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37 /* This file is completely threadsafe - keep it that way! */
46 #include "types/commrec.h"
48 #include "gromacs/utility/futil.h"
53 #include "gromacs/topology/mtop_util.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/pbcutil/ishift.h"
57 #include "gromacs/pbcutil/mshift.h"
58 #include "gromacs/pbcutil/pbc.h"
59 #include "gromacs/utility/fatalerror.h"
60 #include "gromacs/utility/smalloc.h"
62 void init_disres(FILE *fplog, const gmx_mtop_t *mtop,
63 t_inputrec *ir, const t_commrec *cr,
64 t_fcdata *fcd, t_state *state, gmx_bool bIsREMD)
66 int fa, nmol, i, npair, np;
70 gmx_mtop_ilistloop_t iloop;
76 if (gmx_mtop_ftype_count(mtop, F_DISRES) == 0)
85 fprintf(fplog, "Initializing the distance restraints\n");
89 if (ir->eDisre == edrEnsemble)
91 gmx_fatal(FARGS, "Sorry, distance restraints with ensemble averaging over multiple molecules in one system are not functional in this version of GROMACS");
94 dd->dr_weighting = ir->eDisreWeighting;
95 dd->dr_fc = ir->dr_fc;
96 if (EI_DYNAMICS(ir->eI))
98 dd->dr_tau = ir->dr_tau;
104 if (dd->dr_tau == 0.0)
106 dd->dr_bMixed = FALSE;
111 dd->dr_bMixed = ir->bDisreMixed;
112 dd->ETerm = exp(-(ir->delta_t/ir->dr_tau));
114 dd->ETerm1 = 1.0 - dd->ETerm;
116 ip = mtop->ffparams.iparams;
120 iloop = gmx_mtop_ilistloop_init(mtop);
121 while (gmx_mtop_ilistloop_next(iloop, &il, &nmol))
124 for (fa = 0; fa < il[F_DISRES].nr; fa += 3)
127 npair = mtop->ffparams.iparams[il[F_DISRES].iatoms[fa]].disres.npair;
130 dd->nres += (ir->eDisre == edrEnsemble ? 1 : nmol)*npair;
131 dd->npair += nmol*npair;
139 /* Temporary check, will be removed when disre is implemented with DD */
140 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).";
144 fprintf(stderr, "\n%s\n\n", notestr);
148 fprintf(fplog, "%s\n", notestr);
151 if (dd->dr_tau != 0 || ir->eDisre == edrEnsemble || cr->ms != NULL ||
152 dd->nres != dd->npair)
154 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" : "");
156 if (ir->nstdisreout != 0)
160 fprintf(fplog, "\nWARNING: Can not write distance restraint data to energy file with domain decomposition\n\n");
164 fprintf(stderr, "\nWARNING: Can not write distance restraint data to energy file with domain decomposition\n");
170 snew(dd->rt, dd->npair);
172 if (dd->dr_tau != 0.0)
175 /* Set the "history lack" factor to 1 */
176 state->flags |= (1<<estDISRE_INITF);
177 hist->disre_initf = 1.0;
178 /* Allocate space for the r^-3 time averages */
179 state->flags |= (1<<estDISRE_RM3TAV);
180 hist->ndisrepairs = dd->npair;
181 snew(hist->disre_rm3tav, hist->ndisrepairs);
183 /* Allocate space for a copy of rm3tav,
184 * so we can call do_force without modifying the state.
186 snew(dd->rm3tav, dd->npair);
188 /* Allocate Rt_6 and Rtav_6 consecutively in memory so they can be
189 * averaged over the processors in one call (in calc_disre_R_6)
191 snew(dd->Rt_6, 2*dd->nres);
192 dd->Rtav_6 = &(dd->Rt_6[dd->nres]);
194 ptr = getenv("GMX_DISRE_ENSEMBLE_SIZE");
195 if (cr && cr->ms != NULL && ptr != NULL && !bIsREMD)
199 sscanf(ptr, "%d", &dd->nsystems);
202 fprintf(fplog, "Found GMX_DISRE_ENSEMBLE_SIZE set to %d systems per ensemble\n", dd->nsystems);
204 /* This check is only valid on MASTER(cr), so probably
205 * ensemble-averaged distance restraints are broken on more
206 * than one processor per simulation system. */
209 check_multi_int(fplog, cr->ms, dd->nsystems,
210 "the number of systems per ensemble",
213 gmx_bcast_sim(sizeof(int), &dd->nsystems, cr);
215 /* We use to allow any value of nsystems which was a divisor
216 * of ms->nsim. But this required an extra communicator which
217 * was stored in t_fcdata. This pulled in mpi.h in nearly all C files.
