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 #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"
  85 #else
  86 #include "gmx_sse2_single.h"
  87 #endif
  88 #endif
  89
  90
  91 static void global_max(t_commrec *cr,int *n)
  92 {
  93   int *sum,i;
  94
  95   snew(sum,cr->nnodes);
  96   sum[cr->nodeid] = *n;
  97   gmx_sumi(cr->nnodes,sum,cr);
  98   for(i=0; i<cr->nnodes; i++)
  99     *n = max(*n,sum[i]);
 100
 101   sfree(sum);
 102 }
 103
 104 static void realloc_bins(double **bin,int *nbin,int nbin_new)
 105 {
 106   int i;
 107
 108   if (nbin_new != *nbin) {
 109     srenew(*bin,nbin_new);
 110     for(i=*nbin; i<nbin_new; i++)
 111       (*bin)[i] = 0;
 112     *nbin = nbin_new;
 113   }
 114 }
 115
 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,
 119               int nstglobalcomm,
 120               gmx_vsite_t *vsite,gmx_constr_t constr,
 121               int stepout,
 122               t_inputrec *inputrec,
 123               gmx_mtop_t *top_global,t_fcdata *fcd,
 124               t_state *state,
 125               t_mdatoms *mdatoms,
 126               t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 127               gmx_edsam_t ed,
 128               t_forcerec *fr,
 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,
 133               unsigned long Flags,
 134               gmx_runtime_t *runtime)
 135 {
 136   const char *TPI="Test Particle Insertion";
 137   gmx_localtop_t *top;
 138   gmx_groups_t *groups;
 139   gmx_enerdata_t *enerd;
 140   rvec   *f;
 141   real   lambda,t,temp,beta,drmax,epot;
 142   double embU,sum_embU,*sum_UgembU,V,V_all,VembU_all;
 143   t_trxstatus   *status;
 144   t_trxframe rerun_fr;
 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;
 148   rvec   *x_mol;
 149   rvec   mu_tot,x_init,dx,x_tp;
 150   int    nnodes,frame,nsteps,step;
 151   int    i,start,end;
 152   gmx_rng_t tpi_rand;
 153   FILE   *fp_tpi=NULL;
 154   char   *ptr,*dump_pdb,**leg,str[STRLEN],str2[STRLEN];
 155   double dbl,dump_ener;
 156   gmx_bool   bCavity;
 157   int    nat_cavity=0,d;
 158   real   *mass_cavity=NULL,mass_tot;
 159   int    nbin;
 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"};
 164
 165   /* Since there is no upper limit to the insertion energies,
 166    * we need to set an upper limit for the distribution output.
 167    */
 168   real bU_bin_limit      = 50;
 169   real bU_logV_bin_limit = bU_bin_limit + 10;
 170
 171   nnodes = cr->nnodes;
 172
 173   top = gmx_mtop_generate_local_top(top_global,inputrec);
 174
 175   groups = &top_global->groups;
 176
 177   bCavity = (inputrec->eI == eiTPIC);
 178   if (bCavity) {
 179     ptr = getenv("GMX_TPIC_MASSES");
 180     if (ptr == NULL) {
 181       nat_cavity = 1;
 182     } else {
 183       /* Read (multiple) masses from env var GMX_TPIC_MASSES,
 184        * The center of mass of the last atoms is then used for TPIC.
 185        */
 186       nat_cavity = 0;
 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]);
 192         nat_cavity++;
 193         ptr += i;
 194       }
 195       if (nat_cavity == 0)
 196         gmx_fatal(FARGS,"Found %d masses in GMX_TPIC_MASSES",nat_cavity);
 197     }
 198   }
 199
 200   /*
 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 */
 204   fr->ePBC = epbcXYZ;
 205   /* Determine the temperature for the Boltzmann weighting */
 206   temp = inputrec->opts.ref_t[0];
 207   if (fplog) {
 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");
 212       }
 213     }
 214     fprintf(fplog,
 215             "\n  The temperature for test particle insertion is %.3f K\n\n",
 216             temp);
 217   }
 218   beta = 1.0/(BOLTZ*temp);
 219
 220   /* Number of insertions per frame */
 221   nsteps = inputrec->nsteps;
 222
 223   /* Use the same neighborlist with more insertions points
 224    * in a sphere of radius drmax around the initial point
 225    */
 226   /* This should be a proper mdp parameter */
 227   drmax = inputrec->rtpi;
 228
 229   /* An environment variable can be set to dump all configurations
 230    * to pdb with an insertion energy <= this value.
