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 (pre 1.0).
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
# Last resort: simply renormalize all contractions
normed_con_coeffs = _normalized_contractions(obasis)
normed_obasis = GOBasis(obasis.centers, obasis.shell_map, obasis.nprims,
obasis.shell_types, obasis.alphas,
normed_con_coeffs)
if _is_normalized_properly(result['lf'], normed_obasis, permutation,
result['exp_alpha'], result.get('exp_beta')):
if log.do_medium:
log('Detected unnormalized contractions in file. Fixing them...')
result['obasis'] = normed_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 _read_cp2k_contracted_obasis(f):
"""Read a contracted basis set from an open CP2K ATOM output file.
Parameters
----------
f : file
An open readable file object.
Returns
-------
obasis : GOBasis
The orbital basis read from the file.
"""
# Load the relevant data from the file
basis_desc = []
for line in f:
if line.startswith(' *******************'):
break
elif line[3:12] == 'Functions':
shell_type = str_to_shell_types(line[1:2], pure=True)[0]
a = [] # exponents (alpha)
c = [] # contraction coefficients
basis_desc.append((shell_type, a, c))
else:
values = [float(w) for w in line.split()]
a.append(values[0]) # one exponent per line
c.append(values[1:]) # many contraction coefficients per line
# Convert the basis into HORTON format
shell_map = []
shell_types = []
nprims = []
alphas = []
con_coeffs = []
for shell_type, a, c in basis_desc:
# get correction to contraction coefficients. CP2K uses different normalization
# conventions.
corrections = _get_cp2k_norm_corrections(abs(shell_type), np.array(a))
c = np.array(c) / corrections.reshape(-1, 1)
# fill in arrays
for col in c.T:
shell_map.append(0)
shell_types.append(shell_type)
nprims.append(len(col))
alphas.extend(a)
con_coeffs.extend(col)
# Create the basis object
coordinates = np.zeros((1, 3))
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)
obasis = GOBasis(coordinates, shell_map, nprims, shell_types, alphas,
con_coeffs)
return obasis
def apply_to(self, system):
"""Construct a GOBasis object for the system"""
shell_map = []
nprims = []
shell_types = []
alphas = []
con_coeffs = []
def get_basis(i, n):
"""Look up the basis for a given atom"""
basis = self.index_map.get(i)
if basis is not None:
return basis
basis = self.element_map.get(n)
if basis is not None:
return basis
if self.default is None:
raise KeyError('Could not find basis for atom %i.' % i)
else:
return self.default
def translate_basis(basis_x, n):
"""Translate the first argument into a GOBasisAtom instance"""
if isinstance(basis_x, basestring):
basis_fam = go_basis_families.get(basis_x.lower())
if basis_fam is None:
raise ValueError('Unknown basis family: %s' % basis_x)
basis_atom = basis_fam.get(n)
if basis_atom is None:
raise ValueError(
'The basis family %s does not contain element %i.' %
(basis_x, n))
return basis_atom
elif isinstance(basis_x, GOBasisFamily):
basis_atom = basis_x.get(n)
if basis_atom is None:
raise ValueError(
'The basis family %s does not contain element %i.' %
(basis_x.name, n))
return basis_atom
elif isinstance(basis_x, GOBasisAtom):
return basis_x
else:
raise ValueError(
'Can not interpret %s as an atomic basis function.' %
basis_x)
# Loop over the atoms and fill in all the lists
for i in xrange(system.natom):
n = system.numbers[i]
basis_x = get_basis(i, n)
basis_atom = translate_basis(basis_x, n)
basis_atom.extend(i, shell_map, nprims, shell_types, alphas,
con_coeffs, self.pure)
# Return the Gaussian basis object.
return GOBasis(system.coordinates, shell_map, nprims, shell_types,
alphas, con_coeffs)
def normalize(self):
"""Normalize the contraction."""
if self.is_generalized():
raise NotImplementedError("Only segmented contractions can be normalized.")
# Warning! Ugly code ahead to avoid re-implementing the norm of contraction. The
# code below (ab)uses the GOBasis machinery to get that result.
# 1) Constract a GOBasis object with only this contraction.
centers = np.array([[0.0, 0.0, 0.0]])
shell_map = np.array([0])
nprims = np.array([len(self.alphas)])
shell_types = np.array([self.shell_type])
alphas = self.alphas
con_coeffs = self.con_coeffs
gobasis = GOBasis(centers, shell_map, nprims, shell_types, alphas, con_coeffs)
# 2) Get the first diagonal element of the overlap matrix
olpdiag = gobasis.compute_overlap()[0, 0]
# 3) Normalize the contraction
self.con_coeffs /= np.sqrt(olpdiag)
def normalize(self):
"""Normalize the contraction."""
if self.is_generalized():
raise NotImplementedError(
"Only segmented contractions can be normalized.")
