class QuasiHarmonic():
def __init__(self, fname, indexRange, prcntVolume, modePrefix):
"""indexRange is for files' indexing. prcntVolume - coresponding volume
expansions"""
self.qecalc = QECalc(fname)
self.__modePrefix = modePrefix
self.__indexRange = indexRange
self.__prcntVolume = prcntVolume
if len(indexRange) != len(prcntVolume):
raise Exception("QuasiHarmonic dimensions: indexRange != prcntVolume")
self.loadPhonons()
self.__polyOrder = 1
self.fitMatdyn()
def fitFunc(self, p, x):
return p[0] * x
#+ p[1] * x * x
#+ p[2] * x * x * x + p[3] * x * x * x * x
def fitOmega(self, prcntOmega):
# fitfunc = lambda p, x: p[0] * x + p[1] * x * x
errFunc = lambda p, x, y: (y - self.fitFunc(p, x))
# initial parameters:
pinit = [prcntOmega[1]/self.__prcntVolume[1]]
# pinit = [1,0]
v, success = leastsq(errFunc, pinit, args=(self.__prcntVolume, prcntOmega))
if success < 1 or success > 4:
print success
print prcntOmega
print v
# assert success != 1, "fitOmega: Fitting was not successful"
return v
def getQuasiFreqs(prcntVol):
"""Returns array of freqs, corresponding to the provided volume expansion"""
nPoints = shape(self.__coeffOmega)[0]
nModes = shape(self.__coeffOmega)[1]
fittedFreqs = zeros(shape = (nPoints, nModes) )
for i in range( nPoints ):
for j in range( nModes ):
p = self.__coeffOmega[i,j]
fittedFreqs[i,j] = p[0]*prcntVol
return (fittedFreqs+1.0)*self.__omega0
def getFittedFreqs(prcntVol):
nPoints = shape(self.__coeffOmega)[0]
nModes = shape(self.__coeffOmega)[1]
fittedFreqs = zeros(shape = (nPoints, nModes) )
for i in range( nPoints ):
for j in range( nModes ):
p = self.__coeffOmega[i,j]
fittedFreqs[i,j] = fitFunc(p, prcntVol)
return (fittedFreqs+1.0)*self.__omega0
def loadPhonons(self):
fname = self.__modePrefix + str(self.__indexRange[0]) + '.modes'
Pol, Omega, qPoints = self.qecalc.getMultiPhonon(fname)
self.__volOmega = zeros(shape=(len(self.__indexRange), shape(Omega)[0], shape(Omega)[1] ) )
self.__volPol = zeros(shape=(len(self.__indexRange), shape(Pol)[0], shape(Pol)[1], shape(Pol)[2], shape(Pol)[3] ) )
self.__volPol[0] = Pol
self.__volOmega[0] = Omega
for i in range(1,len(indexRange)):
fname = self.__modePrefix + str(self.__indexRange[i]) + '.modes'
Pol, Omega, qPoints = self.qecalc.getMultiPhonon(fname)
self.__volPol[i] = Pol
self.__volOmega[i] = Omega
# return volPol, volOmega, qPoints
def fitMatdyn(self):
# volPol, volOmega, qPoints = loadPhonons(indexRange, prefix)
# prcntVol = array(indexRange)/1000.0
# percent change in Omegas relative to equilibrium
self.__volPrcntOmega = zeros(shape(self.__volOmega))
# introduce Omega0 to get rid of 0s in denominator
Omega0 = copy(self.__volOmega[0])
self.__omega0 = Omega0
for i in range(shape(Omega0)[0]):
for j in range(shape(Omega0)[1]):
if Omega0[i,j] == 0.:
Omega0[i, j] = 1
for i in range(len(self.__indexRange)):
self.__volPrcntOmega[i] = (self.__volOmega[i] - self.__volOmega[0])/Omega0
self.__coeffOmega = zeros( shape = ( shape(Omega0)[0], shape(Omega0)[1], self.__polyOrder) )
nonlinearity = 0
for i in range( shape(Omega0)[0] ):
for j in range( shape(Omega0)[1] ):
self.__coeffOmega[i,j] = self.fitOmega(self.__volPrcntOmega[:,i,j])
if self.__polyOrder > 1:
nonlinearity = nonlinearity + abs(self.__coeffOmega[i,j][1])
# print volPrcntOmega[:,1000,3]
# print fitOmega(prcntVol, volPrcntOmega[:,1000,3])
# plot(volPrcntOmega[:,1000,3])
# show()
# return prcntVol, coeffOmega, volOmega, nonlinearity
def gammaDispersion(self, *pathNPoints):
self.qecalc.dispersion.setPath(*pathNPoints)
self.qecalc.dispersion.setValues(-self.__coeffOmega[:,:,0])
self.qecalc.dispersion.plot()
class QuasiHarmonic():
def __init__(self, fname, indexRange, prcntVolume, modePrefix):
"""indexRange is for files' indexing. prcntVolume - coresponding volume
expansions"""
self.qecalc = QECalc(fname)
self.__modePrefix = modePrefix
self.__indexRange = indexRange
self.__prcntVolume = prcntVolume
if len(indexRange) != len(prcntVolume):
raise Exception(
"QuasiHarmonic dimensions: indexRange != prcntVolume")
self.loadPhonons()
self.__polyOrder = 1
self.fitMatdyn()
def fitFunc(self, p, x):
return p[0] * x
#+ p[1] * x * x
#+ p[2] * x * x * x + p[3] * x * x * x * x
def fitOmega(self, prcntOmega):
# fitfunc = lambda p, x: p[0] * x + p[1] * x * x
errFunc = lambda p, x, y: (y - self.fitFunc(p, x))
# initial parameters:
pinit = [prcntOmega[1] / self.__prcntVolume[1]]
# pinit = [1,0]
v, success = leastsq(errFunc,
pinit,
args=(self.__prcntVolume, prcntOmega))
if success < 1 or success > 4:
print success
print prcntOmega
print v
# assert success != 1, "fitOmega: Fitting was not successful"
return v
def getQuasiFreqs(prcntVol):
"""Returns array of freqs, corresponding to the provided volume expansion"""
nPoints = shape(self.__coeffOmega)[0]
nModes = shape(self.__coeffOmega)[1]
fittedFreqs = zeros(shape=(nPoints, nModes))
for i in range(nPoints):
for j in range(nModes):
p = self.__coeffOmega[i, j]
fittedFreqs[i, j] = p[0] * prcntVol
return (fittedFreqs + 1.0) * self.__omega0
def getFittedFreqs(prcntVol):
nPoints = shape(self.__coeffOmega)[0]
nModes = shape(self.__coeffOmega)[1]
fittedFreqs = zeros(shape=(nPoints, nModes))
for i in range(nPoints):
for j in range(nModes):
p = self.__coeffOmega[i, j]
fittedFreqs[i, j] = fitFunc(p, prcntVol)
return (fittedFreqs + 1.0) * self.__omega0
def loadPhonons(self):
fname = self.__modePrefix + str(self.__indexRange[0]) + '.modes'
Pol, Omega, qPoints = self.qecalc.getMultiPhonon(fname)
self.__volOmega = zeros(shape=(len(self.__indexRange), shape(Omega)[0],
shape(Omega)[1]))
self.__volPol = zeros(shape=(len(self.__indexRange), shape(Pol)[0],
shape(Pol)[1], shape(Pol)[2],
shape(Pol)[3]))
self.__volPol[0] = Pol
self.__volOmega[0] = Omega
for i in range(1, len(indexRange)):
fname = self.__modePrefix + str(self.__indexRange[i]) + '.modes'
Pol, Omega, qPoints = self.qecalc.getMultiPhonon(fname)
self.__volPol[i] = Pol
self.__volOmega[i] = Omega
# return volPol, volOmega, qPoints
def fitMatdyn(self):
# volPol, volOmega, qPoints = loadPhonons(indexRange, prefix)
# prcntVol = array(indexRange)/1000.0
# percent change in Omegas relative to equilibrium
self.__volPrcntOmega = zeros(shape(self.__volOmega))
# introduce Omega0 to get rid of 0s in denominator
Omega0 = copy(self.__volOmega[0])
self.__omega0 = Omega0
for i in range(shape(Omega0)[0]):
for j in range(shape(Omega0)[1]):
if Omega0[i, j] == 0.:
Omega0[i, j] = 1
for i in range(len(self.__indexRange)):
self.__volPrcntOmega[i] = (self.__volOmega[i] -
self.__volOmega[0]) / Omega0
self.__coeffOmega = zeros(shape=(shape(Omega0)[0], shape(Omega0)[1],
self.__polyOrder))
nonlinearity = 0
for i in range(shape(Omega0)[0]):
for j in range(shape(Omega0)[1]):
self.__coeffOmega[i,
j] = self.fitOmega(self.__volPrcntOmega[:, i,
j])
if self.__polyOrder > 1:
nonlinearity = nonlinearity + abs(self.__coeffOmega[i,
j][1])
# print volPrcntOmega[:,1000,3]
# print fitOmega(prcntVol, volPrcntOmega[:,1000,3])
# plot(volPrcntOmega[:,1000,3])
# show()
# return prcntVol, coeffOmega, volOmega, nonlinearity
def gammaDispersion(self, *pathNPoints):
self.qecalc.dispersion.setPath(*pathNPoints)
self.qecalc.dispersion.setValues(-self.__coeffOmega[:, :, 0])
self.qecalc.dispersion.plot()