 231    */
 232   dump_pdb = getenv("GMX_TPI_DUMP");
 233   dump_ener = 0;
 234   if (dump_pdb)
 235     sscanf(dump_pdb,"%lf",&dump_ener);
 236
 237   atoms2md(top_global,inputrec,0,NULL,0,top_global->natoms,mdatoms);
 238   update_mdatoms(mdatoms,inputrec->init_lambda);
 239
 240   snew(enerd,1);
 241   init_enerdata(groups->grps[egcENER].nr,inputrec->n_flambda,enerd);
 242   snew(f,top_global->natoms);
 243
 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);
 249
 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];
 254   if (debug)
 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);
 261
 262   bDispCorr = (inputrec->eDispCorr != edispcNO);
 263   bCharge = FALSE;
 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));
 270   }
 271   bRFExcl = (bCharge && EEL_RF(fr->eeltype) && fr->eeltype!=eelRF_NEC);
 272
 273   calc_cgcm(fplog,cg_tp,cg_tp+1,&(top->cgs),state->x,fr->cg_cm);
 274   if (bCavity) {
 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");
 278     }
 279   } else {
 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]);
 283   }
 284
 285   if (fplog) {
 286     fprintf(fplog,"\nWill insert %d atoms %s partial charges\n",
 287             a_tp1-a_tp0,bCharge ? "with" : "without");
 288
 289     fprintf(fplog,"\nWill insert %d times in each frame of %s\n",
 290             nsteps,opt2fn("-rerun",nfile,fnm));
 291   }
 292
 293     if (!bCavity)
 294     {
 295         if (inputrec->nstlist > 1)
 296         {
 297             if (drmax==0 && a_tp1-a_tp0==1)
 298             {
 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);
 300             }
 301             if (fplog)
 302             {
 303                 fprintf(fplog,"Will use the same neighborlist for %d insertions in a sphere of radius %f\n",inputrec->nstlist,drmax);
 304             }
 305         }
 306     }
 307     else
 308     {
 309         if (fplog)
 310         {
 311             fprintf(fplog,"Will insert randomly in a sphere of radius %f around the center of the cavity\n",drmax);
 312         }
 313     }
 314
 315   ngid = groups->grps[egcENER].nr;
 316   gid_tp = GET_CGINFO_GID(fr->cginfo[cg_tp]);
 317   nener = 1 + ngid;
 318   if (bDispCorr)
 319     nener += 1;
 320   if (bCharge) {
 321     nener += ngid;
 322     if (bRFExcl)
 323       nener += 1;
 324     if (EEL_FULL(fr->eeltype))
 325       nener += 1;
 326   }
 327   snew(sum_UgembU,nener);
 328
 329   /* Initialize random generator */
 330   tpi_rand = gmx_rng_init(inputrec->ld_seed);
 331
 332   if (MASTER(cr)) {
 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);
 337     snew(leg,4+nener);
 338     e = 0;
 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);
 345     sprintf(str,"f. V");
 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);
 353     }
 354     if (bDispCorr) {
 355       sprintf(str,"f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
 356       leg[e++] = strdup(str);
 357     }
 358     if (bCharge) {
 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);
 363       }
 364       if (bRFExcl) {
 365         sprintf(str,"f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
 366         leg[e++] = strdup(str);
 367       }
 368       if (EEL_FULL(fr->eeltype)) {
 369         sprintf(str,"f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
 370         leg[e++] = strdup(str);
 371       }
 372     }
 373     xvgr_legend(fp_tpi,4+nener,(const char**)leg,oenv);
 374     for(i=0; i<4+nener; i++)
 375       sfree(leg[i]);
 376     sfree(leg);
 377   }
 378   clear_rvec(x_init);
 379   V_all = 0;
 380   VembU_all = 0;
 381
 382   invbinw = 10;
 383   nbin = 10;
 384   snew(bin,nbin);
 385
 386   bNotLastFrame = read_first_frame(oenv,&status,opt2fn("-rerun",nfile,fnm),
 387                                    &rerun_fr,TRX_NEED_X);
 388   frame = 0;
 389
 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);
 397
 398   refvolshift = log(det(rerun_fr.box));
 399
 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();
 403 #endif
 404
 405     while (bNotLastFrame)
 406     {
 407         lambda = rerun_fr.lambda;
