell
alpha = float(words[0])
alphas.append(alpha)
con_coeff = renorm_helper(float(words[1]), alpha,
shell_type)
con_coeffs.append(con_coeff)
nprim += 1
else:
if nprim is not None:
nprims.append(nprim)
shell_map.append(center_counter)
# always assume pure basis functions
shell_type = str_to_shell_types(words[1], pure=True)[0]
shell_types.append(shell_type)
in_shell = True
nprim = 0
if nprim is not None:
nprims.append(nprim)
shell_map = np.array(shell_map)
nprims = np.array(nprims)
shell_types = np.array(shell_types)
alphas = np.array(alphas)
con_coeffs = np.array(con_coeffs)
return GOBasis(coordinates, shell_map, nprims, shell_types, alphas,
con_coeffs)
def helper_obasis(f, coordinates, pure):
'''Load the orbital basis'''
shell_types = []
shell_map = []
nprims = []
alphas = []
con_coeffs = []
icenter = 0
in_atom = False
in_shell = False
while True:
last_pos = f.tell()
line = f.readline()
if len(line) == 0:
break
words = line.split()
if len(words) == 0:
in_atom = False
in_shell = False
elif len(words) == 2 and not in_atom:
icenter = int(words[0]) - 1
in_atom = True
in_shell = False
elif len(words) == 3:
in_shell = True
shell_map.append(icenter)
shell_label = words[0].lower()
shell_type = str_to_shell_types(shell_label,
pure.get(shell_label,
False))[0]
shell_types.append(shell_type)
nprims.append(int(words[1]))
elif len(words) == 2 and in_atom:
assert in_shell
alpha = float(words[0].replace('D', 'E'))
alphas.append(alpha)
con_coeff = float(words[1].replace('D', 'E'))
con_coeffs.append(con_coeff)
else:
# done, go back one line
f.seek(last_pos)
break
shell_map = np.array(shell_map)
nprims = np.array(nprims)
shell_types = np.array(shell_types)
alphas = np.array(alphas)
con_coeffs = np.array(con_coeffs)
return GOBasis(coordinates, shell_map, nprims, shell_types, alphas,
con_coeffs)
def helper_obasis(f, coordinates):
'''Load the orbital basis'''
shell_types = []
shell_map = []
nprims = []
alphas = []
con_coeffs = []
icenter = 0
in_atom = False
in_shell = False
while True:
last_pos = f.tell()
line = f.readline()
if len(line) == 0:
break
words = line.split()
if len(words) == 0:
in_atom = False
in_shell = False
elif len(words) == 2 and not in_atom:
icenter = int(words[0])-1
in_atom = True
in_shell = False
elif len(words) == 3:
in_shell = True
shell_map.append(icenter)
# always assume pure basis functions
shell_type = str_to_shell_types(words[0], True)[0]
shell_types.append(shell_type)
nprims.append(int(words[1]))
elif len(words) == 2 and in_atom:
assert in_shell
alpha = float(words[0])
alphas.append(alpha)
con_coeff = renorm_helper(float(words[1]), alpha, shell_type)
con_coeffs.append(con_coeff)
else:
# done, go back one line
f.seek(last_pos)
break
shell_map = np.array(shell_map)
nprims = np.array(nprims)
shell_types = np.array(shell_types)
alphas = np.array(alphas)
con_coeffs = np.array(con_coeffs)
return GOBasis(coordinates, shell_map, nprims, shell_types, alphas, con_coeffs)
def load_wfn(filename, lf):
"""Load data from a WFN file.
**Arguments:**
filename
The filename of the wfn file.
lf
An instance of LinalgFactory, used to initialize the wavefunction
expansions.
**Returns:** a dictionary with ``title``, ``coordinates``, ``numbers``,
``energy``, ``obasis`` and ``exp_alpha``. May contain ``exp_beta``.
"""
title, numbers, coordinates, centers, type_assignment, exponents, \
mo_count, mo_occ, mo_energy, coefficients, energy = load_wfn_low(filename)
permutation = get_permutation_basis(type_assignment)
# permute arrays containing wfn data
type_assignment = type_assignment[permutation]
mask = get_mask(type_assignment)
reduced_size = np.array(mask, int).sum()
num_mo = coefficients.shape[1]
alphas = np.empty(reduced_size)
alphas[:] = exponents[permutation][mask]
assert (centers == centers[permutation]).all()
shell_map = centers[mask]
# cartesian basis: {S:0, P:1, D:2, F:3, G:4, H:5}
shell = {1: 0, 2: 1, 5: 2, 11: 3, 21: 4, 36: 5}
shell_types = type_assignment[mask]
shell_types = np.array([shell[i] for i in shell_types])
assert shell_map.size == shell_types.size == reduced_size
nprims = np.ones(reduced_size, int)
con_coeffs = np.ones(reduced_size)
# build basis set
obasis = GOBasis(coordinates, shell_map, nprims, shell_types, alphas,
con_coeffs)
if lf.default_nbasis is not None and lf.default_nbasis != obasis.nbasis:
raise TypeError(
'The value of lf.default_nbasis does not match nbasis reported in the wfn file.'
