git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12579 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/MC/fix_bond_create.cpp

@@ -374,7 +374,7 @@ void FixBondCreate::post_integrate()
   int *mask = atom->mask;
   int *type = atom->type;
 
-  neighbor->build_one(list->index,1);
+  neighbor->build_one(list,1);
   inum = list->inum;
   ilist = list->ilist;
   numneigh = list->numneigh;

src/MC/fix_bond_swap.cpp

@@ -231,7 +231,7 @@ void FixBondSwap::post_integrate()
   type = atom->type;
   x = atom->x;
 
-  neighbor->build_one(list->index,1);
+  neighbor->build_one(list,1);
   inum = list->inum;
   ilist = list->ilist;
   numneigh = list->numneigh;

src/PERI/fix_peri_neigh.cpp

@@ -179,7 +179,7 @@ void FixPeriNeigh::setup(int vflag)
 
   // build full neighbor list, will copy or build as necessary
 
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/QEQ/fix_qeq.cpp

@@ -268,7 +268,7 @@ void FixQEq::init_list(int id, NeighList *ptr)
 
 void FixQEq::setup_pre_force(int vflag)
 {
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   deallocate_storage();
   allocate_storage();

src/SNAP/compute_sna_atom.cpp

@@ -192,7 +192,7 @@ void ComputeSNAAtom::compute_peratom()
 
   // invoke full neighbor list (will copy or build if necessary)
 
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   const int inum = list->inum;
   const int* const ilist = list->ilist;

src/SNAP/compute_snad_atom.cpp

@@ -196,7 +196,7 @@ void ComputeSNADAtom::compute_peratom()
 
   // invoke full neighbor list (will copy or build if necessary)
 
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   const int inum = list->inum;
   const int* const ilist = list->ilist;

src/SNAP/compute_snav_atom.cpp

@@ -199,7 +199,7 @@ void ComputeSNAVAtom::compute_peratom()
 
   // invoke full neighbor list (will copy or build if necessary)
 
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   const int inum = list->inum;
   const int* const ilist = list->ilist;

src/USER-MISC/compute_ackland_atom.cpp

@@ -114,7 +114,7 @@ void ComputeAcklandAtom::compute_peratom()
 
   // invoke full neighbor list (will copy or build if necessary)
 
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/USER-MISC/compute_basal_atom.cpp

@@ -118,7 +118,7 @@ void ComputeBasalAtom::compute_peratom()
 
   // invoke full neighbor list (will copy or build if necessary)
 
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/USER-REAXC/fix_qeq_reax.cpp

@@ -408,7 +408,7 @@ void FixQEqReax::init_taper()
 
 void FixQEqReax::setup_pre_force(int vflag)
 {
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   deallocate_storage();
   allocate_storage();

src/compute_centro_atom.cpp

@@ -116,7 +116,7 @@ void ComputeCentroAtom::compute_peratom()
 
   // invoke full neighbor list (will copy or build if necessary)
 
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/compute_cluster_atom.cpp

@@ -113,7 +113,7 @@ void ComputeClusterAtom::compute_peratom()
 
   // invoke full neighbor list (will copy or build if necessary)
 
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/compute_cna_atom.cpp

@@ -137,7 +137,7 @@ void ComputeCNAAtom::compute_peratom()
 
   // invoke full neighbor list (will copy or build if necessary)
 
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/compute_contact_atom.cpp

@@ -108,7 +108,7 @@ void ComputeContactAtom::compute_peratom()
 
   // invoke neighbor list (will copy or build if necessary)
 
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/compute_coord_atom.cpp

@@ -141,7 +141,7 @@ void ComputeCoordAtom::compute_peratom()
 
   // invoke full neighbor list (will copy or build if necessary)
 
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/compute_group_group.cpp

@@ -211,7 +211,7 @@ void ComputeGroupGroup::pair_contribution()
 
   // invoke half neighbor list (will copy or build if necessary)
 
