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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,
130 gmx_membed_t *membed,
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 numerical problems can lead to extreme negative energies
166 * when atoms overlap, we need to set a lower limit for beta*U.
168 real bU_neg_limit = -50;
170 /* Since there is no upper limit to the insertion energies,
171 * we need to set an upper limit for the distribution output.
173 real bU_bin_limit = 50;
174 real bU_logV_bin_limit = bU_bin_limit + 10;
178 top = gmx_mtop_generate_local_top(top_global,inputrec);
180 groups = &top_global->groups;
182 bCavity = (inputrec->eI == eiTPIC);
184 ptr = getenv("GMX_TPIC_MASSES");
188 /* Read (multiple) masses from env var GMX_TPIC_MASSES,
189 * The center of mass of the last atoms is then used for TPIC.
192 while (sscanf(ptr,"%lf%n",&dbl,&i) > 0) {
193 srenew(mass_cavity,nat_cavity+1);
194 mass_cavity[nat_cavity] = dbl;
195 fprintf(fplog,"mass[%d] = %f\n",
196 nat_cavity+1,mass_cavity[nat_cavity]);
201 gmx_fatal(FARGS,"Found %d masses in GMX_TPIC_MASSES",nat_cavity);
206 init_em(fplog,TPI,inputrec,&lambda,nrnb,mu_tot,
207 state->box,fr,mdatoms,top,cr,nfile,fnm,NULL,NULL);*/
208 /* We never need full pbc for TPI */
210 /* Determine the temperature for the Boltzmann weighting */
211 temp = inputrec->opts.ref_t[0];
213 for(i=1; (i<inputrec->opts.ngtc); i++) {
214 if (inputrec->opts.ref_t[i] != temp) {
215 fprintf(fplog,"\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
216 fprintf(stderr,"\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
220 "\n The temperature for test particle insertion is %.3f K\n\n",
223 beta = 1.0/(BOLTZ*temp);
225 /* Number of insertions per frame */
226 nsteps = inputrec->nsteps;
228 /* Use the same neighborlist with more insertions points
229 * in a sphere of radius drmax around the initial point
231 /* This should be a proper mdp parameter */
232 drmax = inputrec->rtpi;
234 /* An environment variable can be set to dump all configurations
235 * to pdb with an insertion energy <= this value.
237 dump_pdb = getenv("GMX_TPI_DUMP");
240 sscanf(dump_pdb,"%lf",&dump_ener);
242 atoms2md(top_global,inputrec,0,NULL,0,top_global->natoms,mdatoms);
243 update_mdatoms(mdatoms,inputrec->init_lambda);
246 init_enerdata(groups->grps[egcENER].nr,inputrec->n_flambda,enerd);
247 snew(f,top_global->natoms);
249 /* Print to log file */
250 runtime_start(runtime);
251 print_date_and_time(fplog,cr->nodeid,
252 "Started Test Particle Insertion",runtime);
253 wallcycle_start(wcycle,ewcRUN);
255 /* The last charge group is the group to be inserted */
256 cg_tp = top->cgs.nr - 1;
257 a_tp0 = top->cgs.index[cg_tp];
258 a_tp1 = top->cgs.index[cg_tp+1];
260 fprintf(debug,"TPI cg %d, atoms %d-%d\n",cg_tp,a_tp0,a_tp1);
261 if (a_tp1 - a_tp0 > 1 &&
262 (inputrec->rlist < inputrec->rcoulomb ||
263 inputrec->rlist < inputrec->rvdw))
264 gmx_fatal(FARGS,"Can not do TPI for multi-atom molecule with a twin-range cut-off");
265 snew(x_mol,a_tp1-a_tp0);
267 bDispCorr = (inputrec->eDispCorr != edispcNO);
269 for(i=a_tp0; i<a_tp1; i++) {
270 /* Copy the coordinates of the molecule to be insterted */
271 copy_rvec(state->x[i],x_mol[i-a_tp0]);
272 /* Check if we need to print electrostatic energies */
