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51 #include "chargegroup.h"
56 #include "gmx_fatal.h"
71 #include "gmx_random.h"
76 #include "gmx_wallcycle.h"
77 #include "mtop_util.h"
82 #if ( defined(GMX_IA32_SSE) || defined(GMX_X86_64_SSE) || defined(GMX_X86_64_SSE2) )
83 #if defined(GMX_DOUBLE)
84 #include "gmx_sse2_double.h"
86 #include "gmx_sse2_single.h"
91 static void global_max(t_commrec *cr,int *n)
97 gmx_sumi(cr->nnodes,sum,cr);
98 for(i=0; i<cr->nnodes; i++)
104 static void realloc_bins(double **bin,int *nbin,int nbin_new)
108 if (nbin_new != *nbin) {
109 srenew(*bin,nbin_new);
110 for(i=*nbin; i<nbin_new; i++)
116 double do_tpi(FILE *fplog,t_commrec *cr,
117 int nfile, const t_filenm fnm[],
118 const output_env_t oenv, gmx_bool bVerbose,gmx_bool bCompact,
120 gmx_vsite_t *vsite,gmx_constr_t constr,
122 t_inputrec *inputrec,
123 gmx_mtop_t *top_global,t_fcdata *fcd,
126 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
129 int repl_ex_nst,int repl_ex_seed,
131 real cpt_period,real max_hours,
132 const char *deviceOptions,
134 gmx_runtime_t *runtime)
136 const char *TPI="Test Particle Insertion";
138 gmx_groups_t *groups;
139 gmx_enerdata_t *enerd;
141 real lambda,t,temp,beta,drmax,epot;
142 double embU,sum_embU,*sum_UgembU,V,V_all,VembU_all;
145 gmx_bool bDispCorr,bCharge,bRFExcl,bNotLastFrame,bStateChanged,bNS,bOurStep;
146 tensor force_vir,shake_vir,vir,pres;
147 int cg_tp,a_tp0,a_tp1,ngid,gid_tp,nener,e;
149 rvec mu_tot,x_init,dx,x_tp;
150 int nnodes,frame,nsteps,step;
154 char *ptr,*dump_pdb,**leg,str[STRLEN],str2[STRLEN];
155 double dbl,dump_ener;
158 real *mass_cavity=NULL,mass_tot;
160 double invbinw,*bin,refvolshift,logV,bUlogV;
161 real dvdl,prescorr,enercorr,dvdlcorr;
162 gmx_bool bEnergyOutOfBounds;
163 const char *tpid_leg[2]={"direct","reweighted"};
165 /* Since there is no upper limit to the insertion energies,
166 * we need to set an upper limit for the distribution output.
168 real bU_bin_limit = 50;
169 real bU_logV_bin_limit = bU_bin_limit + 10;
173 top = gmx_mtop_generate_local_top(top_global,inputrec);
175 groups = &top_global->groups;
177 bCavity = (inputrec->eI == eiTPIC);
179 ptr = getenv("GMX_TPIC_MASSES");
183 /* Read (multiple) masses from env var GMX_TPIC_MASSES,
184 * The center of mass of the last atoms is then used for TPIC.
187 while (sscanf(ptr,"%lf%n",&dbl,&i) > 0) {
188 srenew(mass_cavity,nat_cavity+1);
189 mass_cavity[nat_cavity] = dbl;
190 fprintf(fplog,"mass[%d] = %f\n",
191 nat_cavity+1,mass_cavity[nat_cavity]);
196 gmx_fatal(FARGS,"Found %d masses in GMX_TPIC_MASSES",nat_cavity);
201 init_em(fplog,TPI,inputrec,&lambda,nrnb,mu_tot,
202 state->box,fr,mdatoms,top,cr,nfile,fnm,NULL,NULL);*/
203 /* We never need full pbc for TPI */
205 /* Determine the temperature for the Boltzmann weighting */
206 temp = inputrec->opts.ref_t[0];
208 for(i=1; (i<inputrec->opts.ngtc); i++) {
209 if (inputrec->opts.ref_t[i] != temp) {
210 fprintf(fplog,"\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
211 fprintf(stderr,"\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
215 "\n The temperature for test particle insertion is %.3f K\n\n",
218 beta = 1.0/(BOLTZ*temp);
220 /* Number of insertions per frame */
221 nsteps = inputrec->nsteps;
223 /* Use the same neighborlist with more insertions points
224 * in a sphere of radius drmax around the initial point
226 /* This should be a proper mdp parameter */
227 drmax = inputrec->rtpi;
229 /* An environment variable can be set to dump all configurations
230 * to pdb with an insertion energy <= this value.
