def supercell(S, mno):
"""Perform supercell expansion for a structure.
New lattice parameters are multiplied and fractional coordinates
divided by corresponding multiplier. New atoms are grouped with
their source in the original cell.
S -- an instance of Structure from diffpy.Structure.
mno -- sequence of 3 integers for cell multipliers along
the a, b and c axes.
Return a new expanded structure instance.
Raise TypeError when S is not Structure instance.
Raise ValueError for invalid mno argument.
"""
# check arguments
if len(mno) != 3:
emsg = "Argument mno must contain 3 numbers."
raise ValueError, emsg
elif min(mno) < 1:
emsg = "Multipliers must be greater or equal 1"
raise ValueError, emsg
if not isinstance(S, Structure):
emsg = "The first argument must be a Structure instance."
raise TypeError, emsg
# convert mno to a tuple of integers so it can be used as range limit.
mno = (int(mno[0]), int(mno[1]), int(mno[2]))
# create return instance
newS = Structure(S)
if mno == (1, 1, 1):
return newS
# back to business
ijklist = [(i,j,k)
for i in range(mno[0])
for j in range(mno[1])
for k in range(mno[2])]
# numpy.floor returns float array
mnofloats = numpy.array(mno, dtype=float)
# build a list of new atoms
newAtoms = []
for a in S:
for ijk in ijklist:
adup = Atom(a)
adup.xyz = (a.xyz + ijk)/mnofloats
newAtoms.append(adup)
# newS can own references in newAtoms, no need to make copies
newS.__setslice__(0, len(newS), newAtoms, copy=False)
# take care of lattice parameters
newS.lattice.setLatPar(
a=mno[0]*S.lattice.a,
b=mno[1]*S.lattice.b,
c=mno[2]*S.lattice.c )
return newS
def supercell(S, mno):
"""Perform supercell expansion for a structure.
New lattice parameters are multiplied and fractional coordinates
divided by corresponding multiplier. New atoms are grouped with
their source in the original cell.
S -- an instance of Structure from diffpy.Structure.
mno -- sequence of 3 integers for cell multipliers along
the a, b and c axes.
Return a new expanded structure instance.
Raise TypeError when S is not Structure instance.
Raise ValueError for invalid mno argument.
"""
# check arguments
if len(mno) != 3:
emsg = "Argument mno must contain 3 numbers."
raise ValueError, emsg
elif min(mno) < 1:
emsg = "Multipliers must be greater or equal 1"
raise ValueError, emsg
if not isinstance(S, Structure):
emsg = "The first argument must be a Structure instance."
raise TypeError, emsg
# convert mno to a tuple of integers so it can be used as range limit.
mno = (int(mno[0]), int(mno[1]), int(mno[2]))
# create return instance
newS = Structure(S)
if mno == (1, 1, 1):
return newS
# back to business
ijklist = [(i, j, k) for i in range(mno[0]) for j in range(mno[1])
for k in range(mno[2])]
# numpy.floor returns float array
mnofloats = numpy.array(mno, dtype=float)
# build a list of new atoms
newAtoms = []
for a in S:
for ijk in ijklist:
adup = Atom(a)
adup.xyz = (a.xyz + ijk) / mnofloats
newAtoms.append(adup)
# newS can own references in newAtoms, no need to make copies
newS.__setslice__(0, len(newS), newAtoms, copy=False)
# take care of lattice parameters
newS.lattice.setLatPar(a=mno[0] * S.lattice.a,
b=mno[1] * S.lattice.b,
c=mno[2] * S.lattice.c)
return newS
