Image flags in datafile generated by "wirte_data" when having rigid bodies

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1

Dear LAMMPS developers,

I have a question about the image flags of LAMMPS, and could not find the answer in the previously posted lists in the LAMMPS mailing lists.

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 the image 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.”

The following is a description of my question:

I have rigid bodies in my simulation. At the end of the simulation, I generated a datafile using the “write_data” command, and a restart-file using the “write_restart” command. My Questions:
(1) Are the image flags of atoms in rigid bodies in the generated datafile different than they would be if the atoms were not in a rigid body?
(2) Can I use the generated datafile with the image flags for a next simulation with the same rigid bodies?
(3) Can I use the generated restart-file (with the “remap” flag) to continue my simulation with the same rigid bodies?

(4) If I use the generated datafile to run a simulation without rigid bodies, and generate another datafile2 at the end of the simulation, will the image flags in datafile2 be correct? Can I use datafile2 in a simulation with replicate command without worrying about the image flags?

Thank you so much!

Best regards,
Jibao

2

Dear LAMMPS developers,

​please note, that there is no benefit in copying me or steve when posting
to the LAMMPS users mailing list. ​we are both subscribed and gmail will
recognize this and only store one copy. unfortunately, this one copy will
not match the filters for mailing list mail and - for example - clog up my
inbox and requires me to manually sort it into the folder where it belongs.
this is quite annoying.

I have a question about the image flags of LAMMPS, and could not find the
answer in the previously posted lists in the LAMMPS mailing lists.

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 the image 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.