232 dump_pdb = getenv("GMX_TPI_DUMP");
235 sscanf(dump_pdb,"%lf",&dump_ener);
237 atoms2md(top_global,inputrec,0,NULL,0,top_global->natoms,mdatoms);
238 update_mdatoms(mdatoms,inputrec->init_lambda);
241 init_enerdata(groups->grps[egcENER].nr,inputrec->n_flambda,enerd);
242 snew(f,top_global->natoms);
244 /* Print to log file */
245 runtime_start(runtime);
246 print_date_and_time(fplog,cr->nodeid,
247 "Started Test Particle Insertion",runtime);
248 wallcycle_start(wcycle,ewcRUN);
250 /* The last charge group is the group to be inserted */
251 cg_tp = top->cgs.nr - 1;
252 a_tp0 = top->cgs.index[cg_tp];
253 a_tp1 = top->cgs.index[cg_tp+1];
255 fprintf(debug,"TPI cg %d, atoms %d-%d\n",cg_tp,a_tp0,a_tp1);
256 if (a_tp1 - a_tp0 > 1 &&
257 (inputrec->rlist < inputrec->rcoulomb ||
258 inputrec->rlist < inputrec->rvdw))
259 gmx_fatal(FARGS,"Can not do TPI for multi-atom molecule with a twin-range cut-off");
260 snew(x_mol,a_tp1-a_tp0);
262 bDispCorr = (inputrec->eDispCorr != edispcNO);
264 for(i=a_tp0; i<a_tp1; i++) {
265 /* Copy the coordinates of the molecule to be insterted */
266 copy_rvec(state->x[i],x_mol[i-a_tp0]);
267 /* Check if we need to print electrostatic energies */
268 bCharge |= (mdatoms->chargeA[i] != 0 ||
269 (mdatoms->chargeB && mdatoms->chargeB[i] != 0));
271 bRFExcl = (bCharge && EEL_RF(fr->eeltype) && fr->eeltype!=eelRF_NEC);
273 calc_cgcm(fplog,cg_tp,cg_tp+1,&(top->cgs),state->x,fr->cg_cm);
275 if (norm(fr->cg_cm[cg_tp]) > 0.5*inputrec->rlist && fplog) {
276 fprintf(fplog, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
277 fprintf(stderr,"WARNING: Your TPI molecule is not centered at 0,0,0\n");
280 /* Center the molecule to be inserted at zero */
281 for(i=0; i<a_tp1-a_tp0; i++)
282 rvec_dec(x_mol[i],fr->cg_cm[cg_tp]);
286 fprintf(fplog,"\nWill insert %d atoms %s partial charges\n",
287 a_tp1-a_tp0,bCharge ? "with" : "without");
289 fprintf(fplog,"\nWill insert %d times in each frame of %s\n",
290 nsteps,opt2fn("-rerun",nfile,fnm));
295 if (inputrec->nstlist > 1)
297 if (drmax==0 && a_tp1-a_tp0==1)
299 gmx_fatal(FARGS,"Re-using the neighborlist %d times for insertions of a single atom in a sphere of radius %f does not make sense",inputrec->nstlist,drmax);
303 fprintf(fplog,"Will use the same neighborlist for %d insertions in a sphere of radius %f\n",inputrec->nstlist,drmax);
311 fprintf(fplog,"Will insert randomly in a sphere of radius %f around the center of the cavity\n",drmax);
315 ngid = groups->grps[egcENER].nr;
316 gid_tp = GET_CGINFO_GID(fr->cginfo[cg_tp]);
324 if (EEL_FULL(fr->eeltype))
327 snew(sum_UgembU,nener);
329 /* Initialize random generator */
330 tpi_rand = gmx_rng_init(inputrec->ld_seed);
333 fp_tpi = xvgropen(opt2fn("-tpi",nfile,fnm),
334 "TPI energies","Time (ps)",
335 "(kJ mol\\S-1\\N) / (nm\\S3\\N)",oenv);
336 xvgr_subtitle(fp_tpi,"f. are averages over one frame",oenv);
339 sprintf(str,"-kT log(<Ve\\S-\\betaU\\N>/<V>)");
340 leg[e++] = strdup(str);
