def getStatmechData(self, molecule, thermoModel):
"""
Use the previously-loaded frequency database to generate a set of
characteristic group frequencies corresponding to the speficied
`molecule`. The provided thermo data in `thermoModel` is used to fit
some frequencies and all hindered rotors to heat capacity data.
"""
conformer = Conformer()
# Compute spin multiplicity
# For closed-shell molecule the spin multiplicity is 1
# For monoradicals the spin multiplicity is 2
# For higher-order radicals the highest allowed spin multiplicity is assumed
conformer.spinMultiplicity = molecule.getRadicalCount() + 1
# No need to determine rotational and vibrational modes for single atoms
if len(molecule.atoms) < 2:
return (conformer, None, None)
linear = molecule.isLinear()
numRotors = molecule.countInternalRotors()
numVibrations = 3 * len(molecule.atoms) - (5 if linear else
6) - numRotors
# Get characteristic frequency groups and the associated frequencies
groupCount = self.getFrequencyGroups(molecule)
frequencies = []
for entry, count in groupCount.iteritems():
if count != 0 and entry.data is not None:
frequencies.extend(entry.data.generateFrequencies(count))
# Check that we have the right number of degrees of freedom specified
if len(frequencies) > numVibrations:
# We have too many vibrational modes
difference = len(frequencies) - numVibrations
# First try to remove hindered rotor modes until the proper number of modes remain
if numRotors > difference:
numRotors -= difference
numVibrations = len(frequencies)
logging.warning(
'For {0}, more characteristic frequencies were generated than vibrational modes allowed. Removed {1:d} internal rotors to compensate.'
.format(molecule, difference))
# If that won't work, turn off functional groups until the problem is underspecified again
else:
groupsRemoved = 0
freqsRemoved = 0
freqCount = len(frequencies)
while freqCount > numVibrations:
minDegeneracy, minEntry = min([(entry.data.symmetry, entry)
for entry in groupCount
if groupCount[entry] > 0])
if groupCount[minEntry] > 1:
groupCount[minEntry] -= 1
else:
del groupCount[minEntry]
groupsRemoved += 1
freqsRemoved += minDegeneracy
freqCount -= minDegeneracy
# Log warning
logging.warning(
'For {0}, more characteristic frequencies were generated than vibrational modes allowed. Removed {1:d} groups ({2:d} frequencies) to compensate.'
.format(molecule, groupsRemoved, freqsRemoved))
# Regenerate characteristic frequencies
frequencies = []
for entry, count in groupCount.iteritems():
if count != 0:
frequencies.extend(
entry.data.generateFrequencies(count))
# Subtract out contributions to heat capacity from the group frequencies
Tlist = numpy.arange(300.0, 1501.0, 100.0, numpy.float64)
Cv = numpy.array(
[thermoModel.getHeatCapacity(T) / constants.R for T in Tlist],
numpy.float64)
ho = HarmonicOscillator(frequencies=(frequencies, "cm^-1"))
for i in range(Tlist.shape[0]):
Cv[i] -= ho.getHeatCapacity(Tlist[i]) / constants.R
# Subtract out translational modes
Cv -= 1.5
# Subtract out external rotational modes
Cv -= (1.5 if not linear else 1.0)
# Subtract out PV term (Cp -> Cv)
Cv -= 1.0
# Fit remaining frequencies and hindered rotors to the heat capacity data
from statmechfit import fitStatmechToHeatCapacity
modes = fitStatmechToHeatCapacity(Tlist, Cv,
numVibrations - len(frequencies),
numRotors, molecule)
for mode in modes:
if isinstance(mode, HarmonicOscillator):
uncertainties = [0 for f in frequencies
] # probably shouldn't be zero
frequencies.extend(mode.frequencies.value_si)
uncertainties.extend(mode.frequencies.uncertainty)
mode.frequencies.value_si = numpy.array(
frequencies, numpy.float)
mode.frequencies.uncertainty = numpy.array(
uncertainties, numpy.float)
break
else:
modes.insert(
0, HarmonicOscillator(frequencies=(frequencies, "cm^-1")))
conformer.modes = modes
return (conformer, None, None)
def getStatmechData(self, molecule, thermoModel):
"""
Use the previously-loaded frequency database to generate a set of
characteristic group frequencies corresponding to the speficied
`molecule`. The provided thermo data in `thermoModel` is used to fit
some frequencies and all hindered rotors to heat capacity data.
