def dump(self, f):
"""Write all the information about the rotor to a file
This method is part of the PartFun API and should never be called
directly. It will only work properly once the init_part_fun method
is called.
Arguments:
| ``f`` -- A file-like object.
"""
Info.dump(self, f)
# parameters
print >> f, " Dihedral indexes: %s" % " ".join(
str(i) for i in self.rot_scan.dihedral)
print >> f, " Top indexes: %s" % " ".join(
str(i) for i in self.rot_scan.top_indexes)
print >> f, " Rotational symmetry: %i" % self.rotsym
print >> f, " Even potential: %s" % self.even
if self.rot_scan.potential is None:
print >> f, " This is a free rotor"
else:
angles, energies = self.rot_scan.potential
print >> f, " This is a hindered rotor"
print >> f, " Maximum number of cosines in the fit: %i" % self.dofmax
angles, energies = self.potential
fit_energies = self.hb.eval_fn(angles, self.v_coeffs)
rmsd = ((fit_energies - energies)**2).mean()**0.5
rms = (energies**2).mean()**0.5
rrmsd = rmsd / rms
print >> f, " RMSD of the fit [kJ/mol]: %.2f" % (rmsd / kjmol)
print >> f, " Relative RMSD of the fit the fit [%%]: %.1f" % (
rrmsd * 100)
print >> f, " Pearson R^2 of the fit [%%]: %.3f" % (
(1 - rrmsd**2) * 100)
print >> f, " Potential: Angle [deg] Energy [kJ/mol]"
for i in xrange(len(angles)):
print >> f, " % 7.2f %6.1f" % (
angles[i] / deg, energies[i] / kjmol)
print >> f, " Number of QM energy levels: %i" % self.num_levels
# derived quantities
print >> f, " Center [A]: % 8.2f % 8.2f % 8.2f" % tuple(
self.center / angstrom)
print >> f, " Axis [1]: % 8.2f % 8.2f % 8.2f" % tuple(self.axis)
print >> f, " Moment [amu*bohr**2]: %f" % (self.moment / amu)
print >> f, " Reduced moment [amu*bohr**2]: %f" % (
self.reduced_moment / amu)
print >> f, " Cancel wavenumber [1/cm]: %.1f" % (
self.cancel_freq / (lightspeed / centimeter))
print >> f, " The cancelation wavenumber is %s." % self.cancel_method
self.dump_values(f, "Energy levels [kJ/mol]",
self.energy_levels / kjmol, "% 8.2f", 8)
if self.hb is not None:
print >> f, " Number of basis functions: %i" % (self.hb.size)
print >> f, " Zero-point contribution [kJ/mol]: %.7f" % (
self.free_energy(0.0) / kjmol)
def dump(self, f):
"""Write all the information about the rotor to a file
This method is part of the PartFun API and should never be called
directly. It will only work properly once the init_part_fun method
is called.
Arguments:
| ``f`` -- A file-like object.
"""
Info.dump(self, f)
# parameters
print >> f, " Dihedral indexes: %s" % " ".join(str(i) for i in self.rot_scan.dihedral)
print >> f, " Top indexes: %s" % " ".join(str(i) for i in self.rot_scan.top_indexes)
print >> f, " Rotational symmetry: %i" % self.rotsym
print >> f, " Even potential: %s" % self.even
if self.rot_scan.potential is None:
print >> f, " This is a free rotor"
else:
angles, energies = self.rot_scan.potential
print >> f, " This is a hindered rotor"
print >> f, " Maximum number of cosines in the fit: %i" % self.dofmax
angles, energies = self.potential
fit_energies = self.hb.eval_fn(angles, self.v_coeffs)
rmsd = ((fit_energies - energies)**2).mean()**0.5
rms = (energies**2).mean()**0.5
rrmsd = rmsd/rms
print >> f, " RMSD of the fit [kJ/mol]: %.2f" % (rmsd/kjmol)
print >> f, " Relative RMSD of the fit the fit [%%]: %.1f" % (rrmsd*100)
print >> f, " Pearson R^2 of the fit [%%]: %.3f" % ((1-rrmsd**2)*100)
print >> f, " Potential: Angle [deg] Energy [kJ/mol]"
for i in xrange(len(angles)):
print >> f, " % 7.2f %6.1f" % (angles[i]/deg, energies[i]/kjmol)
print >> f, " Number of QM energy levels: %i" % self.num_levels
# derived quantities
print >> f, " Center [A]: % 8.2f % 8.2f % 8.2f" % tuple(self.center/angstrom)
print >> f, " Axis [1]: % 8.2f % 8.2f % 8.2f" % tuple(self.axis)
print >> f, " Moment [amu*bohr**2]: %f" % (self.moment/amu)
print >> f, " Reduced moment [amu*bohr**2]: %f" % (self.reduced_moment/amu)
print >> f, " Cancel wavenumber [1/cm]: %.1f" % (self.cancel_freq/(lightspeed/centimeter))
print >> f, " The cancelation wavenumber is %s." % self.cancel_method
self.dump_values(f, "Energy levels [kJ/mol]", self.energy_levels/kjmol, "% 8.2f", 8)
if self.hb is not None:
print >> f, " Number of basis functions: %i" % (self.hb.size)
print >> f, " Zero-point contribution [kJ/mol]: %.7f" % (self.free_energy(0.0)/kjmol)
def __init__(self,
rot_scan,
molecule=None,
cancel_freq='mbh',
suffix=None,
rotsym=1,
even=False,
num_levels=50,
dofmax=5,
v_threshold=0.01,
large_fixed=False):
"""
Arguments:
| ``rot_scan`` -- A rotational scan object. (free or hindered rotor
information)
Optional arguments:
| ``molecule`` -- Molecule to which the rotor applies, is used to
compute the cancelation frequency. Not required
when the cancel_freq argument is present.
