Calculating short neighbor lists

src/KOKKOS/pair_vashishta_kokkos.cpp

@@ -108,7 +108,7 @@ void PairVashishtaKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   newton_pair = force->newton_pair;
   nall = atom->nlocal + atom->nghost;
 
-  const int inum = list->inum;
+  inum = list->inum;
   const int ignum = inum + list->gnum;
   NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
   d_ilist = k_list->d_ilist;
@@ -121,6 +121,29 @@ void PairVashishtaKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   EV_FLOAT ev;
   EV_FLOAT ev_all;
 
+  int max_neighs = d_neighbors.dimension_1();
+
+  if ((d_neighbors_short_2body.dimension_1() != max_neighs) ||
+     (d_neighbors_short_2body.dimension_0() != ignum)) {
+    d_neighbors_short_2body = Kokkos::View<int**,DeviceType>("Vashishta::neighbors_short_2body",ignum,max_neighs);
+  }
+  if (d_numneigh_short_2body.dimension_0()!=ignum) {
+    d_numneigh_short_2body = Kokkos::View<int*,DeviceType>("Vashishta::numneighs_short_2body",ignum);
+  }
+  
+  if ((d_neighbors_short_3body.dimension_1() != max_neighs) ||
+     (d_neighbors_short_3body.dimension_0() != ignum)) {
+    d_neighbors_short_3body = Kokkos::View<int**,DeviceType>("Vashishta::neighbors_short_3body",ignum,max_neighs);
+  }
+
+  if (d_numneigh_short_3body.dimension_0()!=ignum) {
+    d_numneigh_short_3body = Kokkos::View<int*,DeviceType>("Vashishta::numneighs_short_3body",ignum);
+  }
+
+  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairVashishtaComputeShortNeigh>(0,neighflag==FULL?ignum:inum), *this);
+
+
+
   // loop over neighbor list of my atoms
 
   if (neighflag == HALF) {
@@ -174,6 +197,40 @@ void PairVashishtaKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   copymode = 0;
 }
 
+template<class DeviceType>
+KOKKOS_INLINE_FUNCTION
+void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeShortNeigh, const int& ii) const {
+    const int i = d_ilist[ii];
+    const X_FLOAT xtmp = x(i,0);
+    const X_FLOAT ytmp = x(i,1);
+    const X_FLOAT ztmp = x(i,2);
+
+    const int jnum = d_numneigh[i];
+    int inside_2body = 0;
+    int inside_3body = 0;
+    for (int jj = 0; jj < jnum; jj++) {
+      int j = d_neighbors(i,jj);
+      j &= NEIGHMASK;
+
+      const X_FLOAT delx = xtmp - x(j,0);
+      const X_FLOAT dely = ytmp - x(j,1);
+      const X_FLOAT delz = ztmp - x(j,2);
+      const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
+
+      if (rsq < cutmax*cutmax) {
+        d_neighbors_short_2body(i,inside_2body) = j;
+        inside_2body++;
+      }
+
+      if (rsq < cutmax_3body*cutmax_3body) {
+        d_neighbors_short_3body(i,inside_3body) = j;
+        inside_3body++;
+      }
+    }
+    d_numneigh_short_2body(i) = inside_2body;
+    d_numneigh_short_3body(i) = inside_3body;
+}
+
 template<class DeviceType>
 template<int NEIGHFLAG, int EVFLAG>
 KOKKOS_INLINE_FUNCTION

src/KOKKOS/pair_vashishta_kokkos.h

@@ -34,6 +34,8 @@ struct TagPairVashishtaComputeFullA{};
 template<int NEIGHFLAG, int EVFLAG>
 struct TagPairVashishtaComputeFullB{};
 
+struct TagPairVashishtaComputeShortNeigh{};
+
 namespace LAMMPS_NS {
 
 template<class DeviceType>
@@ -75,6 +77,9 @@ class PairVashishtaKokkos : public PairVashishta {
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairVashishtaComputeFullB<NEIGHFLAG,EVFLAG>, const int&) const;
 
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairVashishtaComputeShortNeigh, const int&) const;
+
   template<int NEIGHFLAG>
   KOKKOS_INLINE_FUNCTION
   void ev_tally(EV_FLOAT &ev, const int &i, const int &j,
@@ -136,7 +141,10 @@ class PairVashishtaKokkos : public PairVashishta {
   int nlocal,nall,eflag,vflag;
 
   int inum;
-
+  Kokkos::View<int**,DeviceType> d_neighbors_short_2body;
+  Kokkos::View<int*,DeviceType> d_numneigh_short_2body;
+  Kokkos::View<int**,DeviceType> d_neighbors_short_3body;
+  Kokkos::View<int*,DeviceType> d_numneigh_short_3body;
   friend void pair_virial_fdotr_compute<PairVashishtaKokkos>(PairVashishtaKokkos*);
 };
 

src/MANYBODY/pair_vashishta.cpp

@@ -532,11 +532,12 @@ void PairVashishta::setup_params()
   }
 
   // set cutmax to max of all params
-
+  cutmax_3body = 0.0;
   cutmax = 0.0;
   for (m = 0; m < nparams; m++) {
     if (params[m].cut > cutmax) cutmax = params[m].cut;
     if (params[m].r0 > cutmax) cutmax = params[m].r0;
+    if (params[m].r0 > cutmax_3body) cutmax_3body = params[m].r0;
   }
 }
 

src/MANYBODY/pair_vashishta.h

@@ -46,6 +46,7 @@ class PairVashishta : public Pair {
   };
  protected:
   double cutmax;                // max cutoff for all elements
+  double cutmax_3body;                // max cutoff for all elements
   int nelements;                // # of unique elements
   char **elements;              // names of unique elements
   int ***elem2param;            // mapping from element triplets to parameters