Merge pull request #3341 from stanmoore1/hybrid_cutoffs

Add pair_modify option to allow separate cutoffs for each neigh list …

doc/src/neighbor.rst

@@ -49,29 +49,27 @@ sometimes be faster.  Either style should give the same answers.
 
 The *multi* style is a modified binning algorithm that is useful for
 systems with a wide range of cutoff distances, e.g. due to different
-size particles. For granular pair styles, cutoffs are set to the
+size particles. For granular pair styles, cutoffs are set to the sum of
-sum of the maximum atomic radii for each atom type.
+the maximum atomic radii for each atom type.  For the *bin* style, the
-For the *bin* style, the bin size is set to 1/2 of
+bin size is set to 1/2 of the largest cutoff distance between any pair
-the largest cutoff distance between any pair of atom types and a
+of atom types and a single set of bins is defined to search over for all
-single set of bins is defined to search over for all atom types.  This
+atom types.  This can be inefficient if one pair of types has a very
-can be inefficient if one pair of types has a very long cutoff, but
+long cutoff, but other type pairs have a much shorter cutoff. The
-other type pairs have a much shorter cutoff. The *multi* style uses
+*multi* style uses different sized bins for collections of different
-different sized bins for collections of different sized particles, where
+sized particles, where "size" may mean the physical size of the particle
-"size" may mean the physical size of the particle or its cutoff
+or its cutoff distance for interacting with other particles. Different
-distance for interacting with other particles. Different
 sets of bins are then used to construct the neighbor lists as as further
 described by Shire, Hanley, and Stratford :ref:`(Shire) <bytype-Shire>`.
-This imposes some extra setup overhead, but the searches themselves
+This imposes some extra setup overhead, but the searches themselves may
-may be much faster. By default, each atom type defines a separate
+be much faster. By default, each atom type defines a separate collection
-collection of particles. For systems where two or more atom types
+of particles. For systems where two or more atom types have the same
-have the same size (either physical size or cutoff distance), the
+size (either physical size or cutoff distance), the definition of
-definition of collections can be customized, which can result in less
+collections can be customized, which can result in less overhead and
-overhead and faster performance. See the :doc:`neigh_modify <neigh_modify>`
+faster performance. See the :doc:`neigh_modify <neigh_modify>` command
-command for how to define custom collections. Whether the collection
+for how to define custom collections. Whether the collection definition
-definition is customized or not, also see the
+is customized or not, also see the :doc:`comm_modify mode multi
-:doc:`comm_modify mode multi <comm_modify>` command for communication
+<comm_modify>` command for communication options that further improve
-options that further improve performance in a manner consistent with
+performance in a manner consistent with neighbor style multi.
-neighbor style multi.
 
 An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest
 cutoff distance and multiple sets of bins are defined to search over for
@@ -80,6 +78,16 @@ algorithm in LAMMPS but was found to be significantly slower than the new
 approach. For now we are keeping the old option in case there are use cases
 where multi/old outperforms the new multi style.
 
+.. note::
+
+   If there are multiple sub-styles in a :doc:`hybrid/overlay pair style
+   <pair_hybrid>` that cover the same atom types, but have significantly
+   different cutoffs, the *multi* style does not apply.  Instead, the
+   :doc:`pair_modify neigh/trim <pair_modify>` setting applies (which is
+   *yes* by default).  Please check the neighbor list summary printed at
+   the beginning of a calculation to verify that the desired set of
+   neighbor list builds is performed.
+
 
 The :doc:`neigh_modify <neigh_modify>` command has additional options
 that control how often neighbor lists are built and which pairs are

doc/src/pair_modify.rst

@@ -13,7 +13,7 @@ Syntax
 * one or more keyword/value pairs may be listed
 * keyword = *pair* or *shift* or *mix* or *table* or *table/disp* or *tabinner*
   or *tabinner/disp* or *tail* or *compute* or *nofdotr* or *special* or
-  *compute/tally*
+  *compute/tally* or *neigh/trim*
 
   .. parsed-literal::
 
@@ -37,6 +37,7 @@ Syntax
           which = *lj/coul* or *lj* or *coul*
           w1,w2,w3 = 1-2, 1-3, 1-4 weights from 0.0 to 1.0 inclusive
        *compute/tally* value = *yes* or *no*
+       *neigh/trim* value = *yes* or *no*
 
 Examples
 """"""""
@@ -283,6 +284,31 @@ the *pair* keyword.  Use *no* to disable, or *yes* to enable.
    The "pair_modify pair compute/tally" command must be issued
    **before** the corresponding compute style is defined.
 
+The *neigh/trim* keyword controls whether an explicit cutoff is set for
+each neighbor list request issued by individual pair sub-styles when
+using :doc:`pair hybrid/overlay <pair_hybrid>`.  When this keyword is
+set to *no*, then the cutoff of each pair sub-style neighbor list will
+be set equal to the largest cutoff, even if a shorter cutoff is
+specified for a particular sub-style.  If possible the neighbor list
+will be copied directly from another list.  When this keyword is set to
+*yes* then the cutoff of the neighbor list will be explicitly set to the
+value requested by the pair sub-style, and if possible the list will be
+created by trimming neighbors from another list with a longer cutoff,
+otherwise a new neighbor list will be created with the specified cutoff.
+The *yes* option can be faster when there are multiple pair styles with
+different cutoffs since the number of pair-wise distance checks between
+neighbors is reduced (but the time required to build the neighbor lists
+is increased). The *no* option could be faster when two or more neighbor
+lists have similar (but not exactly the same) cutoffs.
+
+.. note::
+
+   The "pair_modify neigh/trim" command *only* applies when there are
+   multiple pair sub-styles for the same atoms with different cutoffs,
+   i.e. when using pair style hybrid/overlay.  If you have different
+   cutoffs for different pairs for atoms type, the :doc:`neighbor style
+   multi <neighbor>` should be used to create optimized neighbor lists.
+
 ----------
 
 Restrictions
@@ -298,13 +324,13 @@ Related commands
 
 :doc:`pair_style <pair_style>`, :doc:`pair_style hybrid <pair_hybrid>`,
 :doc:`pair_coeff <pair_coeff>`, :doc:`thermo_style <thermo_style>`,
-:doc:`compute \*/tally <compute_tally>`
+:doc:`compute \*/tally <compute_tally>`, :doc:`neighbor multi <neighbor>`
 
 Default
 """""""
 
 The option defaults are mix = geometric, shift = no, table = 12,
-tabinner = sqrt(2.0), tail = no, and compute = yes.
+tabinner = sqrt(2.0), tail = no, compute = yes, and neigh/trim yes.
 
 Note that some pair styles perform mixing, but only a certain style of
 mixing.  See the doc pages for individual pair styles for details.

doc/utils/sphinx-config/false_positives.txt

@@ -3219,6 +3219,7 @@ Souza
 sp
 spacings
 Spearot
+specieslist
 specular
 spellcheck
 Spellmeyer

src/Depend.sh

@@ -121,6 +121,7 @@ fi
 if (test $1 = "MANYBODY") then
   depend ATC
   depend GPU
+  depend INTEL
   depend KOKKOS
   depend OPT
   depend QEQ

src/INTEL/npair_halffull_newtoff_trim_intel.h

@@ -0,0 +1,44 @@
+// clang-format off
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Stan Moore (SNL)
+------------------------------------------------------------------------- */
+
+// Only used for hybrid to generate list for non-intel style. Use
+// standard routines.
+
+#ifdef NPAIR_CLASS
+// clang-format off
+NPairStyle(halffull/newtoff/trim/intel,
+           NPairHalffullNewtoffTrim,
+           NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF |
+           NP_ORTHO | NP_TRI | NP_TRIM | NP_INTEL);
+
+NPairStyle(halffull/newtoff/skip/trim/intel,
+           NPairHalffullNewtoffTrim,
+           NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF |
+           NP_ORTHO | NP_TRI | NP_SKIP | NP_TRIM | NP_INTEL);
+
+NPairStyle(halffull/newtoff/ghost/trim/intel,
+           NPairHalffullNewtoffTrim,
+           NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF |
+           NP_ORTHO | NP_TRI | NP_GHOST | NP_TRIM | NP_INTEL);
+
+NPairStyle(halffull/newtoff/skip/ghost/trim/intel,
+           NPairHalffullNewtoffTrim,
+           NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF |
+           NP_ORTHO | NP_TRI | NP_SKIP | NP_GHOST | NP_TRIM | NP_INTEL);
+// clang-format on
+#endif

