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_half_bin_newton.h"
16 #include "neigh_list.h"
17 #include "atom.h"
18 #include "atom_vec.h"
19 #include "molecule.h"
20 #include "domain.h"
21 #include "my_page.h"
22 #include "error.h"
23
24 using namespace LAMMPS_NS;
25
26 /* ---------------------------------------------------------------------- */
27
NPairHalfBinNewton(LAMMPS * lmp)28 NPairHalfBinNewton::NPairHalfBinNewton(LAMMPS *lmp) : NPair(lmp) {}
29
30 /* ----------------------------------------------------------------------
31 binned neighbor list construction with full Newton's 3rd law
32 each owned atom i checks its own bin and other bins in Newton stencil
33 every pair stored exactly once by some processor
34 ------------------------------------------------------------------------- */
35
build(NeighList * list)36 void NPairHalfBinNewton::build(NeighList *list)
37 {
38 int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
39 tagint tagprev;
40 double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
41 int *neighptr;
42
43 double **x = atom->x;
44 int *type = atom->type;
45 int *mask = atom->mask;
46 tagint *tag = atom->tag;
47 tagint *molecule = atom->molecule;
48 tagint **special = atom->special;
49 int **nspecial = atom->nspecial;
50 int nlocal = atom->nlocal;
51 if (includegroup) nlocal = atom->nfirst;
52
53 int *molindex = atom->molindex;
54 int *molatom = atom->molatom;
55 Molecule **onemols = atom->avec->onemols;
56 if (molecular == Atom::TEMPLATE) moltemplate = 1;
57 else moltemplate = 0;
58
59 int *ilist = list->ilist;
60 int *numneigh = list->numneigh;
61 int **firstneigh = list->firstneigh;
62 MyPage<int> *ipage = list->ipage;
63
64 int inum = 0;
65 ipage->reset();
66
67 for (i = 0; i < nlocal; i++) {
68 n = 0;
69 neighptr = ipage->vget();
70
71 itype = type[i];
72 xtmp = x[i][0];
73 ytmp = x[i][1];
74 ztmp = x[i][2];
75 if (moltemplate) {
76 imol = molindex[i];
77 iatom = molatom[i];
78 tagprev = tag[i] - iatom - 1;
79 }
80
81 // loop over rest of atoms in i's bin, ghosts are at end of linked list
82 // if j is owned atom, store it, since j is beyond i in linked list
83 // if j is ghost, only store if j coords are "above and to the right" of i
84
85 for (j = bins[i]; j >= 0; j = bins[j]) {
86 if (j >= nlocal) {
87 if (x[j][2] < ztmp) continue;
88 if (x[j][2] == ztmp) {
89 if (x[j][1] < ytmp) continue;
90 if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
91 }
92 }
93
94 jtype = type[j];
95 if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
96
97 delx = xtmp - x[j][0];
98 dely = ytmp - x[j][1];
99 delz = ztmp - x[j][2];
100 rsq = delx*delx + dely*dely + delz*delz;
101
102 if (rsq <= cutneighsq[itype][jtype]) {
103 if (molecular != Atom::ATOMIC) {
104 if (!moltemplate)
105 which = find_special(special[i],nspecial[i],tag[j]);
106 else if (imol >= 0)
107 which = find_special(onemols[imol]->special[iatom],
108 onemols[imol]->nspecial[iatom],
109 tag[j]-tagprev);
110 else which = 0;
111 if (which == 0) neighptr[n++] = j;
112 else if (domain->minimum_image_check(delx,dely,delz))
113 neighptr[n++] = j;
114 else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
115 // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
116 } else neighptr[n++] = j;
117 }
118 }
119
120 // loop over all atoms in other bins in stencil, store every pair
121
122 ibin = atom2bin[i];
123 for (k = 0; k < nstencil; k++) {
124 for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
125 jtype = type[j];
126 if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
127
128 delx = xtmp - x[j][0];
129 dely = ytmp - x[j][1];
130 delz = ztmp - x[j][2];
131 rsq = delx*delx + dely*dely + delz*delz;
132
133 if (rsq <= cutneighsq[itype][jtype]) {
134 if (molecular != Atom::ATOMIC) {
135 if (!moltemplate)
136 which = find_special(special[i],nspecial[i],tag[j]);
137 else if (imol >= 0)
138 which = find_special(onemols[imol]->special[iatom],
139 onemols[imol]->nspecial[iatom],
140 tag[j]-tagprev);
141 else which = 0;
142 if (which == 0) neighptr[n++] = j;
143 else if (domain->minimum_image_check(delx,dely,delz))
144 neighptr[n++] = j;
145 else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
146 // OLD: if (which >= 0) neighptr[n++] = j ^ (which << SBBITS);
147 } else neighptr[n++] = j;
148 }
149 }
150 }
151
152 ilist[inum++] = i;
153 firstneigh[i] = neighptr;
154 numneigh[i] = n;
155 ipage->vgot(n);
156 if (ipage->status())
157 error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
158 }
159
160 list->inum = inum;
161 }
162