219 if (!(cr->ms->nsim == 1 || cr->ms->nsim == dd->nsystems))
221 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);
225 fprintf(fplog, "Our ensemble consists of systems:");
226 for (i = 0; i < dd->nsystems; i++)
228 fprintf(fplog, " %d",
229 (cr->ms->sim/dd->nsystems)*dd->nsystems+i);
231 fprintf(fplog, "\n");
233 snew(dd->Rtl_6, dd->nres);
239 dd->Rtl_6 = dd->Rt_6;
246 fprintf(fplog, "There are %d distance restraints involving %d atom pairs\n", dd->nres, dd->npair);
248 /* Have to avoid g_disre de-referencing cr blindly, mdrun not
249 * doing consistency checks for ensemble-averaged distance
250 * restraints when that's not happening, and only doing those
251 * checks from appropriate processes (since check_multi_int is
252 * too broken to check whether the communication will
254 if (cr && cr->ms && dd->nsystems > 1 && MASTER(cr))
256 check_multi_int(fplog, cr->ms, fcd->disres.nres,
257 "the number of distance restraints",
260 please_cite(fplog, "Tropp80a");
261 please_cite(fplog, "Torda89a");
265 void calc_disres_R_6(int nfa, const t_iatom forceatoms[], const t_iparams ip[],
266 const rvec x[], const t_pbc *pbc,
267 t_fcdata *fcd, history_t *hist)
270 int fa, res, i, pair, ki, kj, m;
273 real *rt, *rm3tav, *Rtl_6, *Rt_6, *Rtav_6;
274 real rt_1, rt_3, rt2;
277 real ETerm, ETerm1, cf1 = 0, cf2 = 0, invn = 0;
281 bTav = (dd->dr_tau != 0);
292 /* scaling factor to smoothly turn on the restraint forces *
293 * when using time averaging */
294 dd->exp_min_t_tau = hist->disre_initf*ETerm;
296 cf1 = dd->exp_min_t_tau;
297 cf2 = 1.0/(1.0 - dd->exp_min_t_tau);
300 if (dd->nsystems > 1)
302 invn = 1.0/dd->nsystems;
305 /* 'loop' over all atom pairs (pair_nr=fa/3) involved in restraints, *
306 * the total number of atoms pairs is nfa/3 */
311 type = forceatoms[fa];
312 npair = ip[type].disres.npair;
317 /* Loop over the atom pairs of 'this' restraint */
319 while (fa < nfa && np < npair)
322 ai = forceatoms[fa+1];
323 aj = forceatoms[fa+2];
327 pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
331 rvec_sub(x[ai], x[aj], dx);
334 rt_1 = gmx_invsqrt(rt2);
335 rt_3 = rt_1*rt_1*rt_1;
337 rt[pair] = sqrt(rt2);
340 /* Here we update rm3tav in t_fcdata using the data
342 * Thus the results stay correct when this routine
343 * is called multiple times.