src/INTEL/npair_halffull_newton_trim_intel.cpp

@@ -0,0 +1,258 @@
+// 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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Stan Moore (SNL)
+------------------------------------------------------------------------- */
+
+#include "npair_halffull_newton_trim_intel.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "modify.h"
+#include "my_page.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalffullNewtonTrimIntel::NPairHalffullNewtonTrimIntel(LAMMPS *lmp) : NPair(lmp) {
+  _fix = static_cast<FixIntel *>(modify->get_fix_by_id("package_intel"));
+  if (!_fix) error->all(FLERR, "The 'package intel' command is required for /intel styles");
+}
+
+/* ----------------------------------------------------------------------
+   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
+------------------------------------------------------------------------- */
+
+template <class flt_t, class acc_t>
+void NPairHalffullNewtonTrimIntel::build_t(NeighList *list,
+                                       IntelBuffers<flt_t,acc_t> *buffers)
+{
+  const int inum_full = list->listfull->inum;
+  const int nlocal = atom->nlocal;
+  const int e_nall = nlocal + atom->nghost;
+  const ATOM_T * _noalias const x = buffers->get_x();
+  int * _noalias const ilist = list->ilist;
+  int * _noalias const numneigh = list->numneigh;
+  int ** _noalias const firstneigh = list->firstneigh;
+  const int * _noalias const ilist_full = list->listfull->ilist;
+  const int * _noalias const numneigh_full = list->listfull->numneigh;
+  const int ** _noalias const firstneigh_full = (const int ** const)list->listfull->firstneigh;  // NOLINT
+
+  const flt_t cutsq_custom = cutoff_custom * cutoff_custom;
+
+  #if defined(_OPENMP)
+  #pragma omp parallel
+  #endif
+  {
+    int tid, ifrom, ito;
+    IP_PRE_omp_range_id(ifrom, ito, tid, inum_full, comm->nthreads);
+
+    // each thread has its own page allocator
+    MyPage<int> &ipage = list->ipage[tid];
+    ipage.reset();
+
+    // loop over parent full list
+    for (int ii = ifrom; ii < ito; ii++) {
+      int n = 0;
+      int *neighptr = ipage.vget();
+
+      const int i = ilist_full[ii];
+      const flt_t xtmp = x[i].x;
+      const flt_t ytmp = x[i].y;
+      const flt_t ztmp = x[i].z;
+
+      // loop over full neighbor list
+
+      const int * _noalias const jlist = firstneigh_full[i];
+      const int jnum = numneigh_full[i];
+
+      #if defined(LMP_SIMD_COMPILER)
+      #pragma vector aligned
+      #pragma ivdep
+      #endif
+      for (int jj = 0; jj < jnum; jj++) {
+        const int joriginal = jlist[jj];
+        const int j = joriginal & NEIGHMASK;
+        int addme = 1;
+        if (j < nlocal) {
+          if (i > j) addme = 0;
+        } else {
+          if (x[j].z < ztmp) addme = 0;
+          if (x[j].z == ztmp) {
+            if (x[j].y < ytmp) addme = 0;
+            if (x[j].y == ytmp && x[j].x < xtmp) addme = 0;
+          }
+        }
+
+        // trim to shorter cutoff
+
+        const flt_t delx = xtmp - x[j].x;
+        const flt_t dely = ytmp - x[j].y;
+        const flt_t delz = ztmp - x[j].z;
+        const flt_t rsq = delx * delx + dely * dely + delz * delz;
+
+        if (rsq > cutsq_custom) addme = 0;
+
+        if (addme)
+          neighptr[n++] = joriginal;
+      }
+
+      ilist[ii] = i;
+      firstneigh[i] = neighptr;
+      numneigh[i] = n;
+
+      int pad_end = n;
+      IP_PRE_neighbor_pad(pad_end, 0);
+      #if defined(LMP_SIMD_COMPILER)
+      #pragma vector aligned
+      #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \
+              avg=INTEL_COMPILE_WIDTH/2
+      #endif
+      for ( ; n < pad_end; n++)
+        neighptr[n] = e_nall;
+
+      ipage.vgot(n);
+      if (ipage.status())
+        error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+    }
+  }
+  list->inum = inum_full;
+}
+
+/* ----------------------------------------------------------------------
+   build half list from full 3-body list and trim to shorter cutoff
+   half list is already stored as first part of 3-body list
+------------------------------------------------------------------------- */
+
+template <class flt_t, class acc_t>
+void NPairHalffullNewtonTrimIntel::build_t3(NeighList *list, int *numhalf,
+                                            IntelBuffers<flt_t,acc_t> *buffers)
+{
+  const int inum_full = list->listfull->inum;
+  const int e_nall = atom->nlocal + atom->nghost;
+  const ATOM_T * _noalias const x = buffers->get_x();
+  int * _noalias const ilist = list->ilist;
+  int * _noalias const numneigh = list->numneigh;
+  int ** _noalias const firstneigh = list->firstneigh;
+  const int * _noalias const ilist_full = list->listfull->ilist;
+  const int * _noalias const numneigh_full = numhalf;
+  const int ** _noalias const firstneigh_full = (const int ** const)list->listfull->firstneigh;  // NOLINT
+
+  const flt_t cutsq_custom = cutoff_custom * cutoff_custom;
+
+  int packthreads = 1;
+  if (comm->nthreads > INTEL_HTHREADS) packthreads = comm->nthreads;
+
+  #if defined(_OPENMP)
+  #pragma omp parallel if (packthreads > 1)
+  #endif
+  {
+    int tid, ifrom, ito;
+    IP_PRE_omp_range_id(ifrom, ito, tid, inum_full, packthreads);
+
+    // each thread has its own page allocator
+    MyPage<int> &ipage = list->ipage[tid];
+    ipage.reset();
+
+    // loop over parent full list
+    for (int ii = ifrom; ii < ito; ii++) {
+      int n = 0;
+      int *neighptr = ipage.vget();
+
+      const int i = ilist_full[ii];
+      const flt_t xtmp = x[i].x;
+      const flt_t ytmp = x[i].y;
+      const flt_t ztmp = x[i].z;
+
+      // loop over full neighbor list
+
+      const int * _noalias const jlist = firstneigh_full[i];
+      const int jnum = numneigh_full[ii];
+
+      #if defined(LMP_SIMD_COMPILER)
+      #pragma vector aligned
+      #pragma ivdep
+      #endif
+      for (int jj = 0; jj < jnum; jj++) {
+        const int joriginal = jlist[jj];
+        const int j = joriginal & NEIGHMASK;
+        int addme = 1;
+
+        // trim to shorter cutoff
+
+        const flt_t delx = xtmp - x[j].x;
+        const flt_t dely = ytmp - x[j].y;
+        const flt_t delz = ztmp - x[j].z;
+        const flt_t rsq = delx * delx + dely * dely + delz * delz;
+
+        if (rsq > cutsq_custom) addme = 0;
+
+        if (addme)
+          neighptr[n++] = joriginal;
+      }
+
+      ilist[ii] = i;
+      firstneigh[i] = neighptr;
+      numneigh[i] = n;
+
+      int pad_end = n;
+      IP_PRE_neighbor_pad(pad_end, 0);
+      #if defined(LMP_SIMD_COMPILER)
+      #pragma vector aligned
+      #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \
+              avg=INTEL_COMPILE_WIDTH/2
+      #endif
+      for ( ; n < pad_end; n++)
+        neighptr[n] = e_nall;
+
+      ipage.vgot(n);
+      if (ipage.status())
+        error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+    }
+  }
+  list->inum = inum_full;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NPairHalffullNewtonTrimIntel::build(NeighList *list)
+{
+  if (_fix->three_body_neighbor() == 0) {
+    if (_fix->precision() == FixIntel::PREC_MODE_MIXED)
+      build_t(list, _fix->get_mixed_buffers());
+    else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE)
+      build_t(list, _fix->get_double_buffers());
+    else
+      build_t(list, _fix->get_single_buffers());
+  } else {
+    int *nhalf, *cnum;
+    if (_fix->precision() == FixIntel::PREC_MODE_MIXED) {
+      _fix->get_mixed_buffers()->get_list_data3(list->listfull, nhalf, cnum);
+      build_t3<float>(list, nhalf, _fix->get_mixed_buffers());
+    } else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
+      _fix->get_double_buffers()->get_list_data3(list->listfull, nhalf, cnum);
+      build_t3<double>(list, nhalf, _fix->get_double_buffers());
+    } else {
+      _fix->get_single_buffers()->get_list_data3(list->listfull, nhalf, cnum);
+      build_t3<float>(list, nhalf, _fix->get_single_buffers());
+    }
+  }
+}

src/INTEL/npair_halffull_newton_trim_intel.h

@@ -0,0 +1,61 @@
+// clang-format off
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Stan Moore (SNL)
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+// clang-format off
+NPairStyle(halffull/newton/trim/intel,
+           NPairHalffullNewtonTrimIntel,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI| NP_TRIM | NP_INTEL);
+
+NPairStyle(halffull/newton/skip/trim/intel,
+           NPairHalffullNewtonTrimIntel,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_SKIP | NP_TRIM | NP_INTEL);
+// clang-format on
+#else
+
+#ifndef LMP_NPAIR_HALFFULL_NEWTON_TRIM_INTEL_H
+#define LMP_NPAIR_HALFFULL_NEWTON_TRIM_INTEL_H
+
+#include "fix_intel.h"
+#include "npair.h"
+
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
+
+namespace LAMMPS_NS {
+
+class NPairHalffullNewtonTrimIntel : public NPair {
+ public:
+  NPairHalffullNewtonTrimIntel(class LAMMPS *);
+  void build(class NeighList *) override;
+
+ protected:
+  FixIntel *_fix;
+
+  template <class flt_t, class acc_t> void build_t(NeighList *, IntelBuffers<flt_t, acc_t> *);
+
+  template <class flt_t, class acc_t> void build_t3(NeighList *, int *, IntelBuffers<flt_t, acc_t> *);
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

