add renieigbor option to fix set

doc/src/Commands_fix.rst

@@ -216,6 +216,7 @@ OPT.
    * :doc:`rigid/small (o) <fix_rigid>`
    * :doc:`rx (k) <fix_rx>`
    * :doc:`saed/vtk <fix_saed_vtk>`
+   * :doc:`set <fix_set>`
    * :doc:`setforce (k) <fix_setforce>`
    * :doc:`setforce/spin <fix_setforce>`
    * :doc:`sgcmc <fix_sgcmc>`

doc/src/fix_set.rst

@@ -8,11 +8,12 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   fix ID group-ID set Nfreq set-args
+   fix ID group-ID set Nfreq rnflag set-args
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * set = style name of this fix command
 * Nfreq = reset per-atom properties every this many timesteps
+* rnflag = 1 to reneighbor on next timestep, 0 to not
 * set-args = identical to args for the :doc:`set <set>` command
 
 Examples
@@ -20,8 +21,8 @@ Examples
 
 .. code-block:: LAMMPS
 
-   fix 10 all set 1 group all i_dump v_new
-   fix 10 all set 1 group all i_dump v_turnoff
+   fix 10 all set 1 0 group all i_dump v_new
+   fix 10 all set 1 0 group all i_dump v_turnoff
 
 Description
 """""""""""
@@ -29,11 +30,30 @@ Description
 Reset one or more properties of one or more atoms once every *Nfreq*
 steps during a simulation.
 
-The args following *Nfreq* are identical to those allowed for the
-:doc:`set <set>` command, as in the examples above and below.
+If the *rnflag* for reneighboring is set to 1, then a reneighboring
+will be triggered on the next timestep (since the fix set operation
+occurs at the end of the current timestep).  This is important to do
+if this command changes per-atom properties that need to be
+communicated to ghost atoms.  If this is not the case, an *rnflag*
+setting of 0 can be used; reneighboring will only be triggered on
+subsequent timesteps by the usual neighbor list criteria; see the
+:doc:`neigh_modify <neigh_modify.html>` command.
+
+Here are two examples where an *rnflag* setting of 1 are needed.  If a
+custom per-atom property is changed and the :doc:`fix property/atom
+<fix_property_atom>` command to create the property used the *ghost
+yes* keyword.  Or if per-atom charges are changed, all pair styles
+which compute Coulombic interactions require charge values for ghost
+atoms.  In both these examples, the re-neighboring will trigger the
+changes in the owned atom properties to be immediately communicated to
+ghost atoms.
+
+The arguments following *Nfreq* and *rnflag* are identical to those
+allowed for the :doc:`set <set>` command, as in the examples above and
+below.
 
 Note that the group-ID setting for this command is ignored.  The
-syntax for the :doc:`set <set>` command allows selection of which
+syntax for the :doc:`set <set>` arguments allows selection of which
 atoms have their properties reset.
 
 This command can only be used to reset an atom property using a
@@ -68,7 +88,7 @@ be output every step for *twindow* timesteps.
    #
    variable        start atom "vx > v_vthresh && i_dump == -1"
    variable        new atom ternary(v_start,step,i_dump)
-   fix             3 all set 1 group all i_dump v_new
+   fix             3 all set 1 0 group all i_dump v_new
    #
    # dump command with thresh which enforces twindow
    #
@@ -112,7 +132,7 @@ longer useful.
    variable        turnon atom ternary(v_start,step,i_dump)
    variable        stop atom "v_turnon >= 0 && (step-v_turnon) < v_twindow"
    variable        turnoff atom ternary(v_stop,v_turnon,-1)
-   fix             3 all set 1 group all i_dump v_turnoff
+   fix             3 all set 1 0 group all i_dump v_turnoff
    #
    # dump command with thresh which enforces twindow
    #

doc/src/run.rst

@@ -103,14 +103,16 @@ must be done.
 
 .. note::
 
-   If your input script changes the system between 2 runs, then the
-   initial setup must be performed to ensure the change is recognized by
-   all parts of the code that are affected.  Examples are adding a
-   :doc:`fix <fix>` or :doc:`dump <dump>` or :doc:`compute <compute>`, changing
-   a :doc:`neighbor <neigh_modify>` list parameter, or writing restart file
-   which can migrate atoms between processors.  LAMMPS has no easy way to
-   check if this has happened, but it is an error to use the *pre no*
-   option in this case.
+   If your input script "changes" the system between 2 runs, then the
+   initial setup typically needs to be performed to ensure the change
+   is recognized by all parts of the code that are affected.  Examples
+   are adding a :doc:`fix <fix>` or :doc:`dump <dump>` or
+   :doc:`compute <compute>`, changing a :doc:`neighbor <neigh_modify>`
+   list parameter, using the :doc:`set <set>` command, or writing a
+   restart file via the :doc:`write_restart <write_restart>` command,
+   which can migrate atoms between processors.  LAMMPS has no easy way
+   to check if this has happened, but it is an error to use the *pre
+   no* option in these cases.
 
 If *post* is specified as "no", the full timing summary is skipped;
 only a one-line summary timing is printed.

src/fix_set.cpp

@@ -16,6 +16,7 @@
 #include "atom.h"
 #include "error.h"
 #include "set.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -26,27 +27,25 @@ enum{SETCOMMAND,FIXSET};     // also used in Set class
 
 FixSet::FixSet(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
 {
-  if (narg < 7) error->all(FLERR, 1, "Illegal fix set command: need at least four arguments");
+  if (narg < 8) error->all(FLERR, 1, "Illegal fix set command: need at least eight arguments");
 
   nevery = utils::inumeric(FLERR, arg[3], false, lmp);
   if (nevery <= 0) error->all(FLERR, "Fix {} Nevery must be > 0", style);
 
+  reneighbor = utils::inumeric(FLERR, arg[4], false, lmp);
+  if (reneighbor = 0 || reneighbor > 1)
+    error->all(FLERR, "Fix {} rnflag must be 0/1", style);
+
   // create instance of Set class
 
   set = new Set(lmp);
 
   // pass remaining args to Set class
   // only keywords which use per-atom variables are currently allowed
-  // NOTE: could also allow when set style = region, since atoms may move in/out of regions
+  // NOTE: could also allow when set style = region,
+  //       since atoms may move in/out of regions
 
-  set->process_args(FIXSET,narg-4,&arg[4]);
-
-  // NOTE: not sure if either of these options for fix set are needed or could be problematic
-  // could add ghost yes keyword/value to trigger
-  //   ghost comm, e.g. if atom types are reset
-  //   this could require an extract() method in Set to query what value(s) to comm
-  // could add reneigh yes keyword/value to trigger
-  //   full reneighbor on next step, e.g. if xyz coords are reset
+  set->process_args(FIXSET,narg-5,&arg[5]);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -79,5 +78,9 @@ void FixSet::end_of_step()
   // loop over list of actions to reset atom attributes
 
   set->invoke_actions();
+
+  // trigger reneighboring on next timestep if requested
+
+  if (reneighbor) next_reneighbor = update->ntimestep + 1;
 }
 

src/fix_set.h

@@ -32,6 +32,8 @@ class FixSet : public Fix {
   void end_of_step() override;
 
  private:
+  int reneighbor;
+
   class Set *set;
 };