Iteration 0019 — 11db74893452 (accepted)

GitHub commit: 11db74893452 Published branch: fermilink-optimize/lammps-neighbor

Change summary

Optimize Neighbor movement tracking by scanning contiguous x/xhold arrays in check_distance() and bulk-copying xhold in build() while keeping the incumbent npair_bin fast path unchanged

Acceptance rationale

Correctness held and weighted_median_neigh_seconds improved from 0.29094 to 0.28487 (-2.09% vs incumbent), 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	08f5ab4a4e02
candidate commit	11db74893452
incumbent metric	0.29094
candidate metric	0.28487
baseline metric	0.36158
Δ vs incumbent	+2.086% (lower-is-better sign)
changed files	src/neighbor.cpp

Diffstat

src/neighbor.cpp | 45 +++++++++++++++++++++++++++++++++++++--------
1 file changed, 37 insertions(+), 8 deletions(-)

Diff

download full diff

diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 6496a8c39a..391afb5899 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -2424,12 +2424,42 @@ int Neighbor::check_distance()
     }
   } else deltasq = triggersq;

-  double **x = atom->x;
+  using dbl3_t = double[3];
+
+  const auto * _noalias const x = (const dbl3_t *) atom->x[0];
+  const auto * _noalias const xhold = (const dbl3_t *) this->xhold[0];
   int nlocal = atom->nlocal;
   if (includegroup) nlocal = atom->nfirst;

   int flag = 0;
-  for (int i = 0; i < nlocal; i++) {
+  int i = 0;
+  for (; i + 3 < nlocal; i += 4) {
+    const double delx0 = x[i][0] - xhold[i][0];
+    const double dely0 = x[i][1] - xhold[i][1];
+    const double delz0 = x[i][2] - xhold[i][2];
+    const double rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
+
+    const double delx1 = x[i+1][0] - xhold[i+1][0];
+    const double dely1 = x[i+1][1] - xhold[i+1][1];
+    const double delz1 = x[i+1][2] - xhold[i+1][2];
+    const double rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
+
+    const double delx2 = x[i+2][0] - xhold[i+2][0];
+    const double dely2 = x[i+2][1] - xhold[i+2][1];
+    const double delz2 = x[i+2][2] - xhold[i+2][2];
+    const double rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
+
+    const double delx3 = x[i+3][0] - xhold[i+3][0];
+    const double dely3 = x[i+3][1] - xhold[i+3][1];
+    const double delz3 = x[i+3][2] - xhold[i+3][2];
+    const double rsq3 = delx3*delx3 + dely3*dely3 + delz3*delz3;
+
+    if ((rsq0 > deltasq) || (rsq1 > deltasq) || (rsq2 > deltasq) || (rsq3 > deltasq)) {
+      flag = 1;
+      break;
+    }
+  }
+  for (; i < nlocal; i++) {
     delx = x[i][0] - xhold[i][0];
     dely = x[i][1] - xhold[i][1];
     delz = x[i][2] - xhold[i][2];
@@ -2472,18 +2502,17 @@ void Neighbor::build(int topoflag)
   // store current atom positions and box size if needed

   if (dist_check) {
-    double **x = atom->x;
+    using dbl3_t = double[3];
+
     if (includegroup) nlocal = atom->nfirst;
     if (atom->nmax > maxhold) {
       maxhold = atom->nmax;
       memory->destroy(xhold);
       memory->create(xhold,maxhold,3,"neigh:xhold");
     }
-    for (i = 0; i < nlocal; i++) {
-      xhold[i][0] = x[i][0];
-      xhold[i][1] = x[i][1];
-      xhold[i][2] = x[i][2];
-    }
+    const auto * _noalias const x = (const dbl3_t *) atom->x[0];
+    auto * _noalias const xhold = (dbl3_t *) this->xhold[0];
+    if (nlocal > 0) std::memcpy(xhold, x, sizeof(dbl3_t) * nlocal);
     if (boxcheck) {
       if (triclinic == 0) {
         boxlo_hold[0] = bboxlo[0];