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: Pavel Elkind (Gothenburg University)
17 ------------------------------------------------------------------------- */
18
19 #include "pair_lj_cut_tip4p_cut.h"
20
21 #include <cmath>
22 #include <cstring>
23 #include "atom.h"
24 #include "force.h"
25 #include "neighbor.h"
26 #include "neigh_list.h"
27 #include "domain.h"
28 #include "angle.h"
29 #include "bond.h"
30 #include "comm.h"
31 #include "math_const.h"
32 #include "memory.h"
33 #include "error.h"
34
35
36 using namespace LAMMPS_NS;
37 using namespace MathConst;
38
39 /* ---------------------------------------------------------------------- */
40
PairLJCutTIP4PCut(LAMMPS * lmp)41 PairLJCutTIP4PCut::PairLJCutTIP4PCut(LAMMPS *lmp) : Pair(lmp)
42 {
43 single_enable = 0;
44 writedata = 1;
45
46 nmax = 0;
47 hneigh = nullptr;
48 newsite = nullptr;
49
50 // TIP4P cannot compute virial as F dot r
51 // due to finding bonded H atoms which are not near O atom
52
53 no_virial_fdotr_compute = 1;
54 }
55
56 /* ---------------------------------------------------------------------- */
57
~PairLJCutTIP4PCut()58 PairLJCutTIP4PCut::~PairLJCutTIP4PCut()
59 {
60 if (allocated) {
61 memory->destroy(setflag);
62 memory->destroy(cutsq);
63
64 memory->destroy(cut_lj);
65 memory->destroy(cut_ljsq);
66 memory->destroy(epsilon);
67 memory->destroy(sigma);
68 memory->destroy(lj1);
69 memory->destroy(lj2);
70 memory->destroy(lj3);
71 memory->destroy(lj4);
72 memory->destroy(offset);
73 }
74
75 memory->destroy(hneigh);
76 memory->destroy(newsite);
77 }
78
79 /* ---------------------------------------------------------------------- */
80
compute(int eflag,int vflag)81 void PairLJCutTIP4PCut::compute(int eflag, int vflag)
82 {
83 int i,j,ii,jj,inum,jnum,itype,jtype;
84 double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
85 double rsq,r2inv,r6inv,forcecoul,forcelj,factor_lj,factor_coul;
86 int *ilist,*jlist,*numneigh,**firstneigh;
87
88 int key;
89 int n,vlist[6];
90 int iH1,iH2,jH1,jH2;
91 double cforce;
92 double fO[3],fH[3],fd[3],v[6];
93 double *x1,*x2,*xH1,*xH2;
94
95 evdwl = ecoul = 0.0;
96 ev_init(eflag,vflag);
97
98 // reallocate hneigh & newsite if necessary
99 // initialize hneigh[0] to -1 on steps when reneighboring occurred
100 // initialize hneigh[2] to 0 every step
101
102 int nlocal = atom->nlocal;
103 int nall = nlocal + atom->nghost;
104
105 if (atom->nmax > nmax) {
106 nmax = atom->nmax;
107 memory->destroy(hneigh);
108 memory->create(hneigh,nmax,3,"pair:hneigh");
109 memory->destroy(newsite);
110 memory->create(newsite,nmax,3,"pair:newsite");
111 }
112 if (neighbor->ago == 0)
113 for (i = 0; i < nall; i++) hneigh[i][0] = -1;
114 for (i = 0; i < nall; i++) hneigh[i][2] = 0;
115
116 double **f = atom->f;
117 double **x = atom->x;
118 double *q = atom->q;
119 tagint *tag = atom->tag;
120 int *type = atom->type;
121 double *special_lj = force->special_lj;
122 double *special_coul = force->special_coul;
123 int newton_pair = force->newton_pair;
124 double qqrd2e = force->qqrd2e;
125
126 inum = list->inum;
127 ilist = list->ilist;
128 numneigh = list->numneigh;
129 firstneigh = list->firstneigh;
130
131 // loop over neighbors of my atoms
132
133 for (ii = 0; ii < inum; ii++) {
134 i = ilist[ii];
135 qtmp = q[i];
136 xtmp = x[i][0];
137 ytmp = x[i][1];
138 ztmp = x[i][2];
139 itype = type[i];
140
141 if (itype == typeO) {
142 if (hneigh[i][0] < 0) {