src/INTEL/npair_trim_intel.cpp

@@ -0,0 +1,138 @@
+// 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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Stan Moore (SNL)
+------------------------------------------------------------------------- */
+
+#include "npair_trim_intel.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "modify.h"
+#include "my_page.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairTrimIntel::NPairTrimIntel(LAMMPS *lmp) : NPair(lmp) {
+  _fix = static_cast<FixIntel *>(modify->get_fix_by_id("package_intel"));
+  if (!_fix) error->all(FLERR, "The 'package intel' command is required for /intel styles");
+}
+
+/* ----------------------------------------------------------------------
+   trim from copy list to shorter cutoff
+------------------------------------------------------------------------- */
+
+template <class flt_t, class acc_t>
+void NPairTrimIntel::build_t(NeighList *list,
+                                       IntelBuffers<flt_t,acc_t> *buffers)
+{
+  const int inum_copy = list->listcopy->inum;
+  const int nlocal = atom->nlocal;
+  const int e_nall = nlocal + atom->nghost;
+  const ATOM_T * _noalias const x = buffers->get_x();
+  int * _noalias const ilist = list->ilist;
+  int * _noalias const numneigh = list->numneigh;
+  int ** _noalias const firstneigh = list->firstneigh;
+  const int * _noalias const ilist_copy = list->listcopy->ilist;
+  const int * _noalias const numneigh_copy = list->listcopy->numneigh;
+  const int ** _noalias const firstneigh_copy = (const int ** const)list->listcopy->firstneigh;  // NOLINT
+
+  const flt_t cutsq_custom = cutoff_custom * cutoff_custom;
+
+  #if defined(_OPENMP)
+  #pragma omp parallel
+  #endif
+  {
+    int tid, ifrom, ito;
+    IP_PRE_omp_range_id(ifrom, ito, tid, inum_copy, comm->nthreads);
+
+    // each thread has its own page allocator
+    MyPage<int> &ipage = list->ipage[tid];
+    ipage.reset();
+
+    // loop over parent copy list
+    for (int ii = ifrom; ii < ito; ii++) {
+      int n = 0;
+      int *neighptr = ipage.vget();
+
+      const int i = ilist_copy[ii];
+      const flt_t xtmp = x[i].x;
+      const flt_t ytmp = x[i].y;
+      const flt_t ztmp = x[i].z;
+
+      // loop over copy neighbor list
+
+      const int * _noalias const jlist = firstneigh_copy[i];
+      const int jnum = numneigh_copy[i];
+
+      #if defined(LMP_SIMD_COMPILER)
+      #pragma vector aligned
+      #pragma ivdep
+      #endif
+      for (int jj = 0; jj < jnum; jj++) {
+        const int joriginal = jlist[jj];
+        const int j = joriginal & NEIGHMASK;
+        int addme = 1;
+
+        // trim to shorter cutoff
+
+        const flt_t delx = xtmp - x[j].x;
+        const flt_t dely = ytmp - x[j].y;
+        const flt_t delz = ztmp - x[j].z;
+        const flt_t rsq = delx * delx + dely * dely + delz * delz;
+
+        if (rsq > cutsq_custom) addme = 0;
+
+        if (addme)
+          neighptr[n++] = joriginal;
+      }
+
+      ilist[ii] = i;
+      firstneigh[i] = neighptr;
+      numneigh[i] = n;
+
+      int pad_end = n;
+      IP_PRE_neighbor_pad(pad_end, 0);
+      #if defined(LMP_SIMD_COMPILER)
+      #pragma vector aligned
+      #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \
+              avg=INTEL_COMPILE_WIDTH/2
+      #endif
+      for ( ; n < pad_end; n++)
+        neighptr[n] = e_nall;
+
+      ipage.vgot(n);
+      if (ipage.status())
+        error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+    }
+  }
+  list->inum = inum_copy;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NPairTrimIntel::build(NeighList *list)
+{
+  if (_fix->precision() == FixIntel::PREC_MODE_MIXED)
+    build_t(list, _fix->get_mixed_buffers());
+  else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE)
+    build_t(list, _fix->get_double_buffers());
+  else
+    build_t(list, _fix->get_single_buffers());
+}

src/INTEL/npair_trim_intel.h

@@ -0,0 +1,53 @@
+// clang-format off
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Stan Moore (SNL)
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+// clang-format off
+NPairStyle(trim/intel,
+           NPairTrimIntel,
+           NP_COPY | NP_TRIM | NP_INTEL);
+// clang-format on
+#else
+
+#ifndef LMP_NPAIR_TRIM_INTEL_H
+#define LMP_NPAIR_TRIM_INTEL_H
+
+#include "fix_intel.h"
+#include "npair.h"
+
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
+
+namespace LAMMPS_NS {
+
+class NPairTrimIntel : public NPair {
+ public:
+  NPairTrimIntel(class LAMMPS *);
+  void build(class NeighList *) override;
+
+ protected:
+  FixIntel *_fix;
+
+  template <class flt_t, class acc_t> void build_t(NeighList *, IntelBuffers<flt_t, acc_t> *);
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

src/KOKKOS/Install.sh

@@ -204,6 +204,8 @@ action npair_halffull_kokkos.cpp
 action npair_halffull_kokkos.h
 action npair_skip_kokkos.cpp
 action npair_skip_kokkos.h
+action npair_trim_kokkos.cpp
+action npair_trim_kokkos.h
 action npair_kokkos.cpp
 action npair_kokkos.h
 action npair_ssa_kokkos.cpp npair_half_bin_newton_ssa.cpp

src/KOKKOS/npair_halffull_kokkos.cpp

@@ -26,8 +26,8 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-template<class DeviceType, int NEWTON>
+template<class DeviceType, int NEWTON, int TRIM>
-NPairHalffullKokkos<DeviceType,NEWTON>::NPairHalffullKokkos(LAMMPS *lmp) : NPair(lmp) {
+NPairHalffullKokkos<DeviceType,NEWTON,TRIM>::NPairHalffullKokkos(LAMMPS *lmp) : NPair(lmp) {
   atomKK = (AtomKokkos *) atom;
   execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
 }
@@ -41,15 +41,17 @@ NPairHalffullKokkos<DeviceType,NEWTON>::NPairHalffullKokkos(LAMMPS *lmp) : NPair
    if ghost, also store neighbors of ghost atoms & set inum,gnum correctly
 ------------------------------------------------------------------------- */
 
-template<class DeviceType, int NEWTON>
+template<class DeviceType, int NEWTON, int TRIM>
-void NPairHalffullKokkos<DeviceType,NEWTON>::build(NeighList *list)
+void NPairHalffullKokkos<DeviceType,NEWTON,TRIM>::build(NeighList *list)
 {
-  if (NEWTON) {
+  if (NEWTON || TRIM) {
     x = atomKK->k_x.view<DeviceType>();
     atomKK->sync(execution_space,X_MASK);
   }
   nlocal = atom->nlocal;
 
+  cutsq_custom = cutoff_custom*cutoff_custom;
+
   NeighListKokkos<DeviceType>* k_list_full = static_cast<NeighListKokkos<DeviceType>*>(list->listfull);
   d_ilist_full = k_list_full->d_ilist;
   d_numneigh_full = k_list_full->d_numneigh;
@@ -76,14 +78,14 @@ void NPairHalffullKokkos<DeviceType,NEWTON>::build(NeighList *list)
   k_list->k_ilist.template modify<DeviceType>();
 }
 
-template<class DeviceType, int NEWTON>
+template<class DeviceType, int NEWTON, int TRIM>
 KOKKOS_INLINE_FUNCTION
-void NPairHalffullKokkos<DeviceType,NEWTON>::operator()(TagNPairHalffullCompute, const int &ii) const {
+void NPairHalffullKokkos<DeviceType,NEWTON,TRIM>::operator()(TagNPairHalffullCompute, const int &ii) const {
   int n = 0;
 
   const int i = d_ilist_full(ii);
   F_FLOAT xtmp,ytmp,ztmp;
-  if (NEWTON) {
+  if (NEWTON || TRIM) {
     xtmp = x(i,0);
     ytmp = x(i,1);
     ztmp = x(i,2);
@@ -108,9 +110,29 @@ void NPairHalffullKokkos<DeviceType,NEWTON>::operator()(TagNPairHalffullCompute,
           if (x(j,1) == ytmp && x(j,0) < xtmp) continue;
         }
       }
+
+      if (TRIM) {
+        const double delx = xtmp - x(j,0);
+        const double dely = ytmp - x(j,1);
+        const double delz = ztmp - x(j,2);
+        const double rsq = delx*delx + dely*dely + delz*delz;
+
+        if (rsq > cutsq_custom) continue;
+      }
+
+      neighbors_i(n++) = joriginal;
+    } else if (j > i) {
+
+      if (TRIM) {
+        const double delx = xtmp - x(j,0);
+        const double dely = ytmp - x(j,1);
+        const double delz = ztmp - x(j,2);
+        const double rsq = delx*delx + dely*dely + delz*delz;
+
+        if (rsq > cutsq_custom) continue;
+      }
+
       neighbors_i(n++) = joriginal;
-    } else {
-      if (j > i) neighbors_i(n++) = joriginal;
     }
   }
 
@@ -119,10 +141,14 @@ void NPairHalffullKokkos<DeviceType,NEWTON>::operator()(TagNPairHalffullCompute,
 }
 
 namespace LAMMPS_NS {
-template class NPairHalffullKokkos<LMPDeviceType,0>;
+template class NPairHalffullKokkos<LMPDeviceType,0,0>;
-template class NPairHalffullKokkos<LMPDeviceType,1>;
+template class NPairHalffullKokkos<LMPDeviceType,0,1>;
+template class NPairHalffullKokkos<LMPDeviceType,1,0>;
+template class NPairHalffullKokkos<LMPDeviceType,1,1>;
 #ifdef LMP_KOKKOS_GPU
-template class NPairHalffullKokkos<LMPHostType,0>;
+template class NPairHalffullKokkos<LMPHostType,0,0>;
-template class NPairHalffullKokkos<LMPHostType,1>;
+template class NPairHalffullKokkos<LMPHostType,0,1>;
+template class NPairHalffullKokkos<LMPHostType,1,0>;
+template class NPairHalffullKokkos<LMPHostType,1,1>;
 #endif
 }

src/KOKKOS/npair_halffull_kokkos.h

@@ -13,27 +13,30 @@
 
 #ifdef NPAIR_CLASS
 // clang-format off
+
+// Trim off
+
 // Newton
 
-typedef NPairHalffullKokkos<LMPDeviceType,1> NPairKokkosHalffullNewtonDevice;
+typedef NPairHalffullKokkos<LMPDeviceType,1,0> NPairKokkosHalffullNewtonDevice;
 NPairStyle(halffull/newton/kk/device,
            NPairKokkosHalffullNewtonDevice,
            NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
            NP_ORTHO | NP_TRI | NP_KOKKOS_DEVICE);
 
