def getThermoData(struct, thermoClass=thermo.ThermoNASAData): # ThermoGAData
"""
Get the thermodynamic data associated with `structure` by looking in the
loaded thermodynamic database.
`thermoClass` is the class of thermo object you want returning; default
is :class:`ThermoNASAData`
"""
import constants
import math
GAthermoData = thermoDatabase.getThermoData(struct)
# Correct entropy for symmetry number
struct.calculateSymmetryNumber()
GAthermoData.S298 -= constants.R * math.log(struct.symmetryNumber)
logging.debug('Group-additivity thermo data: %s' % GAthermoData)
if thermoClass == thermo.ThermoGAData:
return GAthermoData # return here because Wilhoit conversion not wanted
# Convert to Wilhoit
rotors = struct.calculateNumberOfRotors()
atoms = len(struct.atoms())
linear = struct.isLinear()
WilhoitData = thermo.convertGAtoWilhoit(GAthermoData,atoms,rotors,linear)
logging.debug('Wilhoit thermo data: %s' % WilhoitData)
if thermoClass == thermo.ThermoWilhoitData:
return WilhoitData
# Convert to NASA
NASAthermoData = thermo.convertWilhoitToNASA(WilhoitData)
logging.debug('NASA thermo data: %s' % NASAthermoData)
# compute the error for the entire conversion, printing it as info or warning (if it is sufficiently high)
rmsErr = NASAthermoData.rmsErr(GAthermoData)
if(rmsErr > 0.35):
logging.warning("Poor overall GA-to-NASA fit: Overall RMS error in heat capacity fit = %.3f*R." % (rmsErr))
else:
logging.debug("Overall RMS error in heat capacity fit = %.3f*R" % (rmsErr))
if thermoClass == thermo.ThermoNASAData:
return NASAthermoData
# Still not returned?
raise Exception("Cannot convert themo data into class %r"%(required_class))
def getThermoData(struct, required_class=thermo.ThermoNASAData): # ThermoGAData
"""
Get the thermodynamic data associated with `structure` by looking in the
loaded thermodynamic database.
`required_class` is the class of thermo object you want returning; default
is :class:`ThermoNASAData`
"""
import constants
import math
GAthermoData = thermoDatabase.getThermoData(struct)
# Correct entropy for symmetry number
struct.calculateSymmetryNumber()
GAthermoData.S298 -= constants.R * math.log(struct.symmetryNumber)
if required_class==thermo.ThermoGAData:
return GAthermoData # return here because Wilhoit conversion not wanted
# Convert to Wilhoit
rotors = struct.calculateNumberOfRotors()
atoms = len(struct.atoms())
linear = struct.isLinear()
WilhoitData = thermo.convertGAtoWilhoit(GAthermoData,atoms,rotors,linear)
if required_class==thermo.ThermoWilhoitData:
return WilhoitData
# Convert to NASA
NASAthermoData = thermo.convertWilhoitToNASA(WilhoitData)
if required_class==thermo.ThermoNASAData:
return NASAthermoData
# Still not returned?
raise Exception("Cannot convert themo data into class %r"%(required_class))
