compute: bond orientation factor

Thanks for the quick reply. By a full bond list I mean that if I have a
molecule with e.g. 5 C atoms (atom style molecule):

...

Atoms

1 1 1 0.0 0.0 0.0 0.0
2 1 1 0.0 1.5 0.0 0.0
3 1 1 0.0 3.0 0.0 0.0
4 1 1 0.0 4.5 0.0 0.0
5 1 1 0.0 6.0 0.0 0.0

Bonds

1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5

....

I get atom->num_bond[1] is 1 resp. atom->bond_atom[1][0] is atom #3. I would
need something like atom->num_bond[1] as 2 and atoms 1 AND 3 as bonded
atoms. Right now I have loop over nlocal to find all bonded atoms, but I
thought maybe there is a smarter way.

wolfgang

Thanks for the quick reply. By a full bond list I mean that if I have a
molecule with e.g. 5 C atoms (atom style molecule):

...

Atoms

1 1 1 0.0 0.0 0.0 0.0
2 1 1 0.0 1.5 0.0 0.0
3 1 1 0.0 3.0 0.0 0.0
4 1 1 0.0 4.5 0.0 0.0
5 1 1 0.0 6.0 0.0 0.0

Bonds

1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5

....

I get atom->num_bond[1] is 1 resp. atom->bond_atom[1][0] is atom #3. I would
need something like atom->num_bond[1] as 2 and atoms 1 AND 3 as bonded
atoms. Right now I have loop over nlocal to find all bonded atoms, but I
thought maybe there is a smarter way.

you would have to maintain this information by yourself, probably best
as a fix as it has the infrastructure to move this information with
the atoms around as they migrate between (parallel) domains.

have a look at fix property/atom as an example.

axel.

If you set newton bond off, then every atom will
store a list of all its bond partners. Your compute

could check/enforce that that setting was made
in an input script.

Steve