src/mdlib/tpi.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
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  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <string.h>
  41 #include <time.h>
  42 #include <math.h>
  43 #include "sysstuff.h"
  44 #include "string2.h"
  45 #include "network.h"
  46 #include "confio.h"
  47 #include "copyrite.h"
  48 #include "smalloc.h"
  49 #include "nrnb.h"
  50 #include "main.h"
  51 #include "chargegroup.h"
  52 #include "force.h"
  53 #include "macros.h"
  54 #include "random.h"
  55 #include "names.h"
  56 #include "gmx_fatal.h"
  57 #include "txtdump.h"
  58 #include "typedefs.h"
  59 #include "update.h"
  60 #include "random.h"
  61 #include "constr.h"
  62 #include "vec.h"
  63 #include "statutil.h"
  64 #include "tgroup.h"
  65 #include "mdebin.h"
  66 #include "vsite.h"
  67 #include "force.h"
  68 #include "mdrun.h"
  69 #include "domdec.h"
  70 #include "partdec.h"
  71 #include "gmx_random.h"
  72 #include "physics.h"
  73 #include "xvgr.h"
  74 #include "mdatoms.h"
  75 #include "ns.h"
  76 #include "gmx_wallcycle.h"
  77 #include "mtop_util.h"
  78 #include "gmxfio.h"
  79 #include "pme.h"
  80 #include "gbutil.h"
  81
  82
  83 static void global_max(t_commrec *cr,int *n)
  84 {
  85   int *sum,i;
  86
  87   snew(sum,cr->nnodes);
  88   sum[cr->nodeid] = *n;
  89   gmx_sumi(cr->nnodes,sum,cr);
  90   for(i=0; i<cr->nnodes; i++)
  91     *n = max(*n,sum[i]);
  92
  93   sfree(sum);
  94 }
  95
  96 static void realloc_bins(double **bin,int *nbin,int nbin_new)
  97 {
  98   int i;
  99
 100   if (nbin_new != *nbin) {
 101     srenew(*bin,nbin_new);
 102     for(i=*nbin; i<nbin_new; i++)
 103       (*bin)[i] = 0;
 104     *nbin = nbin_new;
 105   }
 106 }
 107
 108 double do_tpi(FILE *fplog,t_commrec *cr,
 109               int nfile, const t_filenm fnm[],
 110               const output_env_t oenv, bool bVerbose,bool bCompact,
 111               int nstglobalcomm,
 112               gmx_vsite_t *vsite,gmx_constr_t constr,
 113               int stepout,
 114               t_inputrec *inputrec,
 115               gmx_mtop_t *top_global,t_fcdata *fcd,
 116               t_state *state,
 117               t_mdatoms *mdatoms,
 118               t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 119               gmx_edsam_t ed,
 120               t_forcerec *fr,
 121               int repl_ex_nst,int repl_ex_seed,
 122               real cpt_period,real max_hours,
 123               const char *deviceOptions,
 124               unsigned long Flags,
 125               gmx_runtime_t *runtime)
 126 {
 127   const char *TPI="Test Particle Insertion";
 128   gmx_localtop_t *top;
 129   gmx_groups_t *groups;
 130   gmx_enerdata_t *enerd;
 131   rvec   *f;
 132   real   lambda,t,temp,beta,drmax,epot;
 133   double embU,sum_embU,*sum_UgembU,V,V_all,VembU_all;
 134   int    status;
 135   t_trxframe rerun_fr;
 136   bool   bDispCorr,bCharge,bRFExcl,bNotLastFrame,bStateChanged,bNS,bOurStep;
 137   tensor force_vir,shake_vir,vir,pres;
 138   int    cg_tp,a_tp0,a_tp1,ngid,gid_tp,nener,e;
 139   rvec   *x_mol;
 140   rvec   mu_tot,x_init,dx,x_tp;
 141   int    nnodes,frame,nsteps,step;
 142   int    i,start,end;
 143   gmx_rng_t tpi_rand;
 144   FILE   *fp_tpi=NULL;
 145   char   *ptr,*dump_pdb,**leg,str[STRLEN],str2[STRLEN];
 146   double dbl,dump_ener;
 147   bool   bCavity;
 148   int    nat_cavity=0,d;
 149   real   *mass_cavity=NULL,mass_tot;
 150   int    nbin;
 151   double invbinw,*bin,refvolshift,logV,bUlogV;
 152   real dvdl,prescorr,enercorr,dvdlcorr;
 153   const char *tpid_leg[2]={"direct","reweighted"};
 154
 155   /* Since numerical problems can lead to extreme negative energies
 156    * when atoms overlap, we need to set a lower limit for beta*U.
