def __init__(self, filename):
self.filename = filename
self.prefix = filename[:-5]
fchk = FCHKFile(filename,
field_labels=[
"Charge",
"Number of basis functions",
"Dipole Moment",
"Number of electrons",
"Number of alpha electrons",
"Number of beta electrons",
"Alpha Orbital Energies",
"Beta Orbital Energies",
])
# for usage 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
# for internal usage
self._hack_fchk = self.restricted and (self.num_alpha != self.num_beta)
if "mp2" in fchk.lot.lower():
self._density_type = "mp2"
elif "mp3" in fchk.lot.lower():
self._density_type = "mp3"
elif "mp4" in fchk.lot.lower():
self._density_type = "mp4"
else:
self._density_type = "scf"
def test_o2_cc_pvtz_cart_num():
tmpdir, fn_fchk = setup_gaussian("o2_cc_pvtz_cart")
fchk = FCHKFile(fn_fchk)
basis = GaussianBasis.from_fchk(fchk)
assert (basis.num_shells == 20)
print basis.num_dof
assert (basis.num_dof == 70)
def test_orb0_hf_sto3g():
tmpdir, fn_fchk = setup_gaussian("hf_sto3g")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
weights = fchk.fields["Alpha MO coefficients"][:basis.num_dof]
points = ref_data_hf_sto3g_orb0[:, :3]
fns = basis.call_gint_grid(gint1_fns_basis, weights.reshape((1, -1)),
points * angstrom, 1)[0]
assert (abs(fns - ref_data_hf_sto3g_orb0[:, 3]).max() < 1e-10)
def load_molecule_g98fchk(fn_freq, fn_ener=None, energy=None):
"""Load a molecule from Gaussian98 formatted checkpoint files.
Arguments:
| ``fn_freq`` -- The formatted checkpoint file of the frequency job.
Optional arguments:
| ``fn_ener`` -- The formatted checkpoint file of a single point
computation for the energy. When not given, the energy
is taken from the frequency job.
| ``energy`` -- Override the energy from the formatted checkpoint file
with the given value.
"""
fchk_freq = FCHKFile(fn_freq,
ignore_errors=True,
field_labels=[
"Cartesian Force Constants", "Total Energy",
"Multiplicity", "Cartesian Gradient"
])
if fn_ener is None:
fchk_ener = fchk_freq
else:
fchk_ener = FCHKFile(fn_ener,
ignore_errors=True,
field_labels=["Total Energy"])
masses = np.array([g98_masses[n - 1] for n in fchk_freq.molecule.numbers])
if energy is None:
energy = fchk_ener.fields["Total Energy"]
return Molecule(
fchk_freq.molecule.numbers,
fchk_freq.molecule.coordinates,
masses,
energy,
np.reshape(np.array(fchk_freq.fields["Cartesian Gradient"]),
(len(fchk_freq.molecule.numbers), 3)),
fchk_freq.get_hessian(),
fchk_freq.fields["Multiplicity"],
None, # gaussian is very poor at computing the rotational symmetry number
False,
)
def test_orb0_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)
weights = fchk.fields["Alpha MO coefficients"][:basis.num_dof]
weights = weights[basis.g03_permutation]
points = ref_data_o2_cc_pvtz_pure_orb0[:, :3]
fns = basis.call_gint_grid(gint1_fns_basis, weights.reshape((1, -1)),
points * angstrom, 1)[0]
assert (abs(fns - ref_data_o2_cc_pvtz_pure_orb0[:, 3]).max() < 1e-10)
def get_mol(self, state, root):
if self.name == "opt":
# load the initial geometry
mol = Molecule.from_file("init/%s.xyz" % state.name)
else:
# load the optimized geometry
fn_fchk = "%s/%s__opt/gaussian.fchk" % (root, state.name)
mol = FCHKFile(fn_fchk, field_labels=[]).molecule
with open("init/%s.fragments" % state.name) as f:
mol.charge_mult = f.readline().split()
mol.tags = f.readline().split()
return mol
def test_orb0_h_sto3g():
tmpdir, fn_fchk = setup_gaussian("h_sto3g")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
# real test for the output
weights = fchk.fields["Alpha MO coefficients"][:basis.num_dof]
points = ref_data_h_sto3g_orb0[:, :3]
fns = basis.call_gint_grid(gint1_fns_basis, weights.reshape((1, -1)),
points * angstrom, 1)[0]
assert (abs(fns - ref_data_h_sto3g_orb0[:, 3]).max() < 1e-10)
# test error mechanism
basis.shell_types[0] = 102
assert_raises(ValueError, basis.call_gint_grid, gint1_fns_basis,
weights.reshape((1, -1)), points * angstrom, 1)
basis.shell_types[0] = -763
assert_raises(ValueError, basis.call_gint_grid, gint1_fns_basis,
weights.reshape((1, -1)), points * angstrom, 1)
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_h_sto3g():
tmpdir, fn_fchk = setup_gaussian("h_sto3g")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
# real test for the output
dmat = fchk.fields["Total SCF Density"]
points = ref_data_h_sto3g_pot[:, :3] * angstrom
radius = numpy.sqrt((points**2).sum(axis=1))
ref_data_h_sto3g_pot[:, 3] -= 1 / radius
potential = -basis.call_gint_grid(gint2_nai_dmat, dmat, points)
assert (abs(potential - ref_data_h_sto3g_pot[:, 3]).max() < 1e-8)
# test error mechanism
basis.shell_types[0] = 102
assert_raises(ValueError, basis.call_gint_grid, gint2_nai_dmat, dmat,
points * angstrom)
basis.shell_types[0] = -763
assert_raises(ValueError, basis.call_gint_grid, gint2_nai_dmat, dmat,
points * angstrom)
def from_file(cls, filename):
"""Construct a molecule object read from the given file.
