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: Julien Devemy (ICCF)
17 ------------------------------------------------------------------------- */
18
19 #include "pair_nm_cut.h"
20
21 #include <cmath>
22 #include <cstring>
23 #include "atom.h"
24 #include "comm.h"
25 #include "force.h"
26 #include "neigh_list.h"
27 #include "math_const.h"
28 #include "memory.h"
29 #include "error.h"
30
31
32 using namespace LAMMPS_NS;
33 using namespace MathConst;
34
35 /* ---------------------------------------------------------------------- */
36
PairNMCut(LAMMPS * lmp)37 PairNMCut::PairNMCut(LAMMPS *lmp) : Pair(lmp)
38 {
39 writedata = 1;
40 }
41
42 /* ---------------------------------------------------------------------- */
43
~PairNMCut()44 PairNMCut::~PairNMCut()
45 {
46 if (allocated) {
47 memory->destroy(setflag);
48 memory->destroy(cutsq);
49
50 memory->destroy(cut);
51 memory->destroy(e0);
52 memory->destroy(r0);
53 memory->destroy(nn);
54 memory->destroy(mm);
55 memory->destroy(nm);
56 memory->destroy(e0nm);
57 memory->destroy(r0n);
58 memory->destroy(r0m);
59 memory->destroy(offset);
60 }
61 }
62
63 /* ---------------------------------------------------------------------- */
64
compute(int eflag,int vflag)65 void PairNMCut::compute(int eflag, int vflag)
66 {
67 int i,j,ii,jj,inum,jnum,itype,jtype;
68 double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
69 double rsq,r2inv,factor_lj;
70 double r,forcenm,rminv,rninv;
71 int *ilist,*jlist,*numneigh,**firstneigh;
72
73 evdwl = 0.0;
74 ev_init(eflag,vflag);
75
76 double **x = atom->x;
77 double **f = atom->f;
78 int *type = atom->type;
79 int nlocal = atom->nlocal;
80 double *special_lj = force->special_lj;
81 int newton_pair = force->newton_pair;
82
83 inum = list->inum;
84 ilist = list->ilist;
85 numneigh = list->numneigh;
86 firstneigh = list->firstneigh;
87
88 // loop over neighbors of my atoms
89
90 for (ii = 0; ii < inum; ii++) {
91 i = ilist[ii];
92 xtmp = x[i][0];
93 ytmp = x[i][1];
94 ztmp = x[i][2];
95 itype = type[i];
96 jlist = firstneigh[i];
97 jnum = numneigh[i];
98
99 for (jj = 0; jj < jnum; jj++) {
100 j = jlist[jj];
101 factor_lj = special_lj[sbmask(j)];
102 j &= NEIGHMASK;
103
104 delx = xtmp - x[j][0];
105 dely = ytmp - x[j][1];
106 delz = ztmp - x[j][2];
107 rsq = delx*delx + dely*dely + delz*delz;
108 jtype = type[j];
109
110 if (rsq < cutsq[itype][jtype]) {
111 r2inv = 1.0/rsq;
112 r = sqrt(rsq);
113
114 rminv = pow(r2inv,mm[itype][jtype]/2.0);
115 rninv = pow(r2inv,nn[itype][jtype]/2.0);
116
117 forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
118 (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
119 r0m[itype][jtype]/pow(r,mm[itype][jtype]));
120 fpair = factor_lj*forcenm*r2inv;
121
122 f[i][0] += delx*fpair;
123 f[i][1] += dely*fpair;
124 f[i][2] += delz*fpair;
125 if (newton_pair || j < nlocal) {
126 f[j][0] -= delx*fpair;
127 f[j][1] -= dely*fpair;
128 f[j][2] -= delz*fpair;
129 }
130
131 if (eflag) {
132 evdwl = e0nm[itype][jtype] *
133 (mm[itype][jtype]*r0n[itype][jtype]*rninv -
134 nn[itype][jtype]*r0m[itype][jtype]*rminv) - offset[itype][jtype];
135 evdwl *= factor_lj;
136 }
137
138 if (evflag) ev_tally(i,j,nlocal,newton_pair,
139 evdwl,0.0,fpair,delx,dely,delz);
140 }
141 }
142 }
143
144 if (vflag_fdotr) virial_fdotr_compute();
145 }
146
147 /* ----------------------------------------------------------------------
