Exemple #1
0
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
Exemple #2
0
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