def reduce(self, ibrav=None):
"""
Reduces a structure instance with nonprimitive lattice ( i.e. solves
for equivalent atomic positions) according to specified lattice type (ibrav).
Each ibrav number corresponds to a specific primitive lattice
(see QE documentation).
"""
ib = self.lattice.ibrav
if ibrav != None:
ib = ibrav
a = self.lattice.diffpy().a
b = self.lattice.diffpy().b
c = self.lattice.diffpy().c
cAB = cosd(self.lattice.diffpy().gamma)
cBC = cosd(self.lattice.diffpy().alpha)
cAC = cosd(self.lattice.diffpy().beta)
if ib > 0:
qeLattice = QELattice(ibrav = ib, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
else:
qeLattice = QELattice(ibrav=ib, base=self.lattice.base)
qeLattice._qeInput = self._qeInput
reducedStructure = QEStructure(self)
reducedStructure.placeInLattice(qeLattice)
# collect atoms that are at equivalent position to some previous atom
duplicates = set([
a1 for i0, a0 in enumerate(reducedStructure)
for a1 in reducedStructure[i0 + 1:] if a0.element == a1.element
and equalPositions(a0.xyz, a1.xyz, eps=1e-4)
])
# Filter out duplicate atoms. Use slice assignment so that
# reducedStructure is not replaced with a list.
self.lattice = qeLattice
self[:] = [a for a in reducedStructure if not a in duplicates]
self._qeInput.structure = self
return
def reduce(self, ibrav = None):
"""
Reduces a structure instance with nonprimitive lattice ( i.e. solves
for equivalent atomic positions) according to specified lattice type (ibrav).
Each ibrav number corresponds to a specific primitive lattice
(see QE documentation).
"""
ib = self.lattice.ibrav
if ibrav != None:
ib = ibrav
a = self.lattice.diffpy().a
b = self.lattice.diffpy().b
c = self.lattice.diffpy().c
cAB = cosd(self.lattice.diffpy().gamma)
cBC = cosd(self.lattice.diffpy().alpha)
cAC = cosd(self.lattice.diffpy().beta)
if ib > 0:
qeLattice = QELattice(ibrav = ib, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
else:
qeLattice = QELattice(ibrav = ib, base = self.lattice.base)
qeLattice._qeInput = self._qeInput
reducedStructure = QEStructure(self)
reducedStructure.placeInLattice( qeLattice )
# collect atoms that are at equivalent position to some previous atom
duplicates = set([a1
for i0, a0 in enumerate(reducedStructure) for a1 in reducedStructure[i0+1:]
if a0.element == a1.element and equalPositions(a0.xyz, a1.xyz, eps=1e-4)])
# Filter out duplicate atoms. Use slice assignment so that
# reducedStructure is not replaced with a list.
self.lattice = qeLattice
self[:] = [a for a in reducedStructure if not a in duplicates]
self._qeInput.structure = self
return
def _setReducedStructureFromDiffpyStructure(self,
structure,
ibrav,
massList=[],
psList=[]):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with potential names
diffpyStructure object will be modified with reduced atomic positions
"""
import copy
diffpyLattice = copy.deepcopy(structure.lattice)
a = diffpyLattice.a
b = diffpyLattice.b
c = diffpyLattice.c
cAB = cosd(diffpyLattice.gamma)
cBC = cosd(diffpyLattice.alpha)
cAC = cosd(diffpyLattice.beta)
qeLattice = QELattice(ibrav = ibrav, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
# make a deep copy:
reducedStructure = Structure(atoms=structure)
reducedStructure.placeInLattice(Lattice(base=qeLattice.diffpy().base))
# collect atoms that are at equivalent position to some previous atom
duplicates = set([
a1 for i0, a0 in enumerate(reducedStructure)
for a1 in reducedStructure[i0 + 1:]
if self._element(a0) == self._element(a1)
and equalPositions(a0.xyz, a1.xyz, eps=1e-4)
])