# Warning! Ugly code ahead to avoid re-implementing the norm of contraction. The
# code below (ab)uses the GOBasis machinery to get that result.
# 1) Constract a GOBasis object with only this contraction.
centers = np.array([[0.0, 0.0, 0.0]])
shell_map = np.array([0])
nprims = np.array([len(self.alphas)])
shell_types = np.array([self.shell_type])
alphas = self.alphas
con_coeffs = self.con_coeffs
gobasis = GOBasis(centers, shell_map, nprims, shell_types, alphas,
con_coeffs)
# 2) Get the first diagonal element of the overlap matrix
olpdiag = gobasis.compute_overlap()[0, 0]
# 3) Normalize the contraction
self.con_coeffs /= np.sqrt(olpdiag)
def _read_cp2k_uncontracted_obasis(f):
"""Read an uncontracted basis set from an open CP2K ATOM output file.
Parameters
----------
f : file
An open readable file object.
Returns
-------
obasis : GOBasis
The orbital basis read from the file.
"""
# Load the relevant data from the file
basis_desc = []
shell_type = None
for line in f:
if line.startswith(' *******************'):
break
elif line[3:13] == 'Exponents:':
shell_type = str_to_shell_types(line[1:2], pure=True)[0]
words = line.split()
if len(words) >= 2:
# read the exponent
alpha = float(words[-1])
basis_desc.append((shell_type, alpha))
# Convert the basis into HORTON format
shell_map = []
shell_types = []
nprims = []
alphas = []
con_coeffs = []
# fill in arrays
for shell_type, alpha in basis_desc:
correction = _get_cp2k_norm_corrections(abs(shell_type), alpha)
shell_map.append(0)
shell_types.append(shell_type)
nprims.append(1)
alphas.append(alpha)
con_coeffs.append(1.0 / correction)
# Create the basis object
centers = np.zeros((1, 3))
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)
obasis = GOBasis(centers, shell_map, nprims, shell_types, alphas,
con_coeffs)
return obasis
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 load_fchk(filename, lf):
'''Load from a formatted checkpoint file.
**Arguments:**
filename
The filename of the Gaussian formatted checkpoint file.
lf
A LinalgFactory instance.
**Returns** a dictionary with: ``title``, ``coordinates``, ``numbers``,
``obasis``, ``exp_alpha``, ``permutation``, ``energy``,
``pseudo_numbers``, ``mulliken_charges``. The dictionary may also
contain: ``npa_charges``, ``esp_charges``, ``exp_beta``, ``dm_full_mp2``,
``dm_spin_mp2``, ``dm_full_mp3``, ``dm_spin_mp3``, ``dm_full_cc``,
``dm_spin_cc``, ``dm_full_ci``, ``dm_spin_ci``, ``dm_full_scf``,
``dm_spin_scf``, ``polar``, ``dipole_moment``, ``quadrupole_moment``.
'''
from horton.gbasis.cext import GOBasis
fchk = FCHKFile(filename, [
"Number of electrons",
"Number of independant functions",
"Number of independent functions",
"Number of alpha electrons",
"Number of beta electrons",
"Atomic numbers",
"Current cartesian coordinates",
"Shell types",
"Shell to atom map",
"Shell to atom map",
"Number of primitives per shell",
"Primitive exponents",
"Contraction coefficients",
"P(S=P) Contraction coefficients",
"Alpha Orbital Energies",
"Alpha MO coefficients",
"Beta Orbital Energies",
"Beta MO coefficients",
"Total Energy",
"Nuclear charges",
'Total SCF Density',
'Spin SCF Density',
'Total MP2 Density',
'Spin MP2 Density',
'Total MP3 Density',
'Spin MP3 Density',
'Total CC Density',
'Spin CC Density',
'Total CI Density',
'Spin CI Density',
'Mulliken Charges',
'ESP Charges',
'NPA Charges',
'Polarizability',
'Dipole Moment',
'Quadrupole Moment',
])
# A) Load the geometry
numbers = fchk["Atomic numbers"]
coordinates = fchk["Current cartesian coordinates"].reshape(-1, 3)
pseudo_numbers = fchk["Nuclear charges"]
# Mask out ghost atoms
mask = pseudo_numbers != 0.0
numbers = numbers[mask]
# Do not overwrite coordinates array, because it is needed to specify basis
system_coordinates = coordinates[mask]
pseudo_numbers = pseudo_numbers[mask]
# B) Load the orbital basis set
shell_types = fchk["Shell types"]
shell_map = fchk["Shell to atom map"] - 1
nprims = fchk["Number of primitives per shell"]
alphas = fchk["Primitive exponents"]
ccoeffs_level1 = fchk["Contraction coefficients"]
ccoeffs_level2 = fchk.get("P(S=P) Contraction coefficients")
my_shell_types = []
my_shell_map = []
my_nprims = []
my_alphas = []
con_coeffs = []
counter = 0
for i, n in enumerate(nprims):
if shell_types[i] == -1:
# Special treatment for SP shell type
my_shell_types.append(0)
my_shell_types.append(1)
my_shell_map.append(shell_map[i])
my_shell_map.append(shell_map[i])
my_nprims.append(nprims[i])
my_nprims.append(nprims[i])
my_alphas.append(alphas[counter:counter + n])
my_alphas.append(alphas[counter:counter + n])
con_coeffs.append(ccoeffs_level1[counter:counter + n])
con_coeffs.append(ccoeffs_level2[counter:counter + n])
else:
my_shell_types.append(shell_types[i])
my_shell_map.append(shell_map[i])
my_nprims.append(nprims[i])
my_alphas.append(alphas[counter:counter + n])
con_coeffs.append(ccoeffs_level1[counter:counter + n])
counter += n
my_shell_types = np.array(my_shell_types)
my_shell_map = np.array(my_shell_map)
my_nprims = np.array(my_nprims)
my_alphas = np.concatenate(my_alphas)
con_coeffs = np.concatenate(con_coeffs)
del shell_map
del shell_types
del nprims
del alphas
obasis = GOBasis(coordinates, my_shell_map, my_nprims, my_shell_types,
my_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 fchk file.'
