Minor updates and documentation

doc/src/comm_modify.rst

@@ -84,13 +84,15 @@ information is available, then also a heuristic based on that bond length
 is computed. It is used as communication cutoff, if there is no pair
 style present and no *comm_modify cutoff* command used. Otherwise a
 warning is printed, if this bond based estimate is larger than the
-communication cutoff used. A
+communication cutoff used.
 
 The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
 communication mode *multi* instead. Since in this case the communication
 cutoffs are determined per atom type, a type specifier is needed and
 cutoff for one or multiple types can be extended. Also ranges of types
-using the usual asterisk notation can be given.
+using the usual asterisk notation can be given. For granular pairstyles, 
+the default cutoff is set to the sum of the current maximum atomic radii
+for each type. 
 
 These are simulation scenarios in which it may be useful or even
 necessary to set a ghost cutoff > neighbor cutoff:

src/npair_half_size_multi_newtoff.cpp

@@ -11,9 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <string.h>
 #include "npair_half_size_multi_newtoff.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
@@ -27,6 +25,7 @@ using namespace LAMMPS_NS;
 NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {}
 
 /* ----------------------------------------------------------------------
+   size particles
    binned neighbor list construction with partial Newton's 3rd law
    each owned atom i checks own bin and other bins in stencil
    multi-type stencil is itype dependent and is distance checked
@@ -46,7 +45,6 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list)
   double *radius = atom->radius;
   int *type = atom->type;
   int *mask = atom->mask;
-  tagint *tag = atom->tag;
   tagint *molecule = atom->molecule;
   int nlocal = atom->nlocal;
   if (includegroup) nlocal = atom->nfirst;
@@ -99,7 +97,7 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list)
         cutdistsq = (radsum+skin) * (radsum+skin);
 
         if (rsq <= cutdistsq) {
-          if (history && rsq < radsum*radsum) 
+          if (history && rsq < radsum*radsum)
             neighptr[n++] = j ^ mask_history;
           else
             neighptr[n++] = j;

src/npair_half_size_multi_newtoff.h

@@ -40,4 +40,7 @@ class NPairHalfSizeMultiNewtoff : public NPair {
 
 /* ERROR/WARNING messages:
 
+E: Neighbor list overflow, boost neigh_modify one
+
+UNDOCUMENTED
 */

src/npair_half_size_multi_newton.cpp

@@ -11,9 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <string.h>
 #include "npair_half_size_multi_newton.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
@@ -27,6 +25,7 @@ using namespace LAMMPS_NS;
 NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {}
 
 /* ----------------------------------------------------------------------
+   size particles
    binned neighbor list construction with full Newton's 3rd law
    each owned atom i checks its own bin and other bins in Newton stencil
    multi-type stencil is itype dependent and is distance checked
@@ -45,7 +44,6 @@ void NPairHalfSizeMultiNewton::build(NeighList *list)
   double *radius = atom->radius;
   int *type = atom->type;
   int *mask = atom->mask;
-  tagint *tag = atom->tag;
   tagint *molecule = atom->molecule;
   int nlocal = atom->nlocal;
   if (includegroup) nlocal = atom->nfirst;

src/npair_half_size_multi_newton.h

@@ -40,4 +40,7 @@ class NPairHalfSizeMultiNewton : public NPair {
 
 /* ERROR/WARNING messages:
 
+E: Neighbor list overflow, boost neigh_modify one
+
+UNDOCUMENTED
 */

src/npair_half_size_multi_newton_tri.cpp

@@ -45,7 +45,6 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list)
   double *radius = atom->radius;
   int *type = atom->type;
   int *mask = atom->mask;
-  tagint *tag = atom->tag;
   tagint *molecule = atom->molecule;
   int nlocal = atom->nlocal;
   if (includegroup) nlocal = atom->nfirst;
@@ -72,7 +71,9 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list)
     radi = radius[i];
 
 
-    // loop over all atoms in bins in stencil
+    // loop over all atoms in bins, including self, in stencil
+    // skip if i,j neighbor cutoff is less than bin distance
+    // bins below self are excluded from stencil
     // pairs for atoms j "below" i are excluded
     // below = lower z or (equal z and lower y) or (equal zy and lower x)
     //         (equal zyx and j <= i)

src/npair_half_size_multi_newton_tri.h

@@ -40,4 +40,7 @@ class NPairHalfSizeMultiNewtonTri : public NPair {
 
 /* ERROR/WARNING messages:
 
+E: Neighbor list overflow, boost neigh_modify one
+
+UNDOCUMENTED
 */