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Document warning about short communication cutoff vs. bond length based estimate

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Axel Kohlmeyer
2020-07-31 11:03:26 -04:00
parent 8cb63194aa
commit 1f1263645e
2 changed files with 34 additions and 0 deletions
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18
doc/src/Errors_warnings.rst
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@ -118,6 +118,24 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
incorrect periodic images of atoms in interaction lists. To avoid, either use
:doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.
*Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*
Since LAMMPS stores topology data with individual atoms, all atoms
comprising a bond, angle, dihedral or improper must be present on any
sub-domain that "owns" the atom with the information, either as a
local or a ghost atom. The communication cutoff is what determines up
to what distance from a sub-domain boundary ghost atoms are created.
The communication cutoff is by default the largest non-bonded cutoff
plus the neighbor skin distance, but for short or non-bonded cutoffs
and/or long bonds, this may not be sufficient. This warning indicates
that there is an increased risk of a simulation stopping unexpectedly
because of Bond/Angle/Dihedral/Improper atoms missing. It can be
silenced by manually setting the communication cutoff via
:doc:`comm_modify cutoff <comm_modify>`. However, since the
heuristic used to determine the estimate is not always accurate, it
is not changed automatically and the warning may be ignored depending
on the specific system being simulated.
*Communication cutoff is too small for SNAP micro load balancing, increased to %lf*
Self-explanatory.

16
src/comm.h
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@ -253,6 +253,22 @@ be generated and LAMMPS may lose atoms or use incorrect periodic images of atoms
interaction lists. To avoid, either define pair style zero with a suitable cutoff
or use comm_modify cutoff.
W: Communication cutoff is shorter than a bond length based estimate. This may lead to errors.
Since LAMMPS stores topology data with individual atoms, all atoms comprising
a bond, angle, dihedral or improper must be present on any sub-domain that
"owns" the atom with the information, either as a local or a ghost atom. The
communication cutoff is what determines up to what distance from a sub-domain
boundary ghost atoms are created. The communication cutoff is by default the
largest non-bonded cutoff plus the neighbor skin distance, but for short or
non-bonded cutoffs and/or long bonds, this may not be sufficient. This warning
indicates that there is an increased risk of a simulation stopping unexpectedly
because of Bond/Angle/Dihedral/Improper atoms missing. It can be silenced by
manually setting the communication cutoff via comm_modify cutoff. However,
since the heuristic used to determine the estimate is not always accurate, it
is not changed automatically and the warning may be ignored depending on the
specific system being simulated.
UNDOCUMENTED
U: OMP_NUM_THREADS environment is not set.