Add trim methods from OPENMP

src/OPENMP/npair_halffull_newtoff_trim_omp.cpp

@@ -0,0 +1,109 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_halffull_newtoff_trim_omp.h"
+
+#include "atom.h"
+#include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalffullNewtoffTrimOmp::NPairHalffullNewtoffTrimOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+   build half list from full list and trim to shorter cutoff
+   pair stored once if i,j are both owned and i < j
+   pair stored by me if j is ghost (also stored by proc owning j)
+   works if full list is a skip list
+------------------------------------------------------------------------- */
+
+void NPairHalffullNewtoffTrimOmp::build(NeighList *list)
+{
+  const int inum_full = list->listfull->inum;
+
+  NPAIR_OMP_INIT;
+
+#if defined(_OPENMP)
+#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
+#endif
+  NPAIR_OMP_SETUP(inum_full);
+
+  int i,j,ii,jj,n,jnum,joriginal;
+  int *neighptr,*jlist;
+  double xtmp,ytmp,ztmp;
+  double delx,dely,delz,rsq;
+
+  double **x = atom->x;
+
+  int *ilist = list->ilist;
+  int *numneigh = list->numneigh;
+  int **firstneigh = list->firstneigh;
+  int *ilist_full = list->listfull->ilist;
+  int *numneigh_full = list->listfull->numneigh;
+  int **firstneigh_full = list->listfull->firstneigh;
+
+  // each thread has its own page allocator
+  MyPage<int> &ipage = list->ipage[tid];
+  ipage.reset();
+
+  double cutsq_custom = cutoff_custom * cutoff_custom;
+
+  // loop over atoms in full list
+
+  for (ii = ifrom; ii < ito; ii++) {
+
+    n = 0;
+    neighptr = ipage.vget();
+
+    // loop over parent full list
+
+    i = ilist_full[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+
+    jlist = firstneigh_full[i];
+    jnum = numneigh_full[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      joriginal = jlist[jj];
+      j = joriginal & NEIGHMASK;
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx * delx + dely * dely + delz * delz;
+
+      if (rsq > cutsq_custom) continue;
+
+      if (j > i) neighptr[n++] = joriginal;
+    }
+
+    ilist[ii] = i;
+    firstneigh[i] = neighptr;
+    numneigh[i] = n;
+    ipage.vgot(n);
+    if (ipage.status())
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+  }
+  NPAIR_OMP_CLOSE;
+  list->inum = inum_full;
+}

src/OPENMP/npair_halffull_newtoff_trim_omp.h

@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+// clang-format off
+NPairStyle(halffull/newtoff/trim/omp,
+           NPairHalffullNewtoffTrimOmp,
+           NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF |
+           NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
+
+NPairStyle(halffull/newtoff/skip/trim/omp,
+           NPairHalffullNewtoffTrimOmp,
+           NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF |
+           NP_ORTHO | NP_TRI | NP_SKIP | NP_TRIM | NP_OMP);
+// clang-format on
+#else
+
+#ifndef LMP_NPAIR_HALFFULL_NEWTOFF_TRIM_OMP_H
+#define LMP_NPAIR_HALFFULL_NEWTOFF_TRIM_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalffullNewtoffTrimOmp : public NPair {
+ public:
+  NPairHalffullNewtoffTrimOmp(class LAMMPS *);
+  void build(class NeighList *) override;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

src/OPENMP/npair_halffull_newton_trim_omp.cpp

@@ -0,0 +1,118 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_halffull_newton_trim_omp.h"
+
+#include "atom.h"
+#include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalffullNewtonTrimOmp::NPairHalffullNewtonTrimOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+   build half list from full list and trim to shorter cutoff
+   pair stored once if i,j are both owned and i < j
+   if j is ghost, only store if j coords are "above and to the right" of i
+   works if full list is a skip list
+------------------------------------------------------------------------- */
+
+void NPairHalffullNewtonTrimOmp::build(NeighList *list)
+{
+  const int inum_full = list->listfull->inum;
+
+  NPAIR_OMP_INIT;
+#if defined(_OPENMP)
+#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
+#endif
+  NPAIR_OMP_SETUP(inum_full);
+
+  int i,j,ii,jj,n,jnum,joriginal;
+  int *neighptr,*jlist;
+  double xtmp,ytmp,ztmp;
+  double delx,dely,delz,rsq;
+
+  double **x = atom->x;
+  int nlocal = atom->nlocal;
+
+  int *ilist = list->ilist;
+  int *numneigh = list->numneigh;
+  int **firstneigh = list->firstneigh;
+  int *ilist_full = list->listfull->ilist;
+  int *numneigh_full = list->listfull->numneigh;
+  int **firstneigh_full = list->listfull->firstneigh;
+
+  // each thread has its own page allocator
+  MyPage<int> &ipage = list->ipage[tid];
+  ipage.reset();
+
+  double cutsq_custom = cutoff_custom * cutoff_custom;
+
+  // loop over parent full list
+
+  for (ii = ifrom; ii < ito; ii++) {
+
+    n = 0;
+    neighptr = ipage.vget();
+
+    i = ilist_full[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+
+    // loop over full neighbor list
+
+    jlist = firstneigh_full[i];
+    jnum = numneigh_full[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      joriginal = jlist[jj];
+      j = joriginal & NEIGHMASK;
+      if (j < nlocal) {
+        if (i > j) continue;
+      } else {
+        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;
+        }
+      }
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx * delx + dely * dely + delz * delz;
+
+      if (rsq > cutsq_custom) continue;
+
+      neighptr[n++] = joriginal;
+    }
+
+    ilist[ii] = i;
+    firstneigh[i] = neighptr;
+    numneigh[i] = n;
+    ipage.vgot(n);
+    if (ipage.status())
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+  }
+  NPAIR_OMP_CLOSE;
+  list->inum = inum_full;
+}