"""
conformer = Conformer()
# Compute spin multiplicity
# For closed-shell molecule the spin multiplicity is 1
# For monoradicals the spin multiplicity is 2
# For higher-order radicals the highest allowed spin multiplicity is assumed
conformer.spinMultiplicity = molecule.getRadicalCount() + 1
# No need to determine rotational and vibrational modes for single atoms
if len(molecule.atoms) < 2:
return (conformer, None, None)
linear = molecule.isLinear()
numRotors = molecule.countInternalRotors()
numVibrations = 3 * len(molecule.atoms) - (5 if linear else 6) - numRotors
# Get characteristic frequency groups and the associated frequencies
groupCount = self.getFrequencyGroups(molecule)
frequencies = []
for entry, count in groupCount.iteritems():
if count != 0 and entry.data is not None: frequencies.extend(entry.data.generateFrequencies(count))
# Check that we have the right number of degrees of freedom specified
if len(frequencies) > numVibrations:
# We have too many vibrational modes
difference = len(frequencies) - numVibrations
# First try to remove hindered rotor modes until the proper number of modes remain
if numRotors > difference:
numRotors -= difference
numVibrations = len(frequencies)
logging.warning('For {0}, more characteristic frequencies were generated than vibrational modes allowed. Removed {1:d} internal rotors to compensate.'.format(molecule, difference))
# If that won't work, turn off functional groups until the problem is underspecified again
else:
groupsRemoved = 0
freqsRemoved = 0
freqCount = len(frequencies)
while freqCount > numVibrations:
minDegeneracy, minEntry = min([(entry.data.symmetry, entry) for entry in groupCount if groupCount[entry] > 0])
if groupCount[minEntry] > 1:
groupCount[minEntry] -= 1
else:
del groupCount[minEntry]
groupsRemoved += 1
freqsRemoved += minDegeneracy
freqCount -= minDegeneracy
# Log warning
logging.warning('For {0}, more characteristic frequencies were generated than vibrational modes allowed. Removed {1:d} groups ({2:d} frequencies) to compensate.'.format(molecule, groupsRemoved, freqsRemoved))
# Regenerate characteristic frequencies
frequencies = []
for entry, count in groupCount.iteritems():
if count != 0: frequencies.extend(entry.data.generateFrequencies(count))
# Subtract out contributions to heat capacity from the group frequencies
Tlist = numpy.arange(300.0, 1501.0, 100.0, numpy.float64)
Cv = numpy.array([thermoModel.getHeatCapacity(T) / constants.R for T in Tlist], numpy.float64)
ho = HarmonicOscillator(frequencies=(frequencies,"cm^-1"))
for i in range(Tlist.shape[0]):
Cv[i] -= ho.getHeatCapacity(Tlist[i]) / constants.R
# Subtract out translational modes
Cv -= 1.5
# Subtract out external rotational modes
Cv -= (1.5 if not linear else 1.0)
# Subtract out PV term (Cp -> Cv)
Cv -= 1.0
# Fit remaining frequencies and hindered rotors to the heat capacity data
from statmechfit import fitStatmechToHeatCapacity
modes = fitStatmechToHeatCapacity(Tlist, Cv, numVibrations - len(frequencies), numRotors, molecule)
for mode in modes:
if isinstance(mode, HarmonicOscillator):
uncertainties = [0 for f in frequencies] # probably shouldn't be zero
frequencies.extend(mode.frequencies.value_si)
uncertainties.extend(mode.frequencies.uncertainty)
mode.frequencies.value_si = numpy.array(frequencies, numpy.float)
mode.frequencies.uncertainty = numpy.array(uncertainties, numpy.float)
break
else:
modes.insert(0, HarmonicOscillator(frequencies=(frequencies,"cm^-1")))
conformer.modes = modes
return (conformer, None, None)