)
lf.default_nbasis = obasis.nbasis
coefficients = coefficients[permutation]
coefficients /= obasis.get_scales().reshape(-1, 1)
# make the wavefunction
if mo_occ.max() > 1.0:
# close shell system
exp_alpha = lf.create_expansion(obasis.nbasis, coefficients.shape[1])
exp_alpha.coeffs[:] = coefficients
exp_alpha.energies[:] = mo_energy
exp_alpha.occupations[:] = mo_occ / 2
exp_beta = None
else:
# open shell system
# counting the number of alpha and beta orbitals
index = 1
while index < num_mo and mo_energy[index] >= mo_energy[
index - 1] and mo_count[index] == mo_count[index - 1] + 1:
index += 1
exp_alpha = lf.create_expansion(obasis.nbasis, index)
exp_alpha.coeffs[:] = coefficients[:, :index]
exp_alpha.energies[:] = mo_energy[:index]
exp_alpha.occupations[:] = mo_occ[:index]
exp_beta = lf.create_expansion(obasis.nbasis, num_mo - index)
exp_beta.coeffs[:] = coefficients[:, index:]
exp_beta.energies[:] = mo_energy[index:]
exp_beta.occupations[:] = mo_occ[index:]
result = {
'title': title,
'coordinates': coordinates,
'exp_alpha': exp_alpha,
'lf': lf,
'numbers': numbers,
'obasis': obasis,
'energy': energy,
}
if exp_beta is not None:
result['exp_beta'] = exp_beta
return result
def load_wfn(filename, lf):
"""Load data from a WFN file.
**Arguments:**
filename
The filename of the wfn file.
lf
An instance of LinalgFactory, used to initialize the wavefunction
expansions.
**Returns:** a dictionary with ``title``, ``coordinates``, ``numbers``,
``energy``, ``obasis`` and ``exp_alpha``. May contain ``exp_beta``.
"""
title, numbers, coordinates, centers, type_assignment, exponents, \
mo_count, mo_occ, mo_energy, coefficients, energy = load_wfn_low(filename)
permutation = get_permutation_basis(type_assignment)
# permute arrays containing wfn data
type_assignment = type_assignment[permutation]
mask = get_mask(type_assignment)
reduced_size = np.array(mask, int).sum()
num_mo = coefficients.shape[1]
alphas = np.empty(reduced_size)
alphas[:] = exponents[permutation][mask]
assert (centers == centers[permutation]).all()
shell_map = centers[mask]
# cartesian basis: {S:0, P:1, D:2, F:3, G:4, H:5}
shell = {1: 0, 2: 1, 5: 2, 11: 3, 21: 4, 36: 5}
shell_types = type_assignment[mask]
shell_types = np.array([shell[i] for i in shell_types])
assert shell_map.size == shell_types.size == reduced_size
nprims = np.ones(reduced_size, int)
con_coeffs = np.ones(reduced_size)
# build basis set
obasis = GOBasis(coordinates, shell_map, nprims, shell_types, alphas, con_coeffs)
if lf.default_nbasis is not None and lf.default_nbasis != obasis.nbasis:
raise TypeError(
'The value of lf.default_nbasis does not match nbasis reported in the wfn file.')
lf.default_nbasis = obasis.nbasis
coefficients = coefficients[permutation]
coefficients /= obasis.get_scales().reshape(-1, 1)
# make the wavefunction
if mo_occ.max() > 1.0:
# close shell system
exp_alpha = lf.create_expansion(obasis.nbasis, coefficients.shape[1])
exp_alpha.coeffs[:] = coefficients
exp_alpha.energies[:] = mo_energy
exp_alpha.occupations[:] = mo_occ / 2
exp_beta = None
else:
# open shell system
# counting the number of alpha and beta orbitals
index = 1
while index < num_mo and mo_energy[index] >= mo_energy[index - 1] and mo_count[index] == mo_count[index - 1] + 1:
index += 1
exp_alpha = lf.create_expansion(obasis.nbasis, index)
exp_alpha.coeffs[:] = coefficients[:, :index]
exp_alpha.energies[:] = mo_energy[:index]
exp_alpha.occupations[:] = mo_occ[:index]
exp_beta = lf.create_expansion(obasis.nbasis, num_mo - index)
exp_beta.coeffs[:] = coefficients[:, index:]
exp_beta.energies[:] = mo_energy[index:]
exp_beta.occupations[:] = mo_occ[index:]
result = {
'title': title,
'coordinates': coordinates,
'exp_alpha': exp_alpha,
'lf': lf,
'numbers': numbers,
'obasis': obasis,
'energy': energy,
}
if exp_beta is not None:
result['exp_beta'] = exp_beta
return result
def load_wfn(filename, lf):
'''Load data from a WFN file
**Arguments:**
filename
The filename of the wfn file.