143 iH1 = atom->map(tag[i] + 1);
144 iH2 = atom->map(tag[i] + 2);
145 if (iH1 == -1 || iH2 == -1)
146 error->one(FLERR,"TIP4P hydrogen is missing");
147 if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
148 error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
149 // set iH1,iH2 to index of closest image to O
150 iH1 = domain->closest_image(i,iH1);
151 iH2 = domain->closest_image(i,iH2);
152 compute_newsite(x[i],x[iH1],x[iH2],newsite[i]);
153 hneigh[i][0] = iH1;
154 hneigh[i][1] = iH2;
155 hneigh[i][2] = 1;
156
157 } else {
158 iH1 = hneigh[i][0];
159 iH2 = hneigh[i][1];
160 if (hneigh[i][2] == 0) {
161 hneigh[i][2] = 1;
162 compute_newsite(x[i],x[iH1],x[iH2],newsite[i]);
163 }
164 }
165 x1 = newsite[i];
166 } else x1 = x[i];
167
168 jlist = firstneigh[i];
169 jnum = numneigh[i];
170
171 for (jj = 0; jj < jnum; jj++) {
172 j = jlist[jj];
173 factor_lj = special_lj[sbmask(j)];
174 factor_coul = special_coul[sbmask(j)];
175 j &= NEIGHMASK;
176
177 delx = xtmp - x[j][0];
178 dely = ytmp - x[j][1];
179 delz = ztmp - x[j][2];
180 rsq = delx*delx + dely*dely + delz*delz;
181 jtype = type[j];
182
183 // LJ interaction based on true rsq
184
185 if (rsq < cut_ljsq[itype][jtype]) {
186 r2inv = 1.0/rsq;
187 r6inv = r2inv*r2inv*r2inv;
188 forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
189 forcelj *= factor_lj * r2inv;
190
191 f[i][0] += delx*forcelj;
192 f[i][1] += dely*forcelj;
193 f[i][2] += delz*forcelj;
194 f[j][0] -= delx*forcelj;
195 f[j][1] -= dely*forcelj;
196 f[j][2] -= delz*forcelj;
197
198 if (eflag) {
199 evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
200 offset[itype][jtype];
201 evdwl *= factor_lj;
202 } else evdwl = 0.0;
203
204 if (evflag) ev_tally(i,j,nlocal,newton_pair,
205 evdwl,0.0,forcelj,delx,dely,delz);
206 }
207
208 // adjust rsq and delxyz for off-site O charge(s) if necessary
209 // but only if they are within reach
210
211 if (rsq < cut_coulsqplus) {
212 if (itype == typeO || jtype == typeO) {
213
214 // if atom J = water O, set x2 = offset charge site
215 // else x2 = x of atom J
216
217 if (jtype == typeO) {
218 if (hneigh[j][0] < 0) {
219 jH1 = atom->map(tag[j] + 1);
220 jH2 = atom->map(tag[j] + 2);
221 if (jH1 == -1 || jH2 == -1)
222 error->one(FLERR,"TIP4P hydrogen is missing");
223 if (atom->type[jH1] != typeH || atom->type[jH2] != typeH)
224 error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
225 // set jH1,jH2 to closest image to O
226 jH1 = domain->closest_image(j,jH1);
227 jH2 = domain->closest_image(j,jH2);
228 compute_newsite(x[j],x[jH1],x[jH2],newsite[j]);
229 hneigh[j][0] = jH1;
230 hneigh[j][1] = jH2;
231 hneigh[j][2] = 1;
232
233 } else {
234 jH1 = hneigh[j][0];
235 jH2 = hneigh[j][1];
236 if (hneigh[j][2] == 0) {
237 hneigh[j][2] = 1;
238 compute_newsite(x[j],x[jH1],x[jH2],newsite[j]);
239 }
240 }
241 x2 = newsite[j];
242 } else x2 = x[j];
243
244 delx = x1[0] - x2[0];
245 dely = x1[1] - x2[1];
246 delz = x1[2] - x2[2];
247 rsq = delx*delx + dely*dely + delz*delz;
248 }
249
250 // Coulombic interaction based on modified rsq
251
252 if (rsq < cut_coulsq) {
253 r2inv = 1.0 / rsq;
254 forcecoul = qqrd2e * qtmp * q[j] * sqrt(r2inv);
255 cforce = factor_coul * forcecoul * r2inv;
256
257 // if i,j are not O atoms, force is applied directly;
258 // if i or j are O atoms, force is on fictitious atom & partitioned
259 // force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
