class VoluPhon():
def __init__(self, prcntVolume, filename = None ):
"""
This class requires a set of "n_matdyn.modes" files
corresponding to different volume expansions
prcntVolume - array with
"""
self.pw = PWTask(filename = filename)
self.matdyn = MatdynTask(filename = filename)
self.__prcntVolume = prcntVolume
def setA(self, values, fitter):
self.a = volufit.ValueFit(self.__prcntVolume, values, fitter)
def setC(self, values, fitter):
self.c = volufit.ValueFit(self.__prcntVolume, values, fitter)
def setEnergy(self, values, fitter):
self.energy = volufit.ValueFit(self.__prcntVolume, values, fitter)
def setPhonons(self, indexRange, fitter):
"""Will read freqs from x_matdyn.modes files and fit the freqs"""
matdynModesName = self.matdyn.setting.get('flvec')
self.matdyn.setting.set('flvec', str(indexRange[0]) + '_' + matdynModesName)
self.matdyn.output.parse()
Pol, Omega, qPoints = self.matdyn.output.property('multi phonon')
volOmega = numpy.zeros(shape=(len(indexRange), numpy.shape(Omega)[0], \
numpy.shape(Omega)[1] ) )
volOmega[0] = Omega
for i in range(1,len(indexRange)):
self.matdyn.setting.set('flvec', str(indexRange[i]) + '_' + matdynModesName)
self.matdyn.output.parse()
Pol, Omega, qPoints = self.matdyn.output.property('multi phonon')
volOmega[i] = Omega
self.matdyn.setting.set('flvec', matdynModesName)
self.freqs = volufit.FreqFit(self.__prcntVolume, volOmega,fitter)
def gammaDispersion(self, *pathNPoints):
#self.pw.input.parse()
#self.matdyn.input.parse()
self.dispersion = PHDispersion( self.pw.input.structure.lattice, self.matdyn)
if self.freqs.fitter.type != 'polynom':
raise Exception('This method is only relevant for polynomial fit')
self.dispersion = PHDispersion( self.pw.input.structure.lattice, self.matdyn)
self.dispersion.setPath(*pathNPoints)
self.dispersion.setValues(-self.freqs.coeff()[:,:,-1])
self.dispersion.save('gamma_disp')
self.dispersion.plot()
def prcntVolume (self):
return self.__prcntVolume
class VoluPhon():
def __init__(self, prcntVolume, filename=None):
"""
This class requires a set of "n_matdyn.modes" files
corresponding to different volume expansions
prcntVolume - array with
"""
self.pw = PWTask(filename=filename)
self.matdyn = MatdynTask(filename=filename)
self.__prcntVolume = prcntVolume
def setA(self, values, fitter):
self.a = volufit.ValueFit(self.__prcntVolume, values, fitter)
def setC(self, values, fitter):
self.c = volufit.ValueFit(self.__prcntVolume, values, fitter)
def setEnergy(self, values, fitter):
self.energy = volufit.ValueFit(self.__prcntVolume, values, fitter)
def setPhonons(self, indexRange, fitter):
"""Will read freqs from x_matdyn.modes files and fit the freqs"""
matdynModesName = self.matdyn.setting.get('flvec')
self.matdyn.setting.set('flvec',
str(indexRange[0]) + '_' + matdynModesName)
self.matdyn.output.parse()
Pol, Omega, qPoints = self.matdyn.output.property('multi phonon')
volOmega = numpy.zeros(shape=(len(indexRange), numpy.shape(Omega)[0], \
numpy.shape(Omega)[1] ) )
volOmega[0] = Omega
for i in range(1, len(indexRange)):
self.matdyn.setting.set('flvec',
str(indexRange[i]) + '_' + matdynModesName)
self.matdyn.output.parse()
Pol, Omega, qPoints = self.matdyn.output.property('multi phonon')
volOmega[i] = Omega
self.matdyn.setting.set('flvec', matdynModesName)
self.freqs = volufit.FreqFit(self.__prcntVolume, volOmega, fitter)
def gammaDispersion(self, *pathNPoints):
#self.pw.input.parse()
#self.matdyn.input.parse()
self.dispersion = PHDispersion(self.pw.input.structure.lattice,
self.matdyn)
if self.freqs.fitter.type != 'polynom':
raise Exception('This method is only relevant for polynomial fit')
self.dispersion = PHDispersion(self.pw.input.structure.lattice,
self.matdyn)
self.dispersion.setPath(*pathNPoints)
self.dispersion.setValues(-self.freqs.coeff()[:, :, -1])
self.dispersion.save('gamma_disp')
self.dispersion.plot()
def prcntVolume(self):
return self.__prcntVolume
# print abs((a.conj()*b).sum())
#
# thrsh_scl = 0.8
# #dispersion = [list(Omegas[0])]
# idxs = [range(Omegas.shape[1])]
# for k in range(1, Omegas.shape[0]):
# omg = []
# idx = []
# for i, o1 in zip( idxs[k-1], Omegas[k-1]):
# for j, o2 in enumerate(Omegas[k]):
# if ( abs((Pol2[k,j,:].conj()*Pol2[k-1,i,:]).sum()) > thrsh_scl):
# #omg.append(o2)
# idx.append(j)
# break
# if len(omg) != 9:
# print "OMG!!! ", k, Omegas[k-1], Omegas[k], omg, '\n'
# #dispersion.append(omg)
# idxs.append(idx)
# dispersion = []
# for k, idx in enumerate(idxs):
# dispersion.append( Omegas[k, idx])
#print dispersion
#print dispersion[0]
#phDisp.dispersion = numpy.array(dispersion)
phDisp.dispersion = phDisp.dispersion*0.1239
phDisp.solveAllCrossings(thrsh_scl = 0.75)
phDisp.plot()
#print phDisp.dispersion
# print abs((a.conj()*b).sum())
#
# thrsh_scl = 0.8
# #dispersion = [list(Omegas[0])]
# idxs = [range(Omegas.shape[1])]
# for k in range(1, Omegas.shape[0]):
# omg = []
# idx = []
# for i, o1 in zip( idxs[k-1], Omegas[k-1]):
# for j, o2 in enumerate(Omegas[k]):
# if ( abs((Pol2[k,j,:].conj()*Pol2[k-1,i,:]).sum()) > thrsh_scl):
# #omg.append(o2)
# idx.append(j)
# break
# if len(omg) != 9:
# print "OMG!!! ", k, Omegas[k-1], Omegas[k], omg, '\n'
# #dispersion.append(omg)
# idxs.append(idx)
# dispersion = []
# for k, idx in enumerate(idxs):
# dispersion.append( Omegas[k, idx])
#print dispersion
#print dispersion[0]
#phDisp.dispersion = numpy.array(dispersion)
phDisp.dispersion = phDisp.dispersion * 0.1239
phDisp.solveAllCrossings(thrsh_scl=0.75)
phDisp.plot()
#print phDisp.dispersion