273 bCharge |= (mdatoms->chargeA[i] != 0 ||
274 (mdatoms->chargeB && mdatoms->chargeB[i] != 0));
276 bRFExcl = (bCharge && EEL_RF(fr->eeltype) && fr->eeltype!=eelRF_NEC);
278 calc_cgcm(fplog,cg_tp,cg_tp+1,&(top->cgs),state->x,fr->cg_cm);
280 if (norm(fr->cg_cm[cg_tp]) > 0.5*inputrec->rlist && fplog) {
281 fprintf(fplog, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
282 fprintf(stderr,"WARNING: Your TPI molecule is not centered at 0,0,0\n");
285 /* Center the molecule to be inserted at zero */
286 for(i=0; i<a_tp1-a_tp0; i++)
287 rvec_dec(x_mol[i],fr->cg_cm[cg_tp]);
291 fprintf(fplog,"\nWill insert %d atoms %s partial charges\n",
292 a_tp1-a_tp0,bCharge ? "with" : "without");
294 fprintf(fplog,"\nWill insert %d times in each frame of %s\n",
295 nsteps,opt2fn("-rerun",nfile,fnm));
300 if (inputrec->nstlist > 1)
302 if (drmax==0 && a_tp1-a_tp0==1)
304 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);
308 fprintf(fplog,"Will use the same neighborlist for %d insertions in a sphere of radius %f\n",inputrec->nstlist,drmax);
316 fprintf(fplog,"Will insert randomly in a sphere of radius %f around the center of the cavity\n",drmax);
320 ngid = groups->grps[egcENER].nr;
321 gid_tp = GET_CGINFO_GID(fr->cginfo[cg_tp]);
329 if (EEL_FULL(fr->eeltype))
332 snew(sum_UgembU,nener);
334 /* Initialize random generator */
335 tpi_rand = gmx_rng_init(inputrec->ld_seed);
338 fp_tpi = xvgropen(opt2fn("-tpi",nfile,fnm),
339 "TPI energies","Time (ps)",
340 "(kJ mol\\S-1\\N) / (nm\\S3\\N)",oenv);
341 xvgr_subtitle(fp_tpi,"f. are averages over one frame",oenv);
344 sprintf(str,"-kT log(<Ve\\S-\\betaU\\N>/<V>)");
345 leg[e++] = strdup(str);
346 sprintf(str,"f. -kT log<e\\S-\\betaU\\N>");
347 leg[e++] = strdup(str);
348 sprintf(str,"f. <e\\S-\\betaU\\N>");
349 leg[e++] = strdup(str);
351 leg[e++] = strdup(str);
352 sprintf(str,"f. <Ue\\S-\\betaU\\N>");
353 leg[e++] = strdup(str);
354 for(i=0; i<ngid; i++) {
355 sprintf(str,"f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
356 *(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
357 leg[e++] = strdup(str);
360 sprintf(str,"f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
361 leg[e++] = strdup(str);
364 for(i=0; i<ngid; i++) {
365 sprintf(str,"f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
366 *(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
367 leg[e++] = strdup(str);
370 sprintf(str,"f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
371 leg[e++] = strdup(str);
373 if (EEL_FULL(fr->eeltype)) {
374 sprintf(str,"f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
375 leg[e++] = strdup(str);
378 xvgr_legend(fp_tpi,4+nener,(const char**)leg,oenv);
379 for(i=0; i<4+nener; i++)
391 bNotLastFrame = read_first_frame(oenv,&status,opt2fn("-rerun",nfile,fnm),
392 &rerun_fr,TRX_NEED_X);
395 if (rerun_fr.natoms - (bCavity ? nat_cavity : 0) !=
396 mdatoms->nr - (a_tp1 - a_tp0))
397 gmx_fatal(FARGS,"Number of atoms in trajectory (%d)%s "
398 "is not equal the number in the run input file (%d) "
399 "minus the number of atoms to insert (%d)\n",
400 rerun_fr.natoms,bCavity ? " minus one" : "",
401 mdatoms->nr,a_tp1-a_tp0);
403 refvolshift = log(det(rerun_fr.box));
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. With tables extreme negative
603 * energies might occur close to r=0.
