fixed bug with pair hybrid/overaly and manybody potentials finding the right skip neighbor method

src/atom_vec_body.cpp

@@ -847,6 +847,7 @@ void AtomVecBody::unpack_border(int n, int first, double *buf)
       inertia[2] = buf[m++];
       bonus[j].ninteger = (int) ubuf(buf[m++]).i;
       bonus[j].ndouble = (int) ubuf(buf[m++]).i;
+      // corresponding put() calls are in clear_bonus()
       bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
       bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
       m += bptr->unpack_border_body(&bonus[j],&buf[m]);
@@ -897,6 +898,7 @@ void AtomVecBody::unpack_border_vel(int n, int first, double *buf)
       inertia[2] = buf[m++];
       bonus[j].ninteger = (int) ubuf(buf[m++]).i;
       bonus[j].ndouble = (int) ubuf(buf[m++]).i;
+      // corresponding put() calls are in clear_bonus()
       bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
       bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
       m += bptr->unpack_border_body(&bonus[j],&buf[m]);
@@ -946,6 +948,7 @@ int AtomVecBody::unpack_border_hybrid(int n, int first, double *buf)
       inertia[2] = buf[m++];
       bonus[j].ninteger = (int) ubuf(buf[m++]).i;
       bonus[j].ndouble = (int) ubuf(buf[m++]).i;
+      // corresponding put() calls are in clear_bonus()
       bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
       bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
       m += bptr->unpack_border_body(&bonus[j],&buf[m]);
@@ -1050,6 +1053,7 @@ int AtomVecBody::unpack_exchange(double *buf)
     inertia[2] = buf[m++];
     bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
     bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
+    // corresponding put() calls are in copy()
     bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
 					  bonus[nlocal_bonus].iindex);
     bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,

src/my_page.h

@@ -57,10 +57,10 @@ namespace LAMMPS_NS {
 
 template<class T>
 class MyPage {
+ public:
   int ndatum;      // total # of stored datums
   int nchunk;      // total # of stored chunks
 
- public:
   MyPage() {
     ndatum = nchunk = 0;
     pages = NULL;

src/neigh_list.cpp

@@ -192,6 +192,7 @@ void NeighList::setup_pages(int pgsize_caller, int oneatom_caller)
      gran calls grow() in granhistory
      respaouter calls grow() in respainner, respamiddle
    triggered by neighbor list build
+   not called if a copy list
 ------------------------------------------------------------------------- */
 
 void NeighList::grow(int nlocal, int nall)

src/neighbor.cpp

@@ -1369,6 +1369,8 @@ int Neighbor::choose_pair(NeighRequest *rq)
                "with ghost neighbors");
 
   // flags for settings the request + system requires of NPair class
+  // some are set to 0/1, others are set to mask bit
+  // comparisons below in loop over classes reflect that
   //   copyflag = no/yes copy request
   //   skipflag = no/yes skip request
   //   halfflag = half request (gran and respa are also half lists)
@@ -1402,7 +1404,7 @@ int Neighbor::choose_pair(NeighRequest *rq)
   // NOTE: exactly one of these request flags is set (see neigh_request.h)
   //       this requires gran/respaouter also set halfflag
   //       can simplify this logic, if follow NOTE in neigh_request.h
-  //       all why do size/off2on and size/off2on/oneside set NP_HALF
+  //       why do size/off2on and size/off2on/oneside set NP_HALF
   //         either should set both half & full, or half should be in file name
   //         to be consistent with how other NP classes use "half"
 
@@ -1433,9 +1435,8 @@ int Neighbor::choose_pair(NeighRequest *rq)
   else if (rq->newton == 1) newtflag = 1;
   else if (rq->newton == 2) newtflag = 0;
 
-  // use flags to match exactly one of NPair class masks, bit by bit
+  // use flags to match exactly one of NPair class masks
-  // copyflag match returns with no further checks
+  // sequence of checks is bit by bit in NeighConst
-  // exactly one of halfflag,fullflag,halffullflag is set and thus must match
 
   int mask;
 
@@ -1447,13 +1448,21 @@ int Neighbor::choose_pair(NeighRequest *rq)
   for (int i = 0; i < npclass; i++) {
     mask = pairmasks[i];
 
-    if (copyflag && (mask & NP_COPY)) {
+    // if copyflag set, return or continue with no further checks
+
+    if (copyflag) {
+      if (!(mask & NP_COPY)) continue;
       if (kokkos_device_flag != (mask & NP_KOKKOS_DEVICE)) continue;
       if (kokkos_host_flag != (mask & NP_KOKKOS_HOST)) continue;
       return i+1;
     }
+
+    // skipflag must match along with other flags, so do not return
+
     if (skipflag != (mask & NP_SKIP)) continue;
 
+    // exactly one of halfflag,fullflag,halffullflag is set and must match
+
     if (halfflag) {
       if (!(mask & NP_HALF)) continue;
     } else if (fullflag) {
@@ -1470,19 +1479,38 @@ int Neighbor::choose_pair(NeighRequest *rq)
     if (ssaflag != (mask & NP_SSA)) continue;
     if (ompflag != (mask & NP_OMP)) continue;
     if (intelflag != (mask & NP_INTEL)) continue;
+
+    // style is one of NSQ,BIN,MULTI and must match
+
+    if (style == NSQ) {
+      if (!(mask & NP_NSQ)) continue;
+    } else if (style == BIN) {
+      if (!(mask & NP_BIN)) continue;
+    } else if (style == MULTI) {
+      if (!(mask & NP_MULTI)) continue;
+    }
+
+    // newtflag is on or off and must match
+
+    if (newtflag) {
+      if (!(mask & NP_NEWTON)) continue;
+    } else if (!newtflag) {
+      if (!(mask & NP_NEWTOFF)) continue;
+    }
+
+    // triclinic flag is on or off and must match
+
+    if (triclinic) {
+      if (!(mask & NP_TRI)) continue;
+    } else if (!triclinic) {
+      if (!(mask & NP_ORTHO)) continue;
+    }
+
+    // Kokkos flags
+
     if (kokkos_device_flag != (mask & NP_KOKKOS_DEVICE)) continue;
     if (kokkos_host_flag != (mask & NP_KOKKOS_HOST)) continue;
 
-    if (style == NSQ && !(mask & NP_NSQ)) continue;
-    if (style == BIN && !(mask & NP_BIN)) continue;
-    if (style == MULTI && !(mask & NP_MULTI)) continue;
-
-    if (newtflag && !(mask & NP_NEWTON)) continue;
-    if (!newtflag && !(mask & NP_NEWTOFF)) continue;
-
-    if (!triclinic && !(mask & NP_ORTHO)) continue;
-    if (triclinic && !(mask & NP_TRI)) continue;
-
     return i+1;
   }
 
@@ -1727,7 +1755,7 @@ void Neighbor::build(int topoflag)
 
   for (i = 0; i < npair_perpetual; i++) {
     m = plist[i];
-    lists[m]->grow(nlocal,nall);
+    if (!lists[m]->copy) lists[m]->grow(nlocal,nall);
     neigh_pair[m]->build_setup();
     neigh_pair[m]->build(lists[m]);
   }

src/npair_skip.h

@@ -15,7 +15,8 @@
 
 NPairStyle(skip,
            NPairSkip,
-           NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | 
+           NP_SKIP | NP_HALF | NP_FULL | NP_HALFFULL |
+           NP_NSQ | NP_BIN | NP_MULTI | 
            NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
 
 #else