Merge pull request lammps#4080 from rbberger/compute_reaxff_atom_over…

…flow_fix

Fix buffer overflow in compute reaxff/atom

src/KOKKOS/compute_reaxff_atom_kokkos.cpp

@@ -67,10 +67,10 @@ void ComputeReaxFFAtomKokkos<DeviceType>::init()
 template<class DeviceType>
 void ComputeReaxFFAtomKokkos<DeviceType>::compute_bonds()
 {
-  if (atom->nlocal > nlocal) {
+  if (atom->nmax > nmax) {
     memory->destroy(array_atom);
-    nlocal = atom->nlocal;
-    memory->create(array_atom, nlocal, 3, "reaxff/atom:array_atom");
+    nmax = atom->nmax;
+    memory->create(array_atom, nmax, 3, "reaxff/atom:array_atom");
   }
 
   // retrieve bond information from kokkos pair style. the data potentially
@@ -85,6 +85,7 @@ void ComputeReaxFFAtomKokkos<DeviceType>::compute_bonds()
   else
     host_pair()->FindBond(maxnumbonds, groupbit);
 
+  const int nlocal = atom->nlocal;
   nbuf = ((store_bonds ? maxnumbonds*2 : 0) + 3)*nlocal;
 
   if (!buf || ((int)k_buf.extent(0) < nbuf)) {
@@ -135,6 +136,7 @@ void ComputeReaxFFAtomKokkos<DeviceType>::compute_local()
   int b = 0;
   int j = 0;
   auto tag = atom->tag;
+  const int nlocal = atom->nlocal;
 
   for (int i = 0; i < nlocal; ++i) {
     const int numbonds = static_cast<int>(buf[j+2]);
@@ -161,6 +163,7 @@ void ComputeReaxFFAtomKokkos<DeviceType>::compute_peratom()
     compute_bonds();
 
   // extract peratom bond information from buffer
+  const int nlocal = atom->nlocal;
 
   int j = 0;
   for (int i = 0; i < nlocal; ++i) {
@@ -180,7 +183,7 @@ void ComputeReaxFFAtomKokkos<DeviceType>::compute_peratom()
 template<class DeviceType>
 double ComputeReaxFFAtomKokkos<DeviceType>::memory_usage()
 {
-  double bytes = (double)(nlocal*3) * sizeof(double);
+  double bytes = (double)(nmax*3) * sizeof(double);
   if (store_bonds)
     bytes += (double)(nbonds*3) * sizeof(double);
   bytes += (double)(nbuf > 0 ? nbuf * sizeof(double) : 0);

src/REAXFF/compute_reaxff_atom.cpp

@@ -43,7 +43,7 @@ ComputeReaxFFAtom::ComputeReaxFFAtom(LAMMPS *lmp, int narg, char **arg) :
 
   // initialize output
 
-  nlocal = -1;
+  nmax = -1;
   nbonds = 0;
   prev_nbonds = -1;
 
@@ -162,20 +162,22 @@ void ComputeReaxFFAtom::compute_bonds()
 {
   invoked_bonds = update->ntimestep;
 
-  if (atom->nlocal > nlocal) {
+  if (atom->nmax > nmax) {
     memory->destroy(abo);
     memory->destroy(neighid);
     memory->destroy(bondcount);
     memory->destroy(array_atom);
-    nlocal = atom->nlocal;
+    nmax = atom->nmax;
     if (store_bonds) {
-      memory->create(abo, nlocal, MAXREAXBOND, "reaxff/atom:abo");
-      memory->create(neighid, nlocal, MAXREAXBOND, "reaxff/atom:neighid");
+      memory->create(abo, nmax, MAXREAXBOND, "reaxff/atom:abo");
+      memory->create(neighid, nmax, MAXREAXBOND, "reaxff/atom:neighid");
     }
-    memory->create(bondcount, nlocal, "reaxff/atom:bondcount");
-    memory->create(array_atom, nlocal, 3, "reaxff/atom:array_atom");
+    memory->create(bondcount, nmax, "reaxff/atom:bondcount");
+    memory->create(array_atom, nmax, 3, "reaxff/atom:array_atom");
   }
 
+  const int nlocal = atom->nlocal;
+
   for (int i = 0; i < nlocal; i++) {
     bondcount[i] = 0;
     for (int j = 0; store_bonds && j < MAXREAXBOND; j++) {
@@ -208,6 +210,8 @@ void ComputeReaxFFAtom::compute_local()
 
   int b = 0;
 
+  const int nlocal = atom->nlocal;
+
   for (int i = 0; i < nlocal; ++i) {
     const int numbonds = bondcount[i];
 
@@ -230,6 +234,8 @@ void ComputeReaxFFAtom::compute_peratom()
     compute_bonds();
   }
 
+  const int nlocal = atom->nlocal;
+
   for (int i = 0; i < nlocal; ++i) {
     auto ptr = array_atom[i];
     ptr[0] = reaxff->api->workspace->total_bond_order[i];
@@ -244,10 +250,10 @@ void ComputeReaxFFAtom::compute_peratom()
 
 double ComputeReaxFFAtom::memory_usage()
 {
-  double bytes = (double)(nlocal*3) * sizeof(double);
-  bytes += (double)(nlocal) * sizeof(int);
+  double bytes = (double)(nmax*3) * sizeof(double);
+  bytes += (double)(nmax) * sizeof(int);
   if (store_bonds) {
-    bytes += (double)(2*nlocal*MAXREAXBOND) * sizeof(double);
+    bytes += (double)(2*nmax*MAXREAXBOND) * sizeof(double);
     bytes += (double)(nbonds*3) * sizeof(double);
   }
   return bytes;

src/REAXFF/compute_reaxff_atom.h

@@ -40,7 +40,7 @@ class ComputeReaxFFAtom : public Compute {
 
  protected:
   bigint invoked_bonds;     // last timestep on which compute_bonds() was invoked
-  int nlocal;
+  int nmax;
   int nbonds;
   int prev_nbonds;
   int nsub;