341 sprintf(str,"f. -kT log<e\\S-\\betaU\\N>");
342 leg[e++] = strdup(str);
343 sprintf(str,"f. <e\\S-\\betaU\\N>");
344 leg[e++] = strdup(str);
346 leg[e++] = strdup(str);
347 sprintf(str,"f. <Ue\\S-\\betaU\\N>");
348 leg[e++] = strdup(str);
349 for(i=0; i<ngid; i++) {
350 sprintf(str,"f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
351 *(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
352 leg[e++] = strdup(str);
355 sprintf(str,"f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
356 leg[e++] = strdup(str);
359 for(i=0; i<ngid; i++) {
360 sprintf(str,"f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
361 *(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
362 leg[e++] = strdup(str);
365 sprintf(str,"f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
366 leg[e++] = strdup(str);
368 if (EEL_FULL(fr->eeltype)) {
369 sprintf(str,"f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
370 leg[e++] = strdup(str);
373 xvgr_legend(fp_tpi,4+nener,(const char**)leg,oenv);
374 for(i=0; i<4+nener; i++)
386 bNotLastFrame = read_first_frame(oenv,&status,opt2fn("-rerun",nfile,fnm),
387 &rerun_fr,TRX_NEED_X);
390 if (rerun_fr.natoms - (bCavity ? nat_cavity : 0) !=
391 mdatoms->nr - (a_tp1 - a_tp0))
392 gmx_fatal(FARGS,"Number of atoms in trajectory (%d)%s "
393 "is not equal the number in the run input file (%d) "
394 "minus the number of atoms to insert (%d)\n",
395 rerun_fr.natoms,bCavity ? " minus one" : "",
396 mdatoms->nr,a_tp1-a_tp0);
398 refvolshift = log(det(rerun_fr.box));
400 #if ( defined(GMX_IA32_SSE) || defined(GMX_X86_64_SSE) || defined(GMX_X86_64_SSE2) )
401 /* Make sure we don't detect SSE overflow generated before this point */
402 gmx_mm_check_and_reset_overflow();
405 while (bNotLastFrame)
407 lambda = rerun_fr.lambda;
411 for(e=0; e<nener; e++)
416 /* Copy the coordinates from the input trajectory */
417 for(i=0; i<rerun_fr.natoms; i++)
419 copy_rvec(rerun_fr.x[i],state->x[i]);
422 V = det(rerun_fr.box);
425 bStateChanged = TRUE;
427 for(step=0; step<nsteps; step++)
429 /* In parallel all nodes generate all random configurations.
430 * In that way the result is identical to a single cpu tpi run.
434 /* Random insertion in the whole volume */
435 bNS = (step % inputrec->nstlist == 0);
438 /* Generate a random position in the box */
439 x_init[XX] = gmx_rng_uniform_real(tpi_rand)*state->box[XX][XX];
440 x_init[YY] = gmx_rng_uniform_real(tpi_rand)*state->box[YY][YY];
441 x_init[ZZ] = gmx_rng_uniform_real(tpi_rand)*state->box[ZZ][ZZ];
443 if (inputrec->nstlist == 1)
445 copy_rvec(x_init,x_tp);
449 /* Generate coordinates within |dx|=drmax of x_init */
452 dx[XX] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
453 dx[YY] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
454 dx[ZZ] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
456 while (norm2(dx) > drmax*drmax);
457 rvec_add(x_init,dx,x_tp);
462 /* Random insertion around a cavity location
463 * given by the last coordinate of the trajectory.