 157    */
 158   real bU_neg_limit = -50;
 159
 160   /* Since there is no upper limit to the insertion energies,
 161    * we need to set an upper limit for the distribution output.
 162    */
 163   real bU_bin_limit      = 50;
 164   real bU_logV_bin_limit = bU_bin_limit + 10;
 165
 166   nnodes = cr->nnodes;
 167
 168   top = gmx_mtop_generate_local_top(top_global,inputrec);
 169
 170   groups = &top_global->groups;
 171
 172   bCavity = (inputrec->eI == eiTPIC);
 173   if (bCavity) {
 174     ptr = getenv("GMX_TPIC_MASSES");
 175     if (ptr == NULL) {
 176       nat_cavity = 1;
 177     } else {
 178       /* Read (multiple) masses from env var GMX_TPIC_MASSES,
 179        * The center of mass of the last atoms is then used for TPIC.
 180        */
 181       nat_cavity = 0;
 182       while (sscanf(ptr,"%lf%n",&dbl,&i) > 0) {
 183         srenew(mass_cavity,nat_cavity+1);
 184         mass_cavity[nat_cavity] = dbl;
 185         fprintf(fplog,"mass[%d] = %f\n",
 186                 nat_cavity+1,mass_cavity[nat_cavity]);
 187         nat_cavity++;
 188         ptr += i;
 189       }
 190       if (nat_cavity == 0)
 191         gmx_fatal(FARGS,"Found %d masses in GMX_TPIC_MASSES",nat_cavity);
 192     }
 193   }
 194
 195   /*
 196   init_em(fplog,TPI,inputrec,&lambda,nrnb,mu_tot,
 197   state->box,fr,mdatoms,top,cr,nfile,fnm,NULL,NULL);*/
 198   /* We never need full pbc for TPI */
 199   fr->ePBC = epbcXYZ;
 200   /* Determine the temperature for the Boltzmann weighting */
 201   temp = inputrec->opts.ref_t[0];
 202   if (fplog) {
 203     for(i=1; (i<inputrec->opts.ngtc); i++) {
 204       if (inputrec->opts.ref_t[i] != temp) {
 205         fprintf(fplog,"\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
 206         fprintf(stderr,"\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
 207       }
 208     }
 209     fprintf(fplog,
 210             "\n  The temperature for test particle insertion is %.3f K\n\n",
 211             temp);
 212   }
 213   beta = 1.0/(BOLTZ*temp);
 214
 215   /* Number of insertions per frame */
 216   nsteps = inputrec->nsteps;
 217
 218   /* Use the same neighborlist with more insertions points
 219    * in a sphere of radius drmax around the initial point
 220    */
 221   /* This should be a proper mdp parameter */
 222   drmax = inputrec->rtpi;
 223
 224   /* An environment variable can be set to dump all configurations
 225    * to pdb with an insertion energy <= this value.