| ``cancel_freq`` -- The frequency to cancel in the vibrational
partition function. This can also be 'mbh' or
'scan' to indicate that the cancel frequency
should be computed using the MBH method or
based on the second order derivative of the
rotational potential. Note that the latter
option is only possible in the case of the
hindered rotor formalism. [default='mbh']
| ``suffix`` -- A name suffix used to distinguish between different
rotors.
| ``rotsym`` -- The rotational symmetry of the rotor. [default=1]
| ``even`` -- True of the rotor is not chiral, i.e. when it has an
even potential
| ``num_levels`` -- The number of energy levels considered in the
QM treatment of the rotor [default=50]
| ``dofmax`` -- The maximum number of cosines used to represent the
torsional potential. if the potential is not even,
the same number of sines is also used. [default=5]
| ``v_threshold`` -- Tolerance on the relative error between the
Fourier expansion and the data points of the
scan. [default=0.01]. Absolute errors smaller
than 1 kJ/mol are always ignored.
| ``large_fixed`` -- When True, assume that the large part of the
system is fixed in space while the small part
rotates. (this means that the absolute moment
of the rotor is used instead of the relative
moment)
In case the Fourier expansion of the potential represents a poor fit
(determined by v_threshold), a ValueError is raised. It means that
you have to check your torsional scan datapoints for errors.
"""
self.rot_scan = rot_scan
self.cancel_freq = cancel_freq
self.cancel_method = 'given by the user'
# the cancelation frequency
if self.cancel_freq == 'mbh':
self.cancel_freq = compute_cancel_frequency_mbh(
molecule, self.rot_scan.dihedral, self.rot_scan.top_indexes)
self.cancel_method = 'computed with mbh'
elif self.cancel_freq == 'scan':
if self.rot_scan.potential is None:
raise RotorError(
"The option cancel_freq='scan' can only be used with hindered rotors."
)
self.cancel_method = 'derived from the torsional potential'
# the actual computation is performed later
else:
raise ValueError("Could not interpret cancel_freq=%s" %
cancel_freq)
#
if suffix is None:
self.suffix = "_".join(str(i) for i in rot_scan.top_indexes)
else:
self.suffix = suffix
self.rotsym = rotsym
self.even = even
self.num_levels = num_levels
self.dofmax = dofmax
self.v_threshold = v_threshold
self.large_fixed = large_fixed
if rot_scan.potential is None:
Info.__init__(self, "free_rotor_%s" % self.suffix)
else:
Info.__init__(self, "hindered_rotor_%s" % self.suffix)
StatFysTerms.__init__(self, 2) # two terms
def __init__(self, rot_scan, molecule=None, cancel_freq='mbh', suffix=None,
rotsym=1, even=False, num_levels=50, dofmax=5,
v_threshold=0.01, large_fixed=False):
"""
Arguments:
| ``rot_scan`` -- A rotational scan object. (free or hindered rotor
information)
Optional arguments:
| ``molecule`` -- Molecule to which the rotor applies, is used to
compute the cancelation frequency. Not required
when the cancel_freq argument is present.
| ``cancel_freq`` -- The frequency to cancel in the vibrational
partition function. This can also be 'mbh' or
'scan' to indicate that the cancel frequency
should be computed using the MBH method or
based on the second order derivative of the
rotational potential. Note that the latter
option is only possible in the case of the
hindered rotor formalism. [default='mbh']
| ``suffix`` -- A name suffix used to distinguish between different
rotors.
| ``rotsym`` -- The rotational symmetry of the rotor. [default=1]
| ``even`` -- True of the rotor is not chiral, i.e. when it has an
even potential
| ``num_levels`` -- The number of energy levels considered in the
QM treatment of the rotor [default=50]
| ``dofmax`` -- The maximum number of cosines used to represent the
torsional potential. if the potential is not even,
the same number of sines is also used. [default=5]
| ``v_threshold`` -- Tolerance on the relative error between the
Fourier expansion and the data points of the
scan. [default=0.01]. Absolute errors smaller
than 1 kJ/mol are always ignored.
| ``large_fixed`` -- When True, assume that the large part of the
system is fixed in space while the small part
rotates. (this means that the absolute moment
of the rotor is used instead of the relative
moment)
In case the Fourier expansion of the potential represents a poor fit
(determined by v_threshold), a ValueError is raised. It means that
you have to check your torsional scan datapoints for errors.
"""
self.rot_scan = rot_scan
self.cancel_freq = cancel_freq
self.cancel_method = 'given by the user'
# the cancelation frequency
if self.cancel_freq == 'mbh':
self.cancel_freq = compute_cancel_frequency_mbh(
molecule, self.rot_scan.dihedral, self.rot_scan.top_indexes
)
self.cancel_method = 'computed with mbh'
elif self.cancel_freq == 'scan':
if self.rot_scan.potential is None:
raise RotorError("The option cancel_freq='scan' can only be used with hindered rotors.")
self.cancel_method = 'derived from the torsional potential'
# the actual computation is performed later
else:
raise ValueError("Could not interpret cancel_freq=%s" % cancel_freq)
#
if suffix is None:
self.suffix = "_".join(str(i) for i in rot_scan.top_indexes)
else:
self.suffix = suffix
self.rotsym = rotsym
self.even = even
self.num_levels = num_levels
self.dofmax = dofmax
self.v_threshold = v_threshold
self.large_fixed = large_fixed
if rot_scan.potential is None:
Info.__init__(self, "free_rotor_%s" % self.suffix)
else:
Info.__init__(self, "hindered_rotor_%s" % self.suffix)
StatFysTerms.__init__(self, 2) # two terms