src/OPENMP/npair_halffull_newton_trim_omp.h

@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+// clang-format off
+NPairStyle(halffull/newton/trim/omp,
+           NPairHalffullNewtonTrimOmp,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
+           NP_ORTHO | NP_TRI| NP_TRIM | NP_OMP);
+
+NPairStyle(halffull/newton/skip/trim/omp,
+           NPairHalffullNewtonTrimOmp,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
+           NP_ORTHO | NP_TRI | NP_SKIP | NP_TRIM | NP_OMP);
+// clang-format on
+#else
+
+#ifndef LMP_NPAIR_HALFFULL_NEWTON_TRIM_OMP_H
+#define LMP_NPAIR_HALFFULL_NEWTON_TRIM_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalffullNewtonTrimOmp : public NPair {
+ public:
+  NPairHalffullNewtonTrimOmp(class LAMMPS *);
+  void build(class NeighList *) override;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

src/OPENMP/npair_trim_omp.cpp

@@ -0,0 +1,108 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "npair_trim_omp.h"
+
+#include "atom.h"
+#include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairTrimOmp::NPairTrimOmp(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+   trim from copy list to shorter cutoff
+------------------------------------------------------------------------- */
+
+void NPairTrimOmp::build(NeighList *list)
+{
+  const int inum_copy = list->listcopy->inum;
+
+  NPAIR_OMP_INIT;
+
+#if defined(_OPENMP)
+#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
+#endif
+  NPAIR_OMP_SETUP(inum_copy);
+
+  int i,j,ii,jj,n,jnum,joriginal;
+  int *neighptr,*jlist;
+  double xtmp,ytmp,ztmp;
+  double delx,dely,delz,rsq;
+
+  double **x = atom->x;
+
+  int *ilist = list->ilist;
+  int *numneigh = list->numneigh;
+  int **firstneigh = list->firstneigh;
+  int *ilist_copy = list->listcopy->ilist;
+  int *numneigh_copy = list->listcopy->numneigh;
+  int **firstneigh_copy = list->listcopy->firstneigh;
+
+  // each thread has its own page allocator
+  MyPage<int> &ipage = list->ipage[tid];
+  ipage.reset();
+
+  double cutsq_custom = cutoff_custom * cutoff_custom;
+
+  // loop over atoms in copy list
+
+  for (ii = ifrom; ii < ito; ii++) {
+
+    n = 0;
+    neighptr = ipage.vget();
+
+    // loop over parent copy list
+
+    i = ilist_copy[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+
+    jlist = firstneigh_copy[i];
+    jnum = numneigh_copy[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      joriginal = jlist[jj];
+      j = joriginal & NEIGHMASK;
+
+      // trim to shorter cutoff
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx * delx + dely * dely + delz * delz;
+
+      if (rsq > cutsq_custom) continue;
+
+      neighptr[n++] = joriginal;
+    }
+
+    ilist[ii] = i;
+    firstneigh[i] = neighptr;
+    numneigh[i] = n;
+    ipage.vgot(n);
+    if (ipage.status())
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+  }
+  NPAIR_OMP_CLOSE;
+  list->inum = inum_copy;
+}

src/OPENMP/npair_trim_omp.h

@@ -0,0 +1,39 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+// clang-format off
+NPairStyle(trim/omp,
+           NPairTrimOmp,
+           NP_COPY | NP_TRIM | NP_OMP)
+
+// clang-format on
+#else
+
+#ifndef LMP_NPAIR_TRIM_OMP_H
+#define LMP_NPAIR_TRIM_OMP_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairTrimOmp : public NPair {
+ public:
+  NPairTrimOmp(class LAMMPS *);
+  void build(class NeighList *) override;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif