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 varnameValue(fname, var, val):
'Dummy! Assumes no comments for a variable in question and one variable per string'
import string
pwscfDic = read_file(fname)
key = find_key_from_string(pwscfDic, var)
pwscfDic[key] = ' ' + var + ' = ' + str(val) + ',\n'
save_dic(pwscfDic, fname)
def getTotalEnergy(self):
'Extract total energy value from pwscf output'
#read Espresso output into memory:
pwscfOut = qe_io_dict.read_file(self.pwscfOutput)
key = qe_io_dict.find_key_from_marker_string(pwscfOut, '!', 'total energy')
words = string.split(pwscfOut[key])
return [float(words[4])]
def getLatticeParameters(self):
'Extract lattice parameters after pwscf geometry optimization'
def vectorLength(v):
from math import sqrt
s = 0.0
for val in v:
s = s + val**2
return sqrt(s)
pwscfOut = qe_io_dict.read_file(self.pwscfOutput)
key_a_0 = qe_io_dict.find_key_from_string(pwscfOut,
'lattice parameter (a_0)')
a_0 = float(string.split(pwscfOut[key_a_0])[4])
keyEnd = max(
qe_io_dict.find_all_keys_from_marker_string(
pwscfOut, '!', 'total energy'))
keyCellPar = qe_io_dict.find_key_from_string_afterkey(pwscfOut, keyEnd, \
'CELL_PARAMETERS (alat)') + 1
a = vectorLength(
[float(valstr) for valstr in string.split(pwscfOut[keyCellPar])])
b = vectorLength([
float(valstr) for valstr in string.split(pwscfOut[keyCellPar + 1])
])
c = vectorLength([
float(valstr) for valstr in string.split(pwscfOut[keyCellPar + 2])
])
return [a * a_0, b * a_0, c * a_0]
def atomic_positions(fname, geometry):
'Dummy! Assumes geometry description is right after "ATOMIC_POSITIONS" (no empty lines)'
import string
pwscfDic = read_file(fname)
key = find_key_from_string(pwscfDic, 'ATOMIC_POSITIONS')
for i in range(len(geometry)):
pwscfDic[key+1+i] = geometry[i] + '\n'
save_dic(pwscfDic, fname)
def k_points(fname, k_points):
'Dummy! Assumes no comments and implies k-point values are in the next line after K_POINTS AUTOMATIC'
import string
pwscfDic = read_file(fname)
key = find_key_from_string(pwscfDic, 'K_POINTS')
k_string = string.join([str(v) + ' ' for v in k_points])
pwscfDic[key+1] = k_string + '\n'
save_dic(pwscfDic, fname)
def getTotalEnergy(self):
'Extract total energy value from pwscf output'
#read Espresso output into memory:
pwscfOut = qe_io_dict.read_file(self.pwscfOutput)
key = qe_io_dict.find_key_from_marker_string(pwscfOut, '!',
'total energy')
words = string.split(pwscfOut[key])
return [float(words[4])]
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]
def getSinglePhonon(self):
'Obtain a list of phonon modes from output generated by dynmat.x'
dynmatOut = qe_io_dict.read_file(self.dynmatOutput)
keyStart = qe_io_dict.find_key_from_marker_string(dynmatOut, '#', 'mode')
modeNum = 1
key = keyStart + 1
words = string.split(dynmatOut[key])
modes = []
while words[0] == str(modeNum):
modes.append( float(words[1]) )
key = key + 1
modeNum = modeNum + 1
words = string.split(dynmatOut[key])
return modes
def getSinglePhonon(self):
'Obtain a list of phonon modes from output generated by dynmat.x'
dynmatOut = qe_io_dict.read_file(self.dynmatOutput)
keyStart = qe_io_dict.find_key_from_marker_string(
dynmatOut, '#', 'mode')
modeNum = 1
key = keyStart + 1
words = string.split(dynmatOut[key])
modes = []
while words[0] == str(modeNum):
modes.append(float(words[1]))
key = key + 1
modeNum = modeNum + 1
words = string.split(dynmatOut[key])
return modes
def getLatticeParameters(self):
'Extract lattice parameters after pwscf geometry optimization'
def vectorLength(v):
from math import sqrt
s = 0.0
for val in v: s = s + val**2
return sqrt( s )
pwscfOut = qe_io_dict.read_file(self.pwscfOutput)
key_a_0 = qe_io_dict.find_key_from_string(pwscfOut, 'lattice parameter (a_0)')
a_0 = float( string.split( pwscfOut[key_a_0] )[4] )
keyEnd = max( qe_io_dict.find_all_keys_from_marker_string(pwscfOut, '!', 'total energy') )
keyCellPar = qe_io_dict.find_key_from_string_afterkey(pwscfOut, keyEnd, \
'CELL_PARAMETERS (alat)') + 1
a = vectorLength( [ float(valstr) for valstr in string.split( pwscfOut[keyCellPar] ) ] )
b = vectorLength( [ float(valstr) for valstr in string.split( pwscfOut[keyCellPar+1] ) ] )
c = vectorLength( [ float(valstr) for valstr in string.split( pwscfOut[keyCellPar+2] ) ] )
return [a*a_0, b*a_0, c*a_0]