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Merge branch 'master' into multi-comm-tiled

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Axel Kohlmeyer
2020-08-03 22:37:23 -04:00
parent ea900b3482 6576c4cbf3
commit f4aede49dc
67 changed files with 3059 additions and 496 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.

6
doc/src/pair_ufm.rst
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@ -94,10 +94,8 @@ of a run:
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
For atom type pairs I,J and I != J, the A coefficient and cutoff
distance for this pair style can be mixed. A is always mixed via a
*geometric* rule. The cutoff is mixed according to the pair_modify
mix value. The default mix value is *geometric*\ . See the
For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff
distance for this pair style can be mixed. The default mix value is *geometric*\ . See the
"pair_modify" command for details.
This pair style support the :doc:`pair_modify <pair_modify>` shift option for the energy of the pair interaction.