605 if (epot != epot || epot*beta < bU_neg_limit)
607 bEnergyOutOfBounds = TRUE;
609 if (bEnergyOutOfBounds)
613 fprintf(debug,"\n time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n",t,step,epot);
619 embU = exp(-beta*epot);
621 /* Determine the weighted energy contributions of each energy group */
623 sum_UgembU[e++] += epot*embU;
626 for(i=0; i<ngid; i++)
629 (enerd->grpp.ener[egBHAMSR][GID(i,gid_tp,ngid)] +
630 enerd->grpp.ener[egBHAMLR][GID(i,gid_tp,ngid)])*embU;
635 for(i=0; i<ngid; i++)
638 (enerd->grpp.ener[egLJSR][GID(i,gid_tp,ngid)] +
639 enerd->grpp.ener[egLJLR][GID(i,gid_tp,ngid)])*embU;
644 sum_UgembU[e++] += enerd->term[F_DISPCORR]*embU;
648 for(i=0; i<ngid; i++)
651 (enerd->grpp.ener[egCOULSR][GID(i,gid_tp,ngid)] +
652 enerd->grpp.ener[egCOULLR][GID(i,gid_tp,ngid)])*embU;
656 sum_UgembU[e++] += enerd->term[F_RF_EXCL]*embU;
658 if (EEL_FULL(fr->eeltype))
660 sum_UgembU[e++] += enerd->term[F_COUL_RECIP]*embU;
665 if (embU == 0 || beta*epot > bU_bin_limit)
671 i = (int)((bU_logV_bin_limit
672 - (beta*epot - logV + refvolshift))*invbinw
680 realloc_bins(&bin,&nbin,i+10);
687 fprintf(debug,"TPI %7d %12.5e %12.5f %12.5f %12.5f\n",
688 step,epot,x_tp[XX],x_tp[YY],x_tp[ZZ]);
691 if (dump_pdb && epot <= dump_ener)
693 sprintf(str,"t%g_step%d.pdb",t,step);
694 sprintf(str2,"t: %f step %d ener: %f",t,step,epot);
695 write_sto_conf_mtop(str,str2,top_global,state->x,state->v,
696 inputrec->ePBC,state->box);
703 /* When running in parallel sum the energies over the processes */
704 gmx_sumd(1, &sum_embU, cr);
705 gmx_sumd(nener,sum_UgembU,cr);
710 VembU_all += V*sum_embU/nsteps;
714 if (bVerbose || frame%10==0 || frame<10)
716 fprintf(stderr,"mu %10.3e <mu> %10.3e\n",
717 -log(sum_embU/nsteps)/beta,-log(VembU_all/V_all)/beta);
720 fprintf(fp_tpi,"%10.3f %12.5e %12.5e %12.5e %12.5e",
722 VembU_all==0 ? 20/beta : -log(VembU_all/V_all)/beta,
723 sum_embU==0 ? 20/beta : -log(sum_embU/nsteps)/beta,
725 for(e=0; e<nener; e++)
727 fprintf(fp_tpi," %12.5e",sum_UgembU[e]/nsteps);
729 fprintf(fp_tpi,"\n");
733 bNotLastFrame = read_next_frame(oenv, status,&rerun_fr);
734 } /* End of the loop */
735 runtime_end(runtime);
741 gmx_fio_fclose(fp_tpi);
747 fprintf(fplog," <V> = %12.5e nm^3\n",V_all/frame);
748 fprintf(fplog," <mu> = %12.5e kJ/mol\n",-log(VembU_all/V_all)/beta);
751 /* Write the Boltzmann factor histogram */
754 /* When running in parallel sum the bins over the processes */
757 realloc_bins(&bin,&nbin,i);
758 gmx_sumd(nbin,bin,cr);
762 fp_tpi = xvgropen(opt2fn("-tpid",nfile,fnm),
763 "TPI energy distribution",
764 "\\betaU - log(V/<V>)","count",oenv);
765 sprintf(str,"number \\betaU > %g: %9.3e",bU_bin_limit,bin[0]);
766 xvgr_subtitle(fp_tpi,str,oenv);
767 xvgr_legend(fp_tpi,2,(const char **)tpid_leg,oenv);
768 for(i=nbin-1; i>0; i--)
770 bUlogV = -i/invbinw + bU_logV_bin_limit - refvolshift + log(V_all/frame);
771 fprintf(fp_tpi,"%6.2f %10d %12.5e\n",
774 bin[i]*exp(-bUlogV)*V_all/VembU_all);
776 gmx_fio_fclose(fp_tpi);
782 runtime->nsteps_done = frame*inputrec->nsteps;