Fixing misc valgrind issues, particularly with resizing ncollections

src/comm.cpp

@@ -58,6 +58,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
   bordergroup = 0;
   cutghostuser = 0.0;
   cutusermulti = nullptr;
+  cutusermultiflag = 0;
   cutusermultiold = nullptr;
   ncollections_prior = 0;
   ghost_velocity = 0;
@@ -348,6 +349,7 @@ void Comm::modify_params(int narg, char **arg)
       // ncollections can be changed by neigh_modify commands
       cut = utils::numeric(FLERR,arg[iarg+2],false,lmp);
       cutghostuser = MAX(cutghostuser,cut);
+      cutusermultiflag = 1;
       if (cut < 0.0)
         error->all(FLERR,"Invalid cutoff in comm_modify command");
       usermultiargs.emplace_back(arg[iarg+1], cut);   

src/comm.h

@@ -33,6 +33,7 @@ class Comm : protected Pointers {
   double cutghost[3];               // cutoffs used for acquiring ghost atoms
   double cutghostuser;              // user-specified ghost cutoff (mode == 0)
   double *cutusermulti;             // per collection user ghost cutoff (mode == 1)
+  int cutusermultiflag;             
   std::vector<std::pair<std::string, double>> usermultiargs; 
                                     // collection args for custom ghost cutoffs  
   double *cutusermultiold;          // per type user ghost cutoff (mode == 2)

src/comm_brick.cpp

@@ -142,6 +142,7 @@ void CommBrick::init()
   // allocate in setup
 
   if (mode == Comm::MULTI && multilo == nullptr) {
+    ncollections = neighbor->ncollections;
     allocate_multi(maxswap);
     memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti");
     ncollections_prior = ncollections;
@@ -205,10 +206,12 @@ void CommBrick::setup()
     
       allocate_multi(maxswap);
       memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti");  
-      memory->grow(cutusermulti,ncollections,"comm:cutusermulti");
+      if(cutusermultiflag) {
-      for(i = ncollections_prior; i < ncollections; i++)
+        memory->grow(cutusermulti,ncollections,"comm:cutusermulti");
-        cutusermulti[i] = -1.0;
+        for(i = ncollections_prior; i < ncollections; i++)
-    
+          cutusermulti[i] = -1.0;
+      }
+      
       ncollections_prior = ncollections;
     }
   

src/comm_tiled.cpp

@@ -104,6 +104,11 @@ void CommTiled::init_buffers()
   cutghostmultiold = nullptr;
   sendbox_multi = nullptr;
   sendbox_multiold = nullptr;
+  
+  // initialize ncollections so grow_swap_send_multi() will not 
+  // construct arrays in init() but will wait for setup()
+  ncollections = 0;
+  ncollections_prior = 0;
 
   maxswap = 6;
   allocate_swap(maxswap);
@@ -194,10 +199,12 @@ void CommTiled::setup()
       for(i = 0; i < maxswap; i ++)
         grow_swap_send_multi(i,DELTA_PROCS);
     
-      memory->grow(cutusermulti,ncollections,"comm:cutusermulti");
+      if(cutusermultiflag){
-      for(i = ncollections_prior; i < ncollections; i++)
+        memory->grow(cutusermulti,ncollections,"comm:cutusermulti");
-        cutusermulti[i] = -1.0;    
+        for(i = ncollections_prior; i < ncollections; i++)
-    
+          cutusermulti[i] = -1.0;    
+      } 
+      
       ncollections_prior = ncollections;    
     }      
 

src/nbin_multi.cpp

@@ -146,7 +146,7 @@ void NBinMulti::setup_bins(int /*style*/)
 
   // Identify smallest collection
   int icollectionmin = 0;
-  for (n = 0; n < maxcollections; n++)
+  for (n = 0; n < ncollections; n++)
     if (cutcollectionsq[n][n] < cutcollectionsq[icollectionmin][icollectionmin]) 
       icollectionmin = n;
 
@@ -188,7 +188,7 @@ void NBinMulti::setup_bins(int /*style*/)
   double binsize_optimal, binsizeinv, coord;
   int mbinxhi,mbinyhi,mbinzhi;
 
-  for (n = 0; n < maxcollections; n++) {
+  for (n = 0; n < ncollections; n++) {
     // binsize_user only relates to smallest collection
     // optimal bin size is roughly 1/2 the collection-collection cutoff
     // special case of all cutoffs = 0.0, binsize = box size
@@ -296,7 +296,7 @@ void NBinMulti::bin_atoms()
   int i,ibin,n;
 
   last_bin = update->ntimestep;
-  for (n = 0; n < maxcollections; n++) {
+  for (n = 0; n < ncollections; n++) {
     for (i = 0; i < mbins_multi[n]; i++) binhead_multi[n][i] = -1;
   }
   // bin in reverse order so linked list will be in forward order

