def test_add_orbitals_to_dmat2():
num_dof = 10
num_orbitals = 5
size = (num_dof*(num_dof+1))/2
orbitals = numpy.random.normal(0, 1, (num_orbitals, num_dof))
dmat = numpy.zeros(size, float)
add_orbitals_to_dmat(orbitals, dmat)
expected_dmat = numpy.dot(orbitals.transpose(), orbitals)
expected_dmat = numpy.concatenate([expected_dmat[i,:i+1] for i in xrange(num_dof)])
assert(abs(dmat - expected_dmat).max() < 1e-10)
def __init__(self, filename, options):
if len(options) == 1:
density_type = options[0]
elif len(options) == 0:
density_type = None
else:
raise ValueError("Only one option is supported for the FCHKWaveFunction")
self.filename = filename
self.options = options
self.prefix = filename[:-5]
fchk = FCHKFile(filename)
# for use by the rest of the program
self.charge = fchk.fields["Charge"]
self.num_orbitals = fchk.fields["Number of basis functions"]
self.dipole = fchk.fields["Dipole Moment"]
self.num_electrons = fchk.fields["Number of electrons"]
self.num_alpha = fchk.fields["Number of alpha electrons"]
self.num_beta = fchk.fields["Number of beta electrons"]
self.restricted = "Beta Orbital Energies" not in fchk.fields
self.molecule = fchk.molecule
self.nuclear_charges = fchk.fields["Nuclear charges"]
# for internal usage
if density_type is None:
if "mp2" in fchk.lot.lower():
density_type = "mp2"
elif "mp3" in fchk.lot.lower():
density_type = "mp3"
elif "mp4" in fchk.lot.lower():
density_type = "mp4"
else:
density_type = "scf"
# electronic structure data
self.basis = GaussianBasis.from_fchk(fchk)
# orbitals
self.alpha_orbital_energies = None
self.beta_orbital_energies = None
self.natural_orbitals = None
self.alpha_orbitals = None
self.beta_orbitals = None
self.alpha_occupations = None
self.beta_occupations = None
self.natural_occupations = None
if density_type == "scf":
# Load orbital stuff only for scf computations.
self.alpha_orbital_energies = fchk.fields["Alpha Orbital Energies"]
self.beta_orbital_energies = fchk.fields.get("Beta Orbital Energies", self.alpha_orbital_energies)
self.alpha_orbitals = fchk.fields["Alpha MO coefficients"].reshape((-1,self.basis.num_dof))
self.alpha_orbitals = self.alpha_orbitals[:,self.basis.g03_permutation]
self.beta_orbitals = fchk.fields.get("Beta MO coefficients")
if self.beta_orbitals is None:
self.beta_orbitals = self.alpha_orbitals
else:
self.beta_orbitals = self.beta_orbitals.reshape((-1,self.basis.num_dof))[:,self.basis.g03_permutation]
self.alpha_occupations = numpy.zeros(self.num_orbitals, float)
self.alpha_occupations[:self.num_alpha] = 1.0
if self.beta_orbitals is None:
self.beta_occupations = self.alpha_occupations
else:
self.beta_occupations = numpy.zeros(self.num_orbitals, float)
self.beta_occupations[:self.num_beta] = 1.0
if self.restricted:
self.natural_orbitals = self.alpha_orbitals
self.natural_occupations = self.alpha_occupations + self.beta_occupations
self.num_natural = max(self.num_alpha, self.num_beta)
# density matrices
hack_fchk = self.restricted and (self.num_alpha != self.num_beta) and density_type == "scf"
if hack_fchk:
