expand/clarify some discussions

doc/src/Errors_details.rst

@@ -395,44 +395,52 @@ Lost atoms ...
 --------------
 
 A simulation stopping with an error due to lost atoms can have multiple
-causes. In the majority of cases, lost atoms are unexpected and a result
+causes.  By default, LAMMPS checks for whether the total number of atoms
-of extremely high velocities causing instabilities in the system, and
+is consistent with the sum of atoms "owned" by MPI processors every time
-those velocities can result from a variety of issues. For ideas on how
+that thermodynamic output is written.  In the majority of cases, lost
-to track down issues with unexpected lost atoms, see :ref:`Fast moving
+atoms are unexpected and a result of extremely high velocities causing
-atoms <hint05>` and :ref:`Neighbor list settings <hint09>` in the
+instabilities in the system, and those velocities can result from a
-general troubleshooting section above. In specific situations however,
+variety of issues.  For ideas on how to track down issues with
-losing atoms is expected material behavior (e.g. with sputtering and
+unexpected lost atoms, see :ref:`Fast moving atoms <hint05>` and
-surface evaporation simulations) and an unwanted crash can be resolved
+:ref:`Neighbor list settings <hint09>` in the general troubleshooting
-by changing the :doc:`thermo_modify lost <thermo_modify>` keyword from
+section above.  In specific situations however, losing atoms is expected
-the default 'error' to 'warn' or 'ignore' (though heed the advice in
+material behavior (e.g. with sputtering and surface evaporation
-:ref:`Ignoring lost atoms <hint06>` above!).
+simulations) and an unwanted crash can be resolved by changing the
+:doc:`thermo_modify lost <thermo_modify>` keyword from the default
+'error' to 'warn' or 'ignore' (though heed the advice in :ref:`Ignoring
+lost atoms <hint06>` above!).
 
 .. _err0009:
 
 Too many neighbor bins
 ----------------------
 
-The simulation box has become too large relative to the size of a
+The simulation box is or has become too large relative to the size of a
-neighbor bin and LAMMPS is unable to store the needed number of
+neighbor bin (which in turn depends on the largest pair-wise cutoff by
-bins. This typically implies the simulation box has expanded too far.
+default) and LAMMPS is unable to store the needed number of bins.  This
-This can happen when some atoms move rapidly apart with shrink-wrap boundaries
+typically implies the simulation box has expanded too far.  That can
-or when a fix (like fix deform or a barostat) excessively grows the simulation
+happen when some atoms move rapidly apart with shrink-wrap boundaries or
-box.
+when a fix (like fix deform or a barostat) excessively grows the
+simulation box.  This can also happen, if the largest pair-wise cutoff
+is small.  In this case, the error can be avoided by using the
+:doc:`neigh_modify command <neigh_modify>` to set the bin width to a
+suitably large value.
 
 .. _err0010:
 
-Unrecognized pair style ... is part of ... package which is not enabled in this LAMMPS binary
+Unrecognized ... style ... is part of ... package which is not enabled in this LAMMPS binary
----------------------------------------------------------------------------------------------
+--------------------------------------------------------------------------------------------
 
-The LAMMPS executable (binary) being used was not compiled with a package
+The LAMMPS executable (binary) being used was not compiled with a
-containing the specified pair style. This indicates that the executable needs to
+package containing the specified style.  This indicates that the
-be re-built after enabling the correct package in the relevant Makefile or CMake
+executable needs to be re-built after enabling the correct package in
-build directory. See :doc:`Section 3. Build LAMMPS <Build>` for more details.
+the relevant Makefile or CMake build directory. See
-One can check if the expected package and pair style is present in the
+:doc:`Section 3. Build LAMMPS <Build>` for more details.  One can check
-executable by running it with the ``-help`` (or ``-h``) flag on the command
+if the expected package and pair style is present in the executable by
-line. One common oversight, especially for beginner LAMMPS users, is to enable
+running it with the ``-help`` (or ``-h``) flag on the command line. One
-the package, but to forget to run commands to rebuild (e.g., to run the final
+common oversight, especially for beginner LAMMPS users, is to enable the
-``make`` or ``cmake`` command).
+package, but to forget to run commands to rebuild (e.g., to run the
+final ``make`` or ``cmake`` command).
 
 If this error is occurring with an executable that the user does not control
 (e.g., through a module on HPC clusters), the user will need to get in contact
@@ -770,9 +778,10 @@ with periodic boundaries or larger than the box with non-periodic
 boundaries.  It means that the positions and image flags have become
 inconsistent.  LAMMPS will still compute bonded interactions based on
 the closest periodic images of the atoms and thus in most cases the
-results will be correct.  Nevertheless, it is good practice to update
+results will be correct.  However they can cause problems when such
-the system so that the message does not appear.  It will help with
+atoms are used with the fix rigid or replicate commands.  Thus, it is
-future manipulations of the system.
+good practice to update the system so that the message does not appear.
+It will help with future manipulations of the system.
 
 There is one case where this warning *must* appear: when you have a
 chain of connected bonds that pass through the entire box and connect