Clarifying variable names

src/nstencil.cpp

@@ -79,9 +79,9 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp)
   stencil_multi = nullptr;  
   maxstencil_multi = nullptr;
  
-  stencil_half = nullptr;
+  flag_half_multi = nullptr;
-  stencil_skip = nullptr;
+  flag_skip_multi = nullptr;
-  stencil_bin_type = nullptr;
+  bin_type_multi = nullptr;
 
   dimension = domain->dimension;
 }
@@ -111,16 +111,16 @@ NStencil::~NStencil()
     memory->destroy(nstencil_multi);
     for (int i = 1; i <= n; i++) {
       for (int j = 0; j <= n; j++) {
-        if (! stencil_skip[i][j]) 
+        if (! flag_skip_multi[i][j]) 
             memory->destroy(stencil_multi[i][j]);
       }
       delete [] stencil_multi[i];
     }
     delete [] stencil_multi;
     memory->destroy(maxstencil_multi);
-    memory->destroy(stencil_half);
+    memory->destroy(flag_half_multi);
-    memory->destroy(stencil_skip);
+    memory->destroy(flag_skip_multi);
-    memory->destroy(stencil_bin_type);
+    memory->destroy(bin_type_multi);
     
     memory->destroy(stencil_sx_multi);
     memory->destroy(stencil_sy_multi);
@@ -272,12 +272,12 @@ void NStencil::create_setup()
     if(nb) copy_bin_info_multi();
 
     // Allocate arrays to store stencil information
-    memory->create(stencil_half, n+1, n+1, 
+    memory->create(flag_half_multi, n+1, n+1, 
-                   "neighstencil:stencil_half");
+                   "neighstencil:flag_half_multi");
-    memory->create(stencil_skip, n+1, n+1, 
+    memory->create(flag_skip_multi, n+1, n+1, 
-                   "neighstencil:stencil_skip");
+                   "neighstencil:flag_skip_multi");
-    memory->create(stencil_bin_type, n+1, n+1, 
+    memory->create(bin_type_multi, n+1, n+1, 
-                   "neighstencil:stencil_bin_type");
+                   "neighstencil:bin_type_multi");
 
     memory->create(stencil_sx_multi, n+1, n+1, 
                    "neighstencil:stencil_sx_multi");               
@@ -303,7 +303,7 @@ void NStencil::create_setup()
     // Skip all stencils by default, initialize smax
     for (i = 1; i <= n; i++) {
       for (j = 1; j <= n; j++) {
-        stencil_skip[i][j] = 1;   
+        flag_skip_multi[i][j] = 1;   
       }
     }
       
@@ -329,10 +329,10 @@ void NStencil::create_setup()
       for (j = 1; j <= n; j++) {
         
         // Skip creation of unused stencils 
-        if (stencil_skip[i][j]) continue;
+        if (flag_skip_multi[i][j]) continue;
            
-        // Copy bin info for this particular pair of types
+        // Copy bin info for this pair of atom types
-        bin_type = stencil_bin_type[i][j];
+        bin_type = bin_type_multi[i][j];
         
         stencil_binsizex_multi[i][j] = binsizex_multi[bin_type];
         stencil_binsizey_multi[i][j] = binsizey_multi[bin_type];

src/nstencil.h

@@ -42,9 +42,9 @@ class NStencil : protected Pointers {
   double cutoff_custom;            // cutoff set by requestor  
   
   // Arrays to store options for multi itype-jtype stencils
-  bool **stencil_half;             // flag creation of a half stencil for itype-jtype
+  bool **flag_half_multi;          // flag creation of a half stencil for itype-jtype
-  bool **stencil_skip;             // skip creation of itype-jtype stencils (for newton on)  
+  bool **flag_skip_multi;          // skip creation of itype-jtype stencils (for newton on)  
-  int **stencil_bin_type;          // what type to use for bin information
+  int **bin_type_multi;            // what type to use for bin information
 
   NStencil(class LAMMPS *);
   virtual ~NStencil();

src/nstencil_full_multi_2d.cpp

@@ -36,9 +36,9 @@ void NStencilFullMulti2d::set_stencil_properties()
 
   for (i = 1; i <= n; i++) {
     for (j = 1; j <= n; j++) {
-      stencil_half[i][j] = 0;
+      flag_half_multi[i][j] = 0;
-      stencil_skip[i][j] = 0;
+      flag_skip_multi[i][j] = 0;
-      stencil_bin_type[i][j] = j;
+      bin_type_multi[i][j] = j;
     }
   }
 }
@@ -56,7 +56,7 @@ void NStencilFullMulti2d::create()
   
   for (itype = 1; itype <= n; itype++) {
     for (jtype = 1; jtype <= n; jtype++) {
-      if (stencil_skip[itype][jtype]) continue;
+      if (flag_skip_multi[itype][jtype]) continue;
       
       ns = 0;
       