# construct density matrices manually because the fchk file
# contains the wrong one. we only do this for scf computations.
n = self.basis.num_dof
size = (n*(n+1))/2
self.density_matrix = numpy.zeros(size, float)
add_orbitals_to_dmat(self.alpha_orbitals[:self.num_alpha], self.density_matrix)
add_orbitals_to_dmat(self.beta_orbitals[:self.num_beta], self.density_matrix)
self.spin_density_matrix = numpy.zeros(size, float)
num_min = min(self.num_alpha, self.num_beta)
num_max = max(self.num_alpha, self.num_beta)
add_orbitals_to_dmat(self.alpha_orbitals[num_min:num_max], self.spin_density_matrix)
else:
self.density_matrix = None
self.spin_density_matrix = None
# load the density matrices
for key in fchk.fields:
if key.startswith("Total") and key.endswith("Density"):
if key[6:-8].lower() != density_type:
continue
assert self.density_matrix is None
dmat = fchk.fields[key]
reorder_dmat(dmat, self.basis.g03_permutation)
self.density_matrix = dmat
elif key.startswith("Spin") and key.endswith("Density"):
if key[5:-8].lower() != density_type:
continue
assert self.spin_density_matrix is None
dmat = fchk.fields[key]
reorder_dmat(dmat, self.basis.g03_permutation)
self.spin_density_matrix = dmat
if self.density_matrix is None:
raise ValueError("Could not find the '%s' density matrix in the fchk file." % self._density_type)
def test_add_orbitals_to_dmat1():
orbitals = numpy.array([[1, 2], [3, 4]])
expected_dmat = numpy.array([10, 14, 20])
dmat = numpy.zeros(3, float)
add_orbitals_to_dmat(orbitals, dmat)
assert(abs(dmat - expected_dmat).max() < 1e-10)
def __init__(self, filename, options):
if len(options) == 1:
density_type = options[0]
elif len(options) == 0:
density_type = None
else:
raise ValueError(
"Only one option is supported for the FCHKWaveFunction")
self.filename = filename
self.options = options
self.prefix = filename[:-5]
fchk = FCHKFile(filename)
# for use by the rest of the program
self.charge = fchk.fields["Charge"]
self.num_orbitals = fchk.fields["Number of basis functions"]
self.dipole = fchk.fields["Dipole Moment"]
self.num_electrons = fchk.fields["Number of electrons"]
self.num_alpha = fchk.fields["Number of alpha electrons"]
self.num_beta = fchk.fields["Number of beta electrons"]
self.restricted = "Beta Orbital Energies" not in fchk.fields
self.molecule = fchk.molecule
self.nuclear_charges = fchk.fields["Nuclear charges"]
# for internal usage
if density_type is None:
if "mp2" in fchk.lot.lower():
density_type = "mp2"
elif "mp3" in fchk.lot.lower():
density_type = "mp3"
elif "mp4" in fchk.lot.lower():
density_type = "mp4"
else:
density_type = "scf"
# electronic structure data
self.basis = GaussianBasis.from_fchk(fchk)
# orbitals
self.alpha_orbital_energies = None
self.beta_orbital_energies = None
self.natural_orbitals = None
self.alpha_orbitals = None
self.beta_orbitals = None
self.alpha_occupations = None
self.beta_occupations = None
self.natural_occupations = None
if density_type == "scf":
# Load orbital stuff only for scf computations.
self.alpha_orbital_energies = fchk.fields["Alpha Orbital Energies"]
self.beta_orbital_energies = fchk.fields.get(
"Beta Orbital Energies", self.alpha_orbital_energies)
self.alpha_orbitals = fchk.fields["Alpha MO coefficients"].reshape(
(-1, self.basis.num_dof))
self.alpha_orbitals = self.alpha_orbitals[:, self.basis.
g03_permutation]
self.beta_orbitals = fchk.fields.get("Beta MO coefficients")
if self.beta_orbitals is None:
self.beta_orbitals = self.alpha_orbitals
else:
self.beta_orbitals = self.beta_orbitals.reshape(
(-1, self.basis.num_dof))[:, self.basis.g03_permutation]
self.alpha_occupations = numpy.zeros(self.num_orbitals, float)
self.alpha_occupations[:self.num_alpha] = 1.0
if self.beta_orbitals is None:
self.beta_occupations = self.alpha_occupations
else:
self.beta_occupations = numpy.zeros(self.num_orbitals, float)
self.beta_occupations[:self.num_beta] = 1.0
if self.restricted:
self.natural_orbitals = self.alpha_orbitals
self.natural_occupations = self.alpha_occupations + self.beta_occupations
self.num_natural = max(self.num_alpha, self.num_beta)
# density matrices
hack_fchk = self.restricted and (
self.num_alpha != self.num_beta) and density_type == "scf"
if hack_fchk:
# construct density matrices manually because the fchk file
# contains the wrong one. we only do this for scf computations.
n = self.basis.num_dof
size = (n * (n + 1)) / 2
self.density_matrix = numpy.zeros(size, float)
add_orbitals_to_dmat(self.alpha_orbitals[:self.num_alpha],
self.density_matrix)
add_orbitals_to_dmat(self.beta_orbitals[:self.num_beta],
self.density_matrix)
self.spin_density_matrix = numpy.zeros(size, float)
num_min = min(self.num_alpha, self.num_beta)
num_max = max(self.num_alpha, self.num_beta)
add_orbitals_to_dmat(self.alpha_orbitals[num_min:num_max],
self.spin_density_matrix)
else:
self.density_matrix = None
self.spin_density_matrix = None
# load the density matrices
for key in fchk.fields:
if key.startswith("Total") and key.endswith("Density"):
if key[6:-8].lower() != density_type:
continue
assert self.density_matrix is None
dmat = fchk.fields[key]
reorder_dmat(dmat, self.basis.g03_permutation)
self.density_matrix = dmat
elif key.startswith("Spin") and key.endswith("Density"):
if key[5:-8].lower() != density_type:
continue
assert self.spin_density_matrix is None
dmat = fchk.fields[key]
reorder_dmat(dmat, self.basis.g03_permutation)
self.spin_density_matrix = dmat
if self.density_matrix is None:
raise ValueError(
"Could not find the '%s' density matrix in the fchk file."
% self._density_type)
