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[lammps-users] Identifying molecules and changing atom types
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[lammps-users] Identifying molecules and changing atom types

From: Tim Lodewyckx <timlodewyckx@...8...>
Date: Wed, 18 Apr 2018 16:37:53 +0000

Dear LAMMPS users,

I am running a script where I have one molecule type that can react with all other molecule types in the same way. The configuration of the first molecule type looks like:

X-X (two particles of type X)

The configuration of all other molecules looks like:

A1-B1-A1 (particles of type A1 and B1)




The X-particles can only react with A-particles and not with B-particles. I would like to implement this by using the fix bond/create command, but it appears that this will not work properly since I would have to use this command multiple times on the same atom type (type X). Since I've read that subsequent fix bond/create commands don't communicate within the same time step, this will probably not give the result that I'm looking for. Therefore I'm thinking about doing it differently. At the start of the simulation I would assign all particles with atom types A1, A2, A3, etc to the same atom type, that is atom type A. This would allow me to use a single fix bond/create command to form all bonds between A and X. After all bonds are formed I would then change the atom types back to their original atom type. This should still be possible, since I didn't change the atom type of the B-particles, so in principle I should be able to identify each A-particle. The only question now is how to do this last step of identifying the B-particles and then assigning the respective A-particles to their original atom type?

Kind regards,