260 // f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
261 // preserves total force and torque on water molecule
262 // virial = sum(r x F) where each water's atoms are near xi and xj
263 // vlist stores 2,4,6 atoms whose forces contribute to virial
264
265 n = 0;
266 key = 0;
267
268 if (itype != typeO) {
269 f[i][0] += delx * cforce;
270 f[i][1] += dely * cforce;
271 f[i][2] += delz * cforce;
272
273 if (vflag) {
274 v[0] = x[i][0] * delx * cforce;
275 v[1] = x[i][1] * dely * cforce;
276 v[2] = x[i][2] * delz * cforce;
277 v[3] = x[i][0] * dely * cforce;
278 v[4] = x[i][0] * delz * cforce;
279 v[5] = x[i][1] * delz * cforce;
280 }
281 vlist[n++] = i;
282
283 } else {
284 key++;
285
286 fd[0] = delx*cforce;
287 fd[1] = dely*cforce;
288 fd[2] = delz*cforce;
289
290 fO[0] = fd[0]*(1.0 - alpha);
291 fO[1] = fd[1]*(1.0 - alpha);
292 fO[2] = fd[2]*(1.0 - alpha);
293
294 fH[0] = 0.5 * alpha * fd[0];
295 fH[1] = 0.5 * alpha * fd[1];
296 fH[2] = 0.5 * alpha * fd[2];
297
298 f[i][0] += fO[0];
299 f[i][1] += fO[1];
300 f[i][2] += fO[2];
301
302 f[iH1][0] += fH[0];
303 f[iH1][1] += fH[1];
304 f[iH1][2] += fH[2];
305
306 f[iH2][0] += fH[0];
307 f[iH2][1] += fH[1];
308 f[iH2][2] += fH[2];
309
310 if (vflag) {
311 xH1 = x[iH1];
312 xH2 = x[iH2];
313 v[0] = x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
314 v[1] = x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
315 v[2] = x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
316 v[3] = x[i][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
317 v[4] = x[i][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
318 v[5] = x[i][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
319 }
320 vlist[n++] = i;
321 vlist[n++] = iH1;
322 vlist[n++] = iH2;
323 }
324
325 if (jtype != typeO) {
326 f[j][0] -= delx * cforce;
327 f[j][1] -= dely * cforce;
328 f[j][2] -= delz * cforce;
329
330 if (vflag) {
331 v[0] -= x[j][0] * delx * cforce;
332 v[1] -= x[j][1] * dely * cforce;
333 v[2] -= x[j][2] * delz * cforce;
334 v[3] -= x[j][0] * dely * cforce;
335 v[4] -= x[j][0] * delz * cforce;
336 v[5] -= x[j][1] * delz * cforce;
337 }
338 vlist[n++] = j;
339
340 } else {
341 key += 2;
342
343 fd[0] = -delx*cforce;
344 fd[1] = -dely*cforce;
345 fd[2] = -delz*cforce;
346
347 fO[0] = fd[0]*(1 - alpha);
348 fO[1] = fd[1]*(1 - alpha);
349 fO[2] = fd[2]*(1 - alpha);
350
351 fH[0] = 0.5 * alpha * fd[0];
352 fH[1] = 0.5 * alpha * fd[1];
353 fH[2] = 0.5 * alpha * fd[2];
354
355 f[j][0] += fO[0];
356 f[j][1] += fO[1];
357 f[j][2] += fO[2];
358
359 f[jH1][0] += fH[0];
360 f[jH1][1] += fH[1];
361 f[jH1][2] += fH[2];
362
363 f[jH2][0] += fH[0];
364 f[jH2][1] += fH[1];
365 f[jH2][2] += fH[2];
366
367 if (vflag) {
368 xH1 = x[jH1];
369 xH2 = x[jH2];
370 v[0] += x[j][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
371 v[1] += x[j][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
372 v[2] += x[j][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
373 v[3] += x[j][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
374 v[4] += x[j][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
375 v[5] += x[j][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
376 }
377 vlist[n++] = j;
378 vlist[n++] = jH1;
379 vlist[n++] = jH2;
380 }
381
382 if (eflag) {
383 ecoul = qqrd2e * qtmp * q[j] * sqrt(r2inv);
384 ecoul *= factor_coul;
385 } else ecoul = 0.0;
386