src/neighbor.cpp

@@ -426,7 +426,7 @@ void Neighbor::init()
         for(i = 1; i <= n; i++){
           cuttmp = sqrt(cutneighsq[i][i]);
           for(icollection = 0; icollection < ncollections; icollection ++){
-            if(collection2cut[icollection] > cuttmp) {
+            if(collection2cut[icollection] >= cuttmp) {
               type2collection[i] = icollection;
               break;
             }
@@ -2503,6 +2503,8 @@ void Neighbor::modify_params(int narg, char **arg)
       if(iarg+2 > narg)
         error->all(FLERR,"Invalid collection/interval command");
       ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
+      if(ncollections < 1)
+        error->all(FLERR,"Invalid collection/interval command");
       if(iarg+1+ncollections > narg)
         error->all(FLERR,"Invalid collection/interval command");
 
@@ -2511,8 +2513,7 @@ void Neighbor::modify_params(int narg, char **arg)
       
       interval_collection_flag = 1;
       custom_collection_flag = 1;
-      if(not collection2cut)
+      memory->grow(collection2cut,ncollections,"neigh:collection2cut");  
-        memory->create(collection2cut,ncollections,"neigh:collection2cut");  
 
       // Set upper cutoff for each collection
       char *id;
@@ -2534,6 +2535,8 @@ void Neighbor::modify_params(int narg, char **arg)
       if(iarg+2 > narg)
         error->all(FLERR,"Invalid collection/type command");
       ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
+      if(ncollections < 1)
+        error->all(FLERR,"Invalid collection/interval command");      
       if(iarg+1+ncollections > narg)
         error->all(FLERR,"Invalid collection/type command");
 

src/nstencil.cpp

@@ -82,6 +82,8 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp)
   flag_half_multi = nullptr;
   flag_skip_multi = nullptr;
   bin_collection_multi = nullptr;
+  
+  maxcollections = 0;
 
   dimension = domain->dimension;
 }
@@ -105,15 +107,12 @@ NStencil::~NStencil()
     delete [] distsq_multi_old;
   }
   
-  if (stencil_multi) {
+  if (maxstencil_multi) {
       
-    int n = ncollections;      
     memory->destroy(nstencil_multi);
-    for (int i = 0; i < n; i++) {
+    for (int i = 0; i < maxcollections; i++) {
-      for (int j = 0; j < n; j++) {
+      for (int j = 0; j < maxcollections; j++)
-        if (! flag_skip_multi[i][j]) 
+          memory->destroy(stencil_multi[i][j]);
-            memory->destroy(stencil_multi[i][j]);
-      }
       delete [] stencil_multi[i];
     }
     delete [] stencil_multi;
@@ -275,47 +274,60 @@ void NStencil::create_setup()
     
     if(nb) copy_bin_info_multi();
 
-    // Allocate arrays to store stencil information
+    // Deallocate arrays if previously allocated
-    memory->create(flag_half_multi, n, n, 
+    if(n > maxcollections and stencil_multi){  
-                   "neighstencil:flag_half_multi");
+      memory->destroy(nstencil_multi);
-    memory->create(flag_skip_multi, n, n, 
+      for (i = 0; i < maxcollections; i++) {
-                   "neighstencil:flag_skip_multi");
+        for (j = 0; j < maxcollections; j++)
-    memory->create(bin_collection_multi, n, n, 
+          memory->destroy(stencil_multi[i][j]);
-                   "neighstencil:bin_collection_multi");
+        delete [] stencil_multi[i];
-
-    memory->create(stencil_sx_multi, n, n, 
-                   "neighstencil:stencil_sx_multi");               
-    memory->create(stencil_sy_multi, n, n, 
-                   "neighstencil:stencil_sy_multi");
-    memory->create(stencil_sz_multi, n, n, 
-                   "neighstencil:stencil_sz_multi");
-
-    memory->create(stencil_binsizex_multi, n, n, 
-                   "neighstencil:stencil_binsizex_multi");
-    memory->create(stencil_binsizey_multi, n, n, 
-                   "neighstencil:stencil_binsizey_multi");
-    memory->create(stencil_binsizez_multi, n, n, 
-                   "neighstencil:stencil_binsizez_multi");
-
-    memory->create(stencil_mbinx_multi, n, n, 
-                   "neighstencil:stencil_mbinx_multi");
-    memory->create(stencil_mbiny_multi, n, n, 
-                   "neighstencil:stencil_mbiny_multi");
-    memory->create(stencil_mbinz_multi, n, n, 
-                   "neighstencil:stencil_mbinz_multi");
-
-    // Skip all stencils by default, initialize smax
-    for (i = 0; i < n; i++) {
-      for (j = 0; j < n; j++) {
-        flag_skip_multi[i][j] = 1;   
       }
-    }
+      delete [] stencil_multi;   
+      memory->destroy(maxstencil_multi);    
+      memory->destroy(flag_half_multi);
+      memory->destroy(flag_skip_multi);
+      memory->destroy(bin_collection_multi);
+      memory->destroy(stencil_sx_multi);
+      memory->destroy(stencil_sy_multi);
+      memory->destroy(stencil_sz_multi);
+      memory->destroy(stencil_binsizex_multi);
+      memory->destroy(stencil_binsizey_multi);
+      memory->destroy(stencil_binsizez_multi);
+      memory->destroy(stencil_mbinx_multi);
+      memory->destroy(stencil_mbiny_multi);
+      memory->destroy(stencil_mbinz_multi);      
+    }      
       
