def test_reorder_dmat1():
# This test uses a very simple small matrix.
dmat = numpy.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0])
permutation = numpy.array([1,2,0])
reorder_dmat(dmat, permutation)
expected_dmat = numpy.array([2.0, 4.0, 5.0, 1.0, 3.0, 0.0])
assert(abs(dmat-expected_dmat).max() < 1e-10)
def test_pot_o2_cc_pvtz_pure():
tmpdir, fn_fchk = setup_gaussian("o2_cc_pvtz_pure")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
dmat = fchk.fields["Total SCF Density"]
reorder_dmat(dmat, basis.g03_permutation)
points = ref_data_o2_cc_pvtz_pure_pot[:,:3]*angstrom
ref_potential = ref_data_o2_cc_pvtz_pure_pot[:,3]
nuc_potential = 0.0
for i in xrange(fchk.molecule.size):
center = fchk.molecule.coordinates[i]
Z = fchk.molecule.numbers[i]
radius = numpy.sqrt(((points-center)**2).sum(axis=1))
nuc_potential += Z/radius
ref_potential -= nuc_potential
potential = -basis.call_gint_grid(gint2_nai_dmat, dmat, points)
assert(abs(potential-ref_potential).max() < 1e-6)
def test_pot_o2_cc_pvtz_pure():
tmpdir, fn_fchk = setup_gaussian("o2_cc_pvtz_pure")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
dmat = fchk.fields["Total SCF Density"]
reorder_dmat(dmat, basis.g03_permutation)
points = ref_data_o2_cc_pvtz_pure_pot[:, :3] * angstrom
ref_potential = ref_data_o2_cc_pvtz_pure_pot[:, 3]
nuc_potential = 0.0
for i in xrange(fchk.molecule.size):
center = fchk.molecule.coordinates[i]
Z = fchk.molecule.numbers[i]
radius = numpy.sqrt(((points - center)**2).sum(axis=1))
nuc_potential += Z / radius
ref_potential -= nuc_potential
potential = -basis.call_gint_grid(gint2_nai_dmat, dmat, points)
assert (abs(potential - ref_potential).max() < 1e-6)
def test_reorder_dmat2():
# This is a test based on a randomly generated matrix.
num_dof = 10
size = (num_dof*(num_dof+1))/2
dmat = numpy.random.normal(0, 1, size)
permutation = numpy.random.permutation(num_dof)
square = numpy.zeros((num_dof, num_dof), float)
j = 0
for i in xrange(num_dof):
square[i,0:i+1] = dmat[j:j+i+1]
square[0:i+1,i] = dmat[j:j+i+1]
j += i+1
square = square[permutation].transpose()[permutation]
expected_dmat = numpy.zeros(size, float)
j = 0
for i in xrange(num_dof):
expected_dmat[j:j+i+1] = square[i,0:i+1]
j += i+1
reorder_dmat(dmat, permutation)
assert(abs(dmat-expected_dmat).max() < 1e-10)
def test_dens_o2_cc_pvtz_pure():
tmpdir, fn_fchk = setup_gaussian("o2_cc_pvtz_pure")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
num_dmat = (basis.num_dof*(basis.num_dof+1))/2
points = ref_data_o2_cc_pvtz_pure_orb0[:,:3]
dmat = fchk.fields["Total SCF Density"][:num_dmat]
reorder_dmat(dmat, basis.g03_permutation)
density = basis.call_gint_grid(gint1_fn_dmat, dmat, points*angstrom)
num_alpha = fchk.fields["Number of alpha electrons"]
weights = fchk.fields["Alpha MO coefficients"][:num_alpha*basis.num_dof]
weights = weights.reshape((num_alpha, basis.num_dof))
weights = weights[:,basis.g03_permutation]
orbitals = basis.call_gint_grid(gint1_fns_basis, weights, points*angstrom, num_alpha)
assert(orbitals.shape == (num_alpha, len(points)))
expected_density = 2*(orbitals**2).sum(axis=0)
assert(abs(density-expected_density).max() < 1e-6)
def test_dens_o2_cc_pvtz_pure():
tmpdir, fn_fchk = setup_gaussian("o2_cc_pvtz_pure")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
num_dmat = (basis.num_dof * (basis.num_dof + 1)) / 2
points = ref_data_o2_cc_pvtz_pure_orb0[:, :3]
dmat = fchk.fields["Total SCF Density"][:num_dmat]
reorder_dmat(dmat, basis.g03_permutation)
density = basis.call_gint_grid(gint1_fn_dmat, dmat, points * angstrom)
num_alpha = fchk.fields["Number of alpha electrons"]
weights = fchk.fields["Alpha MO coefficients"][:num_alpha * basis.num_dof]
weights = weights.reshape((num_alpha, basis.num_dof))
weights = weights[:, basis.g03_permutation]
orbitals = basis.call_gint_grid(gint1_fns_basis, weights,
points * angstrom, num_alpha)
assert (orbitals.shape == (num_alpha, len(points)))
expected_density = 2 * (orbitals**2).sum(axis=0)
assert (abs(density - expected_density).max() < 1e-6)
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 __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)