@@ -66,7 +66,7 @@ void NStencilFullMulti2d::create()
       mbinx = stencil_mbinx_multi[itype][jtype];
       mbiny = stencil_mbiny_multi[itype][jtype];
       
-      bin_type = stencil_bin_type[itype][jtype];
+      bin_type = bin_type_multi[itype][jtype];
       
       cutsq = cutneighsq[itype][jtype];
       

src/nstencil_full_multi_3d.cpp

@@ -37,9 +37,9 @@ void NStencilFullMulti3d::set_stencil_properties()
 
   for (i = 1; i <= n; i++) {
     for (j = 1; j <= n; j++) {
-      stencil_half[i][j] = 0;
+      flag_half_multi[i][j] = 0;
-      stencil_skip[i][j] = 0;
+      flag_skip_multi[i][j] = 0;
-      stencil_bin_type[i][j] = j;
+      bin_type_multi[i][j] = j;
     }
   }
 }
@@ -57,7 +57,7 @@ void NStencilFullMulti3d::create()
   
   for (itype = 1; itype <= n; itype++) {
     for (jtype = 1; jtype <= n; jtype++) {
-      if (stencil_skip[itype][jtype]) continue;
+      if (flag_skip_multi[itype][jtype]) continue;
       
       ns = 0;
       
@@ -69,7 +69,7 @@ void NStencilFullMulti3d::create()
       mbiny = stencil_mbiny_multi[itype][jtype];
       mbinz = stencil_mbinz_multi[itype][jtype];  
       
-      bin_type = stencil_bin_type[itype][jtype];
+      bin_type = bin_type_multi[itype][jtype];
       
       cutsq = cutneighsq[itype][jtype];
       

src/nstencil_half_multi_2d.cpp

@@ -42,14 +42,14 @@ void NStencilHalfMulti2d::set_stencil_properties()
     for (j = 1; j <= n; j++) {
       if(cutneighsq[i][i] > cutneighsq[j][j]) continue;
 
-      stencil_skip[i][j] = 0;
+      flag_skip_multi[i][j] = 0;
       
       if(cutneighsq[i][i] == cutneighsq[j][j]){
-        stencil_half[i][j] = 1;
+        flag_half_multi[i][j] = 1;
-        stencil_bin_type[i][j] = i;
+        bin_type_multi[i][j] = i;
       } else {
-        stencil_half[i][j] = 0;
+        flag_half_multi[i][j] = 0;
-        stencil_bin_type[i][j] = j;
+        bin_type_multi[i][j] = j;
       }
     }
   }
@@ -68,7 +68,7 @@ void NStencilHalfMulti2d::create()
   
   for (itype = 1; itype <= n; itype++) {
     for (jtype = 1; jtype <= n; jtype++) {
-      if (stencil_skip[itype][jtype]) continue;
+      if (flag_skip_multi[itype][jtype]) continue;
       
       ns = 0;
       
@@ -78,11 +78,11 @@ void NStencilHalfMulti2d::create()
       mbinx = stencil_mbinx_multi[itype][jtype];
       mbiny = stencil_mbiny_multi[itype][jtype];
       
-      bin_type = stencil_bin_type[itype][jtype];      
+      bin_type = bin_type_multi[itype][jtype];      
       
       cutsq = cutneighsq[itype][jtype];
       
-      if (stencil_half[itype][jtype]) {
+      if (flag_half_multi[itype][jtype]) {
         for (j = 0; j <= sy; j++)
           for (i = -sx; i <= sx; i++)
             if (j > 0 || (j == 0 && i > 0)) { 

src/nstencil_half_multi_2d_tri.cpp

@@ -42,14 +42,14 @@ void NStencilHalfMulti2dTri::set_stencil_properties()
     for (j = 1; j <= n; j++) {
       if(cutneighsq[i][i] > cutneighsq[j][j]) continue;
 
-      stencil_skip[i][j] = 0;
+      flag_skip_multi[i][j] = 0;
       
       if(cutneighsq[i][i] == cutneighsq[j][j]){
-        stencil_half[i][j] = 1;
+        flag_half_multi[i][j] = 1;
-        stencil_bin_type[i][j] = i;
+        bin_type_multi[i][j] = i;
       } else {
-        stencil_half[i][j] = 0;
+        flag_half_multi[i][j] = 0;
-        stencil_bin_type[i][j] = j;
+        bin_type_multi[i][j] = j;
       }
     }
   }
@@ -68,7 +68,7 @@ void NStencilHalfMulti2dTri::create()
   
   for (itype = 1; itype <= n; itype++) {
     for (jtype = 1; jtype <= n; jtype++) {
-      if (stencil_skip[itype][jtype]) continue;
+      if (flag_skip_multi[itype][jtype]) continue;
       
       ns = 0;
       
