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 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 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,
)
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")
unit = kcalmol / angstrom**2
for row in K:
print(" ".join("% 5.0f" % (v / unit) for v in row))
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,
)
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"
unit = kcalmol/angstrom**2
for row in K:
print " ".join("% 5.0f" % (v/unit) for v in row)