387 if (evflag) ev_tally_tip4p(key,vlist,v,ecoul,alpha);
388 }
389 }
390 }
391 }
392 }
393
394 /* ----------------------------------------------------------------------
395 allocate all arrays
396 ------------------------------------------------------------------------- */
397
allocate()398 void PairLJCutTIP4PCut::allocate()
399 {
400 allocated = 1;
401 int n = atom->ntypes;
402
403 memory->create(setflag,n+1,n+1,"pair:setflag");
404 for (int i = 1; i <= n; i++)
405 for (int j = i; j <= n; j++)
406 setflag[i][j] = 0;
407
408 memory->create(cutsq,n+1,n+1,"pair:cutsq");
409
410 memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
411 memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
412 memory->create(epsilon,n+1,n+1,"pair:epsilon");
413 memory->create(sigma,n+1,n+1,"pair:sigma");
414 memory->create(lj1,n+1,n+1,"pair:lj1");
415 memory->create(lj2,n+1,n+1,"pair:lj2");
416 memory->create(lj3,n+1,n+1,"pair:lj3");
417 memory->create(lj4,n+1,n+1,"pair:lj4");
418 memory->create(offset,n+1,n+1,"pair:offset");
419 }
420
421 /* ----------------------------------------------------------------------
422 global settings
423 ------------------------------------------------------------------------- */
424
settings(int narg,char ** arg)425 void PairLJCutTIP4PCut::settings(int narg, char **arg)
426 {
427 if (narg < 6 || narg > 7) error->all(FLERR,"Illegal pair_style command");
428
429 typeO = utils::inumeric(FLERR,arg[0],false,lmp);
430 typeH = utils::inumeric(FLERR,arg[1],false,lmp);
431 typeB = utils::inumeric(FLERR,arg[2],false,lmp);
432 typeA = utils::inumeric(FLERR,arg[3],false,lmp);
433 qdist = utils::numeric(FLERR,arg[4],false,lmp);
434
435 cut_lj_global = utils::numeric(FLERR,arg[5],false,lmp);
436 if (narg == 6) cut_coul = cut_lj_global;
437 else cut_coul = utils::numeric(FLERR,arg[6],false,lmp);
438
439 cut_coulsq = cut_coul * cut_coul;
440 cut_coulsqplus = (cut_coul + 2.0*qdist) * (cut_coul + 2.0*qdist);
441
442 if (allocated) {
443 int i,j;
444 for (i = 1; i <= atom->ntypes; i++)
445 for (j = i; j <= atom->ntypes; j++)
446 if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
447 }
448 }
449
450 /* ----------------------------------------------------------------------
451 set coeffs for one or more type pairs
452 ------------------------------------------------------------------------- */
453
coeff(int narg,char ** arg)454 void PairLJCutTIP4PCut::coeff(int narg, char **arg)
455 {
456 if (narg < 4 || narg > 5)
457 error->all(FLERR,"Incorrect args for pair coefficients");
458 if (!allocated) allocate();
459
460 int ilo,ihi,jlo,jhi;
461 utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
462 utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
463
464 double epsilon_one = utils::numeric(FLERR,arg[2],false,lmp);
465 double sigma_one = utils::numeric(FLERR,arg[3],false,lmp);
466
467 double cut_lj_one = cut_lj_global;
468 if (narg == 5) cut_lj_one = utils::numeric(FLERR,arg[4],false,lmp);
469
470 int count = 0;
471 for (int i = ilo; i <= ihi; i++) {
472 for (int j = MAX(jlo,i); j <= jhi; j++) {
473 epsilon[i][j] = epsilon_one;
474 sigma[i][j] = sigma_one;
475 cut_lj[i][j] = cut_lj_one;
476 setflag[i][j] = 1;
477 count++;
478 }
479 }
480
481 if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
482 }
483
484 /* ----------------------------------------------------------------------
485 init specific to this pair style
