def _setStructureFromMatterStructure(self, structure, massList = [], psList = [], ibrav = 0):
"""
structure - matter.Structure object
ibrav - Lattice index
psList - list of strings with potential names
matterStructure object will be modified with reduced atomic positions
"""
matterLattice = structure.lattice
qeLattice = QELattice(ibrav = 0, base = matterLattice.base)
qeLattice.a = 1.889725989*qeLattice.a
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
self.lattice.type = 'generic cubic'
atomNames = []
for a in structure:
if a.symbol not in atomNames:
atomNames.append(a.symbol)
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[:] = []
for atom in structure:
self.addNewAtom(atype = atom.symbol, xyz = atom.xyz, \
mass = atomicSpecies[atom.symbol][0], \
potential = atomicSpecies[atom.symbol][1],\
lattice = self.lattice, optConstraint = [])
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.matter().a
b = self.lattice.matter().b
c = self.lattice.matter().c
cAB = cosd(self.lattice.matter().gamma)
cBC = cosd(self.lattice.matter().alpha)
cAC = cosd(self.lattice.matter().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.symbol == a1.symbol 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 _setReducedStructureFromMatterStructure(self, structure, ibrav, massList = [], psList = []):
"""
structure - matter.Structure object
ibrav - Lattice index
psList - list of strings with potential names
matterStructure object will be modified with reduced atomic positions
"""
import copy
matterLattice = copy.deepcopy(structure.lattice)
# there is a big problem with what Nikolay is doing because he is initializing QELattice with abcalbega which
# leaves room for errors in how the basis vectors are chosen compared to the old lattice
a = matterLattice.a
b = matterLattice.b
c = matterLattice.c
cAB = cosd(matterLattice.gamma)
cBC = cosd(matterLattice.alpha)
cAC = cosd(matterLattice.beta)
qeLattice = QELattice(ibrav = ibrav, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
#what he should do is initialize the vectors of QELattice with the vectors of matterLattice
#
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
# make a deep copy:
reducedStructure = Structure(atoms = structure)
reducedStructure.placeInLattice(Lattice(base=qeLattice.matter().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 a0.symbol==a1.symbol 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 a.symbol not in atomNames:
atomNames.append(a.symbol)
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:
self.addNewAtom(atype = atom.symbol, xyz = atom.xyz, \
mass = atomicSpecies[atom.symbol][0], \
potential = atomicSpecies[atom.symbol][1],\
lattice = self.lattice, optConstraint = [])
def _setStructureFromDiffpyStructure(self,
structure,
massList=[],
psList=[],
ibrav=0):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with potential names
diffpyStructure object will be modified with reduced atomic positions
"""
diffpyLattice = structure.lattice
qeLattice = QELattice(ibrav=0, base=diffpyLattice.base)
qeLattice.a = 1.889725989 * qeLattice.a
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
self.lattice.type = 'generic cubic'
atomNames = []
for a in structure:
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[:] = []
for atom in structure:
elem = self._element(atom)
self.addNewAtom(atype = elem, xyz = atom.xyz, \
mass = atomicSpecies[elem][0], \
potential = atomicSpecies[elem][1],\
lattice = self.lattice, optConstraint = [])
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 _setReducedStructureFromMatterStructure(self,
structure,
ibrav,
massList=[],
psList=[]):
"""
structure - matter.Structure object
ibrav - Lattice index
psList - list of strings with potential names
matterStructure object will be modified with reduced atomic positions
"""
import copy
matterLattice = copy.deepcopy(structure.lattice)
# there is a big problem with what Nikolay is doing because he is initializing QELattice with abcalbega which
# leaves room for errors in how the basis vectors are chosen compared to the old lattice
a = matterLattice.a
b = matterLattice.b
c = matterLattice.c
cAB = cosd(matterLattice.gamma)
cBC = cosd(matterLattice.alpha)
cAC = cosd(matterLattice.beta)
qeLattice = QELattice(ibrav = ibrav, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
#what he should do is initialize the vectors of QELattice with the vectors of matterLattice
#
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
# make a deep copy:
reducedStructure = Structure(atoms=structure)
reducedStructure.placeInLattice(Lattice(base=qeLattice.matter().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 a0.symbol == a1.symbol
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 a.symbol not in atomNames:
atomNames.append(a.symbol)
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:
self.addNewAtom(atype = atom.symbol, xyz = atom.xyz, \
mass = atomicSpecies[atom.symbol][0], \
potential = atomicSpecies[atom.symbol][1],\
lattice = self.lattice, optConstraint = [])