@@ -78,11 +78,11 @@ void NStencilHalfMulti2dTri::create()
       mbinx = stencil_mbinx_multi[itype][jtype];
       mbiny = stencil_mbiny_multi[itype][jtype];
       
-      bin_type = stencil_bin_type[itype][jtype];
+      bin_type = bin_type_multi[itype][jtype];
       
       cutsq = cutneighsq[itype][jtype];
       
-      if (stencil_half[itype][jtype]) {
+      if (flag_half_multi[itype][jtype]) {
         for (j = 0; j <= sy; j++)
           for (i = -sx; i <= sx; i++)
             if (bin_distance_multi(i,j,0,bin_type) < cutsq)

src/nstencil_half_multi_3d.cpp

@@ -42,14 +42,14 @@ void NStencilHalfMulti3d::set_stencil_properties()
     for (j = 1; j <= n; j++) {
       if(cutneighsq[i][i] > cutneighsq[j][j]) continue;
 
-      stencil_skip[i][j] = 0;
+      flag_skip_multi[i][j] = 0;
       
       if(cutneighsq[i][i] == cutneighsq[j][j]){
-        stencil_half[i][j] = 1;
+        flag_half_multi[i][j] = 1;
-        stencil_bin_type[i][j] = i;
+        bin_type_multi[i][j] = i;
       } else {
-        stencil_half[i][j] = 0;
+        flag_half_multi[i][j] = 0;
-        stencil_bin_type[i][j] = j;
+        bin_type_multi[i][j] = j;
       }
     }
   }
@@ -68,7 +68,7 @@ void NStencilHalfMulti3d::create()
   
   for (itype = 1; itype <= n; itype++) {
     for (jtype = 1; jtype <= n; jtype++) {
-      if (stencil_skip[itype][jtype]) continue;
+      if (flag_skip_multi[itype][jtype]) continue;
       
       ns = 0;
       
@@ -80,11 +80,11 @@ void NStencilHalfMulti3d::create()
       mbiny = stencil_mbiny_multi[itype][jtype];
       mbinz = stencil_mbinz_multi[itype][jtype];
       
-      bin_type = stencil_bin_type[itype][jtype];
+      bin_type = bin_type_multi[itype][jtype];
       
       cutsq = cutneighsq[itype][jtype];
       
-      if (stencil_half[itype][jtype]) {
+      if (flag_half_multi[itype][jtype]) {
         for (k = 0; k <= sz; k++)
           for (j = -sy; j <= sy; j++)
             for (i = -sx; i <= sx; i++)

src/nstencil_half_multi_3d_tri.cpp

@@ -42,14 +42,14 @@ void NStencilHalfMulti3dTri::set_stencil_properties()
     for (j = 1; j <= n; j++) {
       if(cutneighsq[i][i] > cutneighsq[j][j]) continue;
 
-      stencil_skip[i][j] = 0;
+      flag_skip_multi[i][j] = 0;
       
       if(cutneighsq[i][i] == cutneighsq[j][j]){
-        stencil_half[i][j] = 1;
+        flag_half_multi[i][j] = 1;
-        stencil_bin_type[i][j] = i;
+        bin_type_multi[i][j] = i;
       } else {
-        stencil_half[i][j] = 0;
+        flag_half_multi[i][j] = 0;
-        stencil_bin_type[i][j] = j;
+        bin_type_multi[i][j] = j;
       }
     }
   }
@@ -68,7 +68,7 @@ void NStencilHalfMulti3dTri::create()
   
   for (itype = 1; itype <= n; itype++) {
     for (jtype = 1; jtype <= n; jtype++) {
-      if (stencil_skip[itype][jtype]) continue;
+      if (flag_skip_multi[itype][jtype]) continue;
       
       ns = 0;
       
@@ -80,11 +80,11 @@ void NStencilHalfMulti3dTri::create()
       mbiny = stencil_mbiny_multi[itype][jtype];
       mbinz = stencil_mbinz_multi[itype][jtype];
       
-      bin_type = stencil_bin_type[itype][jtype];
+      bin_type = bin_type_multi[itype][jtype];
       
       cutsq = cutneighsq[itype][jtype];
       
-      if (stencil_half[itype][jtype]) {
+      if (flag_half_multi[itype][jtype]) {
         for (k = 0; k <= sz; k++)
           for (j = -sy; j <= sy; j++)
             for (i = -sx; i <= sx; i++)