simplify logic for checking whether occasional neight list needs to be rebuilt

src/EXTRA-COMPUTE/compute_hexorder_atom.cpp

@@ -148,10 +148,8 @@ void ComputeHexOrderAtom::compute_peratom()
   }
 
   // invoke full neighbor list (will copy or build if necessary)
-  // on the first step of a run, set preflag to one in neighbor->build_one(...)
 
-  if (update->firststep == update->ntimestep) neighbor->build_one(list,1);
-  else neighbor->build_one(list);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/MC/fix_bond_create.cpp

@@ -408,15 +408,15 @@ void FixBondCreate::post_integrate()
   int *mask = atom->mask;
   int *type = atom->type;
 
-  if (constrainflag) {
-    // communicate partner and 1-2 special neighbors
-    // to correctly handle angle constraints
+  // communicate partner and 1-2 special neighbors
+  // to correctly handle angle constraints
 
+  if (constrainflag) {
     commflag = 3;
     comm->forward_comm(this);
   }
 
-  neighbor->build_one(list,1);
+  neighbor->build_one(list);
   inum = list->inum;
   ilist = list->ilist;
   numneigh = list->numneigh;

src/MC/fix_bond_swap.cpp

@@ -229,7 +229,7 @@ void FixBondSwap::post_integrate()
   type = atom->type;
   x = atom->x;
 
-  neighbor->build_one(list,1);
+  neighbor->build_one(list);
   inum = list->inum;
   ilist = list->ilist;
   numneigh = list->numneigh;

src/REACTION/fix_bond_react.cpp

@@ -920,7 +920,7 @@ void FixBondReact::post_integrate()
   tagint *tag = atom->tag;
   int *type = atom->type;
 
-  neighbor->build_one(list,1);
+  neighbor->build_one(list);
 
   // here we define a full special list
   // may need correction for unusual special bond settings

src/RHEO/fix_rheo_thermal.cpp

@@ -654,7 +654,7 @@ void FixRHEOThermal::create_bonds()
   int *num_bond = atom->num_bond;
   double **x = atom->x;
 
-  neighbor->build_one(list, 1);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/compute_aggregate_atom.cpp

@@ -116,12 +116,8 @@ void ComputeAggregateAtom::compute_peratom()
   comm->forward_comm();
 
   // invoke full neighbor list (will copy or build if necessary)
-  // on the first step of a run, set preflag to one in neighbor->build_one(...)
 
-  if (update->firststep == update->ntimestep)
-    neighbor->build_one(list, 1);
-  else
-    neighbor->build_one(list);
+  neighbor->build_one(list);
 
   // if group is dynamic, ensure ghost atom masks are current
 

src/compute_cluster_atom.cpp

@@ -105,12 +105,8 @@ void ComputeClusterAtom::compute_peratom()
   comm->forward_comm();
 
   // invoke full neighbor list (will copy or build if necessary)
-  // on the first step of a run, set preflag to one in neighbor->build_one(...)
 
-  if (update->firststep == update->ntimestep)
-    neighbor->build_one(list, 1);
-  else
-    neighbor->build_one(list);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/create_bonds.cpp

@@ -228,7 +228,7 @@ void CreateBonds::many()
   // build neighbor list this command needs based on earlier request
 
   auto list = neighbor->find_list(this);
-  neighbor->build_one(list, 1);
+  neighbor->build_one(list);
 
   // loop over all neighs of each atom
   // compute distance between two atoms consistently on both procs

src/neighbor.cpp

@@ -163,6 +163,9 @@ pairclass(nullptr), pairnames(nullptr), pairmasks(nullptr)
   npair_perpetual = 0;
   plist = nullptr;
 