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/compute_pair_local.cpp

@@ -155,7 +155,7 @@ int ComputePairLocal::compute_pairs(int flag)
 
   // invoke half neighbor list (will copy or build if necessary)
 
-  if (flag == 0) neighbor->build_one(list->index);
+  if (flag == 0) neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/compute_property_local.cpp

@@ -346,7 +346,7 @@ int ComputePropertyLocal::count_pairs(int allflag, int forceflag)
 
   // invoke half neighbor list (will copy or build if necessary)
 
-  if (allflag == 0) neighbor->build_one(list->index);
+  if (allflag == 0) neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/compute_rdf.cpp

@@ -186,7 +186,7 @@ void ComputeRDF::compute_array()
 
   // invoke half neighbor list (will copy or build if necessary)
 
-  neighbor->build_one(list->index);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/delete_atoms.cpp

@@ -287,7 +287,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
   // build neighbor list this command needs based on earlier request
 
   NeighList *list = neighbor->lists[irequest];
-  neighbor->build_one(irequest);
+  neighbor->build_one(list);
 
   // allocate and initialize deletion list
   // must be after exchange potentially changes nlocal

src/neighbor.cpp

@@ -1491,31 +1491,36 @@ void Neighbor::build_topology()
    called by other classes
 ------------------------------------------------------------------------- */
 
-void Neighbor::build_one(int i, int preflag)
+void Neighbor::build_one(class NeighList *mylist, int preflag)
 {
+  // check if list structure is initialized
+  if (mylist == NULL)
+    error->all(FLERR,"Trying to build an occasional neighbor list "
+               "before initialization is completed.");
+
   // no need to build if already built since last re-neighbor
   // preflag is set by fix bond/create and fix bond/swap
   //   b/c they invoke build_one() on same step neigh list is re-built,
   //   but before re-build, so need to use ">" instead of ">="
 
   if (preflag) {
-    if (lists[i]->last_build > lastcall) return;
+    if (mylist->last_build > lastcall) return;
   } else {
-    if (lists[i]->last_build >= lastcall) return;
+    if (mylist->last_build >= lastcall) return;
   }
 
-  lists[i]->last_build = update->ntimestep;
+  mylist->last_build = update->ntimestep;
 
   // update stencils and grow atom arrays as needed
   // only for relevant settings of stencilflag and growflag
   // grow atom array for this list to current size of perpetual lists
 
-  if (lists[i]->stencilflag) {
-    lists[i]->stencil_allocate(smax,style);
-    (this->*stencil_create[i])(lists[i],sx,sy,sz);
+  if (mylist->stencilflag) {
+    mylist->stencil_allocate(smax,style);
+    (this->*stencil_create[mylist->index])(mylist,sx,sy,sz);
   }
 
-  if (lists[i]->growflag) lists[i]->grow(maxatom);
+  if (mylist->growflag) mylist->grow(maxatom);
 
   // build list I, turning off atom binning
   // binning results from last re-neighbor should be used instead
@@ -1523,7 +1528,7 @@ void Neighbor::build_one(int i, int preflag)
   //   leading to errors or even a crash
 
   binatomflag = 0;
-  (this->*pair_build[i])(lists[i]);
+  (this->*pair_build[mylist->index])(mylist);
   binatomflag = 1;
 }
 

src/neighbor.h

@@ -78,7 +78,7 @@ class Neighbor : protected Pointers {
   void setup_bins();                // setup bins based on box and cutoff
   virtual void build(int topoflag=1);  // create all neighbor lists (pair,bond)
   virtual void build_topology();    // create all topology neighbor lists
-  void build_one(int, int preflag=0);  // create a single neighbor list
+  void build_one(class NeighList *list, int preflag=0);  // create a single neighbor list
   void set(int, char **);           // set neighbor style and skin distance
   void modify_params(int, char**);  // modify parameters that control builds
   bigint memory_usage();