# Filter out duplicate atoms. Use slice assignment so that
# reducedStructure is not replaced with a list.
reducedStructure[:] = [
a for a in reducedStructure if not a in duplicates
]
atomNames = []
for a in reducedStructure:
if self._element(a) not in atomNames:
atomNames.append(self._element(a))
atomicSpecies = {}
for i, elem in enumerate(atomNames):
if len(massList) - 1 < i:
mass = 0
else:
mass = massList[i]
if len(psList) - 1 < i:
ps = ''
else:
ps = psList[i]
atomicSpecies[elem] = (mass, ps)
self[:] = []
# convert to bohr units
self.lattice.setLattice(ibrav, self.lattice.a*1.889725989, \
self.lattice.b*1.889725989,
self.lattice.c*1.889725989)
for atom in reducedStructure:
elem = self._element(atom)
self.addNewAtom(atype = elem, xyz = atom.xyz, \
mass = atomicSpecies[elem][0], \
potential = atomicSpecies[elem][1],\
lattice = self.lattice, optConstraint = [])
def _setReducedStructureFromDiffpyStructure(self, structure, ibrav, massList = [], psList = []):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with potential names
diffpyStructure object will be modified with reduced atomic positions
"""
import copy
diffpyLattice = copy.deepcopy(structure.lattice)
a = diffpyLattice.a
b = diffpyLattice.b
c = diffpyLattice.c
cAB = cosd(diffpyLattice.gamma)
cBC = cosd(diffpyLattice.alpha)
cAC = cosd(diffpyLattice.beta)
qeLattice = QELattice(ibrav = ibrav, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
# make a deep copy:
reducedStructure = Structure(atoms = structure)
reducedStructure.placeInLattice(Lattice(base=qeLattice.diffpy().base))
# collect atoms that are at equivalent position to some previous atom
duplicates = set([a1
for i0, a0 in enumerate(reducedStructure) for a1 in reducedStructure[i0+1:]
if self._element(a0) == self._element(a1) and equalPositions(a0.xyz, a1.xyz, eps=1e-4)])
# Filter out duplicate atoms. Use slice assignment so that
# reducedStructure is not replaced with a list.
reducedStructure[:] = [a for a in reducedStructure if not a in duplicates]
atomNames = []
for a in reducedStructure:
if self._element(a) not in atomNames:
atomNames.append(self._element(a))
atomicSpecies = {}
for i, elem in enumerate(atomNames):
if len(massList) - 1 < i:
mass = 0
else:
mass = massList[i]
if len(psList) - 1 < i:
ps = ''
else:
ps = psList[i]
atomicSpecies[elem] = (mass, ps)
self[:] = []
# convert to bohr units
self.lattice.setLattice(ibrav, self.lattice.a*1.889725989, \
self.lattice.b*1.889725989,
self.lattice.c*1.889725989)
for atom in reducedStructure:
elem = self._element(atom)
self.addNewAtom(atype = elem, xyz = atom.xyz, \
mass = atomicSpecies[elem][0], \
potential = atomicSpecies[elem][1],\
lattice = self.lattice, optConstraint = [])
def setLatticeFromQEVectors(self, ibrav, vectors):
""" Will extract conventional lattice parameters from primitive vectors.
