Iteration 0006 — c4128d3970b2 (accepted)

GitHub commit: c4128d3970b2 Published branch: fermilink-optimize/lammps-neighbor

Change summary

Refine the incumbent NPairBin<1,1,0,0,0>::build() fast path by early-accepting different-molecule pairs and skipping minimum_image_check() for owned same-molecule specials when special_flag[1..3] == 2.

Acceptance rationale

Correctness held and weighted_median_neigh_seconds improved from 0.32842 to 0.31969 (-2.66% vs incumbent), clearing the benchmark contract’s 2.0% promotion gate.

Guardrails & metrics

field	value
decision	ACCEPTED
correctness	ok
correctness mode	field_tolerances
hard reject	no
guardrail errors	0
incumbent commit	380bf2b0146b
candidate commit	c4128d3970b2
incumbent metric	0.32842
candidate metric	0.31969
baseline metric	0.36158
Δ vs incumbent	+2.658% (lower-is-better sign)
changed files	src/npair_bin.cpp

Diffstat

src/npair_bin.cpp | 16 ++++++++++++++++
1 file changed, 16 insertions(+)

Diff

download full diff

diff --git a/src/npair_bin.cpp b/src/npair_bin.cpp
index bd1fc1d338..42917b2dda 100644
--- a/src/npair_bin.cpp
+++ b/src/npair_bin.cpp
@@ -70,12 +70,16 @@ void NPairBin<1, 1, 0, 0, 0>::build(NeighList *list)
   ipage->reset();

   if (!exclude && molecular == Atom::MOLECULAR) {
+    const bool all_special_encoded =
+      (special_flag[1] == 2) && (special_flag[2] == 2) && (special_flag[3] == 2);
+
     for (i = 0; i < nlocal; i++) {
       n = 0;
       neighptr = ipage->vget();

       itype = type[i];
       const double *const cutneighsq_i = cutneighsq[itype];
+      const tagint molecule_i = molecule[i];
       const tagint *const special_i = special[i];
       const int *const nspecial_i = nspecial[i];
       xtmp = x[i][0];
@@ -102,10 +106,16 @@ void NPairBin<1, 1, 0, 0, 0>::build(NeighList *list)
         rsq = delx * delx + dely * dely + delz * delz;

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

         which = find_special(special_i, nspecial_i, tag[j]);
         if (which == 0)
           neighptr[n++] = j;
+        else if (all_special_encoded && (j < nlocal))
+          neighptr[n++] = j ^ (which << SBBITS);
         else if (domain->minimum_image_check(delx, dely, delz))
           neighptr[n++] = j;
         else if (which > 0)
@@ -123,10 +133,16 @@ void NPairBin<1, 1, 0, 0, 0>::build(NeighList *list)
           rsq = delx * delx + dely * dely + delz * delz;

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

           which = find_special(special_i, nspecial_i, tag[j]);
           if (which == 0)
             neighptr[n++] = j;
+          else if (all_special_encoded && (j < nlocal))
+            neighptr[n++] = j ^ (which << SBBITS);
           else if (domain->minimum_image_check(delx, dely, delz))
             neighptr[n++] = j;
           else if (which > 0)