git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10485 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/RIGID/fix_rigid.cpp

@@ -1094,6 +1094,8 @@ void FixRigid::pre_neighbor()
   }
 
   // adjust image flags of any atom in a rigid body whose xcm was remapped
+  // subtracting remapflag = new-old keeps ix,iy,iz near 0
+  //   so body is always in central simulation box
 
   tagint *image = atom->image;
   int nlocal = atom->nlocal;

src/comm.cpp

@@ -116,9 +116,14 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
 #endif
 
   // initialize comm buffers & exchange memory
+  // NOTE: allow for AtomVec to set maxexchange_atom, e.g. for atom_style body
+
+  maxexchange_atom = maxexchange_fix = 0;
+  maxexchange = maxexchange_atom + maxexchange_fix;
+  bufextra = maxexchange + BUFEXTRA;
 
   maxsend = BUFMIN;
-  memory->create(buf_send,maxsend+BUFEXTRA,"comm:buf_send");
+  memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
   maxrecv = BUFMIN;
   memory->create(buf_recv,maxrecv,"comm:buf_recv");
 
@@ -335,11 +340,13 @@ void Comm::init()
   for (int i = 0; i < modify->nfix; i++)
     size_border += modify->fix[i]->comm_border;
   
+  // maxexchange = max # of datums/atom in exchange communication
   // maxforward = # of datums in largest forward communication
   // maxreverse = # of datums in largest reverse communication
   // query pair,fix,compute,dump for their requirements
   // pair style can force reverse comm even if newton off
 
+  maxexchange = BUFMIN + maxexchange_fix;
   maxforward = MAX(size_forward,size_border);
   maxreverse = size_reverse;
 
@@ -537,8 +544,6 @@ void Comm::setup()
     maxneed[0] = MAX(all[0],all[1]);
     maxneed[1] = MAX(all[2],all[3]);
     maxneed[2] = MAX(all[4],all[5]);
-    //if (me == 0) 
-    //printf("MAXNEED %d %d %d\n",maxneed[0],maxneed[1],maxneed[2]);
   }
 
   // allocate comm memory
@@ -826,6 +831,15 @@ void Comm::exchange()
   atom->nghost = 0;
   atom->avec->clear_bonus();
 
+  // insure send buf is large enough for single atom
+  // fixes can change per-atom size requirement on-the-fly
+
+  int bufextra_old = bufextra;
+  maxexchange = maxexchange_atom + maxexchange_fix;
+  bufextra = maxexchange + BUFEXTRA;
+  if (bufextra > bufextra_old)
+    memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
+
   // subbox bounds for orthogonal or triclinic
 
   if (triclinic == 0) {
@@ -1584,7 +1598,7 @@ int Comm::read_lines_from_file(FILE *fp, int nlines, int maxline, char *buf)
 }
 
 /* ----------------------------------------------------------------------
-   realloc the size of the send buffer as needed with BUFFACTOR & BUFEXTRA
+   realloc the size of the send buffer as needed with BUFFACTOR and bufextra
    if flag = 1, realloc
    if flag = 0, don't need to realloc with copy, just free/malloc
 ------------------------------------------------------------------------- */
@@ -1593,10 +1607,10 @@ void Comm::grow_send(int n, int flag)
 {
   maxsend = static_cast<int> (BUFFACTOR * n);
   if (flag)
-    memory->grow(buf_send,(maxsend+BUFEXTRA),"comm:buf_send");
+    memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
   else {
     memory->destroy(buf_send);
-    memory->create(buf_send,maxsend+BUFEXTRA,"comm:buf_send");
+    memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
   }
 }
 
@@ -1888,7 +1902,7 @@ bigint Comm::memory_usage()
   bytes += nprocs * sizeof(int);    // grid2proc
   for (int i = 0; i < nswap; i++)
     bytes += memory->usage(sendlist[i],maxsendlist[i]);
-  bytes += memory->usage(buf_send,maxsend+BUFEXTRA);
+  bytes += memory->usage(buf_send,maxsend+bufextra);
   bytes += memory->usage(buf_recv,maxrecv);
   return bytes;
 }

src/comm.h

@@ -36,6 +36,8 @@ class Comm : protected Pointers {
                                     // -1 if no recv or send
   int other_partition_style;        // 0 = recv layout dims must be multiple of
                                     //     my layout dims
+  int maxexchange_atom;             // max contribution to exchange from AtomVec
+  int maxexchange_fix;              // max contribution to exchange from Fixes
   int nthreads;                     // OpenMP threads per MPI process
 
