Loading doc/src/Errors_warnings.rst +18 −0 Original line number Diff line number Diff line Loading @@ -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. Loading src/comm.h +16 −0 Original line number Diff line number Diff line Loading @@ -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. Loading Loading
doc/src/Errors_warnings.rst +18 −0 Original line number Diff line number Diff line Loading @@ -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. Loading
src/comm.h +16 −0 Original line number Diff line number Diff line Loading @@ -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. Loading