486 ------------------------------------------------------------------------- */
487
init_style()488 void PairLJCutTIP4PCut::init_style()
489 {
490 if (atom->tag_enable == 0)
491 error->all(FLERR,"Pair style lj/cut/tip4p/cut requires atom IDs");
492 if (!force->newton_pair)
493 error->all(FLERR,
494 "Pair style lj/cut/tip4p/cut requires newton pair on");
495 if (!atom->q_flag)
496 error->all(FLERR,
497 "Pair style lj/cut/tip4p/cut requires atom attribute q");
498 if (force->bond == nullptr)
499 error->all(FLERR,"Must use a bond style with TIP4P potential");
500 if (force->angle == nullptr)
501 error->all(FLERR,"Must use an angle style with TIP4P potential");
502
503 neighbor->request(this,instance_me);
504
505 // set alpha parameter
506
507 double theta = force->angle->equilibrium_angle(typeA);
508 double blen = force->bond->equilibrium_distance(typeB);
509 alpha = qdist / (cos(0.5*theta) * blen);
510 }
511
512 /* ----------------------------------------------------------------------
513 init for one type pair i,j and corresponding j,i
514 ------------------------------------------------------------------------- */
515
init_one(int i,int j)516 double PairLJCutTIP4PCut::init_one(int i, int j)
517 {
518 if (setflag[i][j] == 0) {
519 epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
520 sigma[i][i],sigma[j][j]);
521 sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
522 cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
523 }
524
525 // include TIP4P qdist in full cutoff, qdist = 0.0 if not TIP4P
526
527 double cut = MAX(cut_lj[i][j],cut_coul+2.0*qdist);
528 cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
529
530 lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
531 lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
532 lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
533 lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
534
535 if (offset_flag && (cut_lj[i][j] > 0.0)) {
536 double ratio = sigma[i][j] / cut_lj[i][j];
537 offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
538 } else offset[i][j] = 0.0;
539
540 cut_ljsq[j][i] = cut_ljsq[i][j];
541 lj1[j][i] = lj1[i][j];
542 lj2[j][i] = lj2[i][j];
543 lj3[j][i] = lj3[i][j];
544 lj4[j][i] = lj4[i][j];
545 offset[j][i] = offset[i][j];
546
547 // compute I,J contribution to long-range tail correction
548 // count total # of atoms of type I and J via Allreduce
549
550 if (tail_flag) {
551 int *type = atom->type;
552 int nlocal = atom->nlocal;
553
554 double count[2],all[2];
555 count[0] = count[1] = 0.0;
556 for (int k = 0; k < nlocal; k++) {
557 if (type[k] == i) count[0] += 1.0;
558 if (type[k] == j) count[1] += 1.0;
559 }
560 MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
561
562 double sig2 = sigma[i][j]*sigma[i][j];
563 double sig6 = sig2*sig2*sig2;
564 double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
565 double rc6 = rc3*rc3;
566 double rc9 = rc3*rc6;
567 etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
568 sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
569 ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
570 sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
571 }
572
573 // check that LJ epsilon = 0.0 for water H
574 // set LJ cutoff to 0.0 for any interaction involving water H
575 // so LJ term isn't calculated in compute()
576
577 if ((i == typeH && epsilon[i][i] != 0.0) ||
578 (j == typeH && epsilon[j][j] != 0.0))
