def _expandAsymmetricUnit(self):
"""Perform symmetry expansion of self.stru using self.spacegroup.
This method updates data in stru and eau.
No return value.
"""
from diffpy.structure.symmetryutilities import ExpandAsymmetricUnit
# get reverse-ordered unique indices
corepos = [a.xyz for a in self.stru]
coreUijs = [a.U for a in self.stru]
self.eau = ExpandAsymmetricUnit(self.spacegroup, corepos, coreUijs,
eps=self.eps)
# build a nested list of new atoms:
newatoms = []
for i, ca in enumerate(self.stru):
eca = [] # expanded core atom
for j in range(self.eau.multiplicity[i]):
a = Atom(ca)
a.xyz = self.eau.expandedpos[i][j]
if j > 0:
a.label += '_' + str(j + 1)
if a.anisotropy:
a.U = self.eau.expandedUijs[i][j]
eca.append(a)
newatoms.append(eca)
# insert new atoms where they belong
self.stru[:] = sum(newatoms, [])
return
def expandAsymmetricUnit(self, spacegroup, indices, sgoffset=[0,0,0]):
"""Perform symmetry expansion for atoms at given indices.
Temperature factors may be corrected to reflect the symmetry.
All constraints for expanded atoms are erased with the exception
of the occupancy("occ". Constraints of unaffected atoms are adjusted
for new positions self.initial.
spacegroup -- instance of SpaceGroup from diffpy.structure
indices -- list of integer indices of atoms to be expanded
sgoffset -- optional offset of space group origin [0,0,0]
"""
from diffpy.structure.symmetryutilities import ExpandAsymmetricUnit
acd = self._popAtomConstraints()
# get unique, reverse sorted indices
ruindices = dict.fromkeys(indices).keys()
ruindices.sort()
ruindices.reverse()
coreatoms = [self.initial[i] for i in ruindices]
corepos = [a.xyz for a in coreatoms]
coreUijs = [a.U for a in coreatoms]
eau = ExpandAsymmetricUnit(spacegroup, corepos, coreUijs,
sgoffset=sgoffset, eps=self.symposeps)
# build a nested list of new atoms:
newatoms = []
for i in range(len(coreatoms)):
ca = coreatoms[i]
caocc_con = None
if ca in acd and "occ" in acd[ca]:
caocc_con = acd[ca]["occ"]
eca = [] # expanded core atom
for j in range(eau.multiplicity[i]):
a = Atom(ca)
a.xyz = eau.expandedpos[i][j]
a.U = eau.expandedUijs[i][j]
eca.append(a)
if caocc_con is None: continue
# make a copy of occupancy constraint
acd[a] = {"occ" : copy.copy(caocc_con)}
newatoms.append(eca)
# insert new atoms where they belong
for i, atomlist in zip(ruindices, newatoms):
self.initial[i:i+1] = atomlist
# remember this spacegroup as the last one used
self.initial.pdffit["spcgr"] = spacegroup.short_name
self.initial.pdffit["sgoffset"] = list(sgoffset)
# tidy constraints
self._restoreAtomConstraints(acd)
return
def _expandAsymmetricUnit(self, block):
"""Perform symmetry expansion of self.stru using self.spacegroup.
This method updates data in stru and eau.
Parameters
----------
block : CifBlock
The top-level block containing crystal structure data.
"""
from diffpy.structure.symmetryutilities import ExpandAsymmetricUnit
corepos = [a.xyz for a in self.stru]
coreUijs = [a.U for a in self.stru]
self.eau = ExpandAsymmetricUnit(self.spacegroup,
corepos,
coreUijs,
eps=self.eps)
# setup anisotropy according to symmetry requirements
# unless it was already explicitly set
for ca, uisotropy in zip(self.stru, self.eau.Uisotropy):
if not ca.label in self.anisotropy:
ca.anisotropy = not uisotropy
self.anisotropy[ca.label] = ca.anisotropy
# build a nested list of new atoms:
newatoms = []
for i, ca in enumerate(self.stru):
eca = [] # expanded core atom
for j in range(self.eau.multiplicity[i]):
a = Atom(ca)
a.xyz = self.eau.expandedpos[i][j]
if j > 0:
a.label += '_' + str(j + 1)
if a.anisotropy:
a.U = self.eau.expandedUijs[i][j]
eca.append(a)
newatoms.append(eca)
# insert new atoms where they belong
self.stru[:] = sum(newatoms, [])
return