Iteration 0018 — 08f5ab4a4e02 (accepted)

GitHub commit: 08f5ab4a4e02 Published branch: fermilink-optimize/lammps-neighbor

Change summary

Use explicit jnext linked-list traversal with bin/list _noalias aliases and delayed generic-only setup in the incumbent NPairBin<1,1,0,0,0> fast path

Acceptance rationale

Correctness passed and weighted_median_neigh_seconds dropped from 0.31150 to 0.29094 (-6.60% vs incumbent), comfortably clearing the 2.0% promotion gate.

Guardrails & metrics

field	value
decision	ACCEPTED
correctness	ok
correctness mode	field_tolerances
hard reject	no
guardrail errors	0
incumbent commit	8c29b124a2c6
candidate commit	08f5ab4a4e02
incumbent metric	0.3115
candidate metric	0.29094
baseline metric	0.36158
Δ vs incumbent	+6.600% (lower-is-better sign)
changed files	src/npair_bin.cpp

Diffstat

src/npair_bin.cpp | 60 +++++++++++++++++++++++++++++++++++++++----------------
1 file changed, 43 insertions(+), 17 deletions(-)

Diff

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diff --git a/src/npair_bin.cpp b/src/npair_bin.cpp
index 178d975ed0..dbf6866d61 100644
--- a/src/npair_bin.cpp
+++ b/src/npair_bin.cpp
@@ -50,22 +50,19 @@ void NPairBin<1, 1, 0, 0, 0>::build(NeighList *list)

   const auto * _noalias const x = (const dbl3_t *) atom->x[0];
   const int * _noalias const type = atom->type;
-  int * _noalias const mask = atom->mask;
   const tagint * _noalias const tag = atom->tag;
   tagint * _noalias const molecule = atom->molecule;
   tagint * const * _noalias const special = atom->special;
   int * const * _noalias const nspecial = atom->nspecial;
+  const int * _noalias const atom2bin = this->atom2bin;
+  const int * _noalias const bins = this->bins;
+  const int * _noalias const binhead = this->binhead;
+  const int * _noalias const stencil = this->stencil;
   int nlocal = atom->nlocal;
   if (includegroup) nlocal = atom->nfirst;
-
-  const bool moltemplate = (molecular == Atom::TEMPLATE);
-  int *molindex = atom->molindex;
-  int *molatom = atom->molatom;
-  Molecule **onemols = atom->avec->onemols;
-
-  int *ilist = list->ilist;
-  int *numneigh = list->numneigh;
-  int **firstneigh = list->firstneigh;
+  int * _noalias const ilist = list->ilist;
+  int * _noalias const numneigh = list->numneigh;
+  int ** _noalias const firstneigh = list->firstneigh;
   MyPage<int> *ipage = list->ipage;

   int inum = 0;
@@ -90,13 +87,23 @@ void NPairBin<1, 1, 0, 0, 0>::build(NeighList *list)

       ibin = atom2bin[i];

-      for (j = bins[i]; j >= 0; j = bins[j]) {
+      for (j = bins[i]; j >= 0; ) {
+        const int jnext = bins[j];
         const double *const xj = x[j];
         if (j >= nlocal) {
-          if (xj[2] < ztmp) continue;
+          if (xj[2] < ztmp) {
+            j = jnext;
+            continue;
+          }
           if (xj[2] == ztmp) {
-            if (xj[1] < ytmp) continue;
-            if ((xj[1] == ytmp) && (xj[0] < xtmp)) continue;
+            if (xj[1] < ytmp) {
+              j = jnext;
+              continue;
+            }
+            if ((xj[1] == ytmp) && (xj[0] < xtmp)) {
+              j = jnext;
+              continue;
+            }
           }
         }

@@ -107,9 +114,13 @@ void NPairBin<1, 1, 0, 0, 0>::build(NeighList *list)
         delz = ztmp - xj[2];
         rsq = delx * delx + dely * dely + delz * delz;

-        if (rsq > cutneighsq_i[jtype]) continue;
+        if (rsq > cutneighsq_i[jtype]) {
+          j = jnext;
+          continue;
+        }
         if (molecule_i != molecule[j]) {
           neighptr[n++] = j;
+          j = jnext;
           continue;
         }

@@ -122,10 +133,13 @@ void NPairBin<1, 1, 0, 0, 0>::build(NeighList *list)
           neighptr[n++] = j;
         else if (which > 0)
           neighptr[n++] = j ^ (which << SBBITS);
+
+        j = jnext;
       }

       for (k = 1; k < nstencil; k++) {
-        for (j = binhead[ibin + stencil[k]]; j >= 0; j = bins[j]) {
+        for (j = binhead[ibin + stencil[k]]; j >= 0; ) {
+          const int jnext = bins[j];
           const double *const xj = x[j];
           jtype = type[j];

@@ -134,9 +148,13 @@ void NPairBin<1, 1, 0, 0, 0>::build(NeighList *list)
           delz = ztmp - xj[2];
           rsq = delx * delx + dely * dely + delz * delz;

-          if (rsq > cutneighsq_i[jtype]) continue;
+          if (rsq > cutneighsq_i[jtype]) {
+            j = jnext;
+            continue;
+          }
           if (molecule_i != molecule[j]) {
             neighptr[n++] = j;
+            j = jnext;
             continue;
           }

@@ -149,6 +167,8 @@ void NPairBin<1, 1, 0, 0, 0>::build(NeighList *list)
             neighptr[n++] = j;
           else if (which > 0)
             neighptr[n++] = j ^ (which << SBBITS);
+
+          j = jnext;
         }
       }

@@ -163,6 +183,12 @@ void NPairBin<1, 1, 0, 0, 0>::build(NeighList *list)
     return;
   }

+  int * _noalias const mask = atom->mask;
+  const bool moltemplate = (molecular == Atom::TEMPLATE);
+  int * _noalias const molindex = atom->molindex;
+  int * _noalias const molatom = atom->molatom;
+  Molecule **onemols = atom->avec->onemols;
+
   for (i = 0; i < nlocal; i++) {
     n = 0;
     neighptr = ipage->vget();