 408         t = rerun_fr.time;
 409
 410         sum_embU = 0;
 411         for(e=0; e<nener; e++)
 412         {
 413             sum_UgembU[e] = 0;
 414         }
 415
 416         /* Copy the coordinates from the input trajectory */
 417         for(i=0; i<rerun_fr.natoms; i++)
 418         {
 419             copy_rvec(rerun_fr.x[i],state->x[i]);
 420         }
 421
 422         V = det(rerun_fr.box);
 423         logV = log(V);
 424
 425         bStateChanged = TRUE;
 426         bNS = TRUE;
 427         for(step=0; step<nsteps; step++)
 428         {
 429             /* In parallel all nodes generate all random configurations.
 430              * In that way the result is identical to a single cpu tpi run.
 431              */
 432             if (!bCavity)
 433             {
 434                 /* Random insertion in the whole volume */
 435                 bNS = (step % inputrec->nstlist == 0);
 436                 if (bNS)
 437                 {
 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];
 442                 }
 443                 if (inputrec->nstlist == 1)
 444                 {
 445                     copy_rvec(x_init,x_tp);
 446                 }
 447                 else
 448                 {
 449                     /* Generate coordinates within |dx|=drmax of x_init */
 450                     do
 451                     {
 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;
 455                     }
 456                     while (norm2(dx) > drmax*drmax);
 457                     rvec_add(x_init,dx,x_tp);
 458                 }
 459             }
 460             else
 461             {
 462                 /* Random insertion around a cavity location
 463                  * given by the last coordinate of the trajectory.
 464                  */
 465                 if (step == 0)
 466                 {
 467                     if (nat_cavity == 1)
 468                     {
 469                         /* Copy the location of the cavity */
 470                         copy_rvec(rerun_fr.x[rerun_fr.natoms-1],x_init);
 471                     }
 472                     else
 473                     {
 474                         /* Determine the center of mass of the last molecule */
 475                         clear_rvec(x_init);
 476                         mass_tot = 0;
 477                         for(i=0; i<nat_cavity; i++)
 478                         {
 479                             for(d=0; d<DIM; d++)
 480                             {
 481                                 x_init[d] +=
 482                                     mass_cavity[i]*rerun_fr.x[rerun_fr.natoms-nat_cavity+i][d];
 483                             }
 484                             mass_tot += mass_cavity[i];
 485                         }
 486                         for(d=0; d<DIM; d++)
 487                         {
 488                             x_init[d] /= mass_tot;
 489                         }
 490                     }
 491                 }
 492                 /* Generate coordinates within |dx|=drmax of x_init */
 493                 do
 494                 {
 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;
 498                 }
 499                 while (norm2(dx) > drmax*drmax);
 500                 rvec_add(x_init,dx,x_tp);
 501             }
 502
 503             if (a_tp1 - a_tp0 == 1)
 504             {
 505                 /* Insert a single atom, just copy the insertion location */
 506         copy_rvec(x_tp,state->x[a_tp0]);
 507             }
 508             else
 509             {
 510                 /* Copy the coordinates from the top file */
 511                 for(i=a_tp0; i<a_tp1; i++)
 512                 {
 513                     copy_rvec(x_mol[i-a_tp0],state->x[i]);
 514                 }
 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++)
 522                 {
 523                     rvec_inc(state->x[i],x_tp);
 524                 }
 525             }
 526
 527             /* Check if this insertion belongs to this node */
 528             bOurStep = TRUE;
