def Pdefine_bonds(self, cutoff, cutmin=10 ** (-10), atomlist=[], periodicity=False):
bndcnt = 0
for at in self.at():
# print if
if (at.id() % 100) == 0 or at.id() == self.natoms() - 1:
print >>sys.stderr, "...bonding for atom {:d} of {:d} calculated".format(at.id() + 1, self.natoms())
# only check atoms in range
if at.id() in atomlist:
# do bond calculation for periodic structures
if periodicity:
perx = [-1, 0, 1]
pery = [-1, 0, 1]
perz = [-1, 0, 1]
else:
perx = [0]
pery = [0]
perz = [0]
for x in perx:
for y in pery:
for z in perz:
for neigh in self.at():
l = calc.a_dist(at, neigh, per=[x, y, z])
if l > cutmin and l < cutoff:
# print at.id(),neigh.id(),x,y,z,l #infos
at.add_bond(neigh, per=[x, y, z])
bndcnt += 1
return bndcnt
def bondlength(self):
return calc.a_dist(self.atom(), self.neighbor(), self.per())
