def alat2angstroem(self):
for atom in self.at():
coo=[float(0.0),float(0.0),float(0.0)]
# calculate coordinates
coo=calc.scal_vecmult(self.celldm_vec()[0],atom.coord())
# set relative and real coordinates
atom.coord_crystal=atom.coord()
atom.set_pos(coo)
def crystal2angstroem(self):
for atom in self.at():
coo=[float(0.0),float(0.0),float(0.0)]
# calculate coordinates
for dim in range(len(atom.coord())):
coo=calc.vecadd(coo,calc.scal_vecmult(
atom.coord()[dim],self.vec()[dim])
)
# set relative and real coordinates
atom.coord_crystal=atom.coord()
atom.set_pos(coo)
def mol_multiply(self,mx,my,mz,offset=[0,0,0]):
if not hasattr(self,"mol"): self.extend()
# copy the molecules
v=self.vec()
for ix in range(offset[0],mx+offset[0]):
for iy in range(offset[1],my+offset[1]):
for iz in range(offset[2],mz+offset[2]):
x=float(ix)
y=float(iy)
z=float(iz)
shift=[x*v[0][0]+y*v[1][0]+z*v[2][0],
x*v[0][1]+y*v[1][1]+z*v[2][1],
x*v[0][2]+y*v[1][2]+z*v[2][2]]
if not(x==0 and y==0 and z==0):
self.append_submol(self.mol[0],shift)
# reset vectors
self.set_vecs(calc.scal_vecmult(mx,self.celldm_vec()[1][0]),
calc.scal_vecmult(my,self.celldm_vec()[1][1]),
calc.scal_vecmult(mz,self.celldm_vec()[1][2]))
self.extend_set()
return