-    // Determine which stencils need to be built
+    // Allocate arrays 
-    set_stencil_properties(); 
+    if(!maxstencil_multi) {   
-    
+      memory->create(flag_half_multi, n, n, 
-    // Allocate arrays to store stencils
+                     "neighstencil:flag_half_multi");
-    if (!maxstencil_multi) {
+      memory->create(flag_skip_multi, n, n, 
+                     "neighstencil:flag_skip_multi");
+      memory->create(bin_collection_multi, n, n, 
+                     "neighstencil:bin_collection_multi");
+      
+      memory->create(stencil_sx_multi, n, n, 
+                     "neighstencil:stencil_sx_multi");               
+      memory->create(stencil_sy_multi, n, n, 
+                     "neighstencil:stencil_sy_multi");
+      memory->create(stencil_sz_multi, n, n, 
+                     "neighstencil:stencil_sz_multi");
+      
+      memory->create(stencil_binsizex_multi, n, n, 
+                     "neighstencil:stencil_binsizex_multi");
+      memory->create(stencil_binsizey_multi, n, n, 
+                     "neighstencil:stencil_binsizey_multi");
+      memory->create(stencil_binsizez_multi, n, n, 
+                     "neighstencil:stencil_binsizez_multi");
+      
+      memory->create(stencil_mbinx_multi, n, n, 
+                     "neighstencil:stencil_mbinx_multi");
+      memory->create(stencil_mbiny_multi, n, n, 
+                     "neighstencil:stencil_mbiny_multi");
+      memory->create(stencil_mbinz_multi, n, n, 
+                     "neighstencil:stencil_mbinz_multi");
+                     
       memory->create(maxstencil_multi, n, n, "neighstencil::maxstencil_multi");
       memory->create(nstencil_multi, n, n, "neighstencil::nstencil_multi");
       stencil_multi = new int**[n]();
@@ -326,12 +338,22 @@ void NStencil::create_setup()
           nstencil_multi[i][j] = 0;
           stencil_multi[i][j] = nullptr;
         }
+      }       
+      maxcollections = n;      
+    }
+    
+    // Skip all stencils by default, initialize smax
+    for (i = 0; i < n; i++) {
+      for (j = 0; j < n; j++) {
+        flag_skip_multi[i][j] = 1;   
       }
-    }    
+    }
+      
+    // Determine which stencils need to be built
+    set_stencil_properties();  
     
     for (i = 0; i < n; i++) {
       for (j = 0; j < n; j++) {
-        
         // Skip creation of unused stencils 
         if (flag_skip_multi[i][j]) continue;
            
@@ -364,7 +386,8 @@ void NStencil::create_setup()
         
         if (smax > maxstencil_multi[i][j]) {
           maxstencil_multi[i][j] = smax;
-          memory->destroy(stencil_multi[i][j]);
+          if(stencil_multi[i][j])
+            memory->destroy(stencil_multi[i][j]);
           memory->create(stencil_multi[i][j], smax,
 	  	                 "neighstencil::stencil_multi");
         }

src/nstencil.h

@@ -33,6 +33,7 @@ class NStencil : protected Pointers {
   int ** nstencil_multi;           // # bins bins in each igroup-jgroup multi stencil
   int *** stencil_multi;           // list of bin offsets in each multi stencil
   int ** maxstencil_multi;         // max stencil size for each multi stencil
+  int maxcollections;              // size of multi arrays
   
   int sx,sy,sz;                    // extent of stencil in each dim
   int **stencil_sx_multi;         // analogs for each multi stencil
@@ -42,7 +43,7 @@ class NStencil : protected Pointers {
   double cutoff_custom;            // cutoff set by requestor  
   
   // Arrays to store options for multi itype-jtype stencils
-  bool **flag_half_multi;          // flag creation of a half stencil for igroup-jgroup
+  bool **flag_half_multi;          // flag creation of a half stencil for icollection-jcollection
   bool **flag_skip_multi;          // skip creation of icollection-jcollection stencils (for newton on)  
   int **bin_collection_multi;      // what collection to use for bin information
 

src/nstencil_half_multi_2d.cpp

@@ -71,7 +71,7 @@ void NStencilHalfMulti2d::create()
       if (flag_skip_multi[icollection][jcollection]) continue;
       
       ns = 0;
-      
+            
       sx = stencil_sx_multi[icollection][jcollection];
       sy = stencil_sy_multi[icollection][jcollection];