Merge branch 'develop' into region-lookup-refactor

doc/src/Developer_utils.rst

@@ -211,6 +211,9 @@ Convenience functions
 .. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
    :project: progguide
 
+.. doxygenfunction:: errorurl
+   :project: progguide
+
 .. doxygenfunction:: flush_buffers(LAMMPS *lmp)
    :project: progguide
 

doc/src/Errors.rst

@@ -11,6 +11,7 @@ them.
    :maxdepth: 1
 
    Errors_common
+   Errors_details
    Errors_bugs
    Errors_debug
    Errors_messages

doc/src/Errors_details.rst

@@ -0,0 +1,27 @@
+Detailed discussion of errors and warnings
+==========================================
+
+Many errors or warnings are self-explanatory and thus straightforward to
+resolve.  However, there are also cases, where there is no single cause
+and explanation, where LAMMPS can only detect symptoms of an error but
+not the exact cause, or where the explanation needs to be more detailed than
+what can be fit into a message printed by the program.  The following are
+discussions of such cases.
+
+.. _err0001:
+
+Unknown identifier in data file
+-------------------------------
+
+This error happens when LAMMPS encounters a line of text in an unexpected format
+while reading a data file. This is most commonly cause by inconsistent header and
+section data.  The header section informs LAMMPS how many entries or lines are expected in the
+various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of the data file.
+If there is a mismatch, LAMMPS will either keep reading beyond the end of a section
+or stop reading before the section has ended.
+
+Such a mismatch can happen unexpectedly when the first line of the data
+is *not* a comment as required by the format.  That would result in
+LAMMPS expecting, for instance, 0 atoms because the "atoms" header line
+is treated as a comment.
+

doc/src/fix_nve.rst

@@ -35,6 +35,10 @@ consistent with the microcanonical ensemble (NVE) provided there
 are (full) periodic boundary conditions and no other "manipulations"
 of the system (e.g. fixes that modify forces or velocities).
 
+This fix invokes the velocity form of the
+Störmer-Verlet time integration algorithm (velocity-Verlet). Other
+time integration options can be invoked using the :doc:`run_style <run_style>` command.
+
 ----------
 
 .. include:: accel_styles.rst
@@ -57,7 +61,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`
+:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`run_style <run_style>`
 
 Default
 """""""

doc/src/group.rst

@@ -258,11 +258,17 @@ assignment is made at the beginning of the minimization, but not
 during the iterations of the minimizer.
 
 The point in the timestep at which atoms are assigned to a dynamic
-group is after the initial stage of velocity Verlet time integration
-has been performed, and before neighbor lists or forces are computed.
-This is the point in the timestep where atom positions have just
-changed due to the time integration, so the region criterion should be
-accurate, if applied.
+group is after interatomic forces have been computed, but before any
+fixes which alter forces or otherwise update the system have been
+invoked.  This means that atom positions have been updated, neighbor
+lists and ghost atoms are current, and both intermolecular and
+intramolecular forces have been calculated based on the new
+coordinates.  Thus the region criterion, if applied, should be
+accurate.  Also, any computes invoked by an atom-style variable should
+use updated information for that timestep, e.g. potential energy/atom
+or coordination number/atom.  Similarly, fixes or computes which are
+invoked after that point in the timestep, should operate on the new
+group of atoms.
 
 .. note::
 

doc/src/run_style.rst

@@ -67,7 +67,8 @@ Description
 Choose the style of time integrator used for molecular dynamics
 simulations performed by LAMMPS.
 
-The *verlet* style is a standard velocity-Verlet integrator.
+The *verlet* style is the velocity form of the
+Störmer-Verlet time integration algorithm (velocity-Verlet)
 
 ----------