The file format is inferred from the extensions. Currently supported
formats are: ``*.cml``, ``*.fchk``, ``*.pdb``, ``*.sdf``, ``*.xyz``
If a file contains more than one molecule, only the first one is
read.
Argument:
| ``filename`` -- the name of the file containing the molecule
Example usage::
>>> mol = Molecule.from_file("foo.xyz")
"""
# TODO: many different API's to load files. brrr...
if filename.endswith(".cml"):
from molmod.io import load_cml
return load_cml(filename)[0]
elif filename.endswith(".fchk"):
from molmod.io import FCHKFile
fchk = FCHKFile(filename, field_labels=[])
return fchk.molecule
elif filename.endswith(".pdb"):
from molmod.io import load_pdb
return load_pdb(filename)
elif filename.endswith(".sdf"):
from molmod.io import SDFReader
return next(SDFReader(filename))
elif filename.endswith(".xyz"):
from molmod.io import XYZReader
xyz_reader = XYZReader(filename)
title, coordinates = next(xyz_reader)
return Molecule(xyz_reader.numbers,
coordinates,
title,
symbols=xyz_reader.symbols)
else:
raise ValueError("Could not determine file format for %s." %
filename)
def test_dens_h_sto3g():
tmpdir, fn_fchk = setup_gaussian("h_sto3g")
fchk = FCHKFile(fn_fchk)
shutil.rmtree(tmpdir)
basis = GaussianBasis.from_fchk(fchk)
weights = fchk.fields["Alpha MO coefficients"][:basis.num_dof]
weights = weights[basis.g03_permutation]
points = ref_data_h_sto3g_orb0[:, :3]
orb0 = basis.call_gint_grid(gint1_fns_basis, weights.reshape((1, -1)),
points * angstrom, 1)[0]
num_dmat = (basis.num_dof * (basis.num_dof + 1)) / 2
dmat = fchk.fields["Total SCF Density"][:num_dmat]
density = basis.call_gint_grid(gint1_fn_dmat, dmat, points * angstrom)
assert (abs(orb0**2 - density).max() < 1e-10)
# test error mechanism
basis.shell_types[0] = 102
assert_raises(ValueError, basis.call_gint_grid, gint1_fn_dmat, dmat,
points * angstrom, 1)
basis.shell_types[0] = -763
assert_raises(ValueError, basis.call_gint_grid, gint1_fn_dmat, dmat,
points * angstrom, 1)
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)
N3 = coordinates.size
jacobian = numpy.zeros((N3, len(ics)), float)
for j, ic in enumerate(ics):
# Let the ic object fill in each column of the Jacobian.
ic.fill_jacobian_column(jacobian[:, j], coordinates)
return jacobian
# This if block is only executed when this file is ran as a program, and not
# when it is loaded as a module.
if __name__ == "__main__":
# Load the formatted checkpoint file with the frequency computation. This
# file also contains the atomic numbers and the coordinates of the atoms,
# and therefore one can access the dopamine molecule object through
# fchk.molecule.
fchk = FCHKFile("dopamine.fchk")
# Set the default graph for the construction of the internal coordinates:
fchk.molecule.set_default_graph()
# Setup a list of internal coordinates
ics = setup_ics(fchk.molecule.graph)
# Compute the Jacobian.
J = compute_jacobian(ics, fchk.molecule.coordinates)