148 allocate all arrays
149 ------------------------------------------------------------------------- */
150
allocate()151 void PairNMCut::allocate()
152 {
153 allocated = 1;
154 int n = atom->ntypes;
155
156 memory->create(setflag,n+1,n+1,"pair:setflag");
157 for (int i = 1; i <= n; i++)
158 for (int j = i; j <= n; j++)
159 setflag[i][j] = 0;
160
161 memory->create(cutsq,n+1,n+1,"pair:cutsq");
162
163 memory->create(cut,n+1,n+1,"pair:cut");
164 memory->create(e0,n+1,n+1,"pair:e0");
165 memory->create(r0,n+1,n+1,"pair:r0");
166 memory->create(nn,n+1,n+1,"pair:nn");
167 memory->create(mm,n+1,n+1,"pair:mm");
168 memory->create(nm,n+1,n+1,"pair:nm");
169 memory->create(e0nm,n+1,n+1,"pair:e0nm");
170 memory->create(r0n,n+1,n+1,"pair:r0n");
171 memory->create(r0m,n+1,n+1,"pair:r0m");
172 memory->create(offset,n+1,n+1,"pair:offset");
173 }
174
175 /* ----------------------------------------------------------------------
176 global settings
177 ------------------------------------------------------------------------- */
178
settings(int narg,char ** arg)179 void PairNMCut::settings(int narg, char **arg)
180 {
181 if (narg != 1) error->all(FLERR,"Illegal pair_style command");
182
183 cut_global = utils::numeric(FLERR,arg[0],false,lmp);
184
185 // reset cutoffs that have been explicitly set
186
187 if (allocated) {
188 int i,j;
189 for (i = 1; i <= atom->ntypes; i++)
190 for (j = i; j <= atom->ntypes; j++)
191 if (setflag[i][j]) cut[i][j] = cut_global;
192 }
193 }
194
195 /* ----------------------------------------------------------------------
196 set coeffs for one or more type pairs
197 ------------------------------------------------------------------------- */
198
coeff(int narg,char ** arg)199 void PairNMCut::coeff(int narg, char **arg)
200 {
201 if (narg < 6 || narg > 7)
202 error->all(FLERR,"Incorrect args for pair coefficients");
203 if (!allocated) allocate();
204
205 int ilo,ihi,jlo,jhi;
206 utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
207 utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
208
209 double e0_one = utils::numeric(FLERR,arg[2],false,lmp);
210 double r0_one = utils::numeric(FLERR,arg[3],false,lmp);
211 double nn_one = utils::numeric(FLERR,arg[4],false,lmp);
212 double mm_one = utils::numeric(FLERR,arg[5],false,lmp);
213
214 double cut_one = cut_global;
215 if (narg == 7) cut_one = utils::numeric(FLERR,arg[6],false,lmp);
216
217 int count = 0;
218 for (int i = ilo; i <= ihi; i++) {
219 for (int j = MAX(jlo,i); j <= jhi; j++) {
220 e0[i][j] = e0_one;
221 r0[i][j] = r0_one;
222 nn[i][j] = nn_one;
223 mm[i][j] = mm_one;
224 cut[i][j] = cut_one;
225 setflag[i][j] = 1;
226 count++;
227 }
228 }
229
230 if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
231 }
232
233 /* ----------------------------------------------------------------------
234 init for one type pair i,j and corresponding j,i
235 ------------------------------------------------------------------------- */
236
init_one(int i,int j)237 double PairNMCut::init_one(int i, int j)
238 {
239 if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
240
241 nm[i][j] = nn[i][j]*mm[i][j];
242 e0nm[i][j] = e0[i][j]/(nn[i][j]-mm[i][j]);
243 r0n[i][j] = pow(r0[i][j],nn[i][j]);
244 r0m[i][j] = pow(r0[i][j],mm[i][j]);
245
246 if (offset_flag && (cut[i][j] > 0.0)) {
247 offset[i][j] = e0nm[i][j] *