   Comm(class LAMMPS *);
@@ -117,6 +119,9 @@ class Comm : protected Pointers {
   int maxsend,maxrecv;              // current size of send/recv buffer
   int maxforward,maxreverse;        // max # of datums in forward/reverse comm
 
+  int maxexchange;                  // max # of datums/atom in exchange comm 
+  int bufextra;                     // extra space beyond maxsend in send buffer
+
   int updown(int, int, int, double, int, double *);
                                             // compare cutoff to procs
   virtual void grow_send(int, int);         // reallocate send buffer

src/fix_property_atom.cpp

@@ -378,11 +378,14 @@ int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
 int FixPropertyAtom::pack_restart(int i, double *buf)
 {
   buf[0] = nvalue+1;
-  for (int m = 1; m <= nvalue; m++) {
-    if (style[m] == MOLECULE) buf[m] = atom->molecule[i];
-    else if (style[m] == INTEGER) buf[m] = atom->ivector[index[m]][i];
-    else if (style[m] == DOUBLE) buf[m] = atom->dvector[index[m]][i];
+
+  int m = 1;
+  for (int j = 0; j < nvalue; j++) {
+    if (style[j] == MOLECULE) buf[m++] = atom->molecule[i];
+    else if (style[j] == INTEGER) buf[m++] = atom->ivector[index[m]][i];
+    else if (style[j] == DOUBLE) buf[m++] = atom->dvector[index[m]][i];
   }
+
   return nvalue+1;
 }
 
@@ -403,9 +406,9 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth)
   for (int i = 0; i < nvalue; i++) {
     if (style[i] == MOLECULE) 
       atom->molecule[nlocal] = static_cast<int> (extra[nlocal][m++]);
-    else if (style[m] == INTEGER) 
+    else if (style[i] == INTEGER) 
       atom->ivector[index[m]][nlocal] = static_cast<int> (extra[nlocal][m++]);
-    else if (style[m] == DOUBLE)
+    else if (style[i] == DOUBLE)
       atom->dvector[index[m]][nlocal] = extra[nlocal][m++];
   }
 }

src/fix_shear_history.cpp

@@ -246,9 +246,11 @@ void FixShearHistory::pre_exchange()
   }
 
   // set maxtouch = max # of partners of any owned atom
+  // bump up comm->maxexchange_fix if necessary
 
   maxtouch = 0;
   for (i = 0; i < nlocal; i++) maxtouch = MAX(maxtouch,npartner[i]);
+  comm->maxexchange_fix = MAX(comm->maxexchange_fix,4*maxtouch+1);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -421,7 +423,7 @@ void FixShearHistory::unpack_restart(int nlocal, int nth)
 
 int FixShearHistory::maxsize_restart()
 {
-  // maxtouch_all = max touching partners across all procs
+  // maxtouch_all = max # of touching partners across all procs
 
   int maxtouch_all;
   MPI_Allreduce(&maxtouch,&maxtouch_all,1,MPI_INT,MPI_MAX,world);

src/modify.cpp

@@ -995,6 +995,7 @@ void Modify::write_restart(FILE *fp)
 
   for (int i = 0; i < nfix; i++)
     if (fix[i]->restart_peratom) {
+      int maxsize_restart = fix[i]->maxsize_restart();
       if (me == 0) {
         n = strlen(fix[i]->id) + 1;
         fwrite(&n,sizeof(int),1,fp);
@@ -1002,8 +1003,7 @@ void Modify::write_restart(FILE *fp)
         n = strlen(fix[i]->style) + 1;
         fwrite(&n,sizeof(int),1,fp);
         fwrite(fix[i]->style,sizeof(char),n,fp);
-        n = fix[i]->maxsize_restart();
-        fwrite(&n,sizeof(int),1,fp);
+        fwrite(&maxsize_restart,sizeof(int),1,fp);
       }
     }
 }