def elPolarization(self, berryPhase, calcValues, ELEC_BY_VOL_CONST):
'''
Calculate electronic component of polarization
Input: berryPhase[direction 1, 2, 3][spin]
Calculation:
Pel_x = electron charge / unit volume (m) * \
berry phase mean value/2pi * lattice_matrices (diagonal x);
'''
# [OLEG]: check which lattice vectors to use br1 or br2
nspins = numpy.shape(berryPhase)[1]
elP = numpy.zeros((nspins, 3))
for spinIndex in range(0, nspins):
for coordIndex in range(0,
3): # loop over 3 lattice vector direct.
latVec = calcValues['Real primitive lat vectors in bohr'][
coordIndex]
normLatVec = numpy.linalg.norm(latVec) # length of lat. vector
elP[spinIndex,coordIndex] = \
(berryPhase[coordIndex,spinIndex]/(2*numpy.pi)) * \
ELEC_BY_VOL_CONST * \
bohrToMeters(normLatVec)
print("Electronic polarization (C/m2) " +\
"sp(%1i) " % (spinIndex+1), \
"[% e, % e, % e]" % tuple(elP[spinIndex,:]))
print("=" * 87)
return elP
def elPolarization(self, berryPhase, calcValues, ELEC_BY_VOL_CONST):
'''
Calculate electronic component of polarization
Input: berryPhase[direction 1, 2, 3][spin]
Calculation:
Pel_x = electron charge / unit volume (m) * \
berry phase mean value/2pi * lattice_matrices (diagonal x);
'''
latticeConstants = calcValues['Lattice Constants in bohr']
latticeMatrix_x = calcValues['Lattice Matrix in bohr'][0]
latticeMatrix_y = calcValues['Lattice Matrix in bohr'][1]
latticeMatrix_z = calcValues['Lattice Matrix in bohr'][2]
# return the absolute value of the vector sqrt(x^2 + y^2 + z^2)
absVector = lambda vec: math.sqrt(sum([i**2 for i in vec]))
# length of lattice vectors
lattice_x = absVector(latticeMatrix_x)
lattice_y = absVector(latticeMatrix_y)
lattice_z = absVector(latticeMatrix_z)
# Electronic Polarization [OLEG]: check which lattice constants to use
nspins = numpy.shape(berryPhase)[1]
elP = numpy.zeros((nspins, 3))
for spinIndex in range(0, nspins):
for coordIndex in range(0, 3):
elP[spinIndex,coordIndex] = \
(berryPhase[coordIndex,spinIndex]/(2*numpy.pi)) * \
ELEC_BY_VOL_CONST * \
bohrToMeters(latticeConstants[coordIndex])
print "Electronic polarization (C/m2) " +\
"sp(%1i) " % (spinIndex+1), \
"[% e, % e, % e]" % tuple(elP[spinIndex,:])
print "=" * 87
return elP
def elPolarization(self, berryPhase, calcValues, ELEC_BY_VOL_CONST):
'''
Calculate electronic component of polarization
Input: berryPhase[direction 1, 2, 3][spin]
Calculation:
Pel_x = electron charge / unit volume (m) * \
berry phase mean value/2pi * lattice_matrices (diagonal x);
'''
latticeConstants = calcValues['Lattice Constants in bohr']
latticeMatrix_x = calcValues['Lattice Matrix in bohr'][0]
latticeMatrix_y = calcValues['Lattice Matrix in bohr'][1]
latticeMatrix_z = calcValues['Lattice Matrix in bohr'][2]
# return the absolute value of the vector sqrt(x^2 + y^2 + z^2)
absVector = lambda vec: math.sqrt(sum([i**2 for i in vec]))
# length of lattice vectors
lattice_x = absVector(latticeMatrix_x)
lattice_y = absVector(latticeMatrix_y)
lattice_z = absVector(latticeMatrix_z)
# Electronic Polarization [OLEG]: check which lattice constants to use
nspins = numpy.shape(berryPhase)[1]
elP = numpy.zeros((nspins,3))
for spinIndex in range(0,nspins):
for coordIndex in range(0,3):
elP[spinIndex,coordIndex] = \
(berryPhase[coordIndex,spinIndex]/(2*numpy.pi)) * \
ELEC_BY_VOL_CONST * \
bohrToMeters(latticeConstants[coordIndex]);
print "Electronic polarization (C/m2) " +\
"sp(%1i) " % (spinIndex+1), \
"[% e, % e, % e]" % tuple(elP[spinIndex,:]);
print "="*87
return elP; # END elPolarization
def determineIonPolarization(self, fnWrpMethod, args):
'''
INPUT: fnWrpMethod - function that determines the method for
wrapping the phase
args - contains logical variables regarding the
calculation setup
args['so'] - spin-orbit coupling
args['sp'] - spin-polarized calculation
args['orb'] - additional orbital potential (LDA+U)
Calculation:
Pion_x = electron charge / unit volume (m) * lattice_x * (
sum of (
atom valence charge * position(x)
)
)
where atom valence charge = ( core value - spin val 1 - spin val 2 )
'''
print "\n", "CALCULATION OF IONIC POLARIZATION"
ionP = []
calcValues = self.calculationValues()
ELEC_BY_VOL_CONST = self.ELEC_BY_VOL_CONST
latticeConstants = calcValues['Lattice Constants in bohr']
atomListing = calcValues['Atom Listing']
#produce a tuple pair which includes the valence electrons and
#the coordinates for each element
calcIonValues = [] # (coordinates(x,y,z), valence value)
#TODO: include good exception handling for this stage
#construct the calcIonValues for the calculation
if args['sp'] and not args['so']:
nspins = 2
else:
nspins = 1
for atom in atomListing:
for i in range(atom['MULT']):
theElementName = atom['Element Name']
if calcValues['Element Listing'].has_key(theElementName):
theElement = calcValues['Element Listing'][theElementName]
if nspins == 2:
theValence = []
for spin in [1, 2]:
theValence.append( \
atom['Znucl']/2 - theElement['Core Value']/2 \
)
else:
theValence = atom['Znucl'] - theElement['Core Value']
xCoordinate = atom['X-Coord'][i]
yCoordinate = atom['Y-Coord'][i]
zCoordinate = atom['Z-Coord'][i]
#produce tuple from coordinates
coordinates = (xCoordinate, yCoordinate, zCoordinate)
calcIonValues.append(
(theElementName, coordinates, theValence))
else:
print DEFAULT_PREFIX + 'ERROR: Missing element in element list'
print DEFAULT_PREFIX + theElementName
print DEFAULT_PREFIX + calcValues['Element List']
print DEFAULT_PREFIX + 'Exiting....'
