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