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 /* ----------------------------------------------------------------------
16 Contributing author: Trung Dac Nguyen (ORNL)
17 ------------------------------------------------------------------------- */
18
19 #include "pair_lj_gromacs_gpu.h"
20
21 #include "atom.h"
22 #include "domain.h"
23 #include "error.h"
24 #include "force.h"
25 #include "gpu_extra.h"
26 #include "neigh_list.h"
27 #include "neigh_request.h"
28 #include "neighbor.h"
29 #include "suffix.h"
30
31 #include <cmath>
32
33 using namespace LAMMPS_NS;
34
35 // External functions from cuda library for atom decomposition
36
37 int ljgrm_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
38 double **host_lj2, double **host_lj3, double **host_lj4,
39 double *special_lj, const int inum, const int nall,
40 const int max_nbors, const int maxspecial,
41 const double cell_size, int &gpu_mode, FILE *screen,
42 double **host_ljsw1, double **host_ljsw2,
43 double **host_ljsw3, double **host_ljsw4,
44 double **host_ljsw5, double **cut_inner,
45 double **cut_innersq);
46 void ljgrm_gpu_clear();
47 int ** ljgrm_gpu_compute_n(const int ago, const int inum_full, const int nall,
48 double **host_x, int *host_type, double *sublo,
49 double *subhi, tagint *tag, int **nspecial,
50 tagint **special, const bool eflag, const bool vflag,
51 const bool eatom, const bool vatom, int &host_start,
52 int **ilist, int **jnum, const double cpu_time,
53 bool &success);
54 void ljgrm_gpu_compute(const int ago, const int inum_full, const int nall,
55 double **host_x, int *host_type, int *ilist, int *numj,
56 int **firstneigh, const bool eflag, const bool vflag,
57 const bool eatom, const bool vatom, int &host_start,
58 const double cpu_time, bool &success);
59 double ljgrm_gpu_bytes();
60
61 /* ---------------------------------------------------------------------- */
62
PairLJGromacsGPU(LAMMPS * lmp)63 PairLJGromacsGPU::PairLJGromacsGPU(LAMMPS *lmp) :
64 PairLJGromacs(lmp), gpu_mode(GPU_FORCE)
65 {
66 respa_enable = 0;
67 reinitflag = 0;
68 cpu_time = 0.0;
69 suffix_flag |= Suffix::GPU;
70 GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
71 }
72
73 /* ----------------------------------------------------------------------
74 free all arrays
75 ------------------------------------------------------------------------- */
76
~PairLJGromacsGPU()77 PairLJGromacsGPU::~PairLJGromacsGPU()
78 {
79 ljgrm_gpu_clear();
80 }
81
82 /* ---------------------------------------------------------------------- */
83
compute(int eflag,int vflag)84 void PairLJGromacsGPU::compute(int eflag, int vflag)
85 {
86 ev_init(eflag,vflag);
87
88 int nall = atom->nlocal + atom->nghost;
89 int inum, host_start;
90
91 bool success = true;
92 int *ilist, *numneigh, **firstneigh;
93 if (gpu_mode != GPU_FORCE) {
94 double sublo[3],subhi[3];
95 if (domain->triclinic == 0) {
96 sublo[0] = domain->sublo[0];
97 sublo[1] = domain->sublo[1];
98 sublo[2] = domain->sublo[2];
99 subhi[0] = domain->subhi[0];
100 subhi[1] = domain->subhi[1];
101 subhi[2] = domain->subhi[2];
102 } else {
103 domain->bbox(domain->sublo_lamda,domain->subhi_lamda,sublo,subhi);
104 }
105 inum = atom->nlocal;
106 firstneigh = ljgrm_gpu_compute_n(neighbor->ago, inum, nall,
107 atom->x, atom->type, sublo,
108 subhi, atom->tag, atom->nspecial,
109 atom->special, eflag, vflag, eflag_atom,
110 vflag_atom, host_start, &ilist,
111 &numneigh, cpu_time, success);
112 } else {
113 inum = list->inum;
114 ilist = list->ilist;
115 numneigh = list->numneigh;
116 firstneigh = list->firstneigh;
117 ljgrm_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
118 ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
119 vflag_atom, host_start, cpu_time, success);
120 }
121 if (!success)
122 error->one(FLERR,"Insufficient memory on accelerator");
123
124 if (host_start<inum) {
125 cpu_time = MPI_Wtime();