-typedef NPairHalffullKokkos<LMPHostType,1> NPairKokkosHalffullNewtonHost;
+typedef NPairHalffullKokkos<LMPHostType,1,0> NPairKokkosHalffullNewtonHost;
 NPairStyle(halffull/newton/kk/host,
            NPairKokkosHalffullNewtonHost,
            NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
            NP_ORTHO | NP_TRI | NP_KOKKOS_HOST);
 
-typedef NPairHalffullKokkos<LMPDeviceType,1> NPairKokkosHalffullNewtonDevice;
+typedef NPairHalffullKokkos<LMPDeviceType,1,0> NPairKokkosHalffullNewtonDevice;
 NPairStyle(halffull/newton/skip/kk/device,
            NPairKokkosHalffullNewtonDevice,
            NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
            NP_ORTHO | NP_TRI | NP_SKIP | NP_KOKKOS_DEVICE);
 
-typedef NPairHalffullKokkos<LMPHostType,1> NPairKokkosHalffullNewtonHost;
+typedef NPairHalffullKokkos<LMPHostType,1,0> NPairKokkosHalffullNewtonHost;
 NPairStyle(halffull/newton/skip/kk/host,
            NPairKokkosHalffullNewtonHost,
            NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
@@ -41,25 +44,25 @@ NPairStyle(halffull/newton/skip/kk/host,
 
 // Newtoff
 
-typedef NPairHalffullKokkos<LMPDeviceType,0> NPairKokkosHalffullNewtoffDevice;
+typedef NPairHalffullKokkos<LMPDeviceType,0,0> NPairKokkosHalffullNewtoffDevice;
 NPairStyle(halffull/newtoff/kk/device,
            NPairKokkosHalffullNewtoffDevice,
            NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
            NP_ORTHO | NP_TRI | NP_KOKKOS_DEVICE);
 
-typedef NPairHalffullKokkos<LMPHostType,0> NPairKokkosHalffullNewtoffHost;
+typedef NPairHalffullKokkos<LMPHostType,0,0> NPairKokkosHalffullNewtoffHost;
 NPairStyle(halffull/newtoff/kk/host,
            NPairKokkosHalffullNewtoffHost,
            NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
            NP_ORTHO | NP_TRI | NP_KOKKOS_HOST);
 
-typedef NPairHalffullKokkos<LMPDeviceType,0> NPairKokkosHalffullNewtoffDevice;
+typedef NPairHalffullKokkos<LMPDeviceType,0,0> NPairKokkosHalffullNewtoffDevice;
 NPairStyle(halffull/newtoff/skip/kk/device,
            NPairKokkosHalffullNewtoffDevice,
            NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
            NP_ORTHO | NP_TRI | NP_SKIP | NP_KOKKOS_DEVICE);
 
-typedef NPairHalffullKokkos<LMPHostType,0> NPairKokkosHalffullNewtoffHost;
+typedef NPairHalffullKokkos<LMPHostType,0,0> NPairKokkosHalffullNewtoffHost;
 NPairStyle(halffull/newtoff/skip/kk/host,
            NPairKokkosHalffullNewtoffHost,
            NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
@@ -69,25 +72,25 @@ NPairStyle(halffull/newtoff/skip/kk/host,
 
 // Newton
 
-typedef NPairHalffullKokkos<LMPDeviceType,1> NPairKokkosHalffullNewtonGhostDevice;
+typedef NPairHalffullKokkos<LMPDeviceType,1,0> NPairKokkosHalffullNewtonGhostDevice;
 NPairStyle(halffull/newton/ghost/kk/device,
            NPairKokkosHalffullNewtonGhostDevice,
            NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
            NP_ORTHO | NP_TRI | NP_GHOST | NP_KOKKOS_DEVICE);
 
-typedef NPairHalffullKokkos<LMPHostType,1> NPairKokkosHalffullNewtonHost;
+typedef NPairHalffullKokkos<LMPHostType,1,0> NPairKokkosHalffullNewtonHost;
 NPairStyle(halffull/newton/ghost/kk/host,
            NPairKokkosHalffullNewtonHost,
            NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
            NP_ORTHO | NP_TRI | NP_GHOST | NP_KOKKOS_HOST);
 
-typedef NPairHalffullKokkos<LMPDeviceType,1> NPairKokkosHalffullNewtonGhostDevice;
+typedef NPairHalffullKokkos<LMPDeviceType,1,0> NPairKokkosHalffullNewtonGhostDevice;
 NPairStyle(halffull/newton/skip/ghost/kk/device,
            NPairKokkosHalffullNewtonGhostDevice,
            NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
            NP_ORTHO | NP_TRI | NP_GHOST | NP_SKIP | NP_KOKKOS_DEVICE);
 
-typedef NPairHalffullKokkos<LMPHostType,1> NPairKokkosHalffullNewtonHost;
+typedef NPairHalffullKokkos<LMPHostType,1,0> NPairKokkosHalffullNewtonHost;
 NPairStyle(halffull/newton/skip/ghost/kk/host,
            NPairKokkosHalffullNewtonHost,
            NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
@@ -95,29 +98,138 @@ NPairStyle(halffull/newton/skip/ghost/kk/host,
 
 // Newtoff
 
-typedef NPairHalffullKokkos<LMPDeviceType,0> NPairKokkosHalffullNewtoffGhostDevice;
+typedef NPairHalffullKokkos<LMPDeviceType,0,0> NPairKokkosHalffullNewtoffGhostDevice;
 NPairStyle(halffull/newtoff/ghost/kk/device,
            NPairKokkosHalffullNewtoffGhostDevice,
            NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
            NP_ORTHO | NP_TRI | NP_GHOST | NP_KOKKOS_DEVICE);
 
-typedef NPairHalffullKokkos<LMPHostType,0> NPairKokkosHalffullNewtoffHost;
+typedef NPairHalffullKokkos<LMPHostType,0,0> NPairKokkosHalffullNewtoffHost;
 NPairStyle(halffull/newtoff/ghost/kk/host,
            NPairKokkosHalffullNewtoffHost,
            NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
            NP_ORTHO | NP_TRI | NP_GHOST | NP_KOKKOS_HOST);
 
-typedef NPairHalffullKokkos<LMPDeviceType,0> NPairKokkosHalffullNewtoffGhostDevice;
+typedef NPairHalffullKokkos<LMPDeviceType,0,0> NPairKokkosHalffullNewtoffGhostDevice;
 NPairStyle(halffull/newtoff/skip/ghost/kk/device,
            NPairKokkosHalffullNewtoffGhostDevice,
            NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
            NP_ORTHO | NP_TRI | NP_GHOST | NP_SKIP | NP_KOKKOS_DEVICE);
 
