point dipoles connected by bonds

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1

Dear LAMMPS users,

I want to use pair style lj/cut/dipole/cut as shown in the dipole example.
It requires the use of hybrid sphere dipole atom_style,

to integrate by using fix nve/sphere update dipole, which allows for the rotation of dipole moments. However, in this case, if I am not mistaken, it is not possible to assign multiple atoms to one molecule by a standard bond, like a harmonic potential.

Is there any possibility to be able to assign several atoms to one molecule?

Sincerely,
Lukasz Baran

Lukasz Baran
Ph.D. Candidate
Department of Theoretical Chemistry
Institute of Chemical Sciences
Faculty of Chemistry
Maria Curie Skłodowska University in Lublin

2

Why would it not be possible?

3

In the case of atom style hybrid sphere dipole there is no possibility to specify the molecule ID in the read_data command.
Is it possible then to bond by, for instance, bond_style harmonic, atoms that are not assigned to the same molecule?

Sincerely,
Lukasz Baran

Lukasz Baran
Ph.D. Candidate
Department of Theoretical Chemistry
Institute of Chemical Sciences
Faculty of Chemistry
Maria Curie Skłodowska University in Lublin

4

two comments:

  1. molecule IDs are irrelevant for defining molecules, they are just a number assigned to atoms. they have no impact on the physical model.

  2. the real issue at hand is that neither atom style sphere nor atom style dipole allows to store bond information with atoms, so to have the ability to define bonds between atoms you also need to include atom style bond (or angle or molecular or full) in your hybrid style and then you also (automatically) have molecule IDs included.

axel.