 226    */
 227   dump_pdb = getenv("GMX_TPI_DUMP");
 228   dump_ener = 0;
 229   if (dump_pdb)
 230     sscanf(dump_pdb,"%lf",&dump_ener);
 231
 232   atoms2md(top_global,inputrec,0,NULL,0,top_global->natoms,mdatoms);
 233   update_mdatoms(mdatoms,inputrec->init_lambda);
 234
 235   snew(enerd,1);
 236   init_enerdata(groups->grps[egcENER].nr,inputrec->n_flambda,enerd);
 237   snew(f,top_global->natoms);
 238
 239   /* Print to log file  */
 240   runtime_start(runtime);
 241   print_date_and_time(fplog,cr->nodeid,
 242                       "Started Test Particle Insertion",runtime);
 243   wallcycle_start(wcycle,ewcRUN);
 244
 245   /* The last charge group is the group to be inserted */
 246   cg_tp = top->cgs.nr - 1;
 247   a_tp0 = top->cgs.index[cg_tp];
 248   a_tp1 = top->cgs.index[cg_tp+1];
 249   if (debug)
 250     fprintf(debug,"TPI cg %d, atoms %d-%d\n",cg_tp,a_tp0,a_tp1);
 251   if (a_tp1 - a_tp0 > 1 &&
 252       (inputrec->rlist < inputrec->rcoulomb ||
 253        inputrec->rlist < inputrec->rvdw))
 254     gmx_fatal(FARGS,"Can not do TPI for multi-atom molecule with a twin-range cut-off");
 255   snew(x_mol,a_tp1-a_tp0);
 256
 257   bDispCorr = (inputrec->eDispCorr != edispcNO);
 258   bCharge = FALSE;
 259   for(i=a_tp0; i<a_tp1; i++) {
 260     /* Copy the coordinates of the molecule to be insterted */
 261     copy_rvec(state->x[i],x_mol[i-a_tp0]);
 262     /* Check if we need to print electrostatic energies */
 263     bCharge |= (mdatoms->chargeA[i] != 0 ||
 264                 (mdatoms->chargeB && mdatoms->chargeB[i] != 0));
 265   }
 266   bRFExcl = (bCharge && EEL_RF(fr->eeltype) && fr->eeltype!=eelRF_NEC);
 267
 268   calc_cgcm(fplog,cg_tp,cg_tp+1,&(top->cgs),state->x,fr->cg_cm);
 269   if (bCavity) {
 270     if (norm(fr->cg_cm[cg_tp]) > 0.5*inputrec->rlist && fplog) {
 271       fprintf(fplog, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
 272       fprintf(stderr,"WARNING: Your TPI molecule is not centered at 0,0,0\n");
 273     }
 274   } else {
 275     /* Center the molecule to be inserted at zero */
 276      for(i=0; i<a_tp1-a_tp0; i++)
 277       rvec_dec(x_mol[i],fr->cg_cm[cg_tp]);
 278   }
 279
 280   if (fplog) {
 281     fprintf(fplog,"\nWill insert %d atoms %s partial charges\n",
 282             a_tp1-a_tp0,bCharge ? "with" : "without");
 283
 284     fprintf(fplog,"\nWill insert %d times in each frame of %s\n",
 285             nsteps,opt2fn("-rerun",nfile,fnm));
 286   }
 287
 288     if (!bCavity)
 289     {
 290         if (inputrec->nstlist > 1)
 291         {
 292             if (drmax==0 && a_tp1-a_tp0==1)
 293             {
 294                 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);
 295             }
 296             if (fplog)
 297             {
 298                 fprintf(fplog,"Will use the same neighborlist for %d insertions in a sphere of radius %f\n",inputrec->nstlist,drmax);
 299             }
 300         }
 301     }
 302     else
 303     {
 304         if (fplog)
 305         {
 306             fprintf(fplog,"Will insert randomly in a sphere of radius %f around the center of the cavity\n",drmax);
 307         }
 308     }
 309
 310   ngid = groups->grps[egcENER].nr;
 311   gid_tp = GET_CGINFO_GID(fr->cginfo[cg_tp]);
 312   nener = 1 + ngid;
 313   if (bDispCorr)
 314     nener += 1;
 315   if (bCharge) {
 316     nener += ngid;
 317     if (bRFExcl)
 318       nener += 1;
 319     if (EEL_FULL(fr->eeltype))
 320       nener += 1;
 321   }
 322   snew(sum_UgembU,nener);
 323
 324   /* Initialize random generator */
 325   tpi_rand = gmx_rng_init(inputrec->ld_seed);
 326
 327   if (MASTER(cr)) {
 328     fp_tpi = xvgropen(opt2fn("-tpi",nfile,fnm),
 329                       "TPI energies","Time (ps)",
 330                       "(kJ mol\\S-1\\N) / (nm\\S3\\N)",oenv);
 331     xvgr_subtitle(fp_tpi,"f. are averages over one frame",oenv);
 332     snew(leg,4+nener);
 333     e = 0;
 334     sprintf(str,"-kT log(<Ve\\S-\\betaU\\N>/<V>)");
 335     leg[e++] = strdup(str);
 336     sprintf(str,"f. -kT log<e\\S-\\betaU\\N>");
 337     leg[e++] = strdup(str);
 338     sprintf(str,"f. <e\\S-\\betaU\\N>");
 339     leg[e++] = strdup(str);
 340     sprintf(str,"f. V");
 341     leg[e++] = strdup(str);
 342     sprintf(str,"f. <Ue\\S-\\betaU\\N>");