-typedef NPairHalffullKokkos<LMPHostType,0> NPairKokkosHalffullNewtoffHost;
+typedef NPairHalffullKokkos<LMPHostType,0,0> NPairKokkosHalffullNewtoffHost;
 NPairStyle(halffull/newtoff/skip/ghost/kk/host,
            NPairKokkosHalffullNewtoffHost,
            NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
            NP_ORTHO | NP_TRI | NP_GHOST | NP_SKIP | NP_KOKKOS_HOST);
+
+
+//************ Trim **************
+
+// Newton
+
+typedef NPairHalffullKokkos<LMPDeviceType,1,1> NPairKokkosHalffullNewtonTrimDevice;
+NPairStyle(halffull/newton/trim/kk/device,
+           NPairKokkosHalffullNewtonTrimDevice,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_TRIM | NP_KOKKOS_DEVICE);
+
+typedef NPairHalffullKokkos<LMPHostType,1,1> NPairKokkosHalffullNewtonTrimHost;
+NPairStyle(halffull/newton/trim/kk/host,
+           NPairKokkosHalffullNewtonTrimHost,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_TRIM | NP_KOKKOS_HOST);
+
+typedef NPairHalffullKokkos<LMPDeviceType,1,1> NPairKokkosHalffullNewtonTrimDevice;
+NPairStyle(halffull/newton/skip/trim/kk/device,
+           NPairKokkosHalffullNewtonTrimDevice,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_SKIP | NP_TRIM | NP_KOKKOS_DEVICE);
+
+typedef NPairHalffullKokkos<LMPHostType,1,1> NPairKokkosHalffullNewtonTrimHost;
+NPairStyle(halffull/newton/skip/trim/kk/host,
+           NPairKokkosHalffullNewtonTrimHost,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_SKIP | NP_TRIM | NP_KOKKOS_HOST);
+
+// Newtoff
+
+typedef NPairHalffullKokkos<LMPDeviceType,0,1> NPairKokkosHalffullNewtoffTrimDevice;
+NPairStyle(halffull/newtoff/trim/kk/device,
+           NPairKokkosHalffullNewtoffTrimDevice,
+           NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_TRIM | NP_KOKKOS_DEVICE);
+
+typedef NPairHalffullKokkos<LMPHostType,0,1> NPairKokkosHalffullNewtoffTrimHost;
+NPairStyle(halffull/newtoff/trim/kk/host,
+           NPairKokkosHalffullNewtoffTrimHost,
+           NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_TRIM | NP_KOKKOS_HOST);
+
+typedef NPairHalffullKokkos<LMPDeviceType,0,1> NPairKokkosHalffullNewtoffTrimDevice;
+NPairStyle(halffull/newtoff/skip/trim/kk/device,
+           NPairKokkosHalffullNewtoffTrimDevice,
+           NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_SKIP | NP_TRIM | NP_KOKKOS_DEVICE);
+
+typedef NPairHalffullKokkos<LMPHostType,0,1> NPairKokkosHalffullNewtoffTrimHost;
+NPairStyle(halffull/newtoff/skip/trim/kk/host,
+           NPairKokkosHalffullNewtoffTrimHost,
+           NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_SKIP |  NP_TRIM | NP_KOKKOS_HOST);
+
+//************ Ghost **************
+
+// Newton
+
+typedef NPairHalffullKokkos<LMPDeviceType,1,1> NPairKokkosHalffullNewtonGhostTrimDevice;
+NPairStyle(halffull/newton/ghost/trim/kk/device,
+           NPairKokkosHalffullNewtonGhostTrimDevice,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_GHOST | NP_TRIM | NP_KOKKOS_DEVICE);
+
+typedef NPairHalffullKokkos<LMPHostType,1,1> NPairKokkosHalffullNewtonTrimHost;
+NPairStyle(halffull/newton/ghost/trim/kk/host,
+           NPairKokkosHalffullNewtonTrimHost,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_GHOST | NP_TRIM | NP_KOKKOS_HOST);
+
+typedef NPairHalffullKokkos<LMPDeviceType,1,1> NPairKokkosHalffullNewtonGhostTrimDevice;
+NPairStyle(halffull/newton/skip/ghost/trim/kk/device,
+           NPairKokkosHalffullNewtonGhostTrimDevice,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_GHOST | NP_SKIP | NP_TRIM | NP_KOKKOS_DEVICE);
+
+typedef NPairHalffullKokkos<LMPHostType,1,1> NPairKokkosHalffullNewtonTrimHost;
+NPairStyle(halffull/newton/skip/ghost/trim/kk/host,
+           NPairKokkosHalffullNewtonTrimHost,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_GHOST | NP_SKIP | NP_TRIM | NP_KOKKOS_HOST);
+
+// Newtoff
+
+typedef NPairHalffullKokkos<LMPDeviceType,0,1> NPairKokkosHalffullNewtoffGhostTrimDevice;
+NPairStyle(halffull/newtoff/ghost/trim/kk/device,
+           NPairKokkosHalffullNewtoffGhostTrimDevice,
+           NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_GHOST | NP_TRIM | NP_KOKKOS_DEVICE);
+
+typedef NPairHalffullKokkos<LMPHostType,0,1> NPairKokkosHalffullNewtoffTrimHost;
+NPairStyle(halffull/newtoff/ghost/trim/kk/host,
+           NPairKokkosHalffullNewtoffTrimHost,
+           NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_GHOST | NP_TRIM | NP_KOKKOS_HOST);
+
+typedef NPairHalffullKokkos<LMPDeviceType,0,1> NPairKokkosHalffullNewtoffGhostTrimDevice;
+NPairStyle(halffull/newtoff/skip/ghost/trim/kk/device,
+           NPairKokkosHalffullNewtoffGhostTrimDevice,
+           NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_GHOST | NP_SKIP | NP_TRIM | NP_KOKKOS_DEVICE);
+
+typedef NPairHalffullKokkos<LMPHostType,0,1> NPairKokkosHalffullNewtoffTrimHost;
+NPairStyle(halffull/newtoff/skip/ghost/trim/kk/host,
+           NPairKokkosHalffullNewtoffTrimHost,
+           NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
+           NP_ORTHO | NP_TRI | NP_GHOST | NP_SKIP | NP_TRIM | NP_KOKKOS_HOST);
 // clang-format on
 #else
 
@@ -132,7 +244,7 @@ namespace LAMMPS_NS {
 
 struct TagNPairHalffullCompute{};
 
-template<class DeviceType, int NEWTON>
+template<class DeviceType, int NEWTON, int TRIM>
 class NPairHalffullKokkos : public NPair {
  public:
   typedef DeviceType device_type;
@@ -146,6 +258,7 @@ class NPairHalffullKokkos : public NPair {
 
  private:
   int nlocal;
+  double cutsq_custom;
 
   typename AT::t_x_array_randomread x;
 

src/KOKKOS/npair_trim_kokkos.cpp

@@ -0,0 +1,196 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Trimright (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_kokkos.h"
+#include "atom_kokkos.h"
+#include "atom_masks.h"
+#include "neigh_list_kokkos.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+NPairTrimKokkos<DeviceType>::NPairTrimKokkos(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+   create list which is simply a copy of parent list
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void NPairTrimKokkos<DeviceType>::build(NeighList *list)
+{
+  NeighList *listcopy = list->listcopy;
+
+  cutsq_custom = cutoff_custom*cutoff_custom;
+
+  if (list->kokkos) {
+    if (!listcopy->kokkos)
+      error->all(FLERR,"Cannot trim non-Kokkos neighbor list to Kokkos neighbor list");
+    trim_to_kokkos(list);
+  } else {
+    if (!listcopy->kokkos)
+      error->all(FLERR,"Missing Kokkos neighbor list for trim");
+    trim_to_cpu(list);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void NPairTrimKokkos<DeviceType>::trim_to_kokkos(NeighList *list)
+{
+  x = atomKK->k_x.view<DeviceType>();
+  atomKK->sync(execution_space,X_MASK);
+
+  cutsq_custom = cutoff_custom*cutoff_custom;
+
+  NeighListKokkos<DeviceType>* k_list_copy = static_cast<NeighListKokkos<DeviceType>*>(list->listcopy);
+  d_ilist_copy = k_list_copy->d_ilist;
+  d_numneigh_copy = k_list_copy->d_numneigh;
+  d_neighbors_copy = k_list_copy->d_neighbors;
+  int inum_copy = list->listcopy->inum;
+  if (list->ghost) inum_copy += list->listcopy->gnum;
+
+  NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
+  k_list->maxneighs = k_list_copy->maxneighs; // simple, but could be made more memory efficient
+  k_list->grow(atom->nmax);
+  d_ilist = k_list->d_ilist;
+  d_numneigh = k_list->d_numneigh;
+  d_neighbors = k_list->d_neighbors;
+
+  // loop over parent list and trim
+
+  copymode = 1;
+  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagNPairTrim>(0,inum_copy),*this);
+  copymode = 0;
+
+  list->inum = k_list_copy->inum;
+  list->gnum = k_list_copy->gnum;
+
+  k_list->k_ilist.template modify<DeviceType>();
+}
+
+template<class DeviceType>
+KOKKOS_INLINE_FUNCTION
+void NPairTrimKokkos<DeviceType>::operator()(TagNPairTrim, const int &ii) const {
+  int n = 0;
+
+  const int i = d_ilist_copy(ii);
+  const double xtmp = x(i,0);
+  const double ytmp = x(i,1);
+  const double ztmp = x(i,2);
+
+  // loop over copy neighbor list
+
+  const int jnum = d_numneigh_copy(i);
+  const AtomNeighbors neighbors_i = AtomNeighbors(&d_neighbors(i,0),d_numneigh(i),
+                                                  &d_neighbors(i,1)-&d_neighbors(i,0));
+
+  for (int jj = 0; jj < jnum; jj++) {
+    const int joriginal = d_neighbors_copy(i,jj);
+    const int j = joriginal & NEIGHMASK;
+
+    const double delx = xtmp - x(j,0);
+    const double dely = ytmp - x(j,1);
+    const double delz = ztmp - x(j,2);
+    const double rsq = delx*delx + dely*dely + delz*delz;
+
+    if (rsq > cutsq_custom) continue;
+
+    neighbors_i(n++) = joriginal;
+  }
+
+  d_numneigh(i) = n;
+  d_ilist(ii) = i;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void NPairTrimKokkos<DeviceType>::trim_to_cpu(NeighList *list)
+{
+  NeighList *listcopy = list->listcopy;
+  NeighListKokkos<DeviceType>* listcopy_kk = (NeighListKokkos<DeviceType>*) listcopy;
+
+  listcopy_kk->k_ilist.template sync<LMPHostType>();
+
+  double** x = atom->x;
+
+  int inum = listcopy->inum;
+  int gnum = listcopy->gnum;
+  int inum_all = inum;
+  if (list->ghost) inum_all += gnum;
+  auto h_ilist = listcopy_kk->k_ilist.h_view;
+  auto h_numneigh = Kokkos::create_mirror_view_and_copy(LMPHostType(),listcopy_kk->d_numneigh);
+  auto h_neighbors = Kokkos::create_mirror_view_and_copy(LMPHostType(),listcopy_kk->d_neighbors);
+
+  list->inum = inum;
+  list->gnum = gnum;
+  auto ilist = list->ilist;
+  auto numneigh = list->numneigh;
+
+  // Kokkos neighbor data is stored differently than regular CPU,
+  //  must loop over lists
+
+  int *neighptr;
+  int **firstneigh = list->firstneigh;
+  MyPage<int> *ipage = list->ipage;
+  ipage->reset();
+
+  for (int ii = 0; ii < inum_all; ii++) {
+    int n = 0;
+    neighptr = ipage->vget();
+
+    const int i = h_ilist[ii];
+    ilist[ii] = i;
+    const double xtmp = x[i][0];
+    const double ytmp = x[i][1];
+    const double ztmp = x[i][2];
+
+    // loop over Kokkos neighbor list
+
+    const int jnum = h_numneigh[i];
+
+    for (int jj = 0; jj < jnum; jj++) {
+      const int joriginal = h_neighbors(i,jj);
+
+      const int j = joriginal & NEIGHMASK;
+
+      const double delx = xtmp - x[j][0];
+      const double dely = ytmp - x[j][1];
+      const double delz = ztmp - x[j][2];
+      const double rsq = delx*delx + dely*dely + delz*delz;
+
+      if (rsq > cutsq_custom) continue;
+
+      neighptr[n++] = joriginal;
+    }
+
+    firstneigh[i] = neighptr;
+    numneigh[i] = n;
+    ipage->vgot(n);
+    if (ipage->status())
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+  }
+}
+
+namespace LAMMPS_NS {
+template class NPairTrimKokkos<LMPDeviceType>;
+#ifdef LMP_KOKKOS_GPU
+template class NPairTrimKokkos<LMPHostType>;
+#endif
+}