'vectors' - is a list with primitive vectors (in QE notation),
including lattice parameters. For example from PWSCF output"""
from numpy import dot
# default values:
a = b = c = 1.0
cBC = cAC = cAB = 0.0
v = numpy.array(vectors, dtype = float)
if ibrav == 0:
raise NotImplementedError
# sc simple cubic:
if ibrav == 1:
a = v[0,0]
if ibrav == 2:
a = b = c = sqrt( 2.0*dot(v[0,:],v[0,:]) )
if ibrav == 3:
a = b = c = 2.0*sqrt( dot(v[0,:],v[0,:])/3.0)
if ibrav == 4:
a = b = sqrt( dot(v[0,:],v[0,:]))
c = sqrt( dot(v[2,:],v[2,:]))
cAB = cosd(120.0)
if ibrav == 5:
a = b = c = sqrt( dot(v[0,:],v[0,:]))
cBC = cAC = cAB = dot(v[0,:],v[2,:])/a**2
if ibrav == 6:
a = b = sqrt( dot(v[0,:],v[0,:]))
c = sqrt( dot(v[2,:],v[2,:]))
if ibrav == 7:
a = b = v[1,0] - v[2,0]
c = v[1,2] + v[2,2]
if ibrav == 8:
a = v[0,0]
b = v[1,1]
c = v[2,2]
if ibrav == 9:
a = v[0,0] - v[1,0]
b = v[0,1] + v[1,1]
c = v[2,2]
if ibrav == 10:
a = v[2,0] - v[0,0] - v[1,0]
b = v[2,1] - v[0,1] + v[1,1]
c = v[0,2] - v[1,2] + v[2,2]
if ibrav == 11:
a = v[0,0] - v[1,0]
b = v[1,1] - v[2,1]
c = v[0,2] - v[2,2]
if ibrav == 12:
a = v[0,0]
b = sqrt( dot(v[1,:],v[1,:]))
cAB = v[1,0]/b
c = v[2,2]
if ibrav == 13:
a = v[0,0] + v[2,0]
b = sqrt( dot(v[1,:],v[1,:]))
c = v[2,2] - v[0,2]
cAB = v[1,0]/b
if ibrav == 14:
a = v[0,0]
b = sqrt( dot(v[1,:],v[1,:]))
cAB = v[1,0]/b
c = sqrt( dot(v[2,:],v[2,:]))
cAC = v[2,0]/c
cBC = v[2,1]*sqrt(1.0 - cAB**2)/c + cAC*cAB
self.setLattice(ibrav, a, b, c, cBC, cAC, cAB)
def getLatticeParamsFromPWSCF(self, ibrav, fname):
qeConf = QEConfig(fname)
qeConf.parse()
cBC = 0.0
cAC = 0.0
cAB = 0.0
if 'celldm(1)' in qeConf.namelists['system'].params:
self._type = 'celldm' # celldm(i), i=1,6
a = float(qeConf.namelist('system').param('celldm(1)'))
if ibrav == 0:
# lattice is set in the units of celldm(1)
# need to parse CELL_PARAMETERS
cellParLines = qeConf.card('cell_parameters').getLines()
cellParType = qeConf.card('cell_parameters').argument()
if cellParType == 'cubic' or cellParType == None:
self._type = 'generic cubic'
else:
if cellParType == 'hexagonal':
self._type = 'generic hexagonal'
# convert card into list
base = []
for line in cellParLines:
if '!' not in line:
words = line.split()
base.append([float(w) for w in words])
return a, None, None, None, None, None, numpy.array(base)
if ibrav > 0 and ibrav < 4:
return a, a, a, cBC, cAC, cAB, None
if ibrav == 4:
cAB = cosd(120.0)
if ibrav == 4 or ibrav == 6 or ibrav == 7:
c_a = float(qeConf.namelist('system').param('celldm(3)'))
return a, a, c_a*a, cBC, cAC, cAB, None
if ibrav == 5:
cAB = float(qeConf.namelist('system').param('celldm(4)'))
return a, a, a, cAB, cAB, cAB, None
if ibrav > 7 and ibrav < 12:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
return a, b_a*a, c_a*a, cBC, cAC, cAB, None
if ibrav == 12 or ibrav == 13:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
cAB = float(qeConf.namelist('system').param('celldm(4)'))
return a, b_a*a, c_a*a, cBC, cAC, cAB, None
if ibrav == 14:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
cBC = float(qeConf.namelist('system').param('celldm(4)'))
cAC = float(qeConf.namelist('system').param('celldm(5)'))
cAB = float(qeConf.namelist('system').param('celldm(6)'))
return a, b_a*a, c_a*a, cBC, cAC, cAB, None
else:
if ibrav == 0:
print "Should specify celldm(1) if use 'generic' lattice"
raise NotImplementedError
a = float(qeConf.namelist('system').param('A'))
self._type = 'traditional' # A, B, C, cosAB, cosAC, cosBC
if ibrav > 0 and ibrav < 4:
return a, a, a, cBC, cAC, cAB, None
if ibrav == 4:
cAB = cosd(120.0)
if ibrav == 4 or ibrav == 6 or ibrav == 7:
c = float(qeConf.namelist('system').param('C'))
return a, a, c, cBC, cAC, cAB, None
if ibrav == 5:
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, a, a, cAB, cAB, cAB, None