 343     leg[e++] = strdup(str);
 344     for(i=0; i<ngid; i++) {
 345       sprintf(str,"f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
 346               *(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
 347       leg[e++] = strdup(str);
 348     }
 349     if (bDispCorr) {
 350       sprintf(str,"f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
 351       leg[e++] = strdup(str);
 352     }
 353     if (bCharge) {
 354       for(i=0; i<ngid; i++) {
 355         sprintf(str,"f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
 356                 *(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
 357         leg[e++] = strdup(str);
 358       }
 359       if (bRFExcl) {
 360         sprintf(str,"f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
 361         leg[e++] = strdup(str);
 362       }
 363       if (EEL_FULL(fr->eeltype)) {
 364         sprintf(str,"f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
 365         leg[e++] = strdup(str);
 366       }
 367     }
 368     xvgr_legend(fp_tpi,4+nener,leg,oenv);
 369     for(i=0; i<4+nener; i++)
 370       sfree(leg[i]);
 371     sfree(leg);
 372   }
 373   clear_rvec(x_init);
 374   V_all = 0;
 375   VembU_all = 0;
 376
 377   invbinw = 10;
 378   nbin = 10;
 379   snew(bin,nbin);
 380
 381   bNotLastFrame = read_first_frame(oenv,&status,opt2fn("-rerun",nfile,fnm),
 382                                    &rerun_fr,TRX_NEED_X);
 383   frame = 0;
 384
 385   if (rerun_fr.natoms - (bCavity ? nat_cavity : 0) !=
 386       mdatoms->nr - (a_tp1 - a_tp0))
 387     gmx_fatal(FARGS,"Number of atoms in trajectory (%d)%s "
 388               "is not equal the number in the run input file (%d) "
 389               "minus the number of atoms to insert (%d)\n",
 390               rerun_fr.natoms,bCavity ? " minus one" : "",
 391               mdatoms->nr,a_tp1-a_tp0);
 392
 393   refvolshift = log(det(rerun_fr.box));
 394
 395     while (bNotLastFrame)
 396     {
 397         lambda = rerun_fr.lambda;
 398         t = rerun_fr.time;
 399
 400         sum_embU = 0;
 401         for(e=0; e<nener; e++)
 402         {
 403             sum_UgembU[e] = 0;
 404         }
 405
 406         /* Copy the coordinates from the input trajectory */
 407         for(i=0; i<rerun_fr.natoms; i++)
 408         {
 409             copy_rvec(rerun_fr.x[i],state->x[i]);
 410         }
 411
 412         V = det(rerun_fr.box);
 413         logV = log(V);
 414
 415         bStateChanged = TRUE;
 416         bNS = TRUE;
 417         for(step=0; step<nsteps; step++)
 418         {
 419             /* In parallel all nodes generate all random configurations.
 420              * In that way the result is identical to a single cpu tpi run.
 421              */
 422             if (!bCavity)
 423             {
 424                 /* Random insertion in the whole volume */
 425                 bNS = (step % inputrec->nstlist == 0);
 426                 if (bNS)
 427                 {
 428                     /* Generate a random position in the box */
 429                     x_init[XX] = gmx_rng_uniform_real(tpi_rand)*state->box[XX][XX];
 430                     x_init[YY] = gmx_rng_uniform_real(tpi_rand)*state->box[YY][YY];
 431                     x_init[ZZ] = gmx_rng_uniform_real(tpi_rand)*state->box[ZZ][ZZ];
 432                 }
 433                 if (inputrec->nstlist == 1)
 434                 {
 435                     copy_rvec(x_init,x_tp);
 436                 }
 437                 else
 438                 {
 439                     /* Generate coordinates within |dx|=drmax of x_init */
 440                     do
 441                     {
 442                         dx[XX] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
 443                         dx[YY] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
 444                         dx[ZZ] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
 445                     }
 446                     while (norm2(dx) > drmax*drmax);
 447                     rvec_add(x_init,dx,x_tp);
 448                 }
 449             }
 450             else
 451             {
 452                 /* Random insertion around a cavity location
 453                  * given by the last coordinate of the trajectory.