sys.exit(1)
self._calcIonValues = calcIonValues
#### CALCULATION ####
xPolarIon, yPolarIon, zPolarIon = (0., 0., 0.)
print "=" * 87
print "Elem.| Fractional coord. | spin | Zion |", \
" dir(1) ", \
"| ", "dir(2) ", "| ", "dir(3)"
print "-" * 87
print " "*41, "+"+"-"*12, "Ionic phase (rad)", \
"-"*12+"+"
totIonPhase = numpy.zeros((nspins, 3))
for element, iCoord, iValence in calcIonValues:
spinIndex = -1
if isinstance(iValence, collections.Iterable):
pass
else:
iValence = [
iValence,
]
for spinValence in iValence:
spinIndex += 1
ionPhase = numpy.zeros((nspins, 3))
coordIndex = -1
for fcoord in iCoord:
coordIndex += 1
# fractional coordinates used
psi = fcoord * spinValence * 2 * numpy.pi
ionPhase[spinIndex, coordIndex] = psi
if spinIndex == 0:
print "%2s " % element, \
"(%6.4f, %6.4f, %6.4f) " % iCoord, \
"sp(%1i)" % (spinIndex+1), \
"%5.2f" % spinValence, \
"[% e, % e, % e]" % tuple(ionPhase[spinIndex,:])
else:
print " "*29, \
"sp(%1i)" % (spinIndex+1), \
"%5.2f" % spinValence, \
"[% e, % e, % e]" % tuple(ionPhase[spinIndex,:])
totIonPhase[:, :] += ionPhase
print "-" * 87
for spinIndex in range(0, nspins):
print "Total ionic phase (rad)", " "*5, \
"sp(%1i)" % (spinIndex+1), " "*5, \
"[% e, % e, % e]" % tuple(totIonPhase[spinIndex,:])
# warap phases
totIonPhase = fnWrpMethod(totIonPhase)
for spinIndex in range(0, nspins):
print "Total ionic phase wrap. (rad)", \
"sp(%1i)" % (spinIndex+1), " "*5, \
"[% e, % e, % e]" % tuple(totIonPhase[spinIndex,:])
#IONIC Polarization
ionPol = numpy.zeros((nspins, 3))
for spinIndex in range(0, nspins):
for coordIndex in range(0, 3):
psi = totIonPhase[spinIndex, coordIndex]
a = latticeConstants[coordIndex]
ionPol[spinIndex,coordIndex] = \
(psi/(2*numpy.pi)) * ELEC_BY_VOL_CONST * \
bohrToMeters(a)
print "Ionic polarization (C/m2) ", \
"sp(%1i)" % (spinIndex+1), " "*5, \
"[% e, % e, % e]" % tuple(ionPol[spinIndex,:])
print "=" * 87
return ionPol # END determineIonPolarization
def __init__(self, **args):
# spin polarization: yes/no
spCalc = args['sp']
############################
######### PARSING ##########
############################
###Rest of the Files###
#parse all the things!
#### *.struct file parser
parser_struct_handle = open(args['file_struct'], 'r').readlines()
parser_struct_handle = b_PyParse.MainStructParser(parser_struct_handle)
parser_struct_handle.parse()
#### *.scf file parser
parser_scf_handle = open(args['file_scf'], 'r').readlines()
parser_scf_handle = b_PyParse.MainSCFParser(parser_scf_handle)
parser_scf_handle.parse()
#### *.outputd parser
parser_outputd_handle = open(args['file_outputd'], 'r').readlines()
parser_outputd_handle = b_PyParse.MainOutputDParser(
parser_outputd_handle)
parser_outputd_handle.parse()
#### *.outputst parser
parser_outputst_handle = open(args['file_outputst'], 'r').readlines()
parser_outputst_handle = b_PyParse.MainOutputstParser(
parser_outputst_handle)
parser_outputst_handle.parse()
#####################################
############ END Parsing ############
#####################################
#############################
###### Getting Values #######
#############################
self._calculationValues = orderedDict()
#### *.struct handle
# - determine name of atoms
# - determine MULT for each atom
self._calculationValues['Atom Listing'] = \
parser_struct_handle['Atom Listing']
#### *.scf handle
# - Cell Volume
self._calculationValues['Cell Volume in bohr^3'] = \
parser_scf_handle['Cell Volume']
self._calculationValues['Cell Volume in m^3'] = \
bohrToMeters(self._calculationValues['Cell Volume in bohr^3'],3)
#### *.outputd handle
# - BR2_DIR matrix (v_x, v_y, v_z)
# - number of atoms in cell
# - Lattice Constants (x,y,z)
laticematrix = parser_outputd_handle['BR2_DIR Matrix']
latticematrixa1 = laticematrix[0]
self._calculationValues['Lattice Matrix a1 in bohr'] = \
latticematrixa1
latticematrixa2 = laticematrix[1]
self._calculationValues['Lattice Matrix a2 in bohr'] = \
latticematrixa2
latticematrixa3 = laticematrix[2]
self._calculationValues['Lattice Matrix a3 in bohr'] = \
latticematrixa3
self._calculationValues['Lattice Matrix in bohr'] = \
parser_outputd_handle['BR2_DIR Matrix']
self._calculationValues['Lattice Matrix in m'] = \
[[ bohrToMeters(i) for i in j ] for j in \
self._calculationValues['Lattice Matrix in bohr']]
self._calculationValues['Number of Atoms in Unit Cell'] = \
parser_outputd_handle['Number of Atoms in Unit Cell']
self._calculationValues['Lattice Constants in bohr'] = \
parser_outputd_handle['Lattice Constants']
self._calculationValues['Lattice Constants in m'] = \
[ bohrToMeters(i) for i in \
self._calculationValues['Lattice Constants in bohr']]
#### *.outputst handle
# for each element:
# - Core Value
# - Spin Value 1
# - Spin Value 2
self._calculationValues['Element Listing'] = \
