Merge pull request #1099 from jrgissing/bond/react-efficient-competing_reactions

bond/react: efficient competing reactions

src/USER-MISC/fix_bond_react.cpp

@@ -961,6 +961,10 @@ void FixBondReact::superimpose_algorithm()
   local_num_mega = 0;
   ghostly_num_mega = 0;
 
+  // indicates local ghosts of other procs
+  int tmp;
+  localsendlist = (int *) comm->extract("localsendlist",tmp);
+
   // quick description of important global indices you'll see floating about:
   // 'pion' is the pioneer loop index
   // 'neigh' in the first neighbor index
@@ -1857,17 +1861,24 @@ if so, flag for broadcasting for perusal by all processors
 
 void FixBondReact::glove_ghostcheck()
 {
-  // it appears this little loop was deemed important enough for its own function!
-  // noteworthy: it's only relevant for parallel
-
   // here we add glove to either local_mega_glove or ghostly_mega_glove
-  int ghostly = 1;
-  //for (int i = 0; i < onemol->natoms; i++) {
-  //  if (atom->map(glove[i][1]) >= atom->nlocal) {
-  //    ghostly = 1;
-  //    break;
-  //  }
-  //}
+  // ghostly_mega_glove includes atoms that are ghosts, either of this proc or another
+  // 'ghosts of another' indication taken from comm->sendlist
+
+  int ghostly = 0;
+  if (comm->style == 0) {
+    for (int i = 0; i < onemol->natoms; i++) {
+      int ilocal = atom->map(glove[i][1]);
+      if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
+        ghostly = 1;
+        break;
+      }
+    }
+  } else {
+    #if !defined(MPI_STUBS)
+      ghostly = 1;
+    #endif
+  }
 
   if (ghostly == 1) {
     ghostly_mega_glove[0][ghostly_num_mega] = rxnID;

src/USER-MISC/fix_bond_react.h

@@ -122,6 +122,7 @@ class FixBondReact : public Fix {
   tagint **local_mega_glove; // consolidation local of reaction instances
   tagint **ghostly_mega_glove; // consolidation nonlocal of reaction instances
   tagint **global_mega_glove; // consolidation (inter-processor) of gloves containing nonlocal atoms
+  int *localsendlist; // indicates ghosts of other procs
   int local_num_mega; // num of local reaction instances
   int ghostly_num_mega; // num of ghostly reaction instances
   int global_megasize; // num of reaction instances in global_mega_glove

src/comm.h

@@ -112,6 +112,9 @@ class Comm : protected Pointers {
   int read_lines_from_file(FILE *, int, int, char *);
   int read_lines_from_file_universe(FILE *, int, int, char *);
 
+  // extract data useful to other classes
+  virtual void *extract(const char *, int &) {return NULL;}
+
  protected:
   int bordergroup;           // only communicate this group in borders
 

src/comm_brick.cpp

@@ -55,7 +55,8 @@ CommBrick::CommBrick(LAMMPS *lmp) :
   size_reverse_send(NULL), size_reverse_recv(NULL),
   slablo(NULL), slabhi(NULL), multilo(NULL), multihi(NULL),
   cutghostmulti(NULL), pbc_flag(NULL), pbc(NULL), firstrecv(NULL),
-  sendlist(NULL), maxsendlist(NULL), buf_send(NULL), buf_recv(NULL)
+  sendlist(NULL),  localsendlist(NULL), maxsendlist(NULL),
+  buf_send(NULL), buf_recv(NULL)
 {
   style = 0;
   layout = Comm::LAYOUT_UNIFORM;
@@ -74,6 +75,7 @@ CommBrick::~CommBrick()
   }
 
   if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]);
+  if (localsendlist) memory->destroy(localsendlist);
   memory->sfree(sendlist);
   memory->destroy(maxsendlist);
 
@@ -1469,6 +1471,33 @@ void CommBrick::free_multi()
   multilo = multihi = NULL;
 }
 
+/* ----------------------------------------------------------------------
+   extract data potentially useful to other classes
+------------------------------------------------------------------------- */
+
+void *CommBrick::extract(const char *str, int &dim)
+{
+  if (strcmp(str,"localsendlist") == 0) {
+    int i, iswap, isend;
+    if (!localsendlist)
+      memory->create(localsendlist,atom->nlocal,"comm:localsendlist");
+    else
+      memory->grow(localsendlist,atom->nlocal,"comm:localsendlist");
+
+    for (i = 0; i < atom->nlocal; i++)
+      localsendlist[i] = 0;
+
+    for (iswap = 0; iswap < nswap; iswap++)
+      for (isend = 0; isend < sendnum[iswap]; isend++)
+        if (sendlist[iswap][isend] < atom->nlocal)
+          localsendlist[sendlist[iswap][isend]] = 1;
+
+    return (void *) localsendlist;
+  }
+
+  return NULL;
+}
+
 /* ----------------------------------------------------------------------
    return # of bytes of allocated memory
 ------------------------------------------------------------------------- */

src/comm_brick.h

@@ -46,6 +46,7 @@ class CommBrick : public Comm {
 
   void forward_comm_array(int, double **);         // forward comm of array
   int exchange_variable(int, double *, double *&);  // exchange on neigh stencil
+  void *extract(const char *,int &);
   virtual bigint memory_usage();
 
  protected:
@@ -67,6 +68,7 @@ class CommBrick : public Comm {
 
   int *firstrecv;                   // where to put 1st recv atom in each swap
   int **sendlist;                   // list of atoms to send in each swap
+  int *localsendlist;               // indexed list of local sendlist atoms
   int *maxsendlist;                 // max size of send list for each swap
 
   double *buf_send;                 // send buffer for all comm