 454                  */
 455                 if (step == 0)
 456                 {
 457                     if (nat_cavity == 1)
 458                     {
 459                         /* Copy the location of the cavity */
 460                         copy_rvec(rerun_fr.x[rerun_fr.natoms-1],x_init);
 461                     }
 462                     else
 463                     {
 464                         /* Determine the center of mass of the last molecule */
 465                         clear_rvec(x_init);
 466                         mass_tot = 0;
 467                         for(i=0; i<nat_cavity; i++)
 468                         {
 469                             for(d=0; d<DIM; d++)
 470                             {
 471                                 x_init[d] +=
 472                                     mass_cavity[i]*rerun_fr.x[rerun_fr.natoms-nat_cavity+i][d];
 473                             }
 474                             mass_tot += mass_cavity[i];
 475                         }
 476                         for(d=0; d<DIM; d++)
 477                         {
 478                             x_init[d] /= mass_tot;
 479                         }
 480                     }
 481                 }
 482                 /* Generate coordinates within |dx|=drmax of x_init */
 483                 do
 484                 {
 485                     dx[XX] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
 486                     dx[YY] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
 487                     dx[ZZ] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
 488                 }
 489                 while (norm2(dx) > drmax*drmax);
 490                 rvec_add(x_init,dx,x_tp);
 491             }
 492
 493             if (a_tp1 - a_tp0 == 1)
 494             {
 495                 /* Insert a single atom, just copy the insertion location */
 496         copy_rvec(x_tp,state->x[a_tp0]);
 497             }
 498             else
 499             {
 500                 /* Copy the coordinates from the top file */
 501                 for(i=a_tp0; i<a_tp1; i++)
 502                 {
 503                     copy_rvec(x_mol[i-a_tp0],state->x[i]);
 504                 }
 505                 /* Rotate the molecule randomly */
 506                 rotate_conf(a_tp1-a_tp0,state->x+a_tp0,NULL,
 507                             2*M_PI*gmx_rng_uniform_real(tpi_rand),
 508                             2*M_PI*gmx_rng_uniform_real(tpi_rand),
 509                             2*M_PI*gmx_rng_uniform_real(tpi_rand));
 510                 /* Shift to the insertion location */
 511                 for(i=a_tp0; i<a_tp1; i++)
 512                 {
 513                     rvec_inc(state->x[i],x_tp);
 514                 }
 515             }
 516
 517             /* Check if this insertion belongs to this node */
 518             bOurStep = TRUE;
 519             if (PAR(cr))
 520             {
 521                 switch (inputrec->eI)
 522                 {
 523                 case eiTPI:
 524                     bOurStep = ((step / inputrec->nstlist) % nnodes == cr->nodeid);
 525                     break;
 526                 case eiTPIC:
 527                     bOurStep = (step % nnodes == cr->nodeid);
 528                     break;
 529                 default:
 530                     gmx_fatal(FARGS,"Unknown integrator %s",ei_names[inputrec->eI]);
 531                 }
 532             }
 533             if (bOurStep)
 534             {
 535                 /* Clear some matrix variables  */
 536                 clear_mat(force_vir);
 537                 clear_mat(shake_vir);
 538                 clear_mat(vir);
 539                 clear_mat(pres);
 540
 541                 /* Set the charge group center of mass of the test particle */
 542                 copy_rvec(x_init,fr->cg_cm[top->cgs.nr-1]);
 543
 544                 /* Calc energy (no forces) on new positions.
 545                  * Since we only need the intermolecular energy
 546                  * and the RF exclusion terms of the inserted molecule occur
 547                  * within a single charge group we can pass NULL for the graph.
 548                  * This also avoids shifts that would move charge groups
 549                  * out of the box.
 550                  *
 551                  * Some checks above ensure than we can not have
 552                  * twin-range interactions together with nstlist > 1,
 553                  * therefore we do not need to remember the LR energies.