 529             if (PAR(cr))
 530             {
 531                 switch (inputrec->eI)
 532                 {
 533                 case eiTPI:
 534                     bOurStep = ((step / inputrec->nstlist) % nnodes == cr->nodeid);
 535                     break;
 536                 case eiTPIC:
 537                     bOurStep = (step % nnodes == cr->nodeid);
 538                     break;
 539                 default:
 540                     gmx_fatal(FARGS,"Unknown integrator %s",ei_names[inputrec->eI]);
 541                 }
 542             }
 543             if (bOurStep)
 544             {
 545                 /* Clear some matrix variables  */
 546                 clear_mat(force_vir);
 547                 clear_mat(shake_vir);
 548                 clear_mat(vir);
 549                 clear_mat(pres);
 550
 551                 /* Set the charge group center of mass of the test particle */
 552                 copy_rvec(x_init,fr->cg_cm[top->cgs.nr-1]);
 553
 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
 559                  * out of the box.
 560                  *
 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.
 564                  */
 565                 /* Make do_force do a single node force calculation */
 566                 cr->nnodes = 1;
 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));
 575                 cr->nnodes = nnodes;
 576                 bStateChanged = FALSE;
 577                 bNS = FALSE;
 578
 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;
 587
 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())
 593                 {
 594                     if (debug)
 595                     {
 596                         fprintf(debug,"Found an SSE overflow, assuming the energy is out of bounds\n");
 597                     }
 598                     bEnergyOutOfBounds = TRUE;
 599                 }
 600 #endif
 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.
 606                  */
 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.
 614                  */
 615                 if (epot != epot || epot > GMX_REAL_MAX)
 616                 {
 617                     bEnergyOutOfBounds = TRUE;
 618                 }
 619                 if (bEnergyOutOfBounds)
 620                 {
 621                     if (debug)
 622                     {
 623                         fprintf(debug,"\n  time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n",t,step,epot);
 624                     }
 625                     embU = 0;
 626                 }
 627                 else
 628                 {
 629                     embU = exp(-beta*epot);
 630                     sum_embU += embU;
 631                     /* Determine the weighted energy contributions of each energy group */
 632                     e = 0;
 633                     sum_UgembU[e++] += epot*embU;
 634                     if (fr->bBHAM)
 635                     {
 636                         for(i=0; i<ngid; i++)
 637                         {
 638                             sum_UgembU[e++] +=
 639                                 (enerd->grpp.ener[egBHAMSR][GID(i,gid_tp,ngid)] +
 640                                  enerd->grpp.ener[egBHAMLR][GID(i,gid_tp,ngid)])*embU;
 641                         }
 642                     }
 643                     else
 644                     {
 645                         for(i=0; i<ngid; i++)
 646                         {
 647                             sum_UgembU[e++] +=
 648                                 (enerd->grpp.ener[egLJSR][GID(i,gid_tp,ngid)] +
 649                                  enerd->grpp.ener[egLJLR][GID(i,gid_tp,ngid)])*embU;
 650                         }
 651                     }
 652                     if (bDispCorr)
 653                     {
 654                         sum_UgembU[e++] += enerd->term[F_DISPCORR]*embU;
 655                     }
 656                     if (bCharge)
 657                     {
 658                         for(i=0; i<ngid; i++)
 659                         {