src/KOKKOS/npair_trim_kokkos.h

@@ -0,0 +1,70 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Trimright (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/kk/device,
+           NPairTrimKokkos<LMPDeviceType>,
+           NP_COPY | NP_TRIM | NP_KOKKOS_DEVICE);
+
+NPairStyle(trim/kk/host,
+           NPairTrimKokkos<LMPHostType>,
+           NP_COPY | NP_TRIM | NP_KOKKOS_HOST);
+// clang-format on
+#else
+
+// clang-format off
+#ifndef LMP_NPAIR_TRIM_KOKKOS_H
+#define LMP_NPAIR_TRIM_KOKKOS_H
+
+#include "npair.h"
+#include "kokkos_type.h"
+
+namespace LAMMPS_NS {
+
+struct TagNPairTrim{};
+
+template<class DeviceType>
+class NPairTrimKokkos : public NPair {
+ public:
+  typedef DeviceType device_type;
+  typedef ArrayTypes<DeviceType> AT;
+
+  NPairTrimKokkos(class LAMMPS *);
+  void build(class NeighList *) override;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagNPairTrim, const int&) const;
+
+ private:
+  double cutsq_custom;
+
+  typename AT::t_x_array_randomread x;
+
+  typename AT::t_neighbors_2d_const d_neighbors_copy;
+  typename AT::t_int_1d_const d_ilist_copy;
+  typename AT::t_int_1d_const d_numneigh_copy;
+
+  typename AT::t_neighbors_2d d_neighbors;
+  typename AT::t_int_1d d_ilist;
+  typename AT::t_int_1d d_numneigh;
+
+  void trim_to_kokkos(class NeighList *);
+  void trim_to_cpu(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+

src/OPENMP/npair_halffull_newtoff_trim_omp.cpp

@@ -0,0 +1,111 @@
+// 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;
+
+      // 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;
+
+      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 +1,120 @@
+// 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;
+        }
+      }
+
+      // 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_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

src/neigh_list.cpp

@@ -48,6 +48,7 @@ NeighList::NeighList(LAMMPS *lmp) : Pointers(lmp)
   respamiddle = 0;
   respainner = 0;
   copy = 0;
+  trim = 0;
   copymode = 0;
 
   // ptrs
@@ -97,7 +98,8 @@ NeighList::NeighList(LAMMPS *lmp) : Pointers(lmp)
 NeighList::~NeighList()
 {
   if (copymode) return;
-  if (!copy) {
+
+  if (!copy || trim || kk2cpu) {
     memory->destroy(ilist);
     memory->destroy(numneigh);
     memory->sfree(firstneigh);
@@ -144,6 +146,7 @@ void NeighList::post_constructor(NeighRequest *nq)
   respamiddle = nq->respamiddle;
   respainner = nq->respainner;
   copy = nq->copy;
+  trim = nq->trim;
   id = nq->id;
 
   if (nq->copy) {
@@ -286,6 +289,8 @@ void NeighList::print_attributes()
   printf("  %d = skip flag\n",rq->skip);
   printf("  %d = off2on\n",rq->off2on);
   printf("  %d = copy flag\n",rq->copy);
+  printf("  %d = trim flag\n",rq->trim);
+  printf("  %d = kk2cpu flag\n",kk2cpu);
   printf("  %d = half/full\n",rq->halffull);
   printf("\n");
 }

src/neigh_list.h

@@ -42,6 +42,7 @@ class NeighList : protected Pointers {
   int respamiddle;    // 1 if there is also a rRespa middle list
   int respainner;     // 1 if there is also a rRespa inner list
   int copy;           // 1 if this list is copied from another list
+  int trim;           // 1 if this list is trimmed from another list
   int kk2cpu;         // 1 if this list is copied from Kokkos to CPU
   int copymode;       // 1 if this is a Kokkos on-device copy
   int id;             // copied from neighbor list request

src/neigh_request.cpp

@@ -86,6 +86,7 @@ NeighRequest::NeighRequest(LAMMPS *_lmp) : Pointers(_lmp)
   skiplist = -1;
   off2on = 0;
   copy = 0;
+  trim = 0;
   copylist = -1;
   halffull = 0;
   halffulllist = -1;

src/neigh_request.h

@@ -102,6 +102,7 @@ class NeighRequest : protected Pointers {
   int off2on;      // 1 if this is newton on list, but skips from off list
 
   int copy;        // 1 if this list copied from another list
+  int trim;        // 1 if this list trimmed from another list
   int copylist;    // index of list to copy from
 
   int halffull;        // 1 if half list computed from another full list

src/neighbor.cpp

@@ -162,6 +162,7 @@ pairclass(nullptr), pairnames(nullptr), pairmasks(nullptr)
 
   nrequest = maxrequest = 0;
   requests = nullptr;
+  j_sorted = nullptr;
 
   old_nrequest = 0;
   old_requests = nullptr;
@@ -254,6 +255,8 @@ Neighbor::~Neighbor()
     if (old_requests[i]) delete old_requests[i];
   memory->sfree(old_requests);
 
+  delete[] j_sorted;
+
   delete[] binclass;
   delete[] binnames;
   delete[] binmasks;
@@ -842,15 +845,22 @@ int Neighbor::init_pair()
   //   (3) after (2), b/c it adjusts lists created by (2)
   //   (4) after (2) and (3),
   //       b/c (2) may create new full lists, (3) may change them
-  //   (5) last, after all lists are finalized, so all possible copies found
+  //   (5) last, after all lists are finalized, so all possible copies/trims found
 
   int nrequest_original = nrequest;
 
   morph_unique();
   morph_skip();
   morph_granular();     // this method can change flags set by requestor
+
+  // sort requests by cutoff distance for trimming, used by
+  //  morph_halffull and morph_copy_trim. Must come after
+  //  morph_skip() which change the number of requests
+
+  sort_requests();
+
   morph_halffull();
-  morph_copy();
+  morph_copy_trim();
 
   // create new lists, one per request including added requests
   // wait to allocate initial pages until copy lists are detected
@@ -1009,7 +1019,7 @@ int Neighbor::init_pair()
   // allocate initial pages for each list, except if copy flag set
 
   for (i = 0; i < nlist; i++) {
-    if (lists[i]->copy && !lists[i]->kk2cpu)
+    if (lists[i]->copy && !lists[i]->trim && !lists[i]->kk2cpu)
       continue;
     lists[i]->setup_pages(pgsize,oneatom);
   }
@@ -1022,7 +1032,7 @@ int Neighbor::init_pair()
 
   int maxatom = atom->nmax;
   for (i = 0; i < nlist; i++) {
-    if (neigh_pair[i] && (!lists[i]->copy || lists[i]->kk2cpu))
+    if (neigh_pair[i] && (!lists[i]->copy || lists[i]->trim || lists[i]->kk2cpu))
       lists[i]->grow(maxatom,maxatom);
   }
 
@@ -1094,6 +1104,43 @@ int Neighbor::init_pair()
   return same;
 }
 
+/* ----------------------------------------------------------------------
+   sort NeighRequests by cutoff distance
+    to find smallest list for trimming
+------------------------------------------------------------------------- */
+
+void Neighbor::sort_requests()
+{
+  NeighRequest *jrq;
+  int i,j,jmin;
+  double jcut;
+
+  delete[] j_sorted;
+  j_sorted = new int[nrequest];
+
+  for (i = 0; i < nrequest; i++)
+    j_sorted[i] = i;
+
+  for (i = 0; i < nrequest; i++) {
+    double cutoff_min = cutneighmax;
+    jmin = i;
+
+    for (j = i; j < nrequest-1; j++) {
+      jrq = requests[j_sorted[j]];
+      if (jrq->cut) jcut = jrq->cutoff;
+      else jcut = cutneighmax;
+
+      if (jcut <= cutoff_min) {
+        cutoff_min = jcut;
+        jmin = j;
+      }
+    }
+    int tmp = j_sorted[i];
+    j_sorted[i] = j_sorted[jmin];
+    j_sorted[jmin] = tmp;
+  }
+}
+
 /* ----------------------------------------------------------------------
    scan NeighRequests to set additional flags:
    custom cutoff lists and accelerator lists
@@ -1106,10 +1153,23 @@ void Neighbor::morph_unique()
   for (int i = 0; i < nrequest; i++) {
     irq = requests[i];
 
-    // if cut flag set by requestor, set unique flag
+    // if cut flag set by requestor and cutoff is different than default,
+    //  set unique flag, otherwise unset cut flag
     // this forces Pair,Stencil,Bin styles to be instantiated separately
+    // also add skin to cutoff of perpetual lists
 
-    if (irq->cut) irq->unique = 1;
+    if (irq->cut) {
+      if (!irq->occasional)
+        irq->cutoff += skin;
+
+      if (irq->cutoff != cutneighmax) {
+        irq->unique = 1;
+
+      } else {
+        irq->cut = 0;
+        irq->cutoff = 0.0;
+      }
+    }
 
     // avoid flagging a neighbor list as both INTEL and OPENMP
 
@@ -1294,11 +1354,13 @@ void Neighbor::morph_granular()
 
 void Neighbor::morph_halffull()
 {
-  int i,j;
+  int i,j,jj,jmin;
   NeighRequest *irq,*jrq;
+  double icut,jcut;
 
   for (i = 0; i < nrequest; i++) {
     irq = requests[i];
+    int trim_flag = irq->trim;
 
     // only processing half lists
 
@@ -1311,8 +1373,10 @@ void Neighbor::morph_halffull()
 
     // check all other lists
 
-    for (j = 0; j < nrequest; j++) {
+    for (jj = 0; jj < nrequest; jj++) {
-      if (i == j) continue;
+      if (irq->cut) j = j_sorted[jj];
+      else j = jj;
+
       jrq = requests[j];
 
