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36 /* This file is completely threadsafe - keep it that way! */
49 #include "gmx_fatal.h"
54 #include "mtop_util.h"
56 void init_disres(FILE *fplog,const gmx_mtop_t *mtop,
57 t_inputrec *ir,const t_commrec *cr,gmx_bool bPartDecomp,
58 t_fcdata *fcd,t_state *state, gmx_bool bIsREMD)
60 int fa,nmol,i,npair,np;
64 gmx_mtop_ilistloop_t iloop;
70 if (gmx_mtop_ftype_count(mtop,F_DISRES) == 0)
79 fprintf(fplog,"Initializing the distance restraints\n");
83 if (ir->eDisre == edrEnsemble)
85 gmx_fatal(FARGS,"Sorry, distance restraints with ensemble averaging over multiple molecules in one system are not functional in this version of GROMACS");
88 dd->dr_weighting = ir->eDisreWeighting;
89 dd->dr_fc = ir->dr_fc;
90 if (EI_DYNAMICS(ir->eI))
92 dd->dr_tau = ir->dr_tau;
98 if (dd->dr_tau == 0.0)
100 dd->dr_bMixed = FALSE;
105 dd->dr_bMixed = ir->bDisreMixed;
106 dd->ETerm = exp(-(ir->delta_t/ir->dr_tau));
108 dd->ETerm1 = 1.0 - dd->ETerm;
110 ip = mtop->ffparams.iparams;
114 iloop = gmx_mtop_ilistloop_init(mtop);
115 while (gmx_mtop_ilistloop_next(iloop,&il,&nmol)) {
117 for(fa=0; fa<il[F_DISRES].nr; fa+=3)
120 npair = mtop->ffparams.iparams[il[F_DISRES].iatoms[fa]].disres.npair;
123 dd->nres += (ir->eDisre==edrEnsemble ? 1 : nmol)*npair;
124 dd->npair += nmol*npair;
130 if (cr && PAR(cr) && !bPartDecomp)
132 /* Temporary check, will be removed when disre is implemented with DD */
133 const char *notestr="NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd)";
136 fprintf(stderr,"\n%s\n\n",notestr);
138 fprintf(fplog,"%s\n",notestr);
140 if (dd->dr_tau != 0 || ir->eDisre == edrEnsemble || cr->ms != NULL ||
141 dd->nres != dd->npair)
143 gmx_fatal(FARGS,"Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd)");
145 if (ir->nstdisreout != 0)
149 fprintf(fplog,"\nWARNING: Can not write distance restraint data to energy file with domain decomposition\n\n");
153 fprintf(stderr,"\nWARNING: Can not write distance restraint data to energy file with domain decomposition\n");
159 snew(dd->rt,dd->npair);
161 if (dd->dr_tau != 0.0)
164 /* Set the "history lack" factor to 1 */
165 state->flags |= (1<<estDISRE_INITF);
166 hist->disre_initf = 1.0;
167 /* Allocate space for the r^-3 time averages */
168 state->flags |= (1<<estDISRE_RM3TAV);
169 hist->ndisrepairs = dd->npair;
170 snew(hist->disre_rm3tav,hist->ndisrepairs);
172 /* Allocate space for a copy of rm3tav,
173 * so we can call do_force without modifying the state.
175 snew(dd->rm3tav,dd->npair);
177 /* Allocate Rt_6 and Rtav_6 consecutively in memory so they can be
178 * averaged over the processors in one call (in calc_disre_R_6)
180 snew(dd->Rt_6,2*dd->nres);
181 dd->Rtav_6 = &(dd->Rt_6[dd->nres]);
183 ptr = getenv("GMX_DISRE_ENSEMBLE_SIZE");
184 if (cr && cr->ms != NULL && ptr != NULL && !bIsREMD)
188 sscanf(ptr,"%d",&dd->nsystems);
191 fprintf(fplog,"Found GMX_DISRE_ENSEMBLE_SIZE set to %d systems per ensemble\n",dd->nsystems);
193 /* This check is only valid on MASTER(cr), so probably
194 * ensemble-averaged distance restraints are broken on more
195 * than one processor per simulation system. */
198 check_multi_int(fplog,cr->ms,dd->nsystems,
199 "the number of systems per ensemble",
202 gmx_bcast_sim(sizeof(int), &dd->nsystems, cr);
204 /* We use to allow any value of nsystems which was a divisor
205 * of ms->nsim. But this required an extra communicator which
206 * was stored in t_fcdata. This pulled in mpi.h in nearly all C files.