 660                             sum_UgembU[e++] +=
 661                                 (enerd->grpp.ener[egCOULSR][GID(i,gid_tp,ngid)] +
 662                                  enerd->grpp.ener[egCOULLR][GID(i,gid_tp,ngid)])*embU;
 663                         }
 664                         if (bRFExcl)
 665                         {
 666                             sum_UgembU[e++] += enerd->term[F_RF_EXCL]*embU;
 667                         }
 668                         if (EEL_FULL(fr->eeltype))
 669                         {
 670                             sum_UgembU[e++] += enerd->term[F_COUL_RECIP]*embU;
 671                         }
 672                     }
 673                 }
 674
 675                 if (embU == 0 || beta*epot > bU_bin_limit)
 676                 {
 677                     bin[0]++;
 678                 }
 679                 else
 680                 {
 681                     i = (int)((bU_logV_bin_limit
 682                                - (beta*epot - logV + refvolshift))*invbinw
 683                               + 0.5);
 684                     if (i < 0)
 685                     {
 686                         i = 0;
 687                     }
 688                     if (i >= nbin)
 689                     {
 690                         realloc_bins(&bin,&nbin,i+10);
 691                     }
 692                     bin[i]++;
 693                 }
 694
 695                 if (debug)
 696                 {
 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]);
 699                 }
 700
 701                 if (dump_pdb && epot <= dump_ener)
 702                 {
 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);
 707                 }
 708             }
 709         }
 710
 711         if (PAR(cr))
 712         {
 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);
 716         }
 717
 718         frame++;
 719         V_all += V;
 720         VembU_all += V*sum_embU/nsteps;
 721
 722         if (fp_tpi)
 723         {
 724             if (bVerbose || frame%10==0 || frame<10)
 725             {
 726                 fprintf(stderr,"mu %10.3e <mu> %10.3e\n",
 727                         -log(sum_embU/nsteps)/beta,-log(VembU_all/V_all)/beta);
 728             }
 729
 730             fprintf(fp_tpi,"%10.3f %12.5e %12.5e %12.5e %12.5e",
 731                     t,
 732                     VembU_all==0 ? 20/beta : -log(VembU_all/V_all)/beta,
 733                     sum_embU==0  ? 20/beta : -log(sum_embU/nsteps)/beta,
 734                     sum_embU/nsteps,V);
 735             for(e=0; e<nener; e++)
 736             {
 737                 fprintf(fp_tpi," %12.5e",sum_UgembU[e]/nsteps);
 738             }
 739             fprintf(fp_tpi,"\n");
 740             fflush(fp_tpi);
 741         }
 742
 743         bNotLastFrame = read_next_frame(oenv, status,&rerun_fr);
 744     } /* End of the loop  */
 745     runtime_end(runtime);
 746
 747     close_trj(status);
 748
 749     if (fp_tpi != NULL)
 750     {
 751         gmx_fio_fclose(fp_tpi);
 752     }
 753
 754     if (fplog != NULL)
 755     {
 756         fprintf(fplog,"\n");
 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);
 759     }
 760
 761     /* Write the Boltzmann factor histogram */
 762     if (PAR(cr))
 763     {
 764         /* When running in parallel sum the bins over the processes */
 765         i = nbin;
 766         global_max(cr,&i);
 767         realloc_bins(&bin,&nbin,i);
 768         gmx_sumd(nbin,bin,cr);
 769     }
 770     if (MASTER(cr))
 771     {
 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--)
 779         {
 780             bUlogV = -i/invbinw + bU_logV_bin_limit - refvolshift + log(V_all/frame);
 781             fprintf(fp_tpi,"%6.2f %10d %12.5e\n",
 782                     bUlogV,
 783                     (int)(bin[i]+0.5),
 784                     bin[i]*exp(-bUlogV)*V_all/VembU_all);
 785         }
 786         gmx_fio_fclose(fp_tpi);
 787     }
 788     sfree(bin);
 789
 790     sfree(sum_UgembU);
 791
 792     runtime->nsteps_done = frame*inputrec->nsteps;
 793
 794     return 0;
 795 }