parser_outputst_handle['Element List']
####
########################
# get electronic phase #
########################
# get raw list [k-points, phase]
phaseDirSpinPathRaw = args['phases']
# wrap phases in the range [-pi ... +pi]
phaseDirSpinPathWrp11 = self.wrpPhase(phaseDirSpinPathRaw, \
self.wrp11)
# print nice
print "\n","Initial Berry phases and their", \
"wrapped values in the range [-pi ... +pi]"
print "=" * 87
print " "*30, "| init k-point", "| phase raw (rad)", \
"| phase wrap. (rad)"
icoord = -1
for coord in phaseDirSpinPathRaw:
icoord += 1
print "-" * 87
print "direction(%u)" % int(icoord + 1)
ispin = -1
for spin in coord:
ispin += 1
print " " * 12, "spin(%u)" % int(ispin + 1)
ipath = -1
for path in spin:
ipath += 1
# perform wraping using the method privided in input
kpt = phaseDirSpinPathRaw[icoord][ispin][ipath][0]
ph = phaseDirSpinPathRaw[icoord][ispin][ipath][1]
phwrp = phaseDirSpinPathWrp11[icoord][ispin][ipath][1]
print " "*20, "path(%4d) %4d % e % e" \
% (ipath+1, kpt, ph, phwrp)
print "=" * 87
print "\n", "CALCULATION OF ELECTRONIC POLARIZATION"
print "=" * 87
print "Value", " "*25, "| spin ", "| ", "dir(1) ", \
"| ", "dir(2) ", "| ", "dir(3)"
print "-" * 87
# find path-average phase
phaseDirSpinWrp11 = self.pathAvrgPhase(phaseDirSpinPathWrp11)
# wrap the average phase again as it can go out of bounds [-pi..+pi]
phaseDirSpinWrp11 = self.wrp11(phaseDirSpinWrp11)
nspins = numpy.shape(phaseDirSpinWrp11)[1]
for spinIndex in range(0, nspins):
print "Berry phase (rad) [-pi ... +pi] sp(%1i)" \
% (spinIndex+1), \
" [% e, % e, % e]" % tuple(phaseDirSpinWrp11[:,spinIndex])
if not spCalc and not args[
'so']: # in case of non-SP or non-SO calculation...
phaseDirSpinWrp11 = 2 * phaseDirSpinWrp11 # account for the spin degeneracy
nspins = numpy.shape(phaseDirSpinWrp11)[1]
if nspins != 1: # double check
print "Inconsistency detected in the number of spins"
print "Is it spin-polarized calculation? spCalc =", spCalc
print "Number of spins in the electronic phase array", \
nspins
print "Expected 1 spin"
print "Decision is taken to EXIT"
sys.exit(2)
print "Berry phase (rad) up+dn "+ \
"[% e, % e, % e]" % tuple(phaseDirSpinWrp11)
# wrap phases again [-pi ... +pi]
phaseDirSpinWrp11 = self.wrp11(phaseDirSpinWrp11)
print "Berry phase (rad) [-pi ... +pi] " +\
" up+dn [% e, % e, % e]" \
% tuple(phaseDirSpinWrp11)
#electron charge / cell volume
self.ELEC_BY_VOL_CONST = ELECTRON_CHARGE / \
bohrToMeters(self._calculationValues['Cell Volume in bohr^3'], \
dimension = 3.)
# electronic polarization (C/m2)
elP = self.elPolarization(phaseDirSpinWrp11,self._calculationValues, \
self.ELEC_BY_VOL_CONST)
# ionic polarization (C/m2)
ionP = self.determineIonPolarization(self.wrp11, args)
# Total polarization (C/m2) will be returned
# when calling mainCalculation()
self._totalPolarizationVal = self.totalPolarization(elP, ionP)
def determineIonPolarization(self, fnWrpMethod, args):
'''
INPUT: fnWrpMethod - function that determines the method for
wrapping the phase
args - contains logical variables regarding the
calculation setup
args['so'] - spin-orbit coupling
args['sp'] - spin-polarized calculation
args['orb'] - additional orbital potential (LDA+U)
Calculation:
Pion_x = electron charge / unit volume (m) * lattice_x * (
sum of (
atom valence charge * position(x)
)
)
where atom valence charge = ( core value - spin val 1 - spin val 2 )
'''
print("\n\nCALCULATION OF IONIC POLARIZATION",\
"(conventional lattice coordinates)")
ionP = []
calcValues = self.calculationValues()
ELEC_BY_VOL_CONST = self.ELEC_BY_VOL_CONST
latticeConstants = calcValues['Lattice Constants in bohr']
atomListing = calcValues['Atom Listing']
#produce a tuple pair which includes the valence electrons and
#the coordinates for each element
calcIonValues = [] # (coordinates(x,y,z), valence value)
#TODO: include good exception handling for this stage
#construct the calcIonValues for the calculation
if args['sp'] and not args['so']:
nspins = 2
else:
nspins = 1
iatom = -1 # atom index
Zcore = self.calcVal['Atom core charges'] # non-equiv. atoms
for atom in atomListing: # loop over non-equivalent atoms
iatom = iatom + 1
theElementName = atom['Element Name']
for i in range(atom['MULT']):
if nspins == 2:
theValence = []
for spin in [1, 2]:
theValence.append( \
atom['Znucl']/2 - Zcore[iatom]/2 \
)
else:
theValence = atom['Znucl'] - Zcore[iatom]
xCoordinate = atom['X-Coord'][i]
yCoordinate = atom['Y-Coord'][i]
zCoordinate = atom['Z-Coord'][i]
#produce tuple from coordinates
coordinates = (xCoordinate, yCoordinate, zCoordinate)
calcIonValues.append((theElementName, coordinates, theValence))
self._calcIonValues = calcIonValues
#### CALCULATION ####
xPolarIon, yPolarIon, zPolarIon = (0., 0., 0.)