)
lf.default_nbasis = obasis.nbasis
# permutation of the orbital basis functions
permutation_rules = {
-9: np.arange(19),
-8: np.arange(17),
-7: np.arange(15),
-6: np.arange(13),
-5: np.arange(11),
-4: np.arange(9),
-3: np.arange(7),
-2: np.arange(5),
0: np.array([0]),
1: np.arange(3),
2: np.array([0, 3, 4, 1, 5, 2]),
3: np.array([0, 4, 5, 3, 9, 6, 1, 8, 7, 2]),
4: np.arange(15)[::-1],
5: np.arange(21)[::-1],
6: np.arange(28)[::-1],
7: np.arange(36)[::-1],
8: np.arange(45)[::-1],
9: np.arange(55)[::-1],
}
permutation = []
for shell_type in my_shell_types:
permutation.extend(permutation_rules[shell_type] + len(permutation))
permutation = np.array(permutation, dtype=int)
result = {
'title': fchk.title,
'coordinates': system_coordinates,
'lf': lf,
'numbers': numbers,
'obasis': obasis,
'permutation': permutation,
'pseudo_numbers': pseudo_numbers,
}
# C) Load density matrices
def load_dm(label):
if label in fchk:
dm = lf.create_two_index(obasis.nbasis)
start = 0
for i in xrange(obasis.nbasis):
stop = start + i + 1
dm._array[i, :i + 1] = fchk[label][start:stop]
dm._array[:i + 1, i] = fchk[label][start:stop]
start = stop
return dm
# First try to load the post-hf density matrices.
load_orbitals = True
for key in 'MP2', 'MP3', 'CC', 'CI', 'SCF':
dm_full = load_dm('Total %s Density' % key)
if dm_full is not None:
result['dm_full_%s' % key.lower()] = dm_full
dm_spin = load_dm('Spin %s Density' % key)
if dm_spin is not None:
result['dm_spin_%s' % key.lower()] = dm_spin
# D) Load the wavefunction
# Handle small difference in fchk files from g03 and g09
nbasis_indep = fchk.get("Number of independant functions") or \
fchk.get("Number of independent functions")
if nbasis_indep is None:
nbasis_indep = obasis.nbasis
# Load orbitals
nalpha = fchk['Number of alpha electrons']
nbeta = fchk['Number of beta electrons']
if nalpha < 0 or nbeta < 0 or nalpha + nbeta <= 0:
raise ValueError(
'The file %s does not contain a positive number of electrons.' %
filename)
exp_alpha = lf.create_expansion(obasis.nbasis, nbasis_indep)
exp_alpha.coeffs[:] = fchk['Alpha MO coefficients'].reshape(
nbasis_indep, obasis.nbasis).T
exp_alpha.energies[:] = fchk['Alpha Orbital Energies']
exp_alpha.occupations[:nalpha] = 1.0
result['exp_alpha'] = exp_alpha
if 'Beta Orbital Energies' in fchk:
# UHF case
exp_beta = lf.create_expansion(obasis.nbasis, nbasis_indep)
exp_beta.coeffs[:] = fchk['Beta MO coefficients'].reshape(
nbasis_indep, obasis.nbasis).T
exp_beta.energies[:] = fchk['Beta Orbital Energies']
exp_beta.occupations[:nbeta] = 1.0
result['exp_beta'] = exp_beta
elif fchk['Number of beta electrons'] != fchk['Number of alpha electrons']:
# ROHF case
exp_beta = lf.create_expansion(obasis.nbasis, nbasis_indep)
exp_beta.coeffs[:] = fchk['Alpha MO coefficients'].reshape(
nbasis_indep, obasis.nbasis).T
exp_beta.energies[:] = fchk['Alpha Orbital Energies']
exp_beta.occupations[:nbeta] = 1.0
result['exp_beta'] = exp_beta
# Delete dm_full_scf because it is known to be buggy
result.pop('dm_full_scf')
# E) Load properties
result['energy'] = fchk['Total Energy']
if 'Polarizability' in fchk:
result['polar'] = triangle_to_dense(fchk['Polarizability'])
if 'Dipole Moment' in fchk:
result['dipole_moment'] = fchk['Dipole Moment']
if 'Quadrupole Moment' in fchk:
# Convert to HORTON ordering: xx, xy, xz, yy, yz, zz
result['quadrupole_moment'] = fchk['Quadrupole Moment'][[
0, 3, 4, 1, 5, 2
]]
# F) Load optional properties
# Mask out ghost atoms from charges
if 'Mulliken Charges' in fchk:
result['mulliken_charges'] = fchk['Mulliken Charges'][mask]
if 'ESP Charges' in fchk:
result['esp_charges'] = fchk['ESP Charges'][mask]
if 'NPA Charges' in fchk:
result['npa_charges'] = fchk['NPA Charges'][mask]
return result
def load_atom_cp2k(filename, lf):
with open(filename) as f:
# Find the element number
for line in f:
if line.startswith(' Atomic Energy Calculation'):