if ibrav > 7 and ibrav < 12:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
return a, b, c, cBC, cAC, cAB, None
if ibrav == 12 or ibrav == 13:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, b, c, cBC, cAC, cAB, None
if ibrav == 14:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
cBC = float(qeConf.namelist('system').param('cosBC'))
cAC = float(qeConf.namelist('system').param('cosAC'))
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, b, c, cBC, cAC, cAB, None
def setLattice(self, ibrav, a = None, b = None, c = None,
cBC = None, cAC = None, cAB = None, base = None):
""" 'base', numpy array of lattice vectors, and 'a' will only be used
if ibrav == 0. Otherwise, ibrav + lattice parameters will be used"""
from math import acos
# if [ibrav, a,b,c,cBC,cAC,cAB, base] == 8*[None]:
# return None
if ibrav == None:
raise NonImplementedError('ibrav should be specified')
self._ibrav = ibrav
self._a0 = a
if self._ibrav == 0:
# print 'Found "generic" cell:'
if base == None:
raise NonImplementedError('base must be specified')
if a == None: a = 1.0
qeBase = numpy.array(base, dtype = float)*a
# print qeBase
self._a = 1.0
self._primitiveLattice.setLatBase(qeBase)
self._standardLattice.setLatBase(qeBase)
else:
# Make sure all lattice parameters are mutually consistent
# according to ibrav. base array is not used:
if ibrav < 4 or ibrav == 5:
if a is not None:
self._a = self._b = self._c = a
else:
if b is not None:
self._a = self._b = self._c = b
else:
if c is not None:
self._a = self._b = self._c = c
else:
self._b = self._c = self._a
if ibrav < 4:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav == 4 or ibrav == 6 or ibrav == 7:
if a is not None:
self._a = self._b = a
else:
if b is not None:
self._a = self._b = b
else:
self._b = self._a
if c is not None:
self._c = c
if ibrav == 4:
self._cAB = cosd(120.0)
self._cBC = self._cAC = 0.0
if ibrav == 5:
if cBC is not None:
self._cBC = self._cAC = self._cAB = cBC
else:
if cAC is not None:
self._cBC = self._cAC = self._cAB = cAC
else:
if cAB is not None:
self._cBC = self._cAC = self._cAB = cAB
else:
self._cAC = self._cAB = self._cBC
if ibrav == 6 or ibrav == 7:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav > 7 and ibrav <= 14:
if a is not None:
self._a = a
if b is not None:
self._b = b
if c is not None:
self._c = c
if ibrav > 7 and ibrav < 12:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav == 12 or ibrav == 13:
if cAB is not None:
self._cAB = cAB
else:
if cBC is not None or cAC is not None:
raise Exception("Should specify cos(AB) only for" + \
" ibrav = 12 or ibrav = 13" )
self._cBC = self._cAC = 0.0
if ibrav == 14:
if cBC is not None:
self._cBC = cBC
if cAC is not None:
self._cAC = cAC
if cAB is not None:
self._cAB = cAB
# if a is not None: self._a = a
# if b is not None: self._b = b
# if c is not None: self._c = c
# if cBC is not None: self._cBC = cBC
# if cAC is not None: self._cAC = cAC
# if cAB is not None: self._cAB = cAB
qeBaseTuple = self._getQEBaseFromParCos(self._ibrav, self._a, self._b,
self._c, self._cBC, self._cAC, self._cAB)
qeBase = numpy.array(qeBaseTuple[1], dtype = float)*qeBaseTuple[0]
# print 'Found "' + qeBaseTuple[2] + '" cell'
# print 'Setting the base vectors according to QE conventions:'
# print qeBase
self._primitiveLattice.setLatBase(qeBase)
alpha = degrees(acos(self._cBC))
beta = degrees(acos(self._cAC))
gamma = degrees(acos(self._cAB))
self._standardLattice.setLatPar(self._a,self._b,self._c,alpha,beta,gamma)
# print "Standard Lattice:"
# print self._standardLattice.base
self._base = qeBase
def setLattice(self, ibrav, a = None, b = None, c = None,
cBC = None, cAC = None, cAB = None, base = None, updateInput = True):
""" 'base', numpy array of lattice vectors, and 'a' will only be used
if ibrav == 0. Otherwise, ibrav + lattice parameters will be used"""