print("=" * 87)
print("Elem.| Fractional coord. | spin | Zion |", \
" dir(1) ", \
"| ", "dir(2) ", "| ", "dir(3)")
print("-" * 87)
print(" "*41, "+"+"-"*12, "Ionic phase (rad)", \
"-"*12+"+")
totIonPhase = numpy.zeros((nspins, 3))
for element, iCoord, iValence in calcIonValues:
spinIndex = -1
if isinstance(iValence, collections.Iterable):
pass
else:
iValence = [
iValence,
]
for spinValence in iValence:
spinIndex += 1
ionPhase = numpy.zeros((nspins, 3))
coordIndex = -1
for fcoord in iCoord:
coordIndex += 1
# fractional coordinates used
psi = fcoord * spinValence * 2 * numpy.pi
ionPhase[spinIndex, coordIndex] = psi
if spinIndex == 0:
print("%2s " % element, \
"(%6.4f, %6.4f, %6.4f) " % iCoord, \
"sp(%1i)" % (spinIndex+1), \
"%5.2f" % spinValence, \
"[% e, % e, % e]" % tuple(ionPhase[spinIndex,:]))
else:
print(" "*29, \
"sp(%1i)" % (spinIndex+1), \
"%5.2f" % spinValence, \
"[% e, % e, % e]" % tuple(ionPhase[spinIndex,:]))
totIonPhase[:, :] += ionPhase
print("-" * 87)
for spinIndex in range(0, nspins):
print("Total ionic phase (rad)", " "*5, \
"sp(%1i)" % (spinIndex+1), " "*5, \
"[% e, % e, % e]" % tuple(totIonPhase[spinIndex,:]))
# warap phases
totIonPhase = fnWrpMethod(totIonPhase)
for spinIndex in range(0, nspins):
print("Total ionic phase wrap. (rad)", \
"sp(%1i)" % (spinIndex+1), " "*5, \
"[% e, % e, % e]" % tuple(totIonPhase[spinIndex,:]))
#IONIC Polarization
ionPol = numpy.zeros((nspins, 3))
for spinIndex in range(0, nspins):
for coordIndex in range(0,
3): # loop over 3 lattice vector direct.
psi = totIonPhase[spinIndex, coordIndex]
# WIEN2k always uses conventional latt. vec. for ionic positions
latVec = calcValues['Real conventional lat vectors in bohr'][
coordIndex]
normLatVec = numpy.linalg.norm(latVec) # length of lat. vector
ionPol[spinIndex,coordIndex] = \
(psi/(2*numpy.pi)) * ELEC_BY_VOL_CONST * \
bohrToMeters(normLatVec)
print("Ionic polarization (C/m2) ", \
"sp(%1i)" % (spinIndex+1), " "*5, \
"[% e, % e, % e]" % tuple(ionPol[spinIndex,:]))
print("=" * 87)
return ionPol # END determineIonPolarization
def __init__(self, **args):
# spin polarization: yes/no
spCalc = args['sp']
############################
######### PARSING ##########
############################
###Rest of the Files###
#parse all the things!
#### *.struct file parser
parser_struct_handle = open(args['file_struct'], 'r').readlines()
parser_struct_handle = b_PyParse.MainStructParser(parser_struct_handle)
parser_struct_handle.parse()
#### *.inc parser
parser_inc_handle = open(args['file_inc'], 'r').readlines()
parser_inc_handle = b_PyParse.MainIncParser(parser_inc_handle)
parser_inc_handle.parse()
#####################################
############ END Parsing ############
#####################################
#############################
###### Getting Values #######
#############################
self.calcVal = orderedDict()
#### *.struct handle
# - name of atoms
# - MULT for each atom
# - coordinates
# - nuclear charge
self.calcVal['Atom Listing'] = \
parser_struct_handle['Atom Listing']
# - lattice type (P,F,B,CXY,CYZ,CXZ,R,H)
self.calcVal['lattice type'] = \
parser_struct_handle['lattice type']
# - lattice orthogonal (T/F)
self.calcVal['lattice ortho'] = \
parser_struct_handle['lattice ortho']
# - Cell Volume
self.calcVal['Cell Volume in bohr^3'] = \
parser_struct_handle['cell volume']
# - Lattice Constants (a,b,c)
self.calcVal['Lattice Constants in bohr'] = \
parser_struct_handle['lattice constants']
# - lattice vectors BR1_DIR matrix (v_x, v_y, v_z)
self.calcVal['Real conventional lat vectors in bohr'] = \
parser_struct_handle['real space conventional lattice vectors']
# - lattice vectors BR2_DIR matrix (v_x, v_y, v_z)
self.calcVal['Real primitive lat vectors in bohr'] = \
parser_struct_handle['real space primitive lattice vectors']
### *.inc handle
# - core charge for each non-eqivalent atom
self.calcVal['Atom core charges'] = \
parser_inc_handle['core charges']
# check consistency of case.struct and case.inc files
if len(self.calcVal['Atom core charges']) != \
len(self.calcVal['Atom Listing']):
print("Number of non-equivalent atoms in case.struct:", \
len(self.calcVal['Atom Listing']))
print("Number of non-equivalent atoms in case.inc:", \
len(self.calcVal['Atom core charges']))
raise Exception("Inconsistent number of non-equivalent atoms")
# list of pi-wrapping functions that will be applied to wrap the phase
wrpFnList = [self.wrp02, self.wrp11]
for wrpFn in wrpFnList: # iterate over various wrapping functions
if wrpFn == self.wrp11:
print("\n\n~~~~~~~~~~~~~~~~~~~~ " +\
"phases are wrapped in the range [-pi .. +pi]" +\
" ~~~~~~~~~~~~~~~~~~~~~~")
elif wrpFn == self.wrp02:
print("\n\n~~~~~~~~~~~~~~~~~~~~ " +\
"phases are wrapped in the range [0 .. +2pi] " +\
" ~~~~~~~~~~~~~~~~~~~~~")
########################