number = int(line[-5:-1])
break
# Go to the pseudo basis set
for line in f:
if line.startswith(' Pseudopotential Basis'):
break
# TODO: add support for uncontracted and all-electron basis
f.next() # empty line
line = f.next() # Check for GTO
assert line == ' ********************** Contracted Gaussian Type Orbitals **********************\n'
# Load the basis used for the PP wavefn
basis_desc = []
for line in f:
if line.startswith(' *******************'):
break
elif line[3:12] == 'Functions':
shell_type = str_to_shell_types(line[1:2], pure=True)[0]
a = []
c = []
basis_desc.append((shell_type, a, c))
else:
values = [float(w) for w in line.split()]
a.append(values[0])
c.append(values[1:])
# Convert the basis into Horton format
shell_map = []
shell_types = []
nprims = []
alphas = []
con_coeffs = []
for shell_type, a, c in basis_desc:
# get correction to contraction coefficients.
corrections = _get_cp2k_norm_corrections(abs(shell_type), a)
c = np.array(c) / corrections.reshape(-1, 1)
# fill in arrays
for col in c.T:
shell_map.append(0)
shell_types.append(shell_type)
nprims.append(len(col))
alphas.extend(a)
con_coeffs.extend(col)
# Create the basis object
coordinates = np.zeros((1, 3))
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)
obasis = GOBasis(coordinates, shell_map, nprims, shell_types, alphas,
con_coeffs)
# Search for (un)restricted
restricted = None
for line in f:
if line.startswith(' METHOD |'):
if 'Unrestricted' in line:
restricted = False
break
elif 'Restricted' in line:
restricted = True
break
# Search for the core charge (pseudo number)
for line in f:
if line.startswith(' Core Charge'):
pseudo_number = float(line[70:])
assert pseudo_number == int(pseudo_number)
pseudo_number = int(pseudo_number)
break
# Search for energy
for line in f:
if line.startswith(
' Energy components [Hartree] Total Energy ::'):
energy = float(line[60:])
break
# Read orbital energies and occupations
for line in f:
if line.startswith(' Orbital energies'):
break
f.next()
oe_alpha = []
oe_beta = []
empty = 0
while empty < 2:
line = f.next()
words = line.split()
if len(words) == 0:
empty += 1
continue
empty = 0
s = int(words[0])
l = int(words[2 - restricted])
occ = float(words[3 - restricted])
ener = float(words[4 - restricted])
if restricted or words[1] == 'alpha':
oe_alpha.append((l, s, occ, ener))
else:
oe_beta.append((l, s, occ, ener))
# Read orbital expansion coefficients
line = f.next()
assert (line == " Atomic orbital expansion coefficients [Alpha]\n") or \
(line == " Atomic orbital expansion coefficients []\n")
coeffs_alpha = _read_coeffs_helper(f, oe_alpha)
if not restricted:
line = f.next()
assert (line == " Atomic orbital expansion coefficients [Beta]\n")
coeffs_beta = _read_coeffs_helper(f, oe_beta)
# Turn orbital data into a Horton wfn expansion
if restricted:
norb, nel = _helper_norb(oe_alpha)
assert nel % 2 == 0
wfn = RestrictedWFN(lf, obasis.nbasis, norb=norb)
exp_alpha = wfn.init_exp('alpha')
_helper_exp(exp_alpha, oe_alpha, coeffs_alpha, shell_types,
restricted)
else:
norb_alpha, nalpha = _helper_norb(oe_alpha)
norb_beta, nbeta = _helper_norb(oe_beta)
assert norb_alpha == norb_beta
wfn = UnrestrictedWFN(lf, obasis.nbasis, norb=norb_alpha)
exp_alpha = wfn.init_exp('alpha')
exp_beta = wfn.init_exp('beta')
_helper_exp(exp_alpha, oe_alpha, coeffs_alpha, shell_types,
restricted)
_helper_exp(exp_beta, oe_beta, coeffs_beta, shell_types,
restricted)
return {
'obasis': obasis,
'wfn': wfn,
'coordinates': coordinates,
'numbers': np.array([number]),
'extra': {
'energy': energy
},
'pseudo_numbers': np.array([pseudo_number]),
}
def apply_to(self, coordinates, numbers):
"""Construct a GOBasis object for the given molecular geometry
**Arguments:**
coordinates
A (N, 3) float numpy array with Cartesian coordinates of the
atoms.
numbers
A (N,) numpy vector with the atomic numbers.