from math import acos
# if [ibrav, a,b,c,cBC,cAC,cAB, base] == 8*[None]:
# return None
if ibrav == None:
raise NonImplementedError('ibrav should be specified')
self._ibrav = ibrav
if self._ibrav == 0:
# print 'Found "generic" cell:'
if base == None:
raise NonImplementedError('base must be specified')
if a == None:
raise # a and the base must be provided for ibrav = 0
qeBase = numpy.array(base, dtype = float)#*self._a/a
self._a = a
# print qeBase
#self._a = 1.0
if 'generic' not in self._type:
self._type = 'generic cubic'
self.__primitiveLattice.setLatBase(qeBase)
#self._standardLattice.setLatBase(qeBase)
else:
# Make sure all lattice parameters are mutually consistent
# according to ibrav. base array is not used:
if ibrav < 4 or ibrav == 5:
if a is not None:
self._a = self._b = self._c = a
else:
if b is not None:
self._a = self._b = self._c = b
else:
if c is not None:
self._a = self._b = self._c = c
else:
self._b = self._c = self._a
if ibrav < 4:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav == 4 or ibrav == 6 or ibrav == 7:
if a is not None:
self._a = self._b = a
else:
if b is not None:
self._a = self._b = b
else:
self._b = self._a
if c is not None:
self._c = c
if ibrav == 4:
self._cAB = cosd(120.0)
self._cBC = self._cAC = 0.0
if ibrav == 5:
if cBC is not None:
self._cBC = self._cAC = self._cAB = cBC
else:
if cAC is not None:
self._cBC = self._cAC = self._cAB = cAC
else:
if cAB is not None:
self._cBC = self._cAC = self._cAB = cAB
else:
self._cAC = self._cAB = self._cBC
if ibrav == 6 or ibrav == 7:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav > 7 and ibrav <= 14:
if a is not None:
self._a = a
if b is not None:
self._b = b
if c is not None:
self._c = c
if ibrav > 7 and ibrav < 12:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav == 12 or ibrav == 13:
if cAB is not None:
self._cAB = cAB
else:
if cBC is not None or cAC is not None:
raise Exception("Should specify cos(AB) only for" + \
" ibrav = 12 or ibrav = 13" )
self._cBC = self._cAC = 0.0
if ibrav == 14:
if cBC is not None:
self._cBC = cBC
if cAC is not None:
self._cAC = cAC
if cAB is not None:
self._cAB = cAB
qeBaseTuple = self._getQEBaseFromParCos(self._ibrav, self._a, self._b,
self._c, self._cBC, self._cAC, self._cAB)
qeBase = numpy.array(qeBaseTuple[1], dtype = float)*qeBaseTuple[0]
self.__primitiveLattice.setLatBase(qeBase)
alpha = degrees(acos(self._cBC))
beta = degrees(acos(self._cAC))
gamma = degrees(acos(self._cAB))
#self._standardLattice.setLatPar(self._a,self._b,self._c,alpha,beta,gamma)
#self._a0 = a
self._base = qeBase
if self._qeInput != None and updateInput == True:
#self.updatePWInput()
self._qeInput.update( forceUpdate = True )
def setReducedStructureFromDiffpyStructure(self, structure, ibrav, massList = [], psList = []):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with pseudopotential names
diffpyStructure object will be modified with reduced atomic positions
"""
#self.atomicSpecies = OrderedDict()
#self.optConstraints = []
#self.atomicPositionsType = 'crystal'
diffpyLattice = structure.lattice
a = diffpyLattice.a
b = diffpyLattice.b
c = diffpyLattice.c
cAB = cosd(diffpyLattice.gamma)
cBC = cosd(diffpyLattice.alpha)
cAC = cosd(diffpyLattice.beta)
qeLattice = QELattice(ibrav = ibrav, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
self.lattice = qeLattice
# make a deep copy (does not wok now)
#reducedStructure = Structure(diffpyStructure)
reducedStructure = structure
reducedStructure.placeInLattice(Lattice(base=qeLattice.diffpy().base))
# collect atoms that are at equivalent position to some previous atom
duplicates = set([a1
for i0, a0 in enumerate(reducedStructure) for a1 in reducedStructure[i0+1:]
if self._element(a0) == self._element(a1) and equalPositions(a0.xyz, a1.xyz, eps=1e-4)])