# get electronic phase #
########################
# get raw list [k-points, phase]
phaseDirSpinPathRaw = args['phases']
# wrap phases in the range [-pi ... +pi]
phaseDirSpinPathWrp = self.wrpPhase(phaseDirSpinPathRaw, \
wrpFn)
# print nice
print("\n","Initial Berry phases and their", \
"wrapped values")
print("=" * 87)
print(" "*30, "| init k-point", "| phase raw (rad)", \
"| phase wrap. (rad)")
icoord = -1
for coord in phaseDirSpinPathRaw:
icoord += 1
print("-" * 87)
print("direction(%u)" % int(icoord + 1))
ispin = -1
for spin in coord:
ispin += 1
print(" " * 12, "spin(%u)" % int(ispin + 1))
ipath = -1
for path in spin:
ipath += 1
# perform wraping using the method privided in input
kpt = phaseDirSpinPathRaw[icoord][ispin][ipath][0]
ph = phaseDirSpinPathRaw[icoord][ispin][ipath][1]
phwrp = phaseDirSpinPathWrp[icoord][ispin][ipath][1]
print(" "*20, "path(%4d) %4d % e % e" \
% (ipath+1, kpt, ph, phwrp))
print("=" * 87)
print("\n\nCALCULATION OF ELECTRONIC POLARIZATION",\
"(primitive lattice coordinates)")
print("=" * 87)
print("Value", " "*25, "| spin ", "| ", "dir(1) ", \
"| ", "dir(2) ", "| ", "dir(3)")
print("-" * 87)
# find path-average phase
phaseDirSpinWrp = self.pathAvrgPhase(phaseDirSpinPathWrp)
# wrap the average phase again as it can go out of bounds [-pi..+pi]
phaseDirSpinWrp = wrpFn(phaseDirSpinWrp)
nspins = numpy.shape(phaseDirSpinWrp)[1]
for spinIndex in range(0, nspins):
print("Berry phase wrapped (rad) sp(%1i)" \
% (spinIndex+1), \
" [% e, % e, % e]" % tuple(phaseDirSpinWrp[:,spinIndex]))
if not spCalc and not args[
'so']: # in case of non-SP or non-SO calculation...
phaseDirSpinWrp = 2 * phaseDirSpinWrp # account for the spin degeneracy
nspins = numpy.shape(phaseDirSpinWrp)[1]
if nspins != 1: # double check
print("Inconsistency detected in the number of spins")
print("Is it spin-polarized calculation? spCalc =", spCalc)
print("Number of spins in the electronic phase array", \
nspins)
print("Expected 1 spin")
print("Decision is taken to EXIT")
sys.exit(2)
print("Berry phase (rad) up+dn "+ \
"[% e, % e, % e]" % tuple(phaseDirSpinWrp))
# wrap phases again [-pi ... +pi]
phaseDirSpinWrp = wrpFn(phaseDirSpinWrp)
print("Berry phase wrapped (rad)" +\
" up+dn [% e, % e, % e]" \
% tuple(phaseDirSpinWrp))
#electron charge / cell volume
self.ELEC_BY_VOL_CONST = ELECTRON_CHARGE / \
bohrToMeters(self.calcVal['Cell Volume in bohr^3'], \
dimension = 3.)
# electronic polarization (C/m2)
elP = self.elPolarization(phaseDirSpinWrp,self.calcVal, \
self.ELEC_BY_VOL_CONST)
# convert elP from primitive basis to Cart. coordinates
# WIEN2k always uses primitive latt. vec. in constructing Brillouin zone
print("\nThe electronic polarization vector is presented in",\
"this coord. system:")
latVec = numpy.zeros((3, 3))
for i in range(3): # gather lattice vectors into a (3x3) array
latVec[i, :] = self.calcVal[
'Real primitive lat vectors in bohr'][i]
print(" "*4, "dir(%1i) =" % (i+1), \
"[% e, % e, % e] bohr" % tuple(latVec[i,:]))
print("and will be transformed into Cartesian coordinates.")
for i in range(elP.shape[0]): # loop over spin channels
elP[i, :] = vec2cart(elP[i, :], latVec) # prim -> Cartesian
#############################
# ionic polarization (C/m2) #
#############################
ionP = self.determineIonPolarization(wrpFn, args)
# convert ionP from conventional to Cart. coordinates
# WIEN2k always uses conventional latt. vec. for ionic positions
print("\nThe ionic positions and associated polarization vector is",\
"presented in this coord. system:")
latVec = numpy.zeros((3, 3))
for i in range(3): # gather lattice vectors into a (3x3) array
latVec[i, :] = self.calcVal[
'Real conventional lat vectors in bohr'][i]
print(" "*4, "dir(%1i) =" % (i+1), \
"[% e, % e, % e] bohr" % tuple(latVec[i,:]))
for i in range(ionP.shape[0]): # loop over spin channels
ionP[i, :] = vec2cart(ionP[i, :],
latVec) # conventional -> Cartesian
#############################
# total polarization (C/m2) #
#############################
# Total polarization (C/m2) will be returned
# when calling mainCalculation()
self._totalPolarizationVal = self.totalPolarization(elP, ionP)
# Prepare transform polarization from lattice vectors to Cartesian
# coordinates (totP -> totPcart
latVec = numpy.zeros((3, 3))
# END iterate over various wrapping functions
print('''
Notes:
(1) When lattice vectors are _not_ aligned with Cartesian coordinates, an
additional transformation is required to present the polarization vector
in Cartesian coordinates. This can be important when calculating Born
effective charges
Z*_i,j = (Omega/e) * dP_i/dr_j,
where i, j are Cartesian components, Omega is the cell volume (see output
above), and e is the elementary charge. The total polarization vector is
presented in Cartesian coordinates and should be used to determine dP_i.