 554                  */
 555                 /* Make do_force do a single node force calculation */
 556                 cr->nnodes = 1;
 557                 do_force(fplog,cr,inputrec,
 558                          step,nrnb,wcycle,top,top_global,&top_global->groups,
 559                          rerun_fr.box,state->x,&state->hist,
 560                          f,force_vir,mdatoms,enerd,fcd,
 561                          lambda,NULL,fr,NULL,mu_tot,t,NULL,NULL,FALSE,
 562                          GMX_FORCE_NONBONDED |
 563                          (bNS ? GMX_FORCE_NS | GMX_FORCE_DOLR : 0) |
 564                          (bStateChanged ? GMX_FORCE_STATECHANGED : 0));
 565                 cr->nnodes = nnodes;
 566                 bStateChanged = FALSE;
 567                 bNS = FALSE;
 568
 569                 /* Calculate long range corrections to pressure and energy */
 570                 calc_dispcorr(fplog,inputrec,fr,step,top_global->natoms,rerun_fr.box,
 571                               lambda,pres,vir,&prescorr,&enercorr,&dvdlcorr);
 572                 /* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
 573                 enerd->term[F_DISPCORR] = enercorr;
 574                 enerd->term[F_EPOT] += enercorr;
 575                 enerd->term[F_PRES] += prescorr;
 576                 enerd->term[F_DVDL] += dvdlcorr;
 577
 578                 /* If the compiler doesn't optimize this check away
 579                  * we catch the NAN energies. With tables extreme negative
 580                  * energies might occur close to r=0.
 581                  */
 582                 epot = enerd->term[F_EPOT];
 583                 if (epot != epot || epot*beta < bU_neg_limit)
 584                 {
 585                     if (debug)
 586                     {
 587                         fprintf(debug,"\n  time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n",t,step,epot);
 588                     }
 589                     embU = 0;
 590                 }
 591                 else
 592                 {
 593                     embU = exp(-beta*epot);
 594                     sum_embU += embU;
 595                     /* Determine the weighted energy contributions of each energy group */
 596                     e = 0;
 597                     sum_UgembU[e++] += epot*embU;
 598                     if (fr->bBHAM)
 599                     {
 600                         for(i=0; i<ngid; i++)
 601                         {
 602                             sum_UgembU[e++] +=
 603                                 (enerd->grpp.ener[egBHAMSR][GID(i,gid_tp,ngid)] +
 604                                  enerd->grpp.ener[egBHAMLR][GID(i,gid_tp,ngid)])*embU;
 605                         }
 606                     }
 607                     else
 608                     {
 609                         for(i=0; i<ngid; i++)
 610                         {
 611                             sum_UgembU[e++] +=
 612                                 (enerd->grpp.ener[egLJSR][GID(i,gid_tp,ngid)] +
 613                                  enerd->grpp.ener[egLJLR][GID(i,gid_tp,ngid)])*embU;
 614                         }
 615                     }
 616                     if (bDispCorr)
 617                     {
 618                         sum_UgembU[e++] += enerd->term[F_DISPCORR]*embU;
 619                     }
 620                     if (bCharge)
 621                     {
 622                         for(i=0; i<ngid; i++)
 623                         {
 624                             sum_UgembU[e++] +=
 625                                 (enerd->grpp.ener[egCOULSR][GID(i,gid_tp,ngid)] +
 626                                  enerd->grpp.ener[egCOULLR][GID(i,gid_tp,ngid)])*embU;
 627                         }
 628                         if (bRFExcl)
 629                         {
 630                             sum_UgembU[e++] += enerd->term[F_RF_EXCL]*embU;
 631                         }
 632                         if (EEL_FULL(fr->eeltype))
 633                         {
 634                             sum_UgembU[e++] += enerd->term[F_COUL_RECIP]*embU;
