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37 /* This file is completely threadsafe - keep it that way! */
44 #include "types/commrec.h"
46 #include "gromacs/utility/smalloc.h"
49 #include "gromacs/fileio/futil.h"
51 #include "gromacs/utility/fatalerror.h"
56 #include "mtop_util.h"
58 void init_disres(FILE *fplog, const gmx_mtop_t *mtop,
59 t_inputrec *ir, const t_commrec *cr,
60 t_fcdata *fcd, t_state *state, gmx_bool bIsREMD)
62 int fa, nmol, i, npair, np;
66 gmx_mtop_ilistloop_t iloop;
72 if (gmx_mtop_ftype_count(mtop, F_DISRES) == 0)
81 fprintf(fplog, "Initializing the distance restraints\n");
85 if (ir->eDisre == edrEnsemble)
87 gmx_fatal(FARGS, "Sorry, distance restraints with ensemble averaging over multiple molecules in one system are not functional in this version of GROMACS");
90 dd->dr_weighting = ir->eDisreWeighting;
91 dd->dr_fc = ir->dr_fc;
92 if (EI_DYNAMICS(ir->eI))
94 dd->dr_tau = ir->dr_tau;
100 if (dd->dr_tau == 0.0)
102 dd->dr_bMixed = FALSE;
107 dd->dr_bMixed = ir->bDisreMixed;
108 dd->ETerm = exp(-(ir->delta_t/ir->dr_tau));
110 dd->ETerm1 = 1.0 - dd->ETerm;
112 ip = mtop->ffparams.iparams;
116 iloop = gmx_mtop_ilistloop_init(mtop);
117 while (gmx_mtop_ilistloop_next(iloop, &il, &nmol))
120 for (fa = 0; fa < il[F_DISRES].nr; fa += 3)
123 npair = mtop->ffparams.iparams[il[F_DISRES].iatoms[fa]].disres.npair;
126 dd->nres += (ir->eDisre == edrEnsemble ? 1 : nmol)*npair;
127 dd->npair += nmol*npair;
135 /* Temporary check, will be removed when disre is implemented with DD */
136 const char *notestr = "NOTE: atoms involved in distance restraints should be within the same domain. If this is not the case mdrun generates a fatal error. If you encounter this, use a single MPI rank (Verlet+OpenMP+GPUs work fine).";
140 fprintf(stderr, "\n%s\n\n", notestr);
144 fprintf(fplog, "%s\n", notestr);
147 if (dd->dr_tau != 0 || ir->eDisre == edrEnsemble || cr->ms != NULL ||
148 dd->nres != dd->npair)
150 gmx_fatal(FARGS, "Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use a single MPI rank%s", cr->ms ? " per simulation" : "");
152 if (ir->nstdisreout != 0)
156 fprintf(fplog, "\nWARNING: Can not write distance restraint data to energy file with domain decomposition\n\n");
160 fprintf(stderr, "\nWARNING: Can not write distance restraint data to energy file with domain decomposition\n");
166 snew(dd->rt, dd->npair);
168 if (dd->dr_tau != 0.0)
171 /* Set the "history lack" factor to 1 */
172 state->flags |= (1<<estDISRE_INITF);
173 hist->disre_initf = 1.0;
174 /* Allocate space for the r^-3 time averages */
175 state->flags |= (1<<estDISRE_RM3TAV);
176 hist->ndisrepairs = dd->npair;
177 snew(hist->disre_rm3tav, hist->ndisrepairs);
179 /* Allocate space for a copy of rm3tav,
180 * so we can call do_force without modifying the state.
182 snew(dd->rm3tav, dd->npair);
184 /* Allocate Rt_6 and Rtav_6 consecutively in memory so they can be
185 * averaged over the processors in one call (in calc_disre_R_6)
187 snew(dd->Rt_6, 2*dd->nres);
188 dd->Rtav_6 = &(dd->Rt_6[dd->nres]);
190 ptr = getenv("GMX_DISRE_ENSEMBLE_SIZE");
191 if (cr && cr->ms != NULL && ptr != NULL && !bIsREMD)
195 sscanf(ptr, "%d", &dd->nsystems);
198 fprintf(fplog, "Found GMX_DISRE_ENSEMBLE_SIZE set to %d systems per ensemble\n", dd->nsystems);
200 /* This check is only valid on MASTER(cr), so probably
201 * ensemble-averaged distance restraints are broken on more
202 * than one processor per simulation system. */
205 check_multi_int(fplog, cr->ms, dd->nsystems,
206 "the number of systems per ensemble",
209 gmx_bcast_sim(sizeof(int), &dd->nsystems, cr);
211 /* We use to allow any value of nsystems which was a divisor
212 * of ms->nsim. But this required an extra communicator which
213 * was stored in t_fcdata. This pulled in mpi.h in nearly all C files.