It is, however, up to the user to transform the atom displacement vector
components dr_j into Cartesian coordinates. The change in fractional
coordinated should be converted into dr_j using lattice vectors dir(1,2,3)
used in calculation of the ionic polarization (see above). An
Octave/Matlab sctipt can be found in
https://github.com/spichardo/BerryPI/wiki/Tutorial-3:-Non-orthogonal-lattice-vectors
(2) Results are presented for two pi-wrapping options [-pi .. +pi] and
[0 .. +2pi] separated by ~~~~~~. It is designed to assist in situations
when a sudden change in the Berry phase (and associated polarization)
occurs due to a pi-wrapping artefact (see discussion pertaining Fig. 2 in
Ref. [1]). It is up to the user to select the most relevant option. This
decision should be made based on comparing results for _two_ different
structures. The goal is to ensure a smooth change in the phase in response
to a small perturbation.''')
def determineIonPolarization(self, fnWrpMethod, args):
'''
INPUT: fnWrpMethod - function that determines the method for
wrapping the phase
args - contains logical variables regarding the
calculation setup
args['so'] - spin-orbit coupling
args['sp'] - spin-polarized calculation
args['orb'] - additional orbital potential (LDA+U)
Calculation:
Pion_x = electron charge / unit volume (m) * lattice_x * (
sum of (
atom valence charge * position(x)
)
)
where atom valence charge = ( core value - spin val 1 - spin val 2 )
'''
print "\n", "CALCULATION OF IONIC POLARIZATION"
ionP = []
calcValues = self.calculationValues()
ELEC_BY_VOL_CONST = self.ELEC_BY_VOL_CONST
latticeConstants = calcValues['Lattice Constants in bohr']
atomListing = calcValues['Atom Listing']
#produce a tuple pair which includes the valence electrons and
#the coordinates for each element
calcIonValues = [] # (coordinates(x,y,z), valence value)
#TODO: include good exception handling for this stage
#construct the calcIonValues for the calculation
if args['sp'] and not args['so']:
nspins = 2
else:
nspins = 1
for atom in atomListing:
for i in range(atom['MULT']):
theElementName = atom['Element Name']
if calcValues['Element Listing'].has_key(theElementName):
theElement = calcValues['Element Listing'][theElementName]
if nspins == 2:
theValence = []
for spin in [1, 2]:
theValence.append( \
atom['Znucl']/2 - theElement['Core Value']/2 \
);
else:
theValence = atom['Znucl'] - theElement['Core Value'];
xCoordinate = atom['X-Coord'][i]
yCoordinate = atom['Y-Coord'][i]
zCoordinate = atom['Z-Coord'][i]
#produce tuple from coordinates
coordinates = (xCoordinate, yCoordinate, zCoordinate)
calcIonValues.append((theElementName,coordinates, theValence))
else:
print DEFAULT_PREFIX + 'ERROR: Missing element in element list'
print DEFAULT_PREFIX + theElementName
print DEFAULT_PREFIX + calcValues['Element List']
print DEFAULT_PREFIX + 'Exiting....'
sys.exit(1)
self._calcIonValues = calcIonValues
#### CALCULATION ####
xPolarIon, yPolarIon, zPolarIon = (0., 0., 0.)
print "="*87
print "Elem.| Fractional coord. | spin | Zion |", \
" dir(1) ", \
"| ", "dir(2) ", "| ", "dir(3)"
print "-"*87
print " "*41, "+"+"-"*12, "Ionic phase (rad)", \
"-"*12+"+"
totIonPhase = numpy.zeros((nspins,3))
for element, iCoord, iValence in calcIonValues:
spinIndex = -1
if isinstance(iValence, collections.Iterable):
pass
else:
iValence = [iValence, ]
for spinValence in iValence:
spinIndex += 1
ionPhase = numpy.zeros((nspins,3))
coordIndex = -1
for fcoord in iCoord:
coordIndex += 1
# fractional coordinates used
psi = fcoord * spinValence * 2*numpy.pi
ionPhase[ spinIndex , coordIndex ] = psi
if spinIndex == 0:
print "%2s " % element, \
"(%6.4f, %6.4f, %6.4f) " % iCoord, \
"sp(%1i)" % (spinIndex+1), \
"%5.2f" % spinValence, \
"[% e, % e, % e]" % tuple(ionPhase[spinIndex,:]);
else:
print " "*29, \
"sp(%1i)" % (spinIndex+1), \
"%5.2f" % spinValence, \
"[% e, % e, % e]" % tuple(ionPhase[spinIndex,:]);
totIonPhase[:,:] += ionPhase
print "-"*87
for spinIndex in range(0,nspins):
print "Total ionic phase (rad)", " "*5, \
"sp(%1i)" % (spinIndex+1), " "*5, \
"[% e, % e, % e]" % tuple(totIonPhase[spinIndex,:]);
# warap phases
totIonPhase = fnWrpMethod( totIonPhase );
for spinIndex in range(0,nspins):
print "Total ionic phase wrap. (rad)", \
"sp(%1i)" % (spinIndex+1), " "*5, \
"[% e, % e, % e]" % tuple(totIonPhase[spinIndex,:]);
#IONIC Polarization
ionPol = numpy.zeros((nspins,3))
for spinIndex in range(0,nspins):
for coordIndex in range(0,3):
psi = totIonPhase[spinIndex,coordIndex]
a = latticeConstants[coordIndex]
ionPol[spinIndex,coordIndex] = \
(psi/(2*numpy.pi)) * ELEC_BY_VOL_CONST * \
bohrToMeters(a);
print "Ionic polarization (C/m2) ", \
"sp(%1i)" % (spinIndex+1), " "*5, \
"[% e, % e, % e]" % tuple(ionPol[spinIndex,:]);
print "="*87
return ionPol # END determineIonPolarization
def __init__(self, **args):
# spin polarization: yes/no
spCalc = args['sp']
############################
######### PARSING ##########
############################
###Rest of the Files###
#parse all the things!