       // can only derive from a perpetual full list
@@ -1321,10 +1385,20 @@ void Neighbor::morph_halffull()
       if (jrq->occasional) continue;
       if (!jrq->full) continue;
 
+      // trim a list with longer cutoff
+
+      if (irq->cut) icut = irq->cutoff;
+      else icut = cutneighmax;
+
+      if (jrq->cut) jcut = jrq->cutoff;
+      else jcut = cutneighmax;
+
+      if (icut > jcut) continue;
+      else if (icut != jcut) trim_flag = 1;
+
       // these flags must be same,
       //   else 2 lists do not store same pairs
       //   or their data structures are different
-      // this includes custom cutoff set by requestor
 
       if (irq->ghost != jrq->ghost) continue;
       if (irq->size != jrq->size) continue;
@@ -1335,8 +1409,6 @@ void Neighbor::morph_halffull()
       if (irq->kokkos_host != jrq->kokkos_host) continue;
       if (irq->kokkos_device != jrq->kokkos_device) continue;
       if (irq->ssa != jrq->ssa) continue;
-      if (irq->cut != jrq->cut) continue;
-      if (irq->cutoff != jrq->cutoff) continue;
 
       // skip flag must be same
       // if both are skip lists, skip info must match
@@ -1351,25 +1423,28 @@ void Neighbor::morph_halffull()
 
     // if matching list exists, point to it
 
-    if (j < nrequest) {
+    if (jj < nrequest) {
       irq->halffull = 1;
       irq->halffulllist = j;
+      irq->trim = trim_flag;
     }
   }
 }
 
 /* ----------------------------------------------------------------------
-   scan NeighRequests for possible copies
+   scan NeighRequests for possible copies or trims
-   if 2 requests match, turn one into a copy of the other
+   if 2 requests match, turn one into a copy or trim of the other
 ------------------------------------------------------------------------- */
 
-void Neighbor::morph_copy()
+void Neighbor::morph_copy_trim()
 {
-  int i,j,inewton,jnewton;
+  int i,j,jj,jmin,inewton,jnewton;
   NeighRequest *irq,*jrq;
+  double icut,jcut;
 
   for (i = 0; i < nrequest; i++) {
     irq = requests[i];
+    int trim_flag = irq->trim;
 
     // this list is already a copy list due to another morph method
 
@@ -1377,7 +1452,10 @@ void Neighbor::morph_copy()
 
     // check all other lists
 
-    for (j = 0; j < nrequest; j++) {
+    for (jj = 0; jj < nrequest; jj++) {
+      if (irq->cut) j = j_sorted[jj];
+      else j = jj;
+
       if (i == j) continue;
       jrq = requests[j];
 
@@ -1385,13 +1463,24 @@ void Neighbor::morph_copy()
 
       if (jrq->copy && jrq->copylist == i) continue;
 
+      // trim a list with longer cutoff
+
+      if (irq->cut) icut = irq->cutoff;
+      else icut = cutneighmax;
+
+      if (jrq->cut) jcut = jrq->cutoff;
+      else jcut = cutneighmax;
+
+      if (icut > jcut) continue;
+      else if (icut != jcut) trim_flag = 1;
+
       // other list (jrq) to copy from must be perpetual
       // list that becomes a copy list (irq) can be perpetual or occasional
       // if both lists are perpetual, require j < i
       //   to prevent circular dependence with 3 or more copies of a list
 
       if (jrq->occasional) continue;
-      if (!irq->occasional && j > i) continue;
+      if (!irq->occasional && !irq->cut && j > i) continue;
 
       // both lists must be half, or both full
 
@@ -1420,7 +1509,6 @@ void Neighbor::morph_copy()
       // these flags must be same,
       //   else 2 lists do not store same pairs
       //   or their data structures are different
-      // this includes custom cutoff set by requestor
       // no need to check omp b/c it stores same pairs
       // NOTE: need check for 2 Kokkos flags?
 
@@ -1431,8 +1519,6 @@ void Neighbor::morph_copy()
       if (irq->kokkos_host && !jrq->kokkos_host) continue;
       if (irq->kokkos_device && !jrq->kokkos_device) continue;
       if (irq->ssa != jrq->ssa) continue;
-      if (irq->cut != jrq->cut) continue;
-      if (irq->cutoff != jrq->cutoff) continue;
 
       // skip flag must be same
       // if both are skip lists, skip info must match
@@ -1448,10 +1534,13 @@ void Neighbor::morph_copy()
     // turn list I into a copy of list J
     // do not copy a list from another copy list, but from its parent list
 
-    if (j < nrequest) {
+    if (jj < nrequest) {
       irq->copy = 1;
-      if (jrq->copy) irq->copylist = jrq->copylist;
+      irq->trim = trim_flag;
-      else irq->copylist = j;
+      if (jrq->copy && irq->cutoff == requests[jrq->copylist]->cutoff)
+        irq->copylist = jrq->copylist;
+      else
+        irq->copylist = j;
     }
   }
 }
@@ -1666,9 +1755,15 @@ void Neighbor::print_pairwise_info()
 
     // order these to get single output of most relevant
 
-    if (rq->copy)
+    if (rq->copy) {
+      if (rq->trim)
+        out += fmt::format(", trim from ({})",rq->copylist+1);
+      else
         out += fmt::format(", copy from ({})",rq->copylist+1);
-    else if (rq->halffull)
+    } else if (rq->halffull)
+      if (rq->trim)
+        out += fmt::format(", half/full trim from ({})",rq->halffulllist+1);
+      else
         out += fmt::format(", half/full from ({})",rq->halffulllist+1);
     else if (rq->skip)
       out += fmt::format(", skip from ({})",rq->skiplist+1);
@@ -1970,10 +2065,16 @@ int Neighbor::choose_pair(NeighRequest *rq)
     //       pairnames[i],pairmasks[i]);
 
     // if copy request, no further checks needed, just return or continue
-    // Kokkos device/host flags must also match in order to copy
+    // trim and Kokkos device/host flags must also match in order to copy
+    // intel and omp flags must match to trim
 
     if (rq->copy) {
       if (!(mask & NP_COPY)) continue;
+      if (rq->trim) {
+        if (!rq->trim != !(mask & NP_TRIM)) continue;
+        if (!rq->omp != !(mask & NP_OMP)) continue;
+        if (!rq->intel != !(mask & NP_INTEL)) continue;
+      }
       if (rq->kokkos_device || rq->kokkos_host) {
         if (!rq->kokkos_device != !(mask & NP_KOKKOS_DEVICE)) continue;
         if (!rq->kokkos_host != !(mask & NP_KOKKOS_HOST)) continue;
@@ -2025,6 +2126,8 @@ int Neighbor::choose_pair(NeighRequest *rq)
 
     if (!rq->skip != !(mask & NP_SKIP)) continue;
 
+    if (!rq->trim != !(mask & NP_TRIM)) continue;
+
     if (!rq->halffull != !(mask & NP_HALF_FULL)) continue;
     if (!rq->off2on != !(mask & NP_OFF2ON)) continue;
 
@@ -2329,7 +2432,7 @@ void Neighbor::build(int topoflag)
 
   for (i = 0; i < npair_perpetual; i++) {
     m = plist[i];
-    if (!lists[m]->copy || lists[m]->kk2cpu)
+    if (!lists[m]->copy || lists[m]->trim || lists[m]->kk2cpu)
       lists[m]->grow(nlocal,nall);
     neigh_pair[m]->build_setup();
     neigh_pair[m]->build(lists[m]);
@@ -2420,7 +2523,7 @@ void Neighbor::build_one(class NeighList *mylist, int preflag)
 
   // build the list
 
-  if (!mylist->copy || mylist->kk2cpu)
+  if (!mylist->copy || mylist->trim || mylist->kk2cpu)
     mylist->grow(atom->nlocal,atom->nlocal+atom->nghost);
   np->build_setup();
   np->build(mylist);

src/neighbor.h

@@ -94,6 +94,7 @@ class Neighbor : protected Pointers {
   NeighList **lists;
   NeighRequest **requests;        // from Pair,Fix,Compute,Command classes
   NeighRequest **old_requests;    // copy of requests to compare to
+  int* j_sorted;                  // index of requests sorted by cutoff distance
 
   // data from topology neighbor lists
 
@@ -245,11 +246,13 @@ class Neighbor : protected Pointers {
   int init_pair();
   virtual void init_topology();
 