579 error->all(FLERR,"Water H epsilon must be 0.0 for "
580 "pair style lj/cut/tip4p/cut");
581
582 if (i == typeH || j == typeH)
583 cut_ljsq[j][i] = cut_ljsq[i][j] = 0.0;
584
585 return cut;
586 }
587
588 /* ----------------------------------------------------------------------
589 proc 0 writes to restart file
590 ------------------------------------------------------------------------- */
591
write_restart(FILE * fp)592 void PairLJCutTIP4PCut::write_restart(FILE *fp)
593 {
594 write_restart_settings(fp);
595
596 int i,j;
597 for (i = 1; i <= atom->ntypes; i++) {
598 for (j = i; j <= atom->ntypes; j++) {
599 fwrite(&setflag[i][j],sizeof(int),1,fp);
600 if (setflag[i][j]) {
601 fwrite(&epsilon[i][j],sizeof(double),1,fp);
602 fwrite(&sigma[i][j],sizeof(double),1,fp);
603 fwrite(&cut_lj[i][j],sizeof(double),1,fp);
604 }
605 }
606 }
607 }
608
609 /* ----------------------------------------------------------------------
610 proc 0 reads from restart file, bcasts
611 ------------------------------------------------------------------------- */
612
read_restart(FILE * fp)613 void PairLJCutTIP4PCut::read_restart(FILE *fp)
614 {
615 read_restart_settings(fp);
616 allocate();
617
618 int i,j;
619 int me = comm->me;
620 for (i = 1; i <= atom->ntypes; i++) {
621 for (j = i; j <= atom->ntypes; j++) {
622 if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
623 MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
624 if (setflag[i][j]) {
625 if (me == 0) {
626 utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,nullptr,error);
627 utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,nullptr,error);
628 utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,nullptr,error);
629 }
630 MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
631 MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
632 MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
633 }
634 }
635 }
636 }
637
638 /* ----------------------------------------------------------------------
639 proc 0 writes to restart file
640 ------------------------------------------------------------------------- */
641
write_restart_settings(FILE * fp)642 void PairLJCutTIP4PCut::write_restart_settings(FILE *fp)
643 {
644 fwrite(&typeO,sizeof(int),1,fp);
645 fwrite(&typeH,sizeof(int),1,fp);
646 fwrite(&typeB,sizeof(int),1,fp);
647 fwrite(&typeA,sizeof(int),1,fp);
648 fwrite(&qdist,sizeof(double),1,fp);
649
650 fwrite(&cut_lj_global,sizeof(double),1,fp);
651 fwrite(&cut_coul,sizeof(double),1,fp);
652 fwrite(&offset_flag,sizeof(int),1,fp);
653 fwrite(&mix_flag,sizeof(int),1,fp);
654 fwrite(&tail_flag,sizeof(int),1,fp);
655 }
656
657 /* ----------------------------------------------------------------------
658 proc 0 reads from restart file, bcasts
659 ------------------------------------------------------------------------- */
660
read_restart_settings(FILE * fp)661 void PairLJCutTIP4PCut::read_restart_settings(FILE *fp)
662 {
663 if (comm->me == 0) {
664 utils::sfread(FLERR,&typeO,sizeof(int),1,fp,nullptr,error);
665 utils::sfread(FLERR,&typeH,sizeof(int),1,fp,nullptr,error);
666 utils::sfread(FLERR,&typeB,sizeof(int),1,fp,nullptr,error);
667 utils::sfread(FLERR,&typeA,sizeof(int),1,fp,nullptr,error);
668 utils::sfread(FLERR,&qdist,sizeof(double),1,fp,nullptr,error);
669
670 utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,nullptr,error);
671 utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,nullptr,error);