+  npair_occasional = 0;
+  olist = nullptr;
+
   nrequest = maxrequest = 0;
   requests = nullptr;
   j_sorted = nullptr;
@@ -253,6 +256,7 @@ Neighbor::~Neighbor()
 
   delete[] slist;
   delete[] plist;
+  delete[] olist;
 
   for (int i = 0; i < nrequest; i++)
     if (requests[i]) delete requests[i];
@@ -1008,6 +1012,9 @@ int Neighbor::init_pair()
   for (i = 0; i < nrequest; i++) {
     requests[i]->index_pair = -1;
     flag = lists[i]->pair_method;
+
+    // 22 Jul 2024 NOTE, don't think flag = 0 occurs in current code
+
     if (flag == 0) {
       neigh_pair[i] = nullptr;
       continue;
@@ -1054,19 +1061,25 @@ int Neighbor::init_pair()
 
   // plist = indices of perpetual NPair classes
   //         perpetual = non-occasional, re-built at every reneighboring
+  // olist = indices of occasional NPair classes
+  //         occasional = built only when requested
   // slist = indices of perpetual NStencil classes
   //         perpetual = used by any perpetual NPair class
 
-  delete[] slist;
   delete[] plist;
-  nstencil_perpetual = npair_perpetual = 0;
-  slist = new int[nstencil];
+  delete[] olist;
+  delete[] slist;
+  npair_perpetual = npair_occasional = nstencil_perpetual = 0;
   plist = new int[nlist];
+  olist = new int[nlist];
+  slist = new int[nstencil];
 
   for (i = 0; i < nlist; i++) {
     if (lists[i]->occasional == 0 && lists[i]->pair_method)
       plist[npair_perpetual++] = i;
-  }
+    if (lists[i]->occasional)
+      olist[npair_occasional++] = i;
+ }
 
   for (i = 0; i < nstencil; i++) {
     flag = 0;
@@ -1173,7 +1186,7 @@ void Neighbor::morph_unique()
     irq = requests[i];
 
     // if cut flag set by requestor and cutoff is different than default,
-    //  set unique flag, otherwise unset cut flag
+    //   set unique flag, otherwise unset cut flag
     // this forces Pair,Stencil,Bin styles to be instantiated separately
     // also add skin to cutoff of perpetual lists
 
@@ -2416,7 +2429,9 @@ void Neighbor::build(int topoflag)
 
   int nlocal = atom->nlocal;
   int nall = nlocal + atom->nghost;
+
   // rebuild collection array from scratch
+
   if (style == Neighbor::MULTI) build_collection(0);
 
   // check that using special bond flags will not overflow neigh lists
@@ -2488,6 +2503,16 @@ void Neighbor::build(int topoflag)
   // skip if GPU package styles will call it explicitly to overlap with GPU computation.
 
   if ((atom->molecular != Atom::ATOMIC) && topoflag && !overlap_topo) build_topology();
+
+  // reset last_build in all occasional lists
+  // this will force them rebuild on next request
+  // all occasional lists are now out-of-date b/c
+  //   comm->exchange() occurred before neighbor->build()
+
+  for (i = 0; i < npair_occasional; i++) {
+    m = olist[i];
+    neigh_pair[m]->last_build = -1;
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -2524,7 +2549,7 @@ void Neighbor::build_topology()
    called by other classes
 ------------------------------------------------------------------------- */
 
-void Neighbor::build_one(class NeighList *mylist, int preflag)
+void Neighbor::build_one(class NeighList *mylist)
 {
   // check if list structure is initialized
 
@@ -2535,18 +2560,12 @@ void Neighbor::build_one(class NeighList *mylist, int preflag)
 
   if (!mylist->occasional) error->all(FLERR,"Neighbor::build_one() invoked on perpetual list");
 
-  // 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 ">="
+  // no need to build this occasional list if already built
+  //   since last comm->exchange() and re-neighbor which invoked build()
+  // build() method resets last_build for all occasional lists to -1
 
   NPair *np = neigh_pair[mylist->index];
-
-  if (preflag) {
-    if (np->last_build > lastcall) return;
-  } else {
-    if (np->last_build >= lastcall) return;
-  }
+  if (np->last_build >= lastcall) return;
 