469 /* Copy the location of the cavity */
470 copy_rvec(rerun_fr.x[rerun_fr.natoms-1],x_init);
474 /* Determine the center of mass of the last molecule */
477 for(i=0; i<nat_cavity; i++)
482 mass_cavity[i]*rerun_fr.x[rerun_fr.natoms-nat_cavity+i][d];
484 mass_tot += mass_cavity[i];
488 x_init[d] /= mass_tot;
492 /* Generate coordinates within |dx|=drmax of x_init */
495 dx[XX] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
496 dx[YY] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
497 dx[ZZ] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
499 while (norm2(dx) > drmax*drmax);
500 rvec_add(x_init,dx,x_tp);
503 if (a_tp1 - a_tp0 == 1)
505 /* Insert a single atom, just copy the insertion location */
506 copy_rvec(x_tp,state->x[a_tp0]);
510 /* Copy the coordinates from the top file */
511 for(i=a_tp0; i<a_tp1; i++)
513 copy_rvec(x_mol[i-a_tp0],state->x[i]);
515 /* Rotate the molecule randomly */
516 rotate_conf(a_tp1-a_tp0,state->x+a_tp0,NULL,
517 2*M_PI*gmx_rng_uniform_real(tpi_rand),
518 2*M_PI*gmx_rng_uniform_real(tpi_rand),
519 2*M_PI*gmx_rng_uniform_real(tpi_rand));
520 /* Shift to the insertion location */
521 for(i=a_tp0; i<a_tp1; i++)
523 rvec_inc(state->x[i],x_tp);
527 /* Check if this insertion belongs to this node */
531 switch (inputrec->eI)
534 bOurStep = ((step / inputrec->nstlist) % nnodes == cr->nodeid);
537 bOurStep = (step % nnodes == cr->nodeid);
540 gmx_fatal(FARGS,"Unknown integrator %s",ei_names[inputrec->eI]);
545 /* Clear some matrix variables */
546 clear_mat(force_vir);
547 clear_mat(shake_vir);
551 /* Set the charge group center of mass of the test particle */
552 copy_rvec(x_init,fr->cg_cm[top->cgs.nr-1]);
554 /* Calc energy (no forces) on new positions.
555 * Since we only need the intermolecular energy
556 * and the RF exclusion terms of the inserted molecule occur
557 * within a single charge group we can pass NULL for the graph.
558 * This also avoids shifts that would move charge groups
561 * Some checks above ensure than we can not have
562 * twin-range interactions together with nstlist > 1,
563 * therefore we do not need to remember the LR energies.
565 /* Make do_force do a single node force calculation */
567 do_force(fplog,cr,inputrec,
568 step,nrnb,wcycle,top,top_global,&top_global->groups,
569 rerun_fr.box,state->x,&state->hist,
570 f,force_vir,mdatoms,enerd,fcd,
571 lambda,NULL,fr,NULL,mu_tot,t,NULL,NULL,FALSE,
572 GMX_FORCE_NONBONDED |
573 (bNS ? GMX_FORCE_NS | GMX_FORCE_DOLR : 0) |
574 (bStateChanged ? GMX_FORCE_STATECHANGED : 0));
576 bStateChanged = FALSE;
579 /* Calculate long range corrections to pressure and energy */
580 calc_dispcorr(fplog,inputrec,fr,step,top_global->natoms,rerun_fr.box,
581 lambda,pres,vir,&prescorr,&enercorr,&dvdlcorr);
582 /* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
583 enerd->term[F_DISPCORR] = enercorr;
584 enerd->term[F_EPOT] += enercorr;
585 enerd->term[F_PRES] += prescorr;
586 enerd->term[F_DVDL] += dvdlcorr;
588 epot = enerd->term[F_EPOT];
589 bEnergyOutOfBounds = FALSE;
590 #if ( defined(GMX_IA32_SSE) || defined(GMX_X86_64_SSE) || defined(GMX_X86_64_SSE2) )
591 /* With SSE the energy can overflow, check for this */
592 if (gmx_mm_check_and_reset_overflow())
596 fprintf(debug,"Found an SSE overflow, assuming the energy is out of bounds\n");
598 bEnergyOutOfBounds = TRUE;
601 /* If the compiler doesn't optimize this check away
602 * we catch the NAN energies.
603 * The epot>GMX_REAL_MAX check catches inf values,
604 * which should nicely result in embU=0 through the exp below,
605 * but it does not hurt to check anyhow.
607 /* Non-bonded Interaction usually diverge at r=0.
608 * With tabulated interaction functions the first few entries
609 * should be capped in a consistent fashion between
610 * repulsion, dispersion and Coulomb to avoid accidental
611 * negative values in the total energy.
612 * The table generation code in tables.c does this.
613 * With user tbales the user should take care of this.