# Filter out duplicate atoms. Use slice assignment so that
# reducedStructure is not replaced with a list.
reducedStructure[:] = [a for a in reducedStructure if not a in duplicates]
self.structure = reducedStructure
atomNames = []
for a in reducedStructure:
if self._element(a) not in atomNames:
atomNames.append(self._element(a))
#print atomNames
#print len(massList)
for i, elem in enumerate(atomNames):
if len(massList) - 1 < i:
mass = 0
else:
mass = massList[i]
if len(psList) - 1 < i:
ps = ''
else:
ps = psList[i]
#print mass, ps
# atomDict[a] =
# for i, atom in enumerate(reducedStructure):
# elem = self._element(atom)
# if len(massList) - 1 < i:
# mass = 0
# else:
# mass = massList[i]
# if len(psList) - 1 < i:
# ps = ''
# else:
# ps = psList[i]
self.atomicSpecies[elem] = AtomicSpecies(elem, mass, ps)
for atom in reducedStructure:
self.optConstraints.append([])
# convert to bohr units
self.lattice.setLattice(ibrav, self.lattice.a*1.889725989, \
self.lattice.b*1.889725989,
self.lattice.c*1.889725989)
self.nat = len(reducedStructure)
self.ntyp = len(self.atomicSpecies)
def parsePWInput(self, ibrav, qeConf=None):
if qeConf == None:
qeConf = self.qeConf
if qeConf == None:
raise NotImplementedError(
"writeLatticeToPWSCF: qeConf was not properly initialized")
cBC = 0.0
cAC = 0.0
cAB = 0.0
# reset Lattice:
#self.setLattice(1. ,1 , 1, cBC ,cAC ,cAB)
if 'celldm(1)' in qeConf.namelists['system'].params:
self._type = 'celldm' # celldm(i), i=1,6
a = float(qeConf.namelist('system').param('celldm(1)'))
if ibrav == 0:
# lattice is set in the units of celldm(1)
# need to parse CELL_PARAMETERS
#if 'cell_parameters' not in qeConf.cards:
# return #qeConf.createCard('cell_parameters')
cellParLines = qeConf.card('cell_parameters').lines()
#print cellParLines
cellParType = qeConf.card('cell_parameters').arg()
if cellParType == 'cubic' or cellParType == None:
self._type = 'generic cubic'
else:
if cellParType == 'hexagonal':
self._type = 'generic hexagonal'
# convert card into list
base = []
for line in cellParLines:
if '!' not in line:
words = line.split()
base.append([float(w) for w in words])
return a, None, None, None, None, None, numpy.array(base)
if ibrav > 0 and ibrav < 4:
return a, a, a, cBC, cAC, cAB, None
if ibrav == 4:
cAB = cosd(120.0)
if ibrav == 4 or ibrav == 6 or ibrav == 7:
c_a = float(qeConf.namelist('system').param('celldm(3)'))
return a, a, c_a * a, cBC, cAC, cAB, None
if ibrav == 5:
cAB = float(qeConf.namelist('system').param('celldm(4)'))
return a, a, a, cAB, cAB, cAB, None
if ibrav > 7 and ibrav < 12:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
return a, b_a * a, c_a * a, cBC, cAC, cAB, None
if ibrav == 12 or ibrav == 13:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
cAB = float(qeConf.namelist('system').param('celldm(4)'))
return a, b_a * a, c_a * a, cBC, cAC, cAB, None
if ibrav == 14:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
cBC = float(qeConf.namelist('system').param('celldm(4)'))
cAC = float(qeConf.namelist('system').param('celldm(5)'))
cAB = float(qeConf.namelist('system').param('celldm(6)'))
return a, b_a * a, c_a * a, cBC, cAC, cAB, None
else:
if ibrav == 0:
print "Should specify celldm(1) if use 'generic' lattice"
raise NotImplementedError
a = float(qeConf.namelist('system').param('A'))
self._type = 'traditional' # A, B, C, cosAB, cosAC, cosBC
if ibrav > 0 and ibrav < 4:
return a, a, a, cBC, cAC, cAB, None
if ibrav == 4:
cAB = cosd(120.0)
if ibrav == 4 or ibrav == 6 or ibrav == 7:
c = float(qeConf.namelist('system').param('C'))
return a, a, c, cBC, cAC, cAB, None
if ibrav == 5:
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, a, a, cAB, cAB, cAB, None
if ibrav > 7 and ibrav < 12:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
return a, b, c, cBC, cAC, cAB, None
if ibrav == 12 or ibrav == 13:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, b, c, cBC, cAC, cAB, None
if ibrav == 14:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
cBC = float(qeConf.namelist('system').param('cosBC'))
cAC = float(qeConf.namelist('system').param('cosAC'))
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, b, c, cBC, cAC, cAB, None
def parsePWInput(self, ibrav, qeConf = None):
if qeConf == None:
qeConf = self.qeConf
if qeConf == None:
raise NotImplementedError("writeLatticeToPWSCF: qeConf was not properly initialized")
cBC = 0.0
cAC = 0.0
cAB = 0.0
# reset Lattice:
#self.setLattice(1. ,1 , 1, cBC ,cAC ,cAB)
if 'celldm(1)' in qeConf.namelists['system'].params:
self._type = 'celldm' # celldm(i), i=1,6
a = float(qeConf.namelist('system').param('celldm(1)'))
if ibrav == 0:
# lattice is set in the units of celldm(1)
# need to parse CELL_PARAMETERS
#if 'cell_parameters' not in qeConf.cards:
# return #qeConf.createCard('cell_parameters')
cellParLines = qeConf.card('cell_parameters').lines()
#print cellParLines
cellParType = qeConf.card('cell_parameters').arg()
if cellParType == 'cubic' or cellParType == None:
self._type = 'generic cubic'
else:
if cellParType == 'hexagonal':
self._type = 'generic hexagonal'
# convert card into list
base = []
for line in cellParLines:
if '!' not in line:
words = line.split()
base.append([float(w) for w in words])
return a, None, None, None, None, None, numpy.array(base)
if ibrav > 0 and ibrav < 4:
return a, a, a, cBC, cAC, cAB, None
if ibrav == 4:
cAB = cosd(120.0)
if ibrav == 4 or ibrav == 6 or ibrav == 7:
c_a = float(qeConf.namelist('system').param('celldm(3)'))
return a, a, c_a*a, cBC, cAC, cAB, None
if ibrav == 5:
cAB = float(qeConf.namelist('system').param('celldm(4)'))
return a, a, a, cAB, cAB, cAB, None
if ibrav > 7 and ibrav < 12:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
return a, b_a*a, c_a*a, cBC, cAC, cAB, None
if ibrav == 12 or ibrav == 13:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
cAB = float(qeConf.namelist('system').param('celldm(4)'))
return a, b_a*a, c_a*a, cBC, cAC, cAB, None
if ibrav == 14:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
cBC = float(qeConf.namelist('system').param('celldm(4)'))
cAC = float(qeConf.namelist('system').param('celldm(5)'))
cAB = float(qeConf.namelist('system').param('celldm(6)'))
return a, b_a*a, c_a*a, cBC, cAC, cAB, None
else:
if ibrav == 0:
print "Should specify celldm(1) if use 'generic' lattice"
raise NotImplementedError
a = float(qeConf.namelist('system').param('A'))
self._type = 'traditional' # A, B, C, cosAB, cosAC, cosBC
if ibrav > 0 and ibrav < 4:
return a, a, a, cBC, cAC, cAB, None
if ibrav == 4:
cAB = cosd(120.0)
if ibrav == 4 or ibrav == 6 or ibrav == 7:
c = float(qeConf.namelist('system').param('C'))
return a, a, c, cBC, cAC, cAB, None
if ibrav == 5:
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, a, a, cAB, cAB, cAB, None
if ibrav > 7 and ibrav < 12:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
return a, b, c, cBC, cAC, cAB, None
if ibrav == 12 or ibrav == 13:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, b, c, cBC, cAC, cAB, None
if ibrav == 14:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
cBC = float(qeConf.namelist('system').param('cosBC'))
cAC = float(qeConf.namelist('system').param('cosAC'))
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, b, c, cBC, cAC, cAB, None