215 if (!(cr->ms->nsim == 1 || cr->ms->nsim == dd->nsystems))
217 gmx_fatal(FARGS, "GMX_DISRE_ENSEMBLE_SIZE (%d) is not equal to 1 or the number of systems (option -multi) %d", dd->nsystems, cr->ms->nsim);
221 fprintf(fplog, "Our ensemble consists of systems:");
222 for (i = 0; i < dd->nsystems; i++)
224 fprintf(fplog, " %d",
225 (cr->ms->sim/dd->nsystems)*dd->nsystems+i);
227 fprintf(fplog, "\n");
229 snew(dd->Rtl_6, dd->nres);
235 dd->Rtl_6 = dd->Rt_6;
242 fprintf(fplog, "There are %d distance restraints involving %d atom pairs\n", dd->nres, dd->npair);
244 /* Have to avoid g_disre de-referencing cr blindly, mdrun not
245 * doing consistency checks for ensemble-averaged distance
246 * restraints when that's not happening, and only doing those
247 * checks from appropriate processes (since check_multi_int is
248 * too broken to check whether the communication will
250 if (cr && cr->ms && dd->nsystems > 1 && MASTER(cr))
252 check_multi_int(fplog, cr->ms, fcd->disres.nres,
253 "the number of distance restraints",
256 please_cite(fplog, "Tropp80a");
257 please_cite(fplog, "Torda89a");
261 void calc_disres_R_6(int nfa, const t_iatom forceatoms[], const t_iparams ip[],
262 const rvec x[], const t_pbc *pbc,
263 t_fcdata *fcd, history_t *hist)
266 int fa, res, i, pair, ki, kj, m;
269 real *rt, *rm3tav, *Rtl_6, *Rt_6, *Rtav_6;
270 real rt_1, rt_3, rt2;
273 real ETerm, ETerm1, cf1 = 0, cf2 = 0, invn = 0;
277 bTav = (dd->dr_tau != 0);
288 /* scaling factor to smoothly turn on the restraint forces *
289 * when using time averaging */
290 dd->exp_min_t_tau = hist->disre_initf*ETerm;
292 cf1 = dd->exp_min_t_tau;
293 cf2 = 1.0/(1.0 - dd->exp_min_t_tau);
296 if (dd->nsystems > 1)
298 invn = 1.0/dd->nsystems;
301 /* 'loop' over all atom pairs (pair_nr=fa/3) involved in restraints, *
302 * the total number of atoms pairs is nfa/3 */
307 type = forceatoms[fa];
308 npair = ip[type].disres.npair;
313 /* Loop over the atom pairs of 'this' restraint */
315 while (fa < nfa && np < npair)
318 ai = forceatoms[fa+1];
319 aj = forceatoms[fa+2];
323 pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
327 rvec_sub(x[ai], x[aj], dx);
330 rt_1 = gmx_invsqrt(rt2);
331 rt_3 = rt_1*rt_1*rt_1;
333 rt[pair] = sqrt(rt2);
336 /* Here we update rm3tav in t_fcdata using the data
338 * Thus the results stay correct when this routine
339 * is called multiple times.
