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 wrap_atom(self, coord_alat, atom, nwrap):
# calculate shift to box
shift = [0.0, 0.0, 0.0]
outofbox = True
while outofbox == True:
for i in range(ndim):
if coord_alat[i] > 1.0:
for idim in range(ndim):
shift[idim] -= self.vec()[i][idim]
coord_alat[i] -= 1
elif coord_alat[i] < 0.0:
for idim in range(ndim):
shift[idim] += self.vec()[i][idim]
coord_alat[i] += 1
outofbox = False
for i in range(ndim):
if coord_alat[i] > 1.0 or coord_alat[i] < 0.0:
outofbox = True
# reset coordinates
if shift != [0.0, 0.0, 0.0]:
nwrap += 1
atom.set_pos(calc.vecadd(atom.coord(), shift))
return nwrap