#### *.struct file parser
parser_struct_handle = open(args['file_struct'], 'r').readlines()
parser_struct_handle = b_PyParse.MainStructParser(parser_struct_handle)
parser_struct_handle.parse()
#### *.scf file parser
parser_scf_handle = open(args['file_scf'], 'r').readlines()
parser_scf_handle = b_PyParse.MainSCFParser(parser_scf_handle)
parser_scf_handle.parse()
#### *.outputd parser
parser_outputd_handle = open(args['file_outputd'], 'r').readlines()
parser_outputd_handle = b_PyParse.MainOutputDParser(parser_outputd_handle)
parser_outputd_handle.parse()
#### *.outputst parser
parser_outputst_handle = open(args['file_outputst'], 'r').readlines()
parser_outputst_handle = b_PyParse.MainOutputstParser(parser_outputst_handle)
parser_outputst_handle.parse()
#####################################
############ END Parsing ############
#####################################
#############################
###### Getting Values #######
#############################
self._calculationValues = orderedDict();
#### *.struct handle
# - determine name of atoms
# - determine MULT for each atom
self._calculationValues['Atom Listing'] = \
parser_struct_handle['Atom Listing'];
#### *.scf handle
# - Cell Volume
self._calculationValues['Cell Volume in bohr^3'] = \
parser_scf_handle['Cell Volume'];
self._calculationValues['Cell Volume in m^3'] = \
bohrToMeters(self._calculationValues['Cell Volume in bohr^3'],3);
#### *.outputd handle
# - BR2_DIR matrix (v_x, v_y, v_z)
# - number of atoms in cell
# - Lattice Constants (x,y,z)
laticematrix=parser_outputd_handle['BR2_DIR Matrix']
latticematrixa1=laticematrix[0]
self._calculationValues['Lattice Matrix a1 in bohr'] = \
latticematrixa1;
latticematrixa2=laticematrix[1]
self._calculationValues['Lattice Matrix a2 in bohr'] = \
latticematrixa2;
latticematrixa3=laticematrix[2]
self._calculationValues['Lattice Matrix a3 in bohr'] = \
latticematrixa3;
self._calculationValues['Lattice Matrix in bohr'] = \
parser_outputd_handle['BR2_DIR Matrix'];
self._calculationValues['Lattice Matrix in m'] = \
[[ bohrToMeters(i) for i in j ] for j in \
self._calculationValues['Lattice Matrix in bohr']];
self._calculationValues['Number of Atoms in Unit Cell'] = \
parser_outputd_handle['Number of Atoms in Unit Cell'];
self._calculationValues['Lattice Constants in bohr'] = \
parser_outputd_handle['Lattice Constants'];
self._calculationValues['Lattice Constants in m'] = \
[ bohrToMeters(i) for i in \
self._calculationValues['Lattice Constants in bohr']];
#### *.outputst handle
# for each element:
# - Core Value
# - Spin Value 1
# - Spin Value 2
self._calculationValues['Element Listing'] = \
parser_outputst_handle['Element List'];
####
########################
# get electronic phase #
########################
# get raw list [k-points, phase]
phaseDirSpinPathRaw = args['phases']
# wrap phases in the range [-pi ... +pi]
phaseDirSpinPathWrp11 = self.wrpPhase(phaseDirSpinPathRaw, \
self.wrp11);
# print nice
print "\n","Initial Berry phases and their", \
"wrapped values in the range [-pi ... +pi]";
print "="*87
print " "*30, "| init k-point", "| phase raw (rad)", \
"| phase wrap. (rad)"
icoord = -1
for coord in phaseDirSpinPathRaw:
icoord += 1
print "-"*87
print "direction(%u)" % int(icoord + 1)
ispin = -1
for spin in coord:
ispin += 1
print " "*12, "spin(%u)" % int(ispin + 1)
ipath = -1
for path in spin:
ipath += 1
# perform wraping using the method privided in input
kpt = phaseDirSpinPathRaw[icoord][ispin][ipath][0]
ph = phaseDirSpinPathRaw[icoord][ispin][ipath][1]
phwrp = phaseDirSpinPathWrp11[icoord][ispin][ipath][1]
print " "*20, "path(%4d) %4d % e % e" \
% (ipath+1, kpt, ph, phwrp)
print "="*87
print "\n","CALCULATION OF ELECTRONIC POLARIZATION"
print "="*87
print "Value", " "*25, "| spin ", "| ", "dir(1) ", \
"| ", "dir(2) ", "| ", "dir(3)"
print "-"*87
# find path-average phase
phaseDirSpinWrp11 = self.pathAvrgPhase(phaseDirSpinPathWrp11);
# wrap the average phase again as it can go out of bounds [-pi..+pi]
phaseDirSpinWrp11 = self.wrp11(phaseDirSpinWrp11);
nspins = numpy.shape(phaseDirSpinWrp11)[1]
for spinIndex in range(0,nspins):
print "Berry phase (rad) [-pi ... +pi] sp(%1i)" \
% (spinIndex+1), \
" [% e, % e, % e]" % tuple(phaseDirSpinWrp11[:,spinIndex]);
if not spCalc and not args['so']: # in case of non-SP or non-SO calculation...
phaseDirSpinWrp11 = 2*phaseDirSpinWrp11 # account for the spin degeneracy
nspins = numpy.shape(phaseDirSpinWrp11)[1]
if nspins != 1: # double check
print "Inconsistency detected in the number of spins"
print "Is it spin-polarized calculation? spCalc =", spCalc
print "Number of spins in the electronic phase array", \
nspins;
print "Expected 1 spin"
print "Decision is taken to EXIT"
sys.exit(2)
print "Berry phase (rad) up+dn "+ \
"[% e, % e, % e]" % tuple(phaseDirSpinWrp11);
# wrap phases again [-pi ... +pi]
phaseDirSpinWrp11 = self.wrp11(phaseDirSpinWrp11)
print "Berry phase (rad) [-pi ... +pi] " +\
" up+dn [% e, % e, % e]" \
% tuple(phaseDirSpinWrp11);
#electron charge / cell volume
self.ELEC_BY_VOL_CONST = ELECTRON_CHARGE / \
bohrToMeters(self._calculationValues['Cell Volume in bohr^3'], \
dimension = 3.);
# electronic polarization (C/m2)
elP = self.elPolarization(phaseDirSpinWrp11,self._calculationValues, \
self.ELEC_BY_VOL_CONST);
# ionic polarization (C/m2)
ionP = self.determineIonPolarization(self.wrp11,args)
# Total polarization (C/m2) will be returned
# when calling mainCalculation()
self._totalPolarizationVal = self.totalPolarization(elP, ionP)
def __init__(self, **args):
# spin polarization: yes/no
spCalc = args['sp']
############################
######### PARSING ##########
############################
###Rest of the Files###
#parse all the things!
