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_respa_nsq_newton.h"
16 #include "neigh_list.h"
17 #include "atom.h"
18 #include "atom_vec.h"
19 #include "group.h"
20 #include "molecule.h"
21 #include "domain.h"
22 #include "my_page.h"
23 #include "error.h"
24
25 using namespace LAMMPS_NS;
26
27 /* ---------------------------------------------------------------------- */
28
NPairHalfRespaNsqNewton(LAMMPS * lmp)29 NPairHalfRespaNsqNewton::NPairHalfRespaNsqNewton(LAMMPS *lmp) : NPair(lmp) {}
30
31 /* ----------------------------------------------------------------------
32 multiple respa lists
33 N^2 / 2 search for neighbor pairs with full Newton's 3rd law
34 pair added to list if atoms i and j are both owned and i < j
35 if j is ghost only me or other proc adds pair
36 decision based on itag,jtag tests
37 ------------------------------------------------------------------------- */
38
build(NeighList * list)39 void NPairHalfRespaNsqNewton::build(NeighList *list)
40 {
41 int i,j,n,itype,jtype,itag,jtag,n_inner,n_middle,bitmask;
42 int imol,iatom,moltemplate;
43 tagint tagprev;
44 double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
45 int *neighptr,*neighptr_inner,*neighptr_middle;
46
47 double **x = atom->x;
48 int *type = atom->type;
49 int *mask = atom->mask;
50 tagint *tag = atom->tag;
51 tagint *molecule = atom->molecule;
52 tagint **special = atom->special;
53 int **nspecial = atom->nspecial;
54 int nlocal = atom->nlocal;
55 int nall = nlocal + atom->nghost;
56 if (includegroup) {
57 nlocal = atom->nfirst;
58 bitmask = group->bitmask[includegroup];
59 }
60
61 int *molindex = atom->molindex;
62 int *molatom = atom->molatom;
63 Molecule **onemols = atom->avec->onemols;
64 if (molecular == Atom::TEMPLATE) moltemplate = 1;
65 else moltemplate = 0;
66
67 int *ilist = list->ilist;
68 int *numneigh = list->numneigh;
69 int **firstneigh = list->firstneigh;
70 MyPage<int> *ipage = list->ipage;
71
72 int *ilist_inner = list->ilist_inner;
73 int *numneigh_inner = list->numneigh_inner;
74 int **firstneigh_inner = list->firstneigh_inner;
75 MyPage<int> *ipage_inner = list->ipage_inner;
76
77 int *ilist_middle,*numneigh_middle,**firstneigh_middle;
78 MyPage<int> *ipage_middle;
79 int respamiddle = list->respamiddle;
80 if (respamiddle) {
81 ilist_middle = list->ilist_middle;
82 numneigh_middle = list->numneigh_middle;
83 firstneigh_middle = list->firstneigh_middle;
84 ipage_middle = list->ipage_middle;
85 }
86
87 int inum = 0;
88 int which = 0;
89 int minchange = 0;
90 ipage->reset();
91 ipage_inner->reset();
92 if (respamiddle) ipage_middle->reset();
93
94 for (i = 0; i < nlocal; i++) {
95 n = n_inner = 0;
96 neighptr = ipage->vget();
97 neighptr_inner = ipage_inner->vget();
98 if (respamiddle) {
99 n_middle = 0;
100 neighptr_middle = ipage_middle->vget();
101 }
102
103 itag = tag[i];
104 itype = type[i];
105 xtmp = x[i][0];
106 ytmp = x[i][1];
107 ztmp = x[i][2];
108 if (moltemplate) {
109 imol = molindex[i];
110 iatom = molatom[i];
111 tagprev = tag[i] - iatom - 1;
112 }
113
114 // loop over remaining atoms, owned and ghost
115
116 for (j = i+1; j < nall; j++) {
117 if (includegroup && !(mask[j] & bitmask)) continue;
118
119 if (j >= nlocal) {
120 jtag = tag[j];
121 if (itag > jtag) {
122 if ((itag+jtag) % 2 == 0) continue;
123 } else if (itag < jtag) {
124 if ((itag+jtag) % 2 == 1) continue;
125 } else {
126 if (x[j][2] < ztmp) continue;
127 if (x[j][2] == ztmp) {
128 if (x[j][1] < ytmp) continue;
129 if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
130 }
131 }
132 }
133
134 jtype = type[j];
135 if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
136
137 delx = xtmp - x[j][0];
138 dely = ytmp - x[j][1];
139 delz = ztmp - x[j][2];
140 rsq = delx*delx + dely*dely + delz*delz;
141
142 if (rsq <= cutneighsq[itype][jtype]) {
143 if (molecular != Atom::ATOMIC) {
144 if (!moltemplate)
145 which = find_special(special[i],nspecial[i],tag[j]);
146 else if (imol >= 0)
147 which = find_special(onemols[imol]->special[iatom],
148 onemols[imol]->nspecial[iatom],
149 tag[j]-tagprev);
150 else which = 0;
151 if (which == 0) neighptr[n++] = j;
152 else if ((minchange = domain->minimum_image_check(delx,dely,delz)))
153 neighptr[n++] = j;
154 else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
155 } else neighptr[n++] = j;
156
157 if (rsq < cut_inner_sq) {
158 if (which == 0) neighptr_inner[n_inner++] = j;
159 else if (minchange) neighptr_inner[n_inner++] = j;
160 else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS);
161 }
162
163 if (respamiddle &&
164 rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
165 if (which == 0) neighptr_middle[n_middle++] = j;
166 else if (minchange) neighptr_middle[n_middle++] = j;
167 else if (which > 0)
168 neighptr_middle[n_middle++] = j ^ (which << SBBITS);
169 }
170 }
171 }
172
173 ilist[inum] = i;
174 firstneigh[i] = neighptr;
175 numneigh[i] = n;
176 ipage->vgot(n);
177 if (ipage->status())
178 error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
179
180 ilist_inner[inum] = i;
181 firstneigh_inner[i] = neighptr_inner;
182 numneigh_inner[i] = n_inner;
183 ipage_inner->vgot(n_inner);
184 if (ipage_inner->status())
185 error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
186
187 if (respamiddle) {
188 ilist_middle[inum] = i;
189 firstneigh_middle[i] = neighptr_middle;
190 numneigh_middle[i] = n_middle;
191 ipage_middle->vgot(n_middle);
192 if (ipage_middle->status())
193 error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
194 }
195
196 inum++;
197 }
198
199 list->inum = inum;
200 list->inum_inner = inum;
201 if (respamiddle) list->inum_middle = inum;
202 }
203