Note that the geometry specified by the arguments may also contain
ghost atoms.
"""
natom, coordinates, numbers = typecheck_geo(coordinates, numbers, need_pseudo_numbers=False)
shell_map = []
nprims = []
shell_types = []
alphas = []
con_coeffs = []
def get_basis(i, n):
"""Look up the basis for a given atom"""
basis = self.index_map.get(i)
if basis is not None:
return basis
basis = self.element_map.get(n)
if basis is not None:
return basis
if self.default is None:
raise KeyError('Could not find basis for atom %i.' % i)
else:
return self.default
def translate_basis(basis_x, n):
"""Translate the first argument into a GOBasisAtom instance"""
if isinstance(basis_x, basestring):
basis_fam = go_basis_families.get(basis_x.lower())
if basis_fam is None:
raise ValueError('Unknown basis family: %s' % basis_x)
basis_atom = basis_fam.get(n)
if basis_atom is None:
raise ValueError('The basis family %s does not contain element %i.' % (basis_x, n))
return basis_atom
elif isinstance(basis_x, GOBasisFamily):
basis_atom = basis_x.get(n)
if basis_atom is None:
raise ValueError('The basis family %s does not contain element %i.' % (basis_x.name, n))
return basis_atom
elif isinstance(basis_x, GOBasisAtom):
return basis_x
else:
raise ValueError('Can not interpret %s as an atomic basis function.' % basis_x)
# Loop over the atoms and fill in all the lists
for i in xrange(natom):
n = numbers[i]
basis_x = get_basis(i, n)
basis_atom = translate_basis(basis_x, n)
basis_atom.extend(i, shell_map, nprims, shell_types, alphas, con_coeffs, self.pure)
# Return the Gaussian basis object.
return GOBasis(coordinates, shell_map, nprims, shell_types, alphas, con_coeffs)
def project_orbitals_mgs(obasis0, obasis1, orb0, orb1, eps=1e-10):
'''Project the orbitals onto a new basis set with the modified Gram-Schmidt algorithm.
The orbitals in ``orb0`` (w.r.t. ``obasis0``) are projected onto ``obasis1`` and
stored in ``orb1``.
Parameters
----------
obasis0 : GOBasis
The orbital basis for the original wavefunction expansion.
obasis1 : GOBasis
The new orbital basis for the projected wavefunction expansion.
orb0 : Orbitals
The expansion of the original orbitals.
orb1 : Orbitals
An output argument in which the projected orbitals will be stored.
eps : float
A threshold for the renormalization in the Gram-Schmidt procedure
Notes
-----
The projection is based on the Modified Gram-Schmidt (MGS) process. In
each iteration of the MGS, a renormalization is carried out. If the norm
in this step is smaller than ``eps``, an error is raised.
Note that ``orb1`` will be incomplete in several ways. The orbital
energies are not copied. Only the occupied orbitals in ``orb0`` are
projected. Coefficients of higher orbitals are set to zero. The orbital
occupations are simply copied. This should be sufficient to construct
an initial guess in a new orbital basis set based on a previous solution.
If the number of orbitals in ``orb1`` is too small to store all projected
orbitals, an error is raised.
'''
# Compute the overlap matrix of the combined orbital basis
obasis_both = GOBasis.concatenate(obasis0, obasis1)
olp_both = obasis_both.compute_overlap()
# Select the blocks of interest from the big overlap matrix
olp_21 = olp_both[obasis0.nbasis:, :obasis0.nbasis]
olp_22 = olp_both[obasis0.nbasis:, obasis0.nbasis:]
# Construct the projector. This minimizes the L2 norm between the new and old
# orbitals, which does not account for orthonormality.
projector = np.dot(np.linalg.pinv(olp_22), olp_21)
# Project occupied orbitals.
i1 = 0
for i0 in xrange(orb0.nfn):
if orb0.occupations[i0] == 0.0:
continue
if i1 > orb1.nfn:
raise ProjectionError('Not enough functions available in orb1 to store the '
'projected orbitals.')