lf
An instance of LinalgFactory, used to initialize the wavefunction
expansions.
'''
numbers, coordinates, centers, type_assignment, exponents, mo_count, mo_occ, mo_energy, coefficients = load_wfn_low(
filename)
permutation = setup_permutation2(type_assignment)
#Permuting the arrays containing the wfn data
type_assignment = type_assignment[permutation]
mask = setup_mask(type_assignment)
reduced_size = np.array(mask, int).sum()
num_mo = coefficients.shape[1]
alphas = np.empty(reduced_size)
alphas[:] = exponents[permutation][mask]
assert (centers == centers[permutation]).all()
shell_map = centers[mask]
shell = {
1: 0,
2: 1,
5: 2,
11: 3,
21: 4,
36: 5
} #Cartesian: {S:0, P:1, D:2, F:3, G:4, H:5}
shell_types = type_assignment[mask]
shell_types = np.array([shell[i] for i in shell_types])
assert shell_map.size == shell_types.size == reduced_size
nprims = np.ones(reduced_size, int)
con_coeffs = np.ones(reduced_size)
#Building the basis set
from horton.gbasis.gobasis import GOBasis
obasis = GOBasis(coordinates, shell_map, nprims, shell_types, alphas,
con_coeffs)
coefficients = coefficients[permutation]
coefficients /= obasis.get_scales().reshape(-1, 1)
#Making the wavefunction:
if mo_occ.max() > 1.0:
#close shell system
nelec = int(round(mo_occ.sum()))
wfn = RestrictedWFN(lf, obasis.nbasis, norb=coefficients.shape[1])
exp_alpha = wfn.init_exp('alpha')
exp_alpha.coeffs[:] = coefficients
exp_alpha.energies[:] = mo_energy
exp_alpha.occupations[:] = mo_occ / 2
else:
#open shell system
#counting the number of alpha and beta orbitals
index = 1
while index < num_mo and mo_energy[index] >= mo_energy[
index - 1] and mo_count[index] == mo_count[index - 1] + 1:
index += 1
wfn = UnrestrictedWFN(lf, obasis.nbasis)
exp_alpha = wfn.init_exp('alpha', norb=index)
exp_alpha.coeffs[:] = coefficients[:, :index]
exp_alpha.energies[:] = mo_energy[:index]
exp_alpha.occupations[:] = mo_occ[:index]
exp_beta = wfn.init_exp('beta', norb=num_mo - index)
exp_beta.coeffs[:] = coefficients[:, index:]
exp_beta.energies[:] = mo_energy[index:]
exp_beta.occupations[:] = mo_occ[index:]
return {
'coordinates': coordinates,
'numbers': numbers,
'obasis': obasis,
'wfn': wfn,
}
def load_wfn(filename):
"""Load data from a WFN file.
Parameters
----------
filename : str
The filename of the wfn file.
Returns
-------
results : dict
Data loaded from file, with keys ``title``, ``coordinates``, ``numbers``,
``energy``, ``obasis`` and ``orb_alpha``. May contain ``orb_beta``.