# Compute the pseudo-inverse, using a loose threshold for the singular
# values to filter out equivalent internal coordinates.
Jinv = numpy.linalg.pinv(J, 1e-5)
# Get the Hessian in Cartesian coordinates.
H = fchk.get_hessian()
# Transform to internal coordinates.
K = numpy.dot(Jinv, numpy.dot(H, Jinv.transpose()))
# Make a nice printout of K.
print("The Hessian in internal coordinates in kcal/mol/angstrom**2")
def load_ener(fn_fchk):
fchk = FCHKFile(fn_fchk, field_labels=["Total Energy"])
return fchk.fields["Total Energy"]
def load_molecule_g03fchk(fn_freq, fn_ener=None, fn_vdw=None, energy=None, fn_punch=None):
"""Load a molecule from Gaussian03 formatted checkpoint files.
Arguments:
| ``fn_freq`` -- the formatted checkpoint file of the frequency job
Optional arguments:
| ``fn_ener`` -- the formatted checkpoint file of a single point
computation for the energy. When not given, the energy
is taken from the frequency job.
| ``fn_vdw`` -- An orca output file containing a Van der Waals
correction for the energy.
| ``energy`` -- Override the energy from the formatted checkpoint file
with the given value.
| ``punch`` -- A Gaussian derivatives punch file. When given, the
gradient and the Hessian are read from this file
instead.
"""
fchk_freq = FCHKFile(fn_freq, ignore_errors=True, field_labels=[
"Cartesian Force Constants", "Real atomic weights", "Total Energy",
"Multiplicity", "Cartesian Gradient", "MicOpt",
])
if fn_ener is None:
fchk_ener = fchk_freq
else:
fchk_ener = FCHKFile(fn_ener, ignore_errors=True, field_labels=[
"Total Energy"
])
if energy is None:
energy = fchk_ener.fields["Total Energy"]
vdw = 0
if fn_vdw is not None:
from tamkin.io.dispersion import load_dftd_orca
vdw = load_dftd_orca(fn_vdw)
natom = fchk_freq.molecule.size
if fchk_freq.molecule.size == 1 and \
"Cartesian Force Constants" not in fchk_freq.fields:
gradient = np.zeros((1,3), float)
hessian = np.zeros((3,3), float)
elif fn_punch is None:
gradient = fchk_freq.fields["Cartesian Gradient"].copy()
gradient.shape = (natom, 3)
hessian = fchk_freq.get_hessian()
else:
gradient = np.zeros((natom, 3), float)
hessian = np.zeros((3*natom, 3*natom), float)
iterator = iter_floats_file(fn_punch)
for i in xrange(natom):
for j in xrange(3):
gradient[i,j] = iterator.next()
for i in xrange(3*natom):
for j in xrange(i+1):
v = iterator.next()
hessian[i,j] = v
hessian[j,i] = v
if "MicOpt" in fchk_freq.fields:
fixed = (fchk_freq.fields["MicOpt"] == -2).nonzero()[0]
if len(fixed) == 0:
fixed = None
else:
fixed = None
return Molecule(
fchk_freq.molecule.numbers,
fchk_freq.molecule.coordinates,
fchk_freq.fields["Real atomic weights"]*amu,
energy+vdw,
gradient,
hessian,
fchk_freq.fields["Multiplicity"],
None, # gaussian is very poor at computing the rotational symmetry number
False,
title=fchk_freq.title,
fixed=fixed,
)
def test_h_sto3g_num():
tmpdir, fn_fchk = setup_gaussian("h_sto3g")
fchk = FCHKFile(fn_fchk)
basis = GaussianBasis.from_fchk(fchk)
assert (basis.num_shells == 1)
assert (basis.num_dof == 1)
def get_pf(dn, temps):
'''Construct a partition function from a molecule directory.
**Arguments:**
dn
A molecule directory name
temps
A list of temperatures at which the properties of the molecule must be
evaluated.
'''
print ' Loading partition function from', dn
# A1) load the molecule
molecule = load_molecule_g03fchk('%s/freq/gaussian.fchk' % dn)
# A2) if present, load a more accurate energy
fn_sp = '%s/sp/gaussian.fchk' % dn
if os.path.isfile(fn_sp):
from molmod.io import FCHKFile
sp_energy = FCHKFile(fn_sp).fields['Total Energy']
molecule = molecule.copy_with(energy=sp_energy)
# A3) if present add a grimme correction
fn_dftd3 = '%s/dftd3/dftd3.out' % dn
if os.path.isfile(fn_dftd3):
print ' Loading DFT-D3 corrections'
disp_energy = load_dftd3(fn_dftd3)
molecule = molecule.copy_with(energy=molecule.energy + disp_energy)