248 ((mm[i][j]*r0n[i][j] / pow(cut[i][j],nn[i][j])) -
249 (nn[i][j]*r0m[i][j] / pow(cut[i][j],mm[i][j])));
250 } else offset[i][j] = 0.0;
251
252 e0[j][i] = e0[i][j];
253 nn[j][i] = nn[i][j];
254 mm[j][i] = mm[i][j];
255 nm[j][i] = nm[i][j];
256 r0[j][i] = r0[i][j];
257 e0nm[j][i] = e0nm[i][j];
258 r0n[j][i] = r0n[i][j];
259 r0m[j][i] = r0m[i][j];
260 offset[j][i] = offset[i][j];
261
262 // compute I,J contribution to long-range tail correction
263 // count total # of atoms of type I and J via Allreduce
264
265 if (tail_flag) {
266 int *type = atom->type;
267 int nlocal = atom->nlocal;
268
269 double count[2],all[2];
270 count[0] = count[1] = 0.0;
271 for (int k = 0; k < nlocal; k++) {
272 if (type[k] == i) count[0] += 1.0;
273 if (type[k] == j) count[1] += 1.0;
274 }
275 MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
276
277 double cut3 = cut[i][j]*cut[i][j]*cut[i][j];
278 ptail_ij = 2.*MY_PI/3.*all[0]*all[1]*e0nm[i][j]*nm[i][j]*cut3 *
279 (pow(r0[i][j]/cut[i][j],nn[i][j])/(nn[i][j]-3) - pow(r0[i][j]/cut[i][j],mm[i][j])/(mm[i][j]-3));
280 etail_ij = 2.*MY_PI*all[0]*all[1]*e0nm[i][j]*cut3 *
281 (mm[i][j]*pow(r0[i][j]/cut[i][j],nn[i][j])/(nn[i][j]-3) - nn[i][j]*pow(r0[i][j]/cut[i][j],mm[i][j])/(mm[i][j]-3));
282
283 }
284
285 return cut[i][j];
286 }
287
288 /* ----------------------------------------------------------------------
289 proc 0 writes to restart file
290 ------------------------------------------------------------------------- */
291
write_restart(FILE * fp)292 void PairNMCut::write_restart(FILE *fp)
293 {
294 write_restart_settings(fp);
295
296 int i,j;
297 for (i = 1; i <= atom->ntypes; i++)
298 for (j = i; j <= atom->ntypes; j++) {
299 fwrite(&setflag[i][j],sizeof(int),1,fp);
300 if (setflag[i][j]) {
301 fwrite(&e0[i][j],sizeof(double),1,fp);
302 fwrite(&r0[i][j],sizeof(double),1,fp);
303 fwrite(&nn[i][j],sizeof(double),1,fp);
304 fwrite(&mm[i][j],sizeof(double),1,fp);
305 fwrite(&cut[i][j],sizeof(double),1,fp);
306 }
307 }
308 }
309
310 /* ----------------------------------------------------------------------
311 proc 0 reads from restart file, bcasts
312 ------------------------------------------------------------------------- */
313
read_restart(FILE * fp)314 void PairNMCut::read_restart(FILE *fp)
315 {
316 read_restart_settings(fp);
317 allocate();
318
319 int i,j;
320 int me = comm->me;
321 for (i = 1; i <= atom->ntypes; i++)
322 for (j = i; j <= atom->ntypes; j++) {
323 if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
324 MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
325 if (setflag[i][j]) {
326 if (me == 0) {
327 utils::sfread(FLERR,&e0[i][j],sizeof(double),1,fp,nullptr,error);
328 utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,nullptr,error);
329 utils::sfread(FLERR,&nn[i][j],sizeof(double),1,fp,nullptr,error);
330 utils::sfread(FLERR,&mm[i][j],sizeof(double),1,fp,nullptr,error);
331 utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
332 }
333 MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world);
334 MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
335 MPI_Bcast(&nn[i][j],1,MPI_DOUBLE,0,world);
336 MPI_Bcast(&mm[i][j],1,MPI_DOUBLE,0,world);
337 MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
338 }
339 }
340 }
341
342 /* ----------------------------------------------------------------------
343 proc 0 writes to restart file
