creating bonds that stretch beyond the periodic boundary

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1

Dear Lammps users,

I am trying to simulate perfect diamond lattices of poleelectrolyte gels where chains are cross-linked at the ends and the ends(the nodes) form a perfect diamond lattice.
To stop the gel from contracting and provide physically more accurate results I need to bond the atoms through the periodic boundary.

I searched the tools for that in the mailing list but couldn’t find anything.
Do you know if there are any tools to do that task?

So, to simplify the task: given the xyz of the perfect diamond lattice, determine the nearest neighbours (including the neighbours through the periodic image) and connect them with a bond.

Thank you in advance,
Vasilii.

2

Have you tried fix bond/create ?

Arun

3

I have tried, but it works only for the interior atoms, I need the atoms over the periodic boundary as well, I.e

1 – 2 – 3 –4 – 5

So essentially it creates the bonds displayed by dashes, but fails to create bond 5-1

Vasilii.

4

Hello,

I have tried, but it works only for the interior atoms, I need the
atoms over the periodic boundary as well, I.e
1 – 2 – 3 –4 – 5
So essentially it creates the bonds displayed by dashes, but fails to
create bond 5-1

fix bond/create takes into account periodic boundaries when computing the
distance. Did you notice something that suggests otherwise?

Regards,

PIerre