orb1.coeffs[:,i1] = np.dot(projector, orb0.coeffs[:,i0])
orb1.occupations[i1] = orb0.occupations[i0]
i1 += 1
# clear all parts of orb1 that were not touched by the projection loop
ntrans = i1
del i1
orb1.coeffs[:,ntrans:] = 0.0
orb1.occupations[ntrans:] = 0.0
orb1.energies[:] = 0.0
# auxiliary function for the MGS algo
def dot22(a, b):
return np.dot(np.dot(a, olp_22), b)
# Apply the MGS algorithm to orthogonalize the orbitals
for i1 in xrange(ntrans):
orb = orb1.coeffs[:, i1]
# Subtract overlap with previous orbitals
for j1 in xrange(i1):
other = orb1.coeffs[:, j1]
orb -= other*dot22(other, orb)/np.sqrt(dot22(other, other))
# Renormalize
norm = np.sqrt(dot22(orb, orb))
if norm < eps:
raise ProjectionError('The norm of a vector in the MGS algorithm becomes too '
'small. Orbitals are redundant in new basis.')
orb /= norm
def load_atom_cp2k(filename, lf):
'''Load data from a CP2K ATOM computation
**Arguments:**
filename
The name of the cp2k out file
**Returns** a dictionary with ``obasis``, ``exp_alpha``, ``coordinates``,
``numbers``, ``energy``, ``pseudo_numbers``. The dictionary may also
contain: ``exp_beta``.
'''
with open(filename) as f:
# Find the element number
for line in f:
if line.startswith(' Atomic Energy Calculation'):
number = int(line[-5:-1])
break
# Go to the pseudo basis set
for line in f:
if line.startswith(' Pseudopotential Basis'):
break
f.next() # empty line
line = f.next() # Check for GTO
assert line == ' ********************** Contracted Gaussian Type Orbitals **********************\n'
# Load the basis used for the PP wavefn
basis_desc = []
for line in f:
if line.startswith(' *******************'):
break
elif line[3:12] == 'Functions':
shell_type = str_to_shell_types(line[1:2], pure=True)[0]
a = []
c = []
basis_desc.append((shell_type, a, c))
else:
values = [float(w) for w in line.split()]
a.append(values[0])
c.append(values[1:])
# Convert the basis into HORTON format
shell_map = []
shell_types = []
nprims = []
alphas = []
con_coeffs = []
for shell_type, a, c in basis_desc:
# get correction to contraction coefficients.
corrections = _get_cp2k_norm_corrections(abs(shell_type), a)
c = np.array(c)/corrections.reshape(-1,1)
# fill in arrays
for col in c.T:
shell_map.append(0)
shell_types.append(shell_type)
nprims.append(len(col))
alphas.extend(a)
con_coeffs.extend(col)
# Create the basis object
coordinates = np.zeros((1, 3))
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)
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 cp2k.out file.')
lf.default_nbasis = obasis.nbasis
# Search for (un)restricted
restricted = None
for line in f:
if line.startswith(' METHOD |'):
if 'U' in line:
restricted = False
break
elif 'R' in line:
restricted = True
break
# Search for the core charge (pseudo number)
for line in f:
if line.startswith(' Core Charge'):
pseudo_number = float(line[70:])
assert pseudo_number == int(pseudo_number)
pseudo_number = int(pseudo_number)
break
# Search for energy
for line in f:
if line.startswith(' Energy components [Hartree] Total Energy ::'):
energy = float(line[60:])
break
# Read orbital energies and occupations
for line in f:
if line.startswith(' Orbital energies'):
break
f.next()
oe_alpha = []
oe_beta = []
empty = 0
while empty < 2:
line = f.next()
words = line.split()
if len(words) == 0:
empty += 1
continue
empty = 0
s = int(words[0])
l = int(words[2-restricted])
occ = float(words[3-restricted])
ener = float(words[4-restricted])
if restricted or words[1] == 'alpha':
oe_alpha.append((l, s, occ, ener))
else:
oe_beta.append((l, s, occ, ener))
# Read orbital expansion coefficients
line = f.next()
assert (line == " Atomic orbital expansion coefficients [Alpha]\n") or \
(line == " Atomic orbital expansion coefficients []\n")
coeffs_alpha = _read_coeffs_helper(f, oe_alpha)
if not restricted:
line = f.next()
assert (line == " Atomic orbital expansion coefficients [Beta]\n")
coeffs_beta = _read_coeffs_helper(f, oe_beta)
# Turn orbital data into a HORTON orbital expansions
if restricted:
norb, nel = _helper_norb(oe_alpha)
assert nel%2 == 0
exp_alpha = lf.create_expansion(obasis.nbasis, norb)
exp_beta = None
_helper_exp(exp_alpha, oe_alpha, coeffs_alpha, shell_types, restricted)
else:
norb_alpha, nalpha = _helper_norb(oe_alpha)
norb_beta, nbeta = _helper_norb(oe_beta)
assert norb_alpha == norb_beta
exp_alpha = lf.create_expansion(obasis.nbasis, norb_alpha)
exp_beta = lf.create_expansion(obasis.nbasis, norb_beta)
_helper_exp(exp_alpha, oe_alpha, coeffs_alpha, shell_types, restricted)
_helper_exp(exp_beta, oe_beta, coeffs_beta, shell_types, restricted)
result = {
'obasis': obasis,
'lf': lf,
'exp_alpha': exp_alpha,
'coordinates': coordinates,
'numbers': np.array([number]),
'energy': energy,
'pseudo_numbers': np.array([pseudo_number]),
}
if exp_beta is not None:
result['exp_beta'] = exp_beta
return result
def _fix_molden_from_buggy_codes(result, filename):
"""Detect errors in the data loaded from a molden/mkl/... file and correct.
