clean up code and comments

src/compute_property_local.cpp

@@ -405,7 +405,8 @@ int ComputePropertyLocal::count_pairs(int allflag, int forceflag)
       if (!(mask[j] & groupbit)) continue;
 
       // itag = jtag is possible for long cutoffs that include images of self
-
+      // do not need triclinic logic here b/c neighbor list itself is correct
+      
       if (newton_pair == 0 && j >= nlocal) {
         jtag = tag[j];
         if (itag > jtag) {

src/npair_half_bin_newton_tri.cpp

@@ -83,11 +83,12 @@ void NPairHalfBinNewtonTri::build(NeighList *list)
     }
 
     // loop over all atoms in bins in stencil
-    // pairs for atoms j "below" i are excluded
+    // for triclinic, bin stencil is full in all 3 dims
-    // below = lower z or (equal z and lower y) or (equal zy and lower x)
+    // must use itag/jtag to eliminate half the I/J interactions
-    //         (equal zyx and j <= i)
+    // cannot use I/J coord comparision
-    // latter excludes self-self interaction but allows superposed atoms
+    //   b/c transforming orthog -> lambda -> orthog for ghost atoms
-
+    //   with an added PBC offset can shift all 3 coords by epsilon
+    
     ibin = atom2bin[i];
     for (k = 0; k < nstencil; k++) {
       for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
@@ -107,25 +108,9 @@ void NPairHalfBinNewtonTri::build(NeighList *list)
 	    } else {
 	      if (x[j][0] < xtmp) continue;
 	    }
-	    //if (x[j][2] < ztmp) continue;
-	    //if (x[j][2] == ztmp) {
-	    //  if (x[j][1] < ytmp) continue;
-	    //  if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
-	    // }
 	  }
 	}
 
-	/*
-        if (x[j][2] < ztmp) continue;
-        if (x[j][2] == ztmp) {
-          if (x[j][1] < ytmp) continue;
-          if (x[j][1] == ytmp) {
-            if (x[j][0] < xtmp) continue;
-            if (x[j][0] == xtmp && j <= i) continue;
-          }
-        }
-	*/
-	
         jtype = type[j];
         if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
 
@@ -135,8 +120,6 @@ void NPairHalfBinNewtonTri::build(NeighList *list)
         rsq = delx*delx + dely*dely + delz*delz;
 
         if (rsq <= cutneighsq[itype][jtype]) {
-	  //printf("NEIGH i,j %d %d ijtag %d %d dist %g\n",
-	  //	 i,j,tag[i],tag[j],sqrt(rsq));
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);

src/npair_half_nsq_newton.cpp

@@ -89,7 +89,12 @@ void NPairHalfNsqNewton::build(NeighList *list)
     }
 
     // loop over remaining atoms, owned and ghost
+    // use itag/jtap comparision to eliminate half the interactions
     // itag = jtag is possible for long cutoffs that include images of self
+    // for triclinic, must use delta to eliminate half the I/J interactions
+    // cannot use direct I/J coord comparision as for orthog
+    //   b/c transforming orthog -> lambda -> orthog for ghost atoms
+    //   with an added PBC offset can shift all 3 coords by epsilon
 
     for (j = i+1; j < nall; j++) {
       if (includegroup && !(mask[j] & bitmask)) continue;

src/npair_halffull_newton.cpp

@@ -70,6 +70,11 @@ void NPairHalffullNewton::build(NeighList *list)
     ztmp = x[i][2];
 
     // loop over full neighbor list
+    // use i < j < nlocal to eliminate half the local/local interactions
+    // for triclinic, must use delta to eliminate half the local/ghost interactions
+    // cannot use direct I/J coord comparision as for orthog
+    //   b/c transforming orthog -> lambda -> orthog for ghost atoms
+    //   with an added PBC offset can shift all 3 coords by epsilon
 
     jlist = firstneigh_full[i];
     jnum = numneigh_full[i];

src/nstencil_half_bin_2d_tri.cpp

@@ -27,9 +27,17 @@ void NStencilHalfBin2dTri::create()
 {
   int i, j;
 
+  // for triclinic, need to use full stencil in all dims
+  //   not a half stencil in y
+  // b/c transforming orthog -> lambda -> orthog for ghost atoms
+  //   with an added PBC offset can shift both coords by epsilon
+  // thus for an I/J owned/ghost pair, the xy coords
+  //   and bin assignments can be different on I proc vs J proc
+
   nstencil = 0;
 
-  for (j = 0; j <= sy; j++)
+  for (j = -sy; j <= sy; j++)
     for (i = -sx; i <= sx; i++)
-      if (bin_distance(i, j, 0) < cutneighmaxsq) stencil[nstencil++] = j * mbinx + i;
+      if (bin_distance(i, j, 0) < cutneighmaxsq)
+	stencil[nstencil++] = j * mbinx + i;
 }

src/nstencil_half_bin_3d_tri.cpp

@@ -27,9 +27,15 @@ void NStencilHalfBin3dTri::create()
 {
   int i, j, k;
 
+  // for triclinic, need to use full stencil in all dims
+  //   not a half stencil in z
+  // b/c transforming orthog -> lambda -> orthog for ghost atoms
+  //   with an added PBC offset can shift all 3 coords by epsilon
+  // thus for an I/J owned/ghost pair, the xyz coords
+  //   and bin assignments can be different on I proc vs J proc
+  
   nstencil = 0;
 
-  //for (k = 0; k <= sz; k++)
   for (k = -sz; k <= sz; k++)
     for (j = -sy; j <= sy; j++)
       for (i = -sx; i <= sx; i++)