345 rm3tav[pair] = cf2*((ETerm - cf1)*hist->disre_rm3tav[pair] +
353 Rt_6[res] += rt_3*rt_3;
354 Rtav_6[res] += rm3tav[pair]*rm3tav[pair];
359 if (dd->nsystems > 1)
361 Rtl_6[res] = Rt_6[res];
370 real ta_disres(int nfa, const t_iatom forceatoms[], const t_iparams ip[],
371 const rvec x[], rvec f[], rvec fshift[],
372 const t_pbc *pbc, const t_graph *g,
373 real gmx_unused lambda, real gmx_unused *dvdlambda,
374 const t_mdatoms gmx_unused *md, t_fcdata *fcd,
375 int gmx_unused *global_atom_index)
377 const real sixth = 1.0/6.0;
378 const real seven_three = 7.0/3.0;
381 int fa, res, npair, p, pair, ki = CENTRAL, m;
385 real smooth_fc, Rt, Rtav, rt2, *Rtl_6, *Rt_6, *Rtav_6;
386 real k0, f_scal = 0, fmax_scal, fk_scal, fij;
387 real tav_viol, instant_viol, mixed_viol, violtot, vtot;
388 real tav_viol_Rtav7, instant_viol_Rtav7;
390 gmx_bool bConservative, bMixed, bViolation;
397 dr_weighting = dd->dr_weighting;
398 dr_bMixed = dd->dr_bMixed;
403 tav_viol = instant_viol = mixed_viol = tav_viol_Rtav7 = instant_viol_Rtav7 = 0;
405 smooth_fc = dd->dr_fc;
408 /* scaling factor to smoothly turn on the restraint forces *
409 * when using time averaging */
410 smooth_fc *= (1.0 - dd->exp_min_t_tau);
416 /* 'loop' over all atom pairs (pair_nr=fa/3) involved in restraints, *
417 * the total number of atoms pairs is nfa/3 */
422 type = forceatoms[fa];
423 /* Take action depending on restraint, calculate scalar force */
424 npair = ip[type].disres.npair;
425 up1 = ip[type].disres.up1;
426 up2 = ip[type].disres.up2;
427 low = ip[type].disres.low;
428 k0 = smooth_fc*ip[type].disres.kfac;
430 /* save some flops when there is only one pair */
431 if (ip[type].disres.type != 2)
433 bConservative = (dr_weighting == edrwConservative) && (npair > 1);
435 Rt = pow(Rt_6[res], -sixth);
436 Rtav = pow(Rtav_6[res], -sixth);
440 /* When rtype=2 use instantaneous not ensemble avereged distance */
441 bConservative = (npair > 1);
443 Rt = pow(Rtl_6[res], -sixth);
450 tav_viol = Rtav - up1;
455 tav_viol = Rtav - low;
465 * there is no real potential when time averaging is applied
467 vtot += 0.5*k0*sqr(tav_viol);
470 printf("vtot is inf: %f\n", vtot);
474 f_scal = -k0*tav_viol;
475 violtot += fabs(tav_viol);
483 instant_viol = Rt - up1;
494 instant_viol = Rt - low;
507 mixed_viol = sqrt(tav_viol*instant_viol);
508 f_scal = -k0*mixed_viol;
509 violtot += mixed_viol;
516 fmax_scal = -k0*(up2-up1);
517 /* Correct the force for the number of restraints */
520 f_scal = max(f_scal, fmax_scal);
523 f_scal *= Rtav/Rtav_6[res];
527 f_scal /= 2*mixed_viol;
528 tav_viol_Rtav7 = tav_viol*Rtav/Rtav_6[res];
529 instant_viol_Rtav7 = instant_viol*Rt/Rt_6[res];
534 f_scal /= (real)npair;
535 f_scal = max(f_scal, fmax_scal);
538 /* Exert the force ... */
540 /* Loop over the atom pairs of 'this' restraint */
541 for (p = 0; p < npair; p++)
544 ai = forceatoms[fa+1];
545 aj = forceatoms[fa+2];
549 ki = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
553 rvec_sub(x[ai], x[aj], dx);
557 weight_rt_1 = gmx_invsqrt(rt2);
563 weight_rt_1 *= pow(dd->rm3tav[pair], seven_three);
567 weight_rt_1 *= tav_viol_Rtav7*pow(dd->rm3tav[pair], seven_three)+
568 instant_viol_Rtav7*pow(dd->rt[pair], -7);
572 fk_scal = f_scal*weight_rt_1;
576 ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
580 for (m = 0; m < DIM; m++)
586 fshift[ki][m] += fij;
587 fshift[CENTRAL][m] -= fij;
594 /* No violation so force and potential contributions */
600 dd->sumviol = violtot;
606 void update_disres_history(t_fcdata *fcd, history_t *hist)
614 /* Copy the new time averages that have been calculated
615 * in calc_disres_R_6.
617 hist->disre_initf = dd->exp_min_t_tau;
618 for (pair = 0; pair < dd->npair; pair++)
620 hist->disre_rm3tav[pair] = dd->rm3tav[pair];