Parameters
----------
result: dict
A dictionary with the data loaded in the ``load_molden`` function.
This function can recognize erroneous files created by PSI4, ORCA and Turbomole. The
values in `results` for the `obasis` and `signs` keys will be updated accordingly.
"""
obasis = result['obasis']
permutation = result.get('permutation', None)
if _is_normalized_properly(obasis, permutation, result['orb_alpha'],
result.get('orb_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.')
# --- ORCA
if log.do_medium:
log('Trying 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')
if orca_con_coeffs is not None:
# Only try if some changes were made to the contraction coefficients.
orca_obasis = GOBasis(obasis.centers, obasis.shell_map, obasis.nprims,
obasis.shell_types, obasis.alphas,
orca_con_coeffs)
if _is_normalized_properly(orca_obasis,
permutation, result['orb_alpha'],
result.get('orb_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
# --- PSI4
if log.do_medium:
log('Trying to fix it as if it was a file generated by PSI4 (pre 1.0).'
)
psi4_con_coeffs = _get_fixed_con_coeffs(obasis, 'psi4')
if psi4_con_coeffs is not None:
# Only try if some changes were made to the contraction coefficients.
psi4_obasis = GOBasis(obasis.centers, obasis.shell_map, obasis.nprims,
obasis.shell_types, obasis.alphas,
psi4_con_coeffs)
if _is_normalized_properly(psi4_obasis,
permutation, result['orb_alpha'],
result.get('orb_beta')):
if log.do_medium:
log('Detected typical PSI4 errors in file. Fixing them...')
result['obasis'] = psi4_obasis
return
# -- Turbomole
if log.do_medium:
log('Trying to fix it as if it was a file generated by Turbomole.')
tb_con_coeffs = _get_fixed_con_coeffs(obasis, 'turbomole')
if tb_con_coeffs is not None:
# Only try if some changes were made to the contraction coefficients.
tb_obasis = GOBasis(obasis.centers, obasis.shell_map, obasis.nprims,
obasis.shell_types, obasis.alphas, tb_con_coeffs)
if _is_normalized_properly(tb_obasis, permutation, result['orb_alpha'],
result.get('orb_beta')):
if log.do_medium:
log('Detected typical Turbomole errors in file. Fixing them...'
)
result['obasis'] = tb_obasis
return
# --- Renormalized contractions
if log.do_medium:
log('Last resort: trying by renormalizing all contractions')
normed_con_coeffs = _normalized_contractions(obasis)
normed_obasis = GOBasis(obasis.centers, obasis.shell_map, obasis.nprims,
obasis.shell_types, obasis.alphas,
normed_con_coeffs)
if _is_normalized_properly(normed_obasis, permutation, result['orb_alpha'],
result.get('orb_beta')):
if log.do_medium:
log('Detected unnormalized contractions in file. Fixing them...')
result['obasis'] = normed_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 project_orbitals_mgs(obasis0, obasis1, exp0, exp1, eps=1e-10):
'''Project the orbitals in ``exp0`` (wrt ``obasis0``) on ``obasis1`` and store in ``exp1`` with the modified Gram-Schmidt algorithm.
**Arguments:**
obasis0
The orbital basis for the original wavefunction expansion.
obasis1
The new orbital basis for the projected wavefunction expansion.
exp0
The expansion of the original orbitals.
exp1 (output)
An output argument in which the projected orbitals will be stored.
**Optional arguments:**
eps
A threshold for the renormalization in the Gram-Schmidt procedure
The projection is based on the Modified Gram-Schmidt (MGS) process. In
each iteration of the MGS, a renormalization is carried out. If the norm
in this step is smaller than ``eps``, an error is raised.
Note that ``exp1`` will be incomplete in several ways. The orbital
energies are not copied. Only the occupied orbitals in ``exp0`` are
projected. Coefficients of higher orbitals are set to zero. The orbital
occupations are simply copied. This should be sufficient to construct
an initial guess in a new orbital basis set based on a previous solution.
If the number of orbitals in ``exp1`` is too small to store all projected
orbitals, an error is raised.
