def dynmat_modes(self, fname):
matdynDict = io_dict.read_file(fname)
qKeys = io_dict.find_all_keys_from_string(matdynDict, 'q =')
qP = []
for i in qKeys:
qP.append([float(qi) for qi in string.split(matdynDict[i])[2:5]])
qPoints = numpy.array(qP)
# find number of atoms per unit cell and dimensionality
# get frequencies keys for the last q-point:
fKeys = io_dict.find_all_keys_from_string_afterkey(
matdynDict, qKeys[-1], 'omega')
# get sample displacement vector for the first frequency of the last q point and find its dimensionality
# here omegaShift = 1 means no space between displacements and frequencies (2 means 1 extra line ...)
omegaShift = 1
nDim = len(matdynDict[fKeys[0] + omegaShift].split()[1:-1]) / 2
# get number of atoms in unit cell
nAtom = fKeys[1] - fKeys[0] - omegaShift
# qShift = 2 means 1 exra line between q line and frequencies line
qShift = 2
# create numpy array in accordance with idf format specification
# Pol = [ [ [ [ ] ] ] ]
Pol = []
Omegas = []
for i in qKeys:
# Mode = [ [ [ ] ] ]
Mode = []
Omega = []
for iOmega in range(
i + qShift,
nDim * nAtom * (nAtom + omegaShift) + i + qShift,
nAtom + omegaShift):
# get omegas in THz:
# print float( matdynDict[ iOmega].split('=')[1].split()[0] )
Omega.append(float(
matdynDict[iOmega].split('=')[2].split()[0]))
# Atom = [ [ ] ]
Atom = []
for iAtom in range(iOmega + omegaShift,
iOmega + omegaShift + nAtom):
vecStr = matdynDict[iAtom].split()[1:-1]
# vec = [ ]
vec = [
float(v1) + 1.0j * float(v2)
for v1, v2 in zip(vecStr[:-1:2], vecStr[1::2])
]
Atom.append(vec)
Mode.append(Atom)
Pol.append(Mode)
# assume only one q point here
Omegas = Omega
npOmega = numpy.array(Omegas)
npPol = numpy.array(Pol)
# THz2meV = 4.1357 # meV * s
# output Omega in cm-1
return (npPol, None), (npOmega, 'cm-1'), (qPoints, None)
def matdyn(fname):
matdynDict = io_dict.read_file(fname)
qKeys = io_dict.find_all_keys_from_string(matdynDict, 'q =')
qP = []
for i in qKeys:
qP.append( [ float(qi) for qi in string.split( matdynDict[ i ] )[2:5] ] )
qPoints = np.array(qP)
# find number of atoms per unit cell and dimensionality
# get frequencies keys for the last q-point:
fKeys = io_dict.find_all_keys_from_string_afterkey( matdynDict, qKeys[-1], 'omega')
# get sample displacement vector for the first frequency of the last q point and find its dimensionality
# here omegaShift = 1 means no space between displacements and frequencies (2 means 1 extra line ...)
omegaShift = 1
nDim = len( matdynDict[ fKeys[0] + omegaShift ].split()[1:-1] )/2
# get number of atoms in unit cell
nAtom = fKeys[1] - fKeys[0] - omegaShift
# qShift = 2 means 1 exra line between q line and frequencies line
qShift = 2
# create numpy array in accordance with idf format specification
# Pol = [ [ [ [ ] ] ] ]
Pol = []
Omegas = []
for i in qKeys:
# Mode = [ [ [ ] ] ]
Mode = []
Omega = []
for iOmega in range( i + qShift, nDim*nAtom*(nAtom + omegaShift) + i + qShift, nAtom+omegaShift):
# get omegas in THz:
# print float( matdynDict[ iOmega].split('=')[1].split()[0] )
Omega.append( float( matdynDict[ iOmega].split('=')[2].split()[0] ) )
# Atom = [ [ ] ]
Atom = []
for iAtom in range( iOmega + omegaShift, iOmega + omegaShift + nAtom ):
vecStr = matdynDict[ iAtom ].split()[1:-1]
# vec = [ ]
vec = [ float(v1) + 1.0j*float(v2) for v1,v2 in zip( vecStr[:-1:2], vecStr[1::2] ) ]
Atom.append(vec)
Mode.append( Atom )
Pol.append( Mode )
Omegas.append( Omega )
npOmega = np.array(Omegas)
npPol = np.array(Pol)
# THz2meV = 4.1357 # meV * s
# output Omega in cm-1
return [npPol, npOmega, qPoints]