672 utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error);
673 utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
674 utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,nullptr,error);
675 }
676
677 MPI_Bcast(&typeO,1,MPI_INT,0,world);
678 MPI_Bcast(&typeH,1,MPI_INT,0,world);
679 MPI_Bcast(&typeB,1,MPI_INT,0,world);
680 MPI_Bcast(&typeA,1,MPI_INT,0,world);
681 MPI_Bcast(&qdist,1,MPI_DOUBLE,0,world);
682
683 MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
684 MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
685 MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
686 MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
687 MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
688
689 cut_coulsq = cut_coul * cut_coul;
690 cut_coulsqplus = (cut_coul + 2.0*qdist) * (cut_coul + 2.0*qdist);
691 }
692
693 /* ----------------------------------------------------------------------
694 proc 0 writes to data file
695 ------------------------------------------------------------------------- */
696
write_data(FILE * fp)697 void PairLJCutTIP4PCut::write_data(FILE *fp)
698 {
699 for (int i = 1; i <= atom->ntypes; i++)
700 fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]);
701 }
702
703 /* ----------------------------------------------------------------------
704 proc 0 writes all pairs to data file
705 ------------------------------------------------------------------------- */
706
write_data_all(FILE * fp)707 void PairLJCutTIP4PCut::write_data_all(FILE *fp)
708 {
709 for (int i = 1; i <= atom->ntypes; i++)
710 for (int j = i; j <= atom->ntypes; j++)
711 fprintf(fp,"%d %d %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],cut_lj[i][j]);
712 }
713
714 /* ----------------------------------------------------------------------
715 compute position xM of fictitious charge site for O atom and 2 H atoms
716 return it as xM
717 ------------------------------------------------------------------------- */
718
compute_newsite(double * xO,double * xH1,double * xH2,double * xM)719 void PairLJCutTIP4PCut::compute_newsite(double *xO, double *xH1,
720 double *xH2, double *xM)
721 {
722 double delx1 = xH1[0] - xO[0];
723 double dely1 = xH1[1] - xO[1];
724 double delz1 = xH1[2] - xO[2];
725
726 double delx2 = xH2[0] - xO[0];
727 double dely2 = xH2[1] - xO[1];
728 double delz2 = xH2[2] - xO[2];
729
730 xM[0] = xO[0] + alpha * 0.5 * (delx1 + delx2);
731 xM[1] = xO[1] + alpha * 0.5 * (dely1 + dely2);
732 xM[2] = xO[2] + alpha * 0.5 * (delz1 + delz2);
733 }
734
735 /* ---------------------------------------------------------------------- */
736
extract(const char * str,int & dim)737 void *PairLJCutTIP4PCut::extract(const char *str, int &dim)
738 {
739 dim = 0;
740 if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
741 dim = 2;
742 if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
743 if (strcmp(str,"sigma") == 0) return (void *) sigma;
744 return nullptr;
745 }
746 /* ----------------------------------------------------------------------
747 memory usage of hneigh
748 ------------------------------------------------------------------------- */
749
memory_usage()750 double PairLJCutTIP4PCut::memory_usage()
751 {
752 double bytes = (double)maxeatom * sizeof(double);
753 bytes += (double)maxvatom*6 * sizeof(double);
754 bytes += (double)2 * nmax * sizeof(double);
755 return bytes;
756 }
757