'''
# Compute the overlap matrix of the combined orbital basis
obasis_both = GOBasis.concatenate(obasis0, obasis1)
lf = DenseLinalgFactory(obasis_both.nbasis)
olp_both = obasis_both.compute_overlap(lf)
# Select the blocks of interest from the big overlap matrix
olp_21 = olp_both._array[obasis0.nbasis:, :obasis0.nbasis]
olp_22 = olp_both._array[obasis0.nbasis:, obasis0.nbasis:]
# construct the projector
projector = np.dot(np.linalg.pinv(olp_22), olp_21)
# project occupied orbitals
i1 = 0
for i0 in xrange(exp0.nfn):
if exp0.occupations[i0] == 0.0:
continue
if i1 > exp1.nfn:
raise ProjectionError('Not enough functions available in exp1 to store the projected orbitals.')
exp1.coeffs[:,i1] = np.dot(projector, exp0.coeffs[:,i0])
exp1.occupations[i1] = exp0.occupations[i0]
i1 += 1
# clear all parts of exp1 that were not touched by the projection loop
ntrans = i1
del i1
exp1.coeffs[:,ntrans:] = 0.0
exp1.occupations[ntrans:] = 0.0
exp1.energies[:] = 0.0
# auxiliary function for the MGS algo
def dot22(a, b):
return np.dot(np.dot(a, olp_22), b)
# Apply the MGS algorithm to orthogonalize the orbitals
for i1 in xrange(ntrans):
orb = exp1.coeffs[:,i1]
# Subtract overlap with previous orbitals
for j1 in xrange(i1):
other = exp1.coeffs[:,j1]
orb -= other*dot22(other, orb)/np.sqrt(dot22(orb, orb))
# Renormalize
norm = np.sqrt(dot22(orb, orb))
if norm < eps:
raise ProjectionError('The norm of a vector in the MGS algorithm becomes too small. Orbitals are redundant in new basis.')
orb /= norm
def project_orbitals_mgs(obasis0, obasis1, exp0, exp1, eps=1e-10):
'''Project the orbitals onto a new basis set with the modified Gram-Schmidt algorithm.
The orbitals in ``exp0`` (w.r.t. ``obasis0``) are projected onto ``obasis1`` and
stored in ``exp1``.
Parameters
----------
obasis0 : GOBasis
The orbital basis for the original wavefunction expansion.
obasis1 : GOBasis
The new orbital basis for the projected wavefunction expansion.
exp0 : DenseExpansion
The expansion of the original orbitals.
exp1 : DenseExpansion
An output argument in which the projected orbitals will be stored.
eps : float
A threshold for the renormalization in the Gram-Schmidt procedure
Notes
-----
The projection is based on the Modified Gram-Schmidt (MGS) process. In
each iteration of the MGS, a renormalization is carried out. If the norm
in this step is smaller than ``eps``, an error is raised.
Note that ``exp1`` will be incomplete in several ways. The orbital
energies are not copied. Only the occupied orbitals in ``exp0`` are
projected. Coefficients of higher orbitals are set to zero. The orbital
occupations are simply copied. This should be sufficient to construct
an initial guess in a new orbital basis set based on a previous solution.
If the number of orbitals in ``exp1`` is too small to store all projected
orbitals, an error is raised.
'''
# Compute the overlap matrix of the combined orbital basis
obasis_both = GOBasis.concatenate(obasis0, obasis1)
lf = DenseLinalgFactory(obasis_both.nbasis)
olp_both = obasis_both.compute_overlap(lf)
# Select the blocks of interest from the big overlap matrix
olp_21 = olp_both._array[obasis0.nbasis:, :obasis0.nbasis]
olp_22 = olp_both._array[obasis0.nbasis:, obasis0.nbasis:]
# Construct the projector. This minimizes the L2 norm between the new and old
# orbitals, which does not account for orthonormality.
projector = np.dot(np.linalg.pinv(olp_22), olp_21)
# Project occupied orbitals.
i1 = 0
for i0 in xrange(exp0.nfn):
if exp0.occupations[i0] == 0.0:
continue
if i1 > exp1.nfn:
raise ProjectionError(
'Not enough functions available in exp1 to store the '
'projected orbitals.')
exp1.coeffs[:, i1] = np.dot(projector, exp0.coeffs[:, i0])
exp1.occupations[i1] = exp0.occupations[i0]
i1 += 1
# clear all parts of exp1 that were not touched by the projection loop
ntrans = i1
del i1
exp1.coeffs[:, ntrans:] = 0.0
exp1.occupations[ntrans:] = 0.0
exp1.energies[:] = 0.0
# auxiliary function for the MGS algo
def dot22(a, b):
return np.dot(np.dot(a, olp_22), b)
# Apply the MGS algorithm to orthogonalize the orbitals
for i1 in xrange(ntrans):
orb = exp1.coeffs[:, i1]
# Subtract overlap with previous orbitals
for j1 in xrange(i1):
other = exp1.coeffs[:, j1]
orb -= other * dot22(other, orb) / np.sqrt(dot22(other, other))
# Renormalize
norm = np.sqrt(dot22(orb, orb))
if norm < eps:
raise ProjectionError(
'The norm of a vector in the MGS algorithm becomes too '
'small. Orbitals are redundant in new basis.')
orb /= norm