126 cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
127 cpu_time = MPI_Wtime() - cpu_time;
128 }
129 }
130
131 /* ----------------------------------------------------------------------
132 init specific to this pair style
133 ------------------------------------------------------------------------- */
134
init_style()135 void PairLJGromacsGPU::init_style()
136 {
137 if (force->newton_pair)
138 error->all(FLERR,"Pair style lj/gromacs/gpu requires newton pair off");
139
140 // Repeat cutsq calculation because done after call to init_style
141 double maxcut = -1.0;
142 double mcut;
143 for (int i = 1; i <= atom->ntypes; i++) {
144 for (int j = i; j <= atom->ntypes; j++) {
145 if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
146 mcut = init_one(i,j);
147 mcut *= mcut;
148 if (mcut > maxcut)
149 maxcut = mcut;
150 cutsq[i][j] = cutsq[j][i] = mcut;
151 } else
152 cutsq[i][j] = cutsq[j][i] = 0.0;
153 }
154 }
155 double cell_size = sqrt(maxcut) + neighbor->skin;
156
157 int maxspecial=0;
158 if (atom->molecular != Atom::ATOMIC)
159 maxspecial=atom->maxspecial;
160
161 int mnf = 5e-2 * neighbor->oneatom;
162 int success = ljgrm_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
163 force->special_lj, atom->nlocal,
164 atom->nlocal+atom->nghost, mnf, maxspecial,
165 cell_size, gpu_mode, screen, ljsw1, ljsw2,
166 ljsw3, ljsw4, ljsw5, cut_inner, cut_inner_sq);
167 GPU_EXTRA::check_flag(success,error,world);
168
169 if (gpu_mode == GPU_FORCE) {
170 int irequest = neighbor->request(this,instance_me);
171 neighbor->requests[irequest]->half = 0;
172 neighbor->requests[irequest]->full = 1;
173 }
174 }
175
176 /* ---------------------------------------------------------------------- */
177
memory_usage()178 double PairLJGromacsGPU::memory_usage()
179 {
180 double bytes = Pair::memory_usage();
181 return bytes + ljgrm_gpu_bytes();
182 }
183
184 /* ---------------------------------------------------------------------- */
185
cpu_compute(int start,int inum,int eflag,int,int * ilist,int * numneigh,int ** firstneigh)186 void PairLJGromacsGPU::cpu_compute(int start, int inum, int eflag,
187 int /* vflag */, int *ilist,
188 int *numneigh, int **firstneigh)
189 {
190 int i,j,ii,jj,jnum,itype,jtype;
191 double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
192 double rsq,r2inv,r6inv,forcelj,factor_lj;
193 double r,t,fswitch,eswitch;
194 int *jlist;
195
196 double **x = atom->x;
197 double **f = atom->f;
198 int *type = atom->type;
199 double *special_lj = force->special_lj;
200
201 // loop over neighbors of my atoms
202
203 for (ii = start; ii < inum; ii++) {
204 i = ilist[ii];
205 xtmp = x[i][0];
206 ytmp = x[i][1];
207 ztmp = x[i][2];
208 itype = type[i];
209 jlist = firstneigh[i];
210 jnum = numneigh[i];
211
212 for (jj = 0; jj < jnum; jj++) {
213 j = jlist[jj];
214 factor_lj = special_lj[sbmask(j)];
215 j &= NEIGHMASK;
216
217 delx = xtmp - x[j][0];
218 dely = ytmp - x[j][1];
219 delz = ztmp - x[j][2];
220 rsq = delx*delx + dely*dely + delz*delz;
221 jtype = type[j];
222
223 if (rsq < cutsq[itype][jtype]) {
224 r2inv = 1.0/rsq;
225 r6inv = r2inv*r2inv*r2inv;
226 forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
227 if (rsq > cut_inner_sq[itype][jtype]) {
228 r = sqrt(rsq);
229 t = r - cut_inner[itype][jtype];
230 fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);
231 forcelj += fswitch;
232 }
233 fpair = factor_lj*forcelj * r2inv;
234
235 f[i][0] += delx*fpair;
236 f[i][1] += dely*fpair;
237 f[i][2] += delz*fpair;
238
239 if (eflag) {
240 evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
241 evdwl += ljsw5[itype][jtype];
242 if (rsq > cut_inner_sq[itype][jtype]) {
243 eswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t);
244 evdwl += eswitch;
245 }
246 evdwl *= factor_lj;
247 }
248
249 if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
250 }
251 }
252 }
253 }
254