341 rm3tav[pair] = cf2*((ETerm - cf1)*hist->disre_rm3tav[pair] +
349 Rt_6[res] += rt_3*rt_3;
350 Rtav_6[res] += rm3tav[pair]*rm3tav[pair];
355 if (dd->nsystems > 1)
357 Rtl_6[res] = Rt_6[res];
366 real ta_disres(int nfa, const t_iatom forceatoms[], const t_iparams ip[],
367 const rvec x[], rvec f[], rvec fshift[],
368 const t_pbc *pbc, const t_graph *g,
369 real gmx_unused lambda, real gmx_unused *dvdlambda,
370 const t_mdatoms gmx_unused *md, t_fcdata *fcd,
371 int gmx_unused *global_atom_index)
373 const real sixth = 1.0/6.0;
374 const real seven_three = 7.0/3.0;
377 int fa, res, npair, p, pair, ki = CENTRAL, m;
381 real smooth_fc, Rt, Rtav, rt2, *Rtl_6, *Rt_6, *Rtav_6;
382 real k0, f_scal = 0, fmax_scal, fk_scal, fij;
383 real tav_viol, instant_viol, mixed_viol, violtot, vtot;
384 real tav_viol_Rtav7, instant_viol_Rtav7;
386 gmx_bool bConservative, bMixed, bViolation;
393 dr_weighting = dd->dr_weighting;
394 dr_bMixed = dd->dr_bMixed;
399 tav_viol = instant_viol = mixed_viol = tav_viol_Rtav7 = instant_viol_Rtav7 = 0;
401 smooth_fc = dd->dr_fc;
404 /* scaling factor to smoothly turn on the restraint forces *
405 * when using time averaging */
406 smooth_fc *= (1.0 - dd->exp_min_t_tau);
412 /* 'loop' over all atom pairs (pair_nr=fa/3) involved in restraints, *
413 * the total number of atoms pairs is nfa/3 */
418 type = forceatoms[fa];
419 /* Take action depending on restraint, calculate scalar force */
420 npair = ip[type].disres.npair;
421 up1 = ip[type].disres.up1;
422 up2 = ip[type].disres.up2;
423 low = ip[type].disres.low;
424 k0 = smooth_fc*ip[type].disres.kfac;
426 /* save some flops when there is only one pair */
427 if (ip[type].disres.type != 2)
429 bConservative = (dr_weighting == edrwConservative) && (npair > 1);
431 Rt = pow(Rt_6[res], -sixth);
432 Rtav = pow(Rtav_6[res], -sixth);
436 /* When rtype=2 use instantaneous not ensemble avereged distance */
437 bConservative = (npair > 1);
439 Rt = pow(Rtl_6[res], -sixth);
446 tav_viol = Rtav - up1;
451 tav_viol = Rtav - low;
461 * there is no real potential when time averaging is applied
463 vtot += 0.5*k0*sqr(tav_viol);
466 printf("vtot is inf: %f\n", vtot);
470 f_scal = -k0*tav_viol;
471 violtot += fabs(tav_viol);
479 instant_viol = Rt - up1;
490 instant_viol = Rt - low;
503 mixed_viol = sqrt(tav_viol*instant_viol);
504 f_scal = -k0*mixed_viol;
505 violtot += mixed_viol;
512 fmax_scal = -k0*(up2-up1);
513 /* Correct the force for the number of restraints */
516 f_scal = max(f_scal, fmax_scal);
519 f_scal *= Rtav/Rtav_6[res];
523 f_scal /= 2*mixed_viol;
524 tav_viol_Rtav7 = tav_viol*Rtav/Rtav_6[res];
525 instant_viol_Rtav7 = instant_viol*Rt/Rt_6[res];
530 f_scal /= (real)npair;
531 f_scal = max(f_scal, fmax_scal);
534 /* Exert the force ... */
536 /* Loop over the atom pairs of 'this' restraint */
537 for (p = 0; p < npair; p++)
540 ai = forceatoms[fa+1];
541 aj = forceatoms[fa+2];
545 ki = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
549 rvec_sub(x[ai], x[aj], dx);
553 weight_rt_1 = gmx_invsqrt(rt2);
559 weight_rt_1 *= pow(dd->rm3tav[pair], seven_three);
563 weight_rt_1 *= tav_viol_Rtav7*pow(dd->rm3tav[pair], seven_three)+
564 instant_viol_Rtav7*pow(dd->rt[pair], -7);
568 fk_scal = f_scal*weight_rt_1;
572 ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
576 for (m = 0; m < DIM; m++)
582 fshift[ki][m] += fij;
583 fshift[CENTRAL][m] -= fij;
590 /* No violation so force and potential contributions */
596 dd->sumviol = violtot;
602 void update_disres_history(t_fcdata *fcd, history_t *hist)
610 /* Copy the new time averages that have been calculated
611 * in calc_disres_R_6.
613 hist->disre_initf = dd->exp_min_t_tau;
614 for (pair = 0; pair < dd->npair; pair++)
616 hist->disre_rm3tav[pair] = dd->rm3tav[pair];