344 ------------------------------------------------------------------------- */
345
write_restart_settings(FILE * fp)346 void PairNMCut::write_restart_settings(FILE *fp)
347 {
348 fwrite(&cut_global,sizeof(double),1,fp);
349 fwrite(&offset_flag,sizeof(int),1,fp);
350 fwrite(&mix_flag,sizeof(int),1,fp);
351 fwrite(&tail_flag,sizeof(int),1,fp);
352 }
353
354 /* ----------------------------------------------------------------------
355 proc 0 reads from restart file, bcasts
356 ------------------------------------------------------------------------- */
357
read_restart_settings(FILE * fp)358 void PairNMCut::read_restart_settings(FILE *fp)
359 {
360 if (comm->me == 0) {
361 utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
362 utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error);
363 utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
364 utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,nullptr,error);
365 }
366 MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
367 MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
368 MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
369 MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
370 }
371
372 /* ----------------------------------------------------------------------
373 proc 0 writes to data file
374 ------------------------------------------------------------------------- */
375
write_data(FILE * fp)376 void PairNMCut::write_data(FILE *fp)
377 {
378 for (int i = 1; i <= atom->ntypes; i++)
379 fprintf(fp,"%d %g %g %g %g\n",i,e0[i][i],r0[i][i],nn[i][i],mm[i][i]);
380 }
381
382 /* ----------------------------------------------------------------------
383 proc 0 writes all pairs to data file
384 ------------------------------------------------------------------------- */
385
write_data_all(FILE * fp)386 void PairNMCut::write_data_all(FILE *fp)
387 {
388 for (int i = 1; i <= atom->ntypes; i++)
389 for (int j = i; j <= atom->ntypes; j++)
390 fprintf(fp,"%d %d %g %g %g %g %g\n",i,j,
391 e0[i][j],r0[i][j],nn[i][j],mm[i][j],cut[i][j]);
392 }
393
394 /* ---------------------------------------------------------------------- */
395
single(int,int,int itype,int jtype,double rsq,double,double factor_lj,double & fforce)396 double PairNMCut::single(int /*i*/, int /*j*/, int itype, int jtype,
397 double rsq, double /*factor_coul*/, double factor_lj,
398 double &fforce)
399 {
400 double r2inv,r,forcenm,phinm;
401
402 r2inv = 1.0/rsq;
403 r = sqrt(rsq);
404
405 forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
406 (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
407 r0m[itype][jtype]/pow(r,mm[itype][jtype]));
408 fforce = factor_lj*forcenm*r2inv;
409
410 phinm = e0nm[itype][jtype] *
411 (mm[itype][jtype] * r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
412 nn[itype][jtype]*r0m[itype][jtype] /pow(r,mm[itype][jtype])) -
413 offset[itype][jtype];
414 return factor_lj*phinm;
415 }
416
417 /* ---------------------------------------------------------------------- */
418
extract(const char * str,int & dim)419 void *PairNMCut::extract(const char *str, int &dim)
420 {
421 dim = 2;
422 if (strcmp(str,"e0") == 0) return (void *) e0;
423 if (strcmp(str,"r0") == 0) return (void *) r0;
424 if (strcmp(str,"nn") == 0) return (void *) nn;
425 if (strcmp(str,"mm") == 0) return (void *) mm;
426 return nullptr;
427 }
428