def loadConfiguration(energyLog, geomLog, statesLog, extSymmetry, spinMultiplicity, freqScaleFactor, linear, rotors, atoms, bonds, E0=None, TS=False):
logging.debug(' Reading optimized geometry...')
log = GaussianLog(geomLog)
geom = log.loadGeometry()
logging.debug(' Reading energy...')
if E0 is None:
if energyLog is not None: log = GaussianLog(energyLog)
E0 = log.loadEnergy()
else:
E0 *= 4.35974394e-18 * constants.Na # Hartree/particle to J/mol
E0 = applyEnergyCorrections(E0, modelChemistry, atoms, bonds)
logging.debug(' E0 (0 K) = %g kcal/mol' % (E0 / 4184))
logging.debug(' Reading molecular degrees of freedom...')
log = GaussianLog(statesLog)
states = log.loadStates(symmetry=extSymmetry)
states.spinMultiplicity = spinMultiplicity
F = log.loadForceConstantMatrix()
if F is not None and len(geom.mass) > 1 and len(rotors) > 0:
logging.debug(' Fitting %i hindered rotors...' % len(rotors))
for scanLog, pivots, top, symmetry in rotors:
log = GaussianLog(scanLog)
fourier = log.fitFourierSeriesPotential()
inertia = geom.getInternalReducedMomentOfInertia(pivots, top)
rotor = HinderedRotor(inertia=(inertia*constants.Na*1e23,"amu*angstrom^2"), symmetry=symmetry, fourier=(fourier,"J/mol"))
states.modes.append(rotor)
#import numpy
#import pylab
#import math
#Vlist = log.loadScanEnergies()
#Vlist = Vlist[:-1]
#angle = numpy.arange(0.0, 2*math.pi+0.00001, 2*math.pi/(len(Vlist)-1), numpy.float64)
#phi = numpy.arange(0, 6.3, 0.02, numpy.float64)
#pylab.plot(angle, Vlist / 4184, 'ok')
#pylab.plot(phi, rotor.getPotential(phi) / 4184, '-k')
#pylab.show()
logging.debug(' Determining frequencies from reduced force constant matrix...')
frequencies = list(projectRotors(geom, F, rotors, linear, TS))
elif len(states.modes) > 2:
frequencies = states.modes[2].frequencies.values
rotors = []
else:
frequencies = []
rotors = []
for mode in states.modes:
if isinstance(mode, HarmonicOscillator):
mode.frequencies.values = numpy.array(frequencies, numpy.float) * freqScaleFactor
return E0, geom, states
def loadConfiguration(energyLog, geomLog, statesLog, extSymmetry, spinMultiplicity, freqScaleFactor, linear, rotors, atoms, bonds, E0=None, TS=False):
logging.debug(' Reading optimized geometry...')
log = GaussianLog(geomLog)
geom = log.loadGeometry()
logging.debug(' Reading energy...')
if E0 is None:
if energyLog is not None: log = GaussianLog(energyLog)
E0 = log.loadEnergy()
else:
E0 *= 4.35974394e-18 * constants.Na # Hartree/particle to J/mol
E0 = applyEnergyCorrections(E0, modelChemistry, atoms, bonds)
logging.debug(' E0 (0 K) = %g kcal/mol' % (E0 / 4184))
logging.debug(' Reading molecular degrees of freedom...')
log = GaussianLog(statesLog)
states = log.loadStates(symmetry=extSymmetry)
states.spinMultiplicity = spinMultiplicity
F = log.loadForceConstantMatrix()
if F is not None and len(geom.mass) > 1 and len(rotors) > 0:
logging.debug(' Fitting %i hindered rotors...' % len(rotors))
for scanLog, pivots, top, symmetry in rotors:
log = GaussianLog(scanLog)
Vlist, angle = log.loadScanEnergies()
inertia = geom.getInternalReducedMomentOfInertia(pivots, top)
barr, symm = log.fitCosinePotential()
cosineRotor = HinderedRotor(inertia=(inertia*constants.Na*1e23,"amu*angstrom^2"), symmetry=symm, barrier=(barr/4184.,"kcal/mol"))
fourier = log.fitFourierSeriesPotential()
fourierRotor = HinderedRotor(inertia=(inertia*constants.Na*1e23,"amu*angstrom^2"), symmetry=symmetry, fourier=(fourier,"J/mol"))
Vlist_cosine = cosineRotor.getPotential(angle)
Vlist_fourier = fourierRotor.getPotential(angle)
rms_cosine = numpy.sqrt(numpy.sum((Vlist_cosine - Vlist) * (Vlist_cosine - Vlist)) / (len(Vlist) - 1)) / 4184.
rms_fourier = numpy.sqrt(numpy.sum((Vlist_fourier - Vlist) * (Vlist_fourier - Vlist))/ (len(Vlist) - 1)) / 4184.
print rms_cosine, rms_fourier, symm, symmetry
# Keep the rotor with the most accurate potential
rotor = cosineRotor if rms_cosine < rms_fourier else fourierRotor
# However, keep the cosine rotor if it is accurate enough, the
# fourier rotor is not significantly more accurate, and the cosine
# rotor has the correct symmetry
if rms_cosine < 0.05 and rms_cosine / rms_fourier > 0.25 and rms_cosine / rms_fourier < 4.0 and symmetry == symm:
rotor = cosineRotor
states.modes.append(rotor)
import pylab
phi = numpy.arange(0, 6.3, 0.02, numpy.float64)
fig = pylab.figure()
pylab.plot(angle, Vlist / 4184, 'ok')
linespec = '-r' if rotor is cosineRotor else '--r'
pylab.plot(phi, cosineRotor.getPotential(phi) / 4184, linespec)
linespec = '-b' if rotor is fourierRotor else '--b'
pylab.plot(phi, fourierRotor.getPotential(phi) / 4184, linespec)
pylab.legend(['scan', 'cosine', 'fourier'], loc=1)
pylab.xlim(0, 2*math.pi)
axes = fig.get_axes()[0]
axes.set_xticks([float(j*math.pi/4) for j in range(0,9)])
axes.set_xticks([float(j*math.pi/8) for j in range(0,17)], minor=True)
axes.set_xticklabels(['$0$', '$\pi/4$', '$\pi/2$', '$3\pi/4$', '$\pi$', '$5\pi/4$', '$3\pi/2$', '$7\pi/4$', '$2\pi$'])
pylab.show()
logging.debug(' Determining frequencies from reduced force constant matrix...')
frequencies = list(projectRotors(geom, F, rotors, linear, TS))
elif len(states.modes) > 2:
frequencies = states.modes[2].frequencies.values
rotors = []
else:
frequencies = []
rotors = []
for mode in states.modes:
if isinstance(mode, HarmonicOscillator):
mode.frequencies.values = numpy.array(frequencies, numpy.float) * freqScaleFactor
return E0, geom, states