Incomplete and/or empty dump custom files

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1

Dear all,

I am running a simulation with LAMMPS (version 5 June 2019)
involving a cubic box of 1000 particles (all of the same type)
interacting according to a hybrid/overlay pair_style. The latter
comprises a DLVO type force, Fast Lubrication Dynamics (for long range hydrodynamic forces),
lubrication and brownian forces in the overdamped limit (lubricateU pair style) and granular forces.

For this case study, I wrote by myself a DLVO pair_style potential
and also a fix regarding a dynamic update of the simulation timestep.

The run is thermodynamically stable but post-processing the dump

files with OVITO I realized that there are some dump files empty and some others
with some information (on particle position or velocity or whatever…) missing.

This, obviously, causes OVITO to crash.

This is how I print out the dump custom files in my script:

“dump dmp_atom all custom 100000 data_dump/atom*.dat id c_chcl c_clust fx fy fz x y z vx vy vz”

with “chcl” and “clust” referring to a cluster/atom and a chunk/atom compute, respectively.
Do you have any idea what might be the cause for this error in printing out the dump custom files?

Thank you all in advance,
all the best

Gianluca

2

There is no reason from inside of LAMMPS why there should be incomplete files.
however, this can happen if - for example - you are running on cluster and your calculation gets terminated due to wall time limits, or you accidentally run two simulations in the same folder that would concurrently overwrite each other’s files, or there is some file system issue (this can happen more often on networked file systems like NFS).

axel.

3

Dear Axel,
Thanks for your reply.
Effectively, this problem arises only when I run the simulations from a cluster.

I’ll see what I can do.
Thanks again,
Gianluca