   // if this is copy list and parent is occasional list,
   // or this is halffull and parent is occasional list,
@@ -2554,11 +2573,11 @@ void Neighbor::build_one(class NeighList *mylist, int preflag)
   // ensure parent is current
 
   if (mylist->listcopy && mylist->listcopy->occasional)
-    build_one(mylist->listcopy,preflag);
+    build_one(mylist->listcopy);
   if (mylist->listfull && mylist->listfull->occasional)
-    build_one(mylist->listfull,preflag);
+    build_one(mylist->listfull);
   if (mylist->listskip && mylist->listskip->occasional)
-    build_one(mylist->listskip,preflag);
+    build_one(mylist->listskip);
 
   // create stencil if hasn't been created since last setup_bins() call
 

src/neighbor.h

@@ -126,18 +126,22 @@ class Neighbor : protected Pointers {
   virtual void init();
 
   // old API for creating neighbor list requests
+
   int request(void *, int instance = 0);
 
   // new API for creating neighbor list requests
+
   NeighRequest *add_request(class Pair *, int flags = 0);
   NeighRequest *add_request(class Fix *, int flags = 0);
   NeighRequest *add_request(class Compute *, int flags = 0);
   NeighRequest *add_request(class Command *, const char *, int flags = 0);
 
   // set neighbor list request OpenMP flag
+
   void set_omp_neighbor(int);
 
   // report if we have INTEL package neighbor lists
+
   bool has_intel_request() const;
 
   int decide();                     // decide whether to build or not
@@ -145,8 +149,8 @@ class Neighbor : protected Pointers {
   void setup_bins();                // setup bins based on box and cutoff
   virtual void build(int);          // build all perpetual neighbor lists
   virtual void build_topology();    // pairwise topology neighbor lists
-  // create a one-time pairwise neigh list
-  void build_one(class NeighList *list, int preflag = 0);
+
+  void build_one(class NeighList *list);      // create an occasional pairwise neigh list
   void set(int, char **);                     // set neighbor style and skin distance
   void reset_timestep(bigint);                // reset of timestep counter
   void modify_params(int, char **);           // modify params that control builds
@@ -155,18 +159,18 @@ class Neighbor : protected Pointers {
   void exclusion_group_group_delete(int, int);    // rm a group-group exclusion
   int exclude_setting();                          // return exclude value to accelerator pkg
 
-  // Option to call build_topology (e.g. from gpu styles instead for overlapped computation)
+  // option to call build_topology (e.g. from gpu styles instead for overlapped computation)
 
   int overlap_topo;    // 0 for default/old non-overlap mode
   void set_overlap_topo(int);
 
-  // find a neighbor list based on requestor
+  // find a neighbor list or request based on requestor
+
   NeighList *find_list(void *, const int id = 0) const;
-  // find a neighbor request based on requestor
   NeighRequest *find_request(void *, const int id = 0) const;
 
   const std::vector<NeighRequest *> get_pair_requests() const;
-  int any_full();                // Check if any old requests had full neighbor lists
+  int any_full();                // check if any old requests had full neighbor lists
   void build_collection(int);    // build peratom collection array starting at the given index
 
   bigint get_nneigh_full();    // return number of neighbors in a regular full neighbor list
@@ -205,10 +209,13 @@ class Neighbor : protected Pointers {
   int old_pgsize, old_oneatom;     // used to avoid re-creating neigh lists
 
   int nstencil_perpetual;    // # of perpetual NeighStencil classes
-  int npair_perpetual;       // #x of perpetual NeighPair classes
+  int npair_perpetual;       // # of perpetual NeighPair classes
   int *slist;                // indices of them in neigh_stencil
   int *plist;                // indices of them in neigh_pair
 
+  int npair_occasional;      // # of occasional NeighPair classes
+  int *olist;                // indices of them in neigh_pair
+
   int maxex_type;     // max # in exclusion type list
   int maxex_group;    // max # in exclusion group list
   int maxex_mol;      // max # in exclusion molecule list