# B) Load all rotors and keep directories of each rotor (dns_rotor).
rotors = []
dns_rotor = []
# B1) load all rotors computed with Gaussian
for dn_rotor in glob('%s/rotor_g_*' % dn):
print ' Loading rotor', dn_rotor
dns_rotor.append(dn_rotor)
fn_log = '%s/gaussian.log' % dn_rotor
# Load the config file
rotor_cfg = load_cfg(os.path.join(dn_rotor, 'rotor.cfg'))
# Load the rotational scan data from the Gaussian log file.
rotor_scan = load_rotscan_g03log(fn_log,
get_atom_indexes(rotor_cfg, 'top'))
# Construct a Rotor object (solves Schrodinger equation etc.)
rotor = Rotor(rotor_scan,
molecule,
suffix=os.path.basename(dn_rotor)[6:],
rotsym=rotor_cfg.get('rotsym', 1),
even=rotor_cfg.get('even', False),
num_levels=rotor_cfg.get('num_levels', 50),
dofmax=rotor_cfg.get('dofmax', 5),
v_threshold=v_threshold)
rotors.append(rotor)
# B2) load all free rotors
for dn_rotor in glob('%s/rotor_f_*' % dn):
print ' Loading rotor', dn_rotor
dns_rotor.append(dn_rotor)
fn_cfg = '%s/rotor.cfg' % dn_rotor
# Load the config file
rotor_cfg = load_cfg(fn_cfg)
# Construct a Rotor object (solves Schrodinger equation etc.)
rotor_scan = RotScan(get_atom_indexes(rotor_cfg, 'dihed'), molecule,
get_atom_indexes(rotor_cfg, 'top'))
rotor = Rotor(rotor_scan,
molecule,
suffix=os.path.basename(dn_rotor)[6:],
rotsym=rotor_cfg.get('rotsym', 1),
num_levels=rotor_cfg.get('num_levels', 50),
dofmax=rotor_cfg.get('dofmax', 5),
v_threshold=v_threshold)
rotors.append(rotor)
# B3) load all custom rotors
for dn_rotor in glob('%s/rotor_c_*' % dn):
print ' Loading rotor', dn_rotor
dns_rotor.append(dn_rotor)
fn_dat = '%s/rotor.dat' % dn_rotor
# Load the potential data
potential = np.loadtxt(fn_dat).T
# Load the config file
rotor_cfg = load_cfg(os.path.join(dn_rotor, 'rotor.cfg'))
# Construct a Rotor object (solves Schrodinger equation etc.)
rotor_scan = RotScan(get_atom_indexes(rotor_cfg, 'dihed'), molecule,
get_atom_indexes(rotor_cfg, 'top'), potential)
rotor = Rotor(rotor_scan,
molecule,
suffix=os.path.basename(dn_rotor)[6:],
rotsym=rotor_cfg.get('rotsym', 1),
even=rotor_cfg.get('even', False),
num_levels=rotor_cfg.get('num_levels', 50),
dofmax=rotor_cfg.get('dofmax', 5),
v_threshold=v_threshold)
rotors.append(rotor)
# C) Perform a normal mode analysis
if molecule.fixed is None:
print ' Performing NMA with fixed external degrees of freedom'
nma = NMA(molecule,
ConstrainExt(gradient_threshold=gradient_threshold))
else:
print ' Performing NMA with fixed atoms: %s' % molecule.fixed
nma = NMA(molecule, PHVA(molecule.fixed))
# D) Define the partition function
mol_cfg = load_cfg('%s/molecule.cfg' % dn)
pf_contributions = [
Vibrations(freq_scaling=mol_cfg.get('freq_scaling', 1.0),
zp_scaling=mol_cfg.get('zp_scaling', 1.0))
]
if molecule.fixed is None:
pf_contributions.append(ExtTrans())
pf_contributions.append(ExtRot(mol_cfg.get('symnum', None)))
pf_contributions.extend(rotors)
pf = PartFun(nma, pf_contributions)
# Store the atomic numbers as an attribute of the partition function (used
# to check that no atoms get lost in a reaction.
pf.numbers = molecule.numbers
# E) Make plots of the rotor
for dn_rotor, rotor in zip(dns_rotor, rotors):
rotor.plot_levels('%s/levels.png' % dn_rotor, 300)
# F) Write a partf.txt file
pf.write_to_file('%s/partf.txt' % dn)
# G) Write a thermo analysis if temperatures are provided
if len(temps) > 0:
ta = ThermoAnalysis(pf, temps)
ta.write_to_file('%s/thermo.csv' % dn)
return pf
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)