 635                         }
 636                     }
 637                 }
 638
 639                 if (embU == 0 || beta*epot > bU_bin_limit)
 640                 {
 641                     bin[0]++;
 642                 }
 643                 else
 644                 {
 645                     i = (int)((bU_logV_bin_limit
 646                                - (beta*epot - logV + refvolshift))*invbinw
 647                               + 0.5);
 648                     if (i < 0)
 649                     {
 650                         i = 0;
 651                     }
 652                     if (i >= nbin)
 653                     {
 654                         realloc_bins(&bin,&nbin,i+10);
 655                     }
 656                     bin[i]++;
 657                 }
 658
 659                 if (debug)
 660                 {
 661                     fprintf(debug,"TPI %7d %12.5e %12.5f %12.5f %12.5f\n",
 662                             step,epot,x_tp[XX],x_tp[YY],x_tp[ZZ]);
 663                 }
 664
 665                 if (dump_pdb && epot <= dump_ener)
 666                 {
 667                     sprintf(str,"t%g_step%d.pdb",t,step);
 668                     sprintf(str2,"t: %f step %d ener: %f",t,step,epot);
 669                     write_sto_conf_mtop(str,str2,top_global,state->x,state->v,
 670                                         inputrec->ePBC,state->box);
 671                 }
 672             }
 673         }
 674
 675         if (PAR(cr))
 676         {
 677             /* When running in parallel sum the energies over the processes */
 678             gmx_sumd(1,    &sum_embU, cr);
 679             gmx_sumd(nener,sum_UgembU,cr);
 680         }
 681
 682         frame++;
 683         V_all += V;
 684         VembU_all += V*sum_embU/nsteps;
 685
 686         if (fp_tpi)
 687         {
 688             if (bVerbose || frame%10==0 || frame<10)
 689             {
 690                 fprintf(stderr,"mu %10.3e <mu> %10.3e\n",
 691                         -log(sum_embU/nsteps)/beta,-log(VembU_all/V_all)/beta);
 692             }
 693
 694             fprintf(fp_tpi,"%10.3f %12.5e %12.5e %12.5e %12.5e",
 695                     t,
 696                     VembU_all==0 ? 20/beta : -log(VembU_all/V_all)/beta,
 697                     sum_embU==0  ? 20/beta : -log(sum_embU/nsteps)/beta,
 698                     sum_embU/nsteps,V);
 699             for(e=0; e<nener; e++)
 700             {
 701                 fprintf(fp_tpi," %12.5e",sum_UgembU[e]/nsteps);
 702             }
 703             fprintf(fp_tpi,"\n");
 704             fflush(fp_tpi);
 705         }
 706
 707         bNotLastFrame = read_next_frame(oenv, status,&rerun_fr);
 708     } /* End of the loop  */
 709   runtime_end(runtime);
 710
 711   close_trj(status);
 712
 713   if (fp_tpi)
 714     gmx_fio_fclose(fp_tpi);
 715
 716   if (fplog) {
 717     fprintf(fplog,"\n");
 718     fprintf(fplog,"  <V>  = %12.5e nm^3\n",V_all/frame);
 719     fprintf(fplog,"  <mu> = %12.5e kJ/mol\n",-log(VembU_all/V_all)/beta);
 720   }
 721
 722   /* Write the Boltzmann factor histogram */
 723   if (PAR(cr)) {
 724     /* When running in parallel sum the bins over the processes */
 725     i = nbin;
 726     global_max(cr,&i);
 727     realloc_bins(&bin,&nbin,i);
 728     gmx_sumd(nbin,bin,cr);
 729   }
 730   fp_tpi = xvgropen(opt2fn("-tpid",nfile,fnm),
 731                     "TPI energy distribution",
 732                     "\\betaU - log(V/<V>)","count",oenv);
 733   sprintf(str,"number \\betaU > %g: %9.3e",bU_bin_limit,bin[0]);
 734   xvgr_subtitle(fp_tpi,str,oenv);
 735   xvgr_legend(fp_tpi,2,(char **)tpid_leg,oenv);
 736   for(i=nbin-1; i>0; i--) {
 737     bUlogV = -i/invbinw + bU_logV_bin_limit - refvolshift + log(V_all/frame);
 738     fprintf(fp_tpi,"%6.2f %10d %12.5e\n",
 739             bUlogV,
 740             (int)(bin[i]+0.5),
 741             bin[i]*exp(-bUlogV)*V_all/VembU_all);
 742   }
 743   gmx_fio_fclose(fp_tpi);
 744   sfree(bin);
 745
 746   sfree(sum_UgembU);
 747
 748   runtime->nsteps_done = frame*inputrec->nsteps;
 749
 750   return 0;
 751 }