Greetings,
My simulation was first interrupted by "Bond atoms %d %d missing on proc %d at step %ld", so I applied "communicate cutoff" command to solve the problem. Now another error is "Domain too large for neighbor bins" which couldn't be fixed by trying different values of cutoff and it seems the source of problem may be some where else. Any guidance is highly appreciate since I couldn't find any solution by searching the archive.
Here is parts of my input file:
boundary p p p
pair_style lj/cut/coul/long 12.5
pair_modify tail yes
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
Thank you in advance,
Negin
Greetings,
My simulation was first interrupted by "Bond atoms %d %d missing on proc %d at step %ld", so I applied "communicate cutoff" command to solve the problem. Now another error is "Domain too large for neighbor bins" which couldn't be fixed by trying different values of cutoff and it seems the source of problem may be some where else. Any guidance is highly appreciate since I couldn't find any solution by searching the archive.
impossible to say much with so little information. but most likely
your initial geometry and/or force field parameters are bad and thus
you are trying to cure the symptoms and not the cause.
regardless, the answer to your question is that you can manually set
the domain size. but as noted above, this is likely the wrong
approach.
axel.
This is almost certainly caused by a bond that is much longer than the
normal 1-3 angstroms, which is almost certainly an error in your data
file.
The “domain too large for neighbor bins” error is
caused by a very huge simulation box, which typically
occurs when using shrink-wrap boundaries and exploding
an atom(s) out of the box. I.e. bad dynamics.
Steve
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