208 if (!(cr->ms->nsim == 1 || cr->ms->nsim == dd->nsystems))
210 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);
214 fprintf(fplog,"Our ensemble consists of systems:");
215 for(i=0; i<dd->nsystems; i++)
218 (cr->ms->sim/dd->nsystems)*dd->nsystems+i);
222 snew(dd->Rtl_6,dd->nres);
228 dd->Rtl_6 = dd->Rt_6;
234 fprintf(fplog,"There are %d distance restraints involving %d atom pairs\n",dd->nres,dd->npair);
236 /* Have to avoid g_disre de-referencing cr blindly, mdrun not
237 * doing consistency checks for ensemble-averaged distance
238 * restraints when that's not happening, and only doing those
239 * checks from appropriate processes (since check_multi_int is
240 * too broken to check whether the communication will
242 if (cr && cr->ms && dd->nsystems > 1 && MASTER(cr))
244 check_multi_int(fplog,cr->ms,fcd->disres.nres,
245 "the number of distance restraints",
248 please_cite(fplog,"Tropp80a");
249 please_cite(fplog,"Torda89a");
253 void calc_disres_R_6(const gmx_multisim_t *ms,
254 int nfa,const t_iatom forceatoms[],const t_iparams ip[],
255 const rvec x[],const t_pbc *pbc,
256 t_fcdata *fcd,history_t *hist)
259 int fa,res,i,pair,ki,kj,m;
262 real *rt,*rm3tav,*Rtl_6,*Rt_6,*Rtav_6;
266 real ETerm,ETerm1,cf1=0,cf2=0,invn=0;
270 bTav = (dd->dr_tau != 0);
281 /* scaling factor to smoothly turn on the restraint forces *
282 * when using time averaging */
283 dd->exp_min_t_tau = hist->disre_initf*ETerm;
285 cf1 = dd->exp_min_t_tau;
286 cf2 = 1.0/(1.0 - dd->exp_min_t_tau);
289 if (dd->nsystems > 1)
291 invn = 1.0/dd->nsystems;
294 /* 'loop' over all atom pairs (pair_nr=fa/3) involved in restraints, *
295 * the total number of atoms pairs is nfa/3 */
300 type = forceatoms[fa];
301 npair = ip[type].disres.npair;
306 /* Loop over the atom pairs of 'this' restraint */
308 while (fa < nfa && np < npair)
311 ai = forceatoms[fa+1];
312 aj = forceatoms[fa+2];
316 pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
320 rvec_sub(x[ai],x[aj],dx);
323 rt_1 = gmx_invsqrt(rt2);
324 rt_3 = rt_1*rt_1*rt_1;
326 rt[pair] = sqrt(rt2);
329 /* Here we update rm3tav in t_fcdata using the data
331 * Thus the results stay correct when this routine
332 * is called multiple times.
334 rm3tav[pair] = cf2*((ETerm - cf1)*hist->disre_rm3tav[pair] +
342 Rt_6[res] += rt_3*rt_3;
343 Rtav_6[res] += rm3tav[pair]*rm3tav[pair];
348 if (dd->nsystems > 1)
350 Rtl_6[res] = Rt_6[res];
359 if (dd->nsystems > 1)
361 gmx_sum_sim(2*dd->nres,Rt_6,ms);
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 lambda,real *dvdlambda,
370 const t_mdatoms *md,t_fcdata *fcd,
371 int *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);
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];