Updating from master to 19May17

src/neighbor.cpp

@@ -640,6 +640,24 @@ int Neighbor::init_pair()
   delete [] neigh_stencil;
   delete [] neigh_pair;
 
+  // error check on requests
+  // do not allow occasional, ghost, bin list
+  //   b/c it still uses variant of coord2bin() in NPair() method
+  //     instead of atom2bin, this could cause error b/c stoms have
+  //     moved out of proc domain by time occasional list is built
+  //   solution would be to use a different NBin variant
+  //     that used Npair::coord2bin(x,ix,iy,iz) (then delete it from NPair)
+  //     and stored the ix,iy,iz values for all atoms (including ghosts)
+  //     at time of binning when neighbor lists are rebuilt,
+  //     similar to what vanilla Nbin::coord2atom() does now in atom2bin
+
+  if (style == BIN) {
+    for (i = 0; i < nrequest; i++)
+      if (requests[i]->occasional && requests[i]->ghost)
+        error->all(FLERR,"Cannot request an occasional binned neighbor list "
+                   "with ghost info");
+  }
+
   // morph requests in various ways
   // purpose is to avoid duplicate or inefficient builds
   // may add new requests if a needed request to derive from does not exist
@@ -667,7 +685,7 @@ int Neighbor::init_pair()
     
   // create new lists, one per request including added requests
   // wait to allocate initial pages until copy lists are detected
-  // NOTE: can I allocation now, instead of down below?
+  // NOTE: can I allocate now, instead of down below?
 
   nlist = nrequest;
   
@@ -1216,7 +1234,7 @@ void Neighbor::morph_copy()
     
     // check all other lists
 
-    for (j = 0; j < i; j++) {
+    for (j = 0; j < nrequest; j++) {
       if (i == j) continue;
       jrq = requests[j];
 
@@ -1224,10 +1242,13 @@ void Neighbor::morph_copy()
 
       if (jrq->copy && jrq->copylist == i) continue;
 
-      // parent list must be perpetual
-      // copied list can be perpetual or occasional
+      // other list (jrq) to copy from must be perpetual
+      // list that becomes a copy list (irq) can be perpetual or occasional
+      // if both lists are perpetual, require j < i
+      //   to prevent circular dependence with 3 or more copies of a list
 
       if (jrq->occasional) continue;
+      if (!irq->occasional && j > i) continue;
 
       // both lists must be half, or both full
 
@@ -1279,7 +1300,7 @@ void Neighbor::morph_copy()
     // turn list I into a copy of list J
     // do not copy a list from another copy list, but from its parent list
 
-    if (j < i) {
+    if (j < nrequest) {
       irq->copy = 1;
       if (jrq->copy) irq->copylist = jrq->copylist;
       else irq->copylist = j;
@@ -1666,7 +1687,6 @@ int Neighbor::choose_stencil(NeighRequest *rq)
   else if (rq->newton == 1) newtflag = 1;
   else if (rq->newton == 2) newtflag = 0;
 
-
   //printf("STENCIL RQ FLAGS: hff %d %d n %d g %d s %d newtflag %d\n",
   //       rq->half,rq->full,rq->newton,rq->ghost,rq->ssa,
   //       newtflag);
@@ -2084,7 +2104,7 @@ void Neighbor::build(int topoflag)
   }
 
   // bin atoms for all NBin instances
-  // not just NBin associated with perpetual lists
+  // not just NBin associated with perpetual lists, also occasional lists
   // b/c cannot wait to bin occasional lists in build_one() call
   // if bin then, atoms may have moved outside of proc domain & bin extent,
   //   leading to errors or even a crash
@@ -2190,6 +2210,7 @@ void Neighbor::build_one(class NeighList *mylist, int preflag)
 
   // build the list
 
+  if (!mylist->copy) mylist->grow(atom->nlocal,atom->nlocal+atom->nghost);
   np->build_setup();
   np->build(mylist);
 }