+  void sort_requests();
+
   void morph_unique();
   void morph_skip();
   void morph_granular();
   void morph_halffull();
-  void morph_copy();
+  void morph_copy_trim();
 
   void print_pairwise_info();
   void requests_new2old();
@@ -323,7 +326,8 @@ namespace NeighConst {
     NP_SKIP = 1 << 22,
     NP_HALF_FULL = 1 << 23,
     NP_OFF2ON = 1 << 24,
-    NP_MULTI_OLD = 1 << 25
+    NP_MULTI_OLD = 1 << 25,
+    NP_TRIM = 1 << 26
   };
 
   enum {

src/npair_halffull_newtoff_trim.cpp

@@ -0,0 +1,101 @@
+/* ----------------------------------------------------------------------
+   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.h"
+
+#include "atom.h"
+#include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalffullNewtoffTrim::NPairHalffullNewtoffTrim(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+   build half list from full list
+   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
+   works for owned (non-ghost) list, also for ghost list
+   if ghost, also store neighbors of ghost atoms & set inum,gnum correctly
+------------------------------------------------------------------------- */
+
+void NPairHalffullNewtoffTrim::build(NeighList *list)
+{
+  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;
+  MyPage<int> *ipage = list->ipage;
+
+  int *ilist_full = list->listfull->ilist;
+  int *numneigh_full = list->listfull->numneigh;
+  int **firstneigh_full = list->listfull->firstneigh;
+  int inum_full = list->listfull->inum;
+  if (list->ghost) inum_full += list->listfull->gnum;
+
+  int inum = 0;
+  ipage->reset();
+
+  double cutsq_custom = cutoff_custom * cutoff_custom;
+
+  // loop over atoms in full list
+
+  for (ii = 0; ii < inum_full; 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;
+      if (j > i) {
+        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[inum++] = i;
+    firstneigh[i] = neighptr;
+    numneigh[i] = n;
+    ipage->vgot(n);
+    if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
+  }
+
+  list->inum = inum;
+  if (list->ghost) list->gnum = list->listfull->gnum;
+}

src/npair_halffull_newtoff_trim.h

@@ -0,0 +1,54 @@
+/* -*- 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,
+           NPairHalffullNewtoffTrim,
+           NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF |
+           NP_ORTHO | NP_TRI | NP_TRIM);
+
+NPairStyle(halffull/newtoff/skip/trim,
+           NPairHalffullNewtoffTrim,
+           NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF |
+           NP_ORTHO | NP_TRI | NP_SKIP | NP_TRIM);
+
+NPairStyle(halffull/newtoff/ghost/trim,
+           NPairHalffullNewtoffTrim,
+           NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF |
+           NP_ORTHO | NP_TRI | NP_GHOST | NP_TRIM);
+
+NPairStyle(halffull/newtoff/skip/ghost/trim,
+           NPairHalffullNewtoffTrim,
+           NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF |
+           NP_ORTHO | NP_TRI | NP_SKIP | NP_GHOST | NP_TRIM);
+// clang-format on
+#else
+
+#ifndef LMP_NPAIR_HALFFULL_NEWTOFF_TRIM_H
+#define LMP_NPAIR_HALFFULL_NEWTOFF_TRIM_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalffullNewtoffTrim : public NPair {
+ public:
+  NPairHalffullNewtoffTrim(class LAMMPS *);
+  void build(class NeighList *) override;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

src/npair_halffull_newton_trim.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_halffull_newton_trim.h"
+
+#include "atom.h"
+#include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairHalffullNewtonTrim::NPairHalffullNewtonTrim(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+   build half list from full list
+   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 NPairHalffullNewtonTrim::build(NeighList *list)
+{
+  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;
+  MyPage<int> *ipage = list->ipage;
+
+  int *ilist_full = list->listfull->ilist;
+  int *numneigh_full = list->listfull->numneigh;
+  int **firstneigh_full = list->listfull->firstneigh;
+  int inum_full = list->listfull->inum;
+
+  int inum = 0;
+  ipage->reset();
+
+  double cutsq_custom = cutoff_custom * cutoff_custom;
+
+  // loop over parent full list
+
+  for (ii = 0; ii < inum_full; 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[inum++] = i;
+    firstneigh[i] = neighptr;
+    numneigh[i] = n;
+    ipage->vgot(n);
+    if (ipage->status())
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+  }
+
+  list->inum = inum;
+}

src/npair_halffull_newton_trim.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,
+           NPairHalffullNewtonTrim,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
+           NP_ORTHO | NP_TRI | NP_TRIM);
+
+NPairStyle(halffull/newton/skip/trim,
+           NPairHalffullNewtonTrim,
+           NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
+           NP_ORTHO | NP_TRI | NP_SKIP | NP_TRIM);
+// clang-format on
+#else
+
+#ifndef LMP_NPAIR_HALFFULL_NEWTON_TRIM_H
+#define LMP_NPAIR_HALFFULL_NEWTON_TRIM_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairHalffullNewtonTrim : public NPair {
+ public:
+  NPairHalffullNewtonTrim(class LAMMPS *);
+  void build(class NeighList *) override;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

src/npair_trim.cpp

@@ -0,0 +1,92 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Trimright (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.h"
+#include "neigh_list.h"
+#include "atom.h"
+#include "error.h"
+#include "my_page.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+NPairTrim::NPairTrim(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+   create list which is a trimmed version of parent list
+------------------------------------------------------------------------- */
+
+void NPairTrim::build(NeighList *list)
+{
+  NeighList *listcopy = list->listcopy;
+
+  double cutsq_custom = cutoff_custom * cutoff_custom;
+
+  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;
+  MyPage<int> *ipage = list->ipage;
+  ipage->reset();
+
+  int *ilist_copy = listcopy->ilist;
+  int *numneigh_copy = listcopy->numneigh;
+  int **firstneigh_copy = listcopy->firstneigh;
+  int inum = listcopy->inum;
+
+  list->inum = inum;
+  list->gnum = listcopy->gnum;
+
+  for (ii = 0; ii < inum; ii++) {
+    n = 0;
+    neighptr = ipage->vget();
+
+    const int i = ilist_copy[ii];
+    ilist[i] = i;
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+
+    // loop over copy list with larger cutoff and trim to shorter cutoff
+
+    jlist = firstneigh_copy[i];
+    jnum = numneigh_copy[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;
+
+      neighptr[n++] = joriginal;
+    }
+
+    firstneigh[i] = neighptr;
+    numneigh[i] = n;
+    ipage->vgot(n);
+    if (ipage->status())
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+  }
+}

src/npair_trim.h

@@ -0,0 +1,38 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Trimright (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,
+           NPairTrim,
+           NP_COPY | NP_TRIM);
+// clang-format on
+#else
+
+#ifndef LMP_NPAIR_TRIM_H
+#define LMP_NPAIR_TRIM_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+class NPairTrim : public NPair {
+ public:
+  NPairTrim(class LAMMPS *);
+  void build(class NeighList *) override;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

src/pair.cpp

@@ -97,6 +97,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
   tabinner_disp = sqrt(2.0);
   ftable = nullptr;
   fdisptable = nullptr;
+  trim_flag = 1;
 
   allocated = 0;
   suffix_flag = Suffix::NONE;
@@ -204,6 +205,10 @@ void Pair::modify_params(int narg, char **arg)
     } else if (strcmp(arg[iarg],"nofdotr") == 0) {
       no_virial_fdotr_compute = 1;
       ++iarg;
+    } else if (strcmp(arg[iarg],"neigh/trim") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");
+      trim_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
+      iarg += 2;
     } else error->all(FLERR,"Illegal pair_modify command");
   }
 }

src/pair.h

@@ -82,6 +82,7 @@ class Pair : protected Pointers {
   int tail_flag;          // pair_modify flag for LJ tail correction
   double etail, ptail;    // energy/pressure tail corrections
   double etail_ij, ptail_ij;
+  int trim_flag;          // pair_modify flag for trimming neigh list
 
   int evflag;    // energy,virial settings
   int eflag_either, eflag_global, eflag_atom;

src/pair_hybrid.cpp

@@ -35,7 +35,7 @@ using namespace LAMMPS_NS;
 
 PairHybrid::PairHybrid(LAMMPS *lmp) : Pair(lmp),
   styles(nullptr), keywords(nullptr), multiple(nullptr), nmap(nullptr),
-  map(nullptr), special_lj(nullptr), special_coul(nullptr), compute_tally(nullptr)
+  map(nullptr), special_lj(nullptr), special_coul(nullptr), compute_tally(nullptr), cutmax_style(nullptr)
 {
   nstyles = 0;
 
@@ -56,6 +56,7 @@ PairHybrid::~PairHybrid()
     }
   }
   delete[] styles;
+  delete[] cutmax_style;
   delete[] keywords;
   delete[] multiple;
 
@@ -304,6 +305,8 @@ void PairHybrid::settings(int narg, char **arg)
   // allocate list of sub-styles as big as possibly needed if no extra args
 
   styles = new Pair *[narg];
+  cutmax_style = new double[narg];
+  memset(cutmax_style, 0.0, narg*sizeof(double));
   keywords = new char *[narg];
   multiple = new int[narg];
 
@@ -722,6 +725,24 @@ double PairHybrid::init_one(int i, int j)
       ptail_ij += styles[map[i][j][k]]->ptail_ij;
     }
     cutmax = MAX(cutmax,cut);
+
+    int istyle;
+    for (istyle = 0; istyle < nstyles; istyle++)
+      if (styles[istyle] == styles[map[i][j][k]]) break;
+
+    if (styles[istyle]->trim_flag) {
+
+      if (cut > cutmax_style[istyle]) {
+        cutmax_style[istyle] = cut;
+
+        for (auto &request : neighbor->get_pair_requests()) {
+          if (styles[istyle] == request->get_requestor() && styles[istyle]->trim_flag) {
+            request->set_cutoff(cutmax_style[istyle]);
+            break;
+          }
+        }
+      }
+    }
   }
 
   return cutmax;
@@ -784,6 +805,8 @@ void PairHybrid::read_restart(FILE *fp)
   delete[] compute_tally;
 
   styles = new Pair*[nstyles];
+  cutmax_style = new double[nstyles];
+  memset(cutmax_style, 0.0, nstyles*sizeof(double));
   keywords = new char*[nstyles];
   multiple = new int[nstyles];
 

src/pair_hybrid.h

@@ -71,6 +71,7 @@ class PairHybrid : public Pair {
  protected:
   int nstyles;           // # of sub-styles
   Pair **styles;         // list of Pair style classes
+  double *cutmax_style;  // max cutoff for each style
   char **keywords;       // style name of each Pair style
   int *multiple;         // 0 if style used once, else Mth instance
 

src/pair_hybrid_scaled.cpp

@@ -276,6 +276,8 @@ void PairHybridScaled::settings(int narg, char **arg)
   // allocate list of sub-styles as big as possibly needed if no extra args
 
   styles = new Pair *[narg];
+  cutmax_style = new double[narg];
+  memset(cutmax_style, 0.0, narg*sizeof(double));
   keywords = new char *[narg];
   multiple = new int[narg];