Dear LAMMPS developers,
In the manual of lammps for replicate command, there is a statement:
Replicating a system that has rigid bodies (defined via the fix rigid command), either currently defined or that created the restart file which was read in before replicating, can cause problems if there is a bond between a pair of rigid bodies that straddle a periodic boundary. This is because the periodic image information for particles in the rigid bodies are set differently than for a non-rigid system and can result in a new bond being created that spans the periodic box. Thus you cannot use the replicate command in this scenario.
However, I learned from Axel’s answer to my earlier questions that there is no special treatments of image flags for rigid bodies (see the following for the details of my earlier question and Axel’s answer). So my question is, with the latest version of lammps, can I replicate a system that has rigid bodies (defined via the fix rigid command), either currently defined or that created the restart file which was read in before replicating?
I noticed there is clarification from Axel in the mailing lists: “IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are modified when the center-of-mass of the rigid body moves across a periodic boundary. They are not incremented/decremented as they would be for non-rigid atoms. This change does not affect dynamics, but means that any diagnostic computation based on the atomic image flag values must be adjusted accordingly. For example, the compute msd will not compute the expected mean-squared displacement for such atoms, and theimage flag values written to a dump file will be different than they would be if the atoms were not in a rigid body. It also means that if you have bonds between a pair of rigid bodies and the bond straddles a periodic boundary, you cannot use the replicate command to increase the system size.”
this statement is only true for older versions of LAMMPS. as of version 30 Jan 2015, there is no special treatments of image flags for rigid bodies. the necessary accounting is now done internally in the rigid fixes.
axel.
Thank you so much!
Best,
Jibao