#### *.struct file parser
parser_struct_handle = open(args['file_struct'], 'r').readlines()
parser_struct_handle = b_PyParse.MainStructParser(parser_struct_handle)
parser_struct_handle.parse()
#### *.inc parser
parser_inc_handle = open(args['file_inc'], 'r').readlines()
parser_inc_handle = b_PyParse.MainIncParser(parser_inc_handle)
parser_inc_handle.parse()
#####################################
############ END Parsing ############
#####################################
#############################
###### Getting Values #######
#############################
self._calculationValues = orderedDict()
#### *.struct handle
# - name of atoms
# - MULT for each atom
# - coordinates
# - nuclear charge
self._calculationValues['Atom Listing'] = \
parser_struct_handle['Atom Listing']
# - Cell Volume
self._calculationValues['Cell Volume in bohr^3'] = \
parser_struct_handle['cell volume']
# - Lattice Constants (a,b,c)
self._calculationValues['Lattice Constants in bohr'] = \
parser_struct_handle['lattice constants']
# - lattice vectors BR2_DIR matrix (v_x, v_y, v_z)
self._calculationValues['Lattice Matrix in bohr'] = \
parser_struct_handle['real space lattice vectors']
### *.inc handle
# - core charge for each non-eqivalent atom
self._calculationValues['Atom core charges'] = \
parser_inc_handle['core charges']
# check consistency of case.struct and case.inc files
if len(self._calculationValues['Atom core charges']) != \
len(self._calculationValues['Atom Listing']):
print("Number of non-equivalent atoms in case.struct:", \
len(self._calculationValues['Atom Listing']))
print("Number of non-equivalent atoms in case.inc:", \
len(self._calculationValues['Atom core charges']))
raise Exception("Inconsistent number of non-equivalent atoms")
########################
# get electronic phase #
########################
# get raw list [k-points, phase]
phaseDirSpinPathRaw = args['phases']
# wrap phases in the range [-pi ... +pi]
phaseDirSpinPathWrp11 = self.wrpPhase(phaseDirSpinPathRaw, \
self.wrp11)
# print nice
print("\n","Initial Berry phases and their", \
"wrapped values in the range [-pi ... +pi]")
print("=" * 87)
print(" "*30, "| init k-point", "| phase raw (rad)", \
"| phase wrap. (rad)")
icoord = -1
for coord in phaseDirSpinPathRaw:
icoord += 1
print("-" * 87)
print("direction(%u)" % int(icoord + 1))
ispin = -1
for spin in coord:
ispin += 1
print(" " * 12, "spin(%u)" % int(ispin + 1))
ipath = -1
for path in spin:
ipath += 1
# perform wraping using the method privided in input
kpt = phaseDirSpinPathRaw[icoord][ispin][ipath][0]
ph = phaseDirSpinPathRaw[icoord][ispin][ipath][1]
phwrp = phaseDirSpinPathWrp11[icoord][ispin][ipath][1]
print(" "*20, "path(%4d) %4d % e % e" \
% (ipath+1, kpt, ph, phwrp))
print("=" * 87)
print("\n", "CALCULATION OF ELECTRONIC POLARIZATION")
print("=" * 87)
print("Value", " "*25, "| spin ", "| ", "dir(1) ", \
"| ", "dir(2) ", "| ", "dir(3)")
print("-" * 87)
# find path-average phase
phaseDirSpinWrp11 = self.pathAvrgPhase(phaseDirSpinPathWrp11)
# wrap the average phase again as it can go out of bounds [-pi..+pi]
phaseDirSpinWrp11 = self.wrp11(phaseDirSpinWrp11)
nspins = numpy.shape(phaseDirSpinWrp11)[1]
for spinIndex in range(0, nspins):
print("Berry phase (rad) [-pi ... +pi] sp(%1i)" \
% (spinIndex+1), \
" [% e, % e, % e]" % tuple(phaseDirSpinWrp11[:,spinIndex]))
if not spCalc and not args[
'so']: # in case of non-SP or non-SO calculation...
phaseDirSpinWrp11 = 2 * phaseDirSpinWrp11 # account for the spin degeneracy
nspins = numpy.shape(phaseDirSpinWrp11)[1]
if nspins != 1: # double check
print("Inconsistency detected in the number of spins")
print("Is it spin-polarized calculation? spCalc =", spCalc)
print("Number of spins in the electronic phase array", \
nspins)
print("Expected 1 spin")
print("Decision is taken to EXIT")
sys.exit(2)
print("Berry phase (rad) up+dn "+ \
"[% e, % e, % e]" % tuple(phaseDirSpinWrp11))
# wrap phases again [-pi ... +pi]
phaseDirSpinWrp11 = self.wrp11(phaseDirSpinWrp11)
print("Berry phase (rad) [-pi ... +pi] " +\
" up+dn [% e, % e, % e]" \
% tuple(phaseDirSpinWrp11))
#electron charge / cell volume
self.ELEC_BY_VOL_CONST = ELECTRON_CHARGE / \
bohrToMeters(self._calculationValues['Cell Volume in bohr^3'], \
dimension = 3.)
# electronic polarization (C/m2)
elP = self.elPolarization(phaseDirSpinWrp11,self._calculationValues, \
self.ELEC_BY_VOL_CONST)
# ionic polarization (C/m2)
ionP = self.determineIonPolarization(self.wrp11, args)
# Total polarization (C/m2) will be returned
# when calling mainCalculation()
self._totalPolarizationVal = self.totalPolarization(elP, ionP)