"""
title, numbers, coordinates, centers, type_assignment, exponents, \
mo_count, mo_occ, mo_energy, coefficients, energy = load_wfn_low(filename)
permutation = get_permutation_basis(type_assignment)
# permute arrays containing wfn data
type_assignment = type_assignment[permutation]
mask = get_mask(type_assignment)
reduced_size = np.array(mask, int).sum()
num_mo = coefficients.shape[1]
alphas = np.empty(reduced_size)
alphas[:] = exponents[permutation][mask]
assert (centers == centers[permutation]).all()
shell_map = centers[mask]
# cartesian basis: {S:0, P:1, D:2, F:3, G:4, H:5}
shell = {1: 0, 2: 1, 5: 2, 11: 3, 21: 4, 36: 5}
shell_types = type_assignment[mask]
shell_types = np.array([shell[i] for i in shell_types])
assert shell_map.size == shell_types.size == reduced_size
nprims = np.ones(reduced_size, int)
con_coeffs = np.ones(reduced_size)
# build basis set
obasis = GOBasis(coordinates, shell_map, nprims, shell_types, alphas, con_coeffs)
coefficients = coefficients[permutation]
coefficients /= obasis.get_scales().reshape(-1, 1)
# make the wavefunction
if mo_occ.max() > 1.0:
# close shell system
orb_alpha = Orbitals(obasis.nbasis, coefficients.shape[1])
orb_alpha.coeffs[:] = coefficients
orb_alpha.energies[:] = mo_energy
orb_alpha.occupations[:] = mo_occ / 2
orb_beta = None
else:
# open shell system
# counting the number of alpha and beta orbitals
index = 1
while index < num_mo and mo_energy[index] >= mo_energy[index - 1] and mo_count[index] == mo_count[index - 1] + 1:
index += 1
orb_alpha = Orbitals(obasis.nbasis, index)
orb_alpha.coeffs[:] = coefficients[:, :index]
orb_alpha.energies[:] = mo_energy[:index]
orb_alpha.occupations[:] = mo_occ[:index]
orb_beta = Orbitals(obasis.nbasis, num_mo - index)
orb_beta.coeffs[:] = coefficients[:, index:]
orb_beta.energies[:] = mo_energy[index:]
orb_beta.occupations[:] = mo_occ[index:]
result = {
'title': title,
'coordinates': coordinates,
'orb_alpha': orb_alpha,
'numbers': numbers,
'obasis': obasis,
'energy': energy,
}
if orb_beta is not None:
result['orb_beta'] = orb_beta
return result
def load_wfn(filename, lf):
'''Load data from a WFN file
**Arguments:**
filename
The filename of the wfn file.
lf
An instance of LinalgFactory, used to initialize the wavefunction
expansions.
'''
numbers, coordinates, centers, type_assignment, exponents, mo_count, mo_occ, mo_energy, coefficients = load_wfn_low(filename)
permutation = setup_permutation2(type_assignment)
#Permuting the arrays containing the wfn data
type_assignment = type_assignment[permutation]
mask = setup_mask(type_assignment)
reduced_size = np.array(mask, int).sum()
num_mo = coefficients.shape[1]
alphas = np.empty(reduced_size)
alphas[:] = exponents[permutation][mask]
assert (centers == centers[permutation]).all()
shell_map = centers[mask]
shell = {1:0, 2:1, 5:2, 11:3, 21:4, 36:5} #Cartesian: {S:0, P:1, D:2, F:3, G:4, H:5}
shell_types = type_assignment[mask]
shell_types = np.array([shell[i] for i in shell_types])
assert shell_map.size == shell_types.size == reduced_size
nprims = np.ones(reduced_size, int)
con_coeffs = np.ones(reduced_size)
#Building the basis set
from horton.gbasis.gobasis import GOBasis
obasis = GOBasis(coordinates, shell_map, nprims, shell_types, alphas, con_coeffs)
coefficients = coefficients[permutation]
coefficients /= obasis.get_scales().reshape(-1,1)
#Making the wavefunction:
if mo_occ.max() > 1.0:
#close shell system
nelec = int(round(mo_occ.sum()))
wfn = RestrictedWFN(lf, obasis.nbasis, norb=coefficients.shape[1])
exp_alpha = wfn.init_exp('alpha')
exp_alpha.coeffs[:] = coefficients
exp_alpha.energies[:] = mo_energy
exp_alpha.occupations[:] = mo_occ/2
else:
#open shell system
#counting the number of alpha and beta orbitals
index = 1
while index < num_mo and mo_energy[index] >= mo_energy[index-1] and mo_count[index] == mo_count[index-1]+1:
index += 1
wfn = UnrestrictedWFN(lf, obasis.nbasis)
exp_alpha = wfn.init_exp('alpha', norb=index)
exp_alpha.coeffs[:] = coefficients[:,:index]
exp_alpha.energies[:] = mo_energy[:index]
exp_alpha.occupations[:] = mo_occ[:index]
exp_beta = wfn.init_exp('beta', norb=num_mo-index)
exp_beta.coeffs[:] = coefficients[:,index:]
exp_beta.energies[:] = mo_energy[index:]
exp_beta.occupations[:] = mo_occ[index:]
return {
'coordinates': coordinates,
'numbers': numbers,
'obasis': obasis,
'wfn': wfn,
}