Using "fix bond/break" with "run 0"

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1

Dear LAMMPS users,

I am trying to update the topology of my system using fix bond/break without evolving the system in time. Initially I have tried using the

fix bond/break
run 0

commands, however, I have found that the fix only works if the simulation is run for 1 or more timesteps. Currently I am using the

fix move linear 0 0 0
fix bond/break
run 1

combination, but it does not seem optimal as it requires twice as much time (two timesteps instead of one). Do you know if there is a way to apply the “fix bond/break” command while only simulating the initial step i.e. run 0? I am updating the topology statically quite a lot so the decrease in simulation time would be very helpful.

Best regards
Jacek Golebiowski

2

Dear LAMMPS users,

I am trying to update the topology of my system using fix bond/break without evolving the system in time. Initially I have tried using the

fix bond/break
run 0

commands, however, I have found that the fix only works if the simulation is run for 1 or more timesteps. Currently I am using the

fix move linear 0 0 0
fix bond/break
run 1

combination, but it does not seem optimal as it requires twice as much time (two timesteps instead of one). Do you know if there is a way to apply the “fix bond/break” command while only simulating the initial step i.e. run 0? I am updating the topology statically quite a lot so the decrease in simulation time would be very helpful.

why use fix bond/break and not delete_bonds?

axel.

3

I want to delete the bond between two atoms as well as all the angles and dihedrals that this bond is a part of. This is done by the bond/break fix, however, the delete_bond command only turns off the interactions if all atoms in the angle or dihedral are in the specified group. Since I only have two atoms that I wish to de-bond, I would have to iterate over all of the interactions they are a part of and switch them off individually by updating the group. The alternative is using the any keyword, however, then all of the interactions those two atoms are a part off are switched off which I don’t want, the goal is just to delete the interactions between two specified atoms.

Jacek

4

fix bond/break is run during the post integrate hook, so you need to
run at least one MD step for this to work.

the only way i can see to reduce computational cost would be to
temporarily switch the pair style to zero, which skips the most time
consuming step (but defines the cutoff needed for fix bond/break to
work properly) and disable any time integration fix(es). (you can do
the same for bonds and beyond, but that is probably not going to save
you much).

axel.

5

Thank you, I will try to apply it.

Best
Jacek