615 if (epot != epot || epot > GMX_REAL_MAX)
617 bEnergyOutOfBounds = TRUE;
619 if (bEnergyOutOfBounds)
623 fprintf(debug,"\n time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n",t,step,epot);
629 embU = exp(-beta*epot);
631 /* Determine the weighted energy contributions of each energy group */
633 sum_UgembU[e++] += epot*embU;
636 for(i=0; i<ngid; i++)
639 (enerd->grpp.ener[egBHAMSR][GID(i,gid_tp,ngid)] +
640 enerd->grpp.ener[egBHAMLR][GID(i,gid_tp,ngid)])*embU;
645 for(i=0; i<ngid; i++)
648 (enerd->grpp.ener[egLJSR][GID(i,gid_tp,ngid)] +
649 enerd->grpp.ener[egLJLR][GID(i,gid_tp,ngid)])*embU;
654 sum_UgembU[e++] += enerd->term[F_DISPCORR]*embU;
658 for(i=0; i<ngid; i++)
661 (enerd->grpp.ener[egCOULSR][GID(i,gid_tp,ngid)] +
662 enerd->grpp.ener[egCOULLR][GID(i,gid_tp,ngid)])*embU;
666 sum_UgembU[e++] += enerd->term[F_RF_EXCL]*embU;
668 if (EEL_FULL(fr->eeltype))
670 sum_UgembU[e++] += enerd->term[F_COUL_RECIP]*embU;
675 if (embU == 0 || beta*epot > bU_bin_limit)
681 i = (int)((bU_logV_bin_limit
682 - (beta*epot - logV + refvolshift))*invbinw
690 realloc_bins(&bin,&nbin,i+10);
697 fprintf(debug,"TPI %7d %12.5e %12.5f %12.5f %12.5f\n",
698 step,epot,x_tp[XX],x_tp[YY],x_tp[ZZ]);
701 if (dump_pdb && epot <= dump_ener)
703 sprintf(str,"t%g_step%d.pdb",t,step);
704 sprintf(str2,"t: %f step %d ener: %f",t,step,epot);
705 write_sto_conf_mtop(str,str2,top_global,state->x,state->v,
706 inputrec->ePBC,state->box);
713 /* When running in parallel sum the energies over the processes */
714 gmx_sumd(1, &sum_embU, cr);
715 gmx_sumd(nener,sum_UgembU,cr);
720 VembU_all += V*sum_embU/nsteps;
724 if (bVerbose || frame%10==0 || frame<10)
726 fprintf(stderr,"mu %10.3e <mu> %10.3e\n",
727 -log(sum_embU/nsteps)/beta,-log(VembU_all/V_all)/beta);
730 fprintf(fp_tpi,"%10.3f %12.5e %12.5e %12.5e %12.5e",
732 VembU_all==0 ? 20/beta : -log(VembU_all/V_all)/beta,
733 sum_embU==0 ? 20/beta : -log(sum_embU/nsteps)/beta,
735 for(e=0; e<nener; e++)
737 fprintf(fp_tpi," %12.5e",sum_UgembU[e]/nsteps);
739 fprintf(fp_tpi,"\n");
743 bNotLastFrame = read_next_frame(oenv, status,&rerun_fr);
744 } /* End of the loop */
745 runtime_end(runtime);
751 gmx_fio_fclose(fp_tpi);
757 fprintf(fplog," <V> = %12.5e nm^3\n",V_all/frame);
758 fprintf(fplog," <mu> = %12.5e kJ/mol\n",-log(VembU_all/V_all)/beta);
761 /* Write the Boltzmann factor histogram */
764 /* When running in parallel sum the bins over the processes */
767 realloc_bins(&bin,&nbin,i);
768 gmx_sumd(nbin,bin,cr);
772 fp_tpi = xvgropen(opt2fn("-tpid",nfile,fnm),
773 "TPI energy distribution",
774 "\\betaU - log(V/<V>)","count",oenv);
775 sprintf(str,"number \\betaU > %g: %9.3e",bU_bin_limit,bin[0]);
776 xvgr_subtitle(fp_tpi,str,oenv);
777 xvgr_legend(fp_tpi,2,(const char **)tpid_leg,oenv);
778 for(i=nbin-1; i>0; i--)
780 bUlogV = -i/invbinw + bU_logV_bin_limit - refvolshift + log(V_all/frame);
781 fprintf(fp_tpi,"%6.2f %10d %12.5e\n",
784 bin[i]*exp(-bUlogV)*V_all/VembU_all);
786 gmx_fio_fclose(fp_tpi);
792 runtime->nsteps_done = frame*inputrec->nsteps;