1 // clang-format off
2 /* ----------------------------------------------------------------------
3 LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
4 https://www.lammps.org/, Sandia National Laboratories
5 Steve Plimpton, sjplimp@sandia.gov
6
7 Copyright (2003) Sandia Corporation. Under the terms of Contract
8 DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
9 certain rights in this software. This software is distributed under
10 the GNU General Public License.
11
12 See the README file in the top-level LAMMPS directory.
13 ------------------------------------------------------------------------- */
14
15 #include "npair_full_bin_atomonly_omp.h"
16
17 #include "atom.h"
18 #include "error.h"
19 #include "my_page.h"
20 #include "neigh_list.h"
21 #include "npair_omp.h"
22
23 #include "omp_compat.h"
24
25 using namespace LAMMPS_NS;
26
27 /* ---------------------------------------------------------------------- */
28
NPairFullBinAtomonlyOmp(LAMMPS * lmp)29 NPairFullBinAtomonlyOmp::NPairFullBinAtomonlyOmp(LAMMPS *lmp) : NPair(lmp) {}
30
31 /* ----------------------------------------------------------------------
32 binned neighbor list construction for all neighbors
33 every neighbor pair appears in list of both atoms i and j
34 ------------------------------------------------------------------------- */
35
build(NeighList * list)36 void NPairFullBinAtomonlyOmp::build(NeighList *list)
37 {
38 const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
39
40 NPAIR_OMP_INIT;
41 #if defined(_OPENMP)
42 #pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
43 #endif
44 NPAIR_OMP_SETUP(nlocal);
45
46 int i,j,k,n,itype,jtype,ibin;
47 double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
48 int *neighptr;
49
50 double **x = atom->x;
51 int *type = atom->type;
52 int *mask = atom->mask;
53 tagint *molecule = atom->molecule;
54
55 int *ilist = list->ilist;
56 int *numneigh = list->numneigh;
57 int **firstneigh = list->firstneigh;
58
59 // each thread has its own page allocator
60 MyPage<int> &ipage = list->ipage[tid];
61 ipage.reset();
62
63 // loop over owned atoms, storing neighbors
64
65 for (i = ifrom; i < ito; i++) {
66
67 n = 0;
68 neighptr = ipage.vget();
69
70 itype = type[i];
71 xtmp = x[i][0];
72 ytmp = x[i][1];
73 ztmp = x[i][2];
74
75 // loop over all atoms in surrounding bins in stencil including self
76 // skip i = j
77
78 ibin = atom2bin[i];
79
80 for (k = 0; k < nstencil; k++) {
81 for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
82 if (i == j) continue;
83
84 jtype = type[j];
85 if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
86
87 delx = xtmp - x[j][0];
88 dely = ytmp - x[j][1];
89 delz = ztmp - x[j][2];
90 rsq = delx*delx + dely*dely + delz*delz;
91
92 if (rsq <= cutneighsq[itype][jtype]) neighptr[n++] = j;
93 }
94 }
95
96 ilist[i] = i;
97 firstneigh[i] = neighptr;
98 numneigh[i] = n;
99 ipage.vgot(n);
100 if (ipage.status())
101 error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
102 }
103 NPAIR_OMP_CLOSE;
104 list->inum = nlocal;
105 list->gnum = 0;
106 }
107