src/gromacs/mdlib/force.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.2.0
  11  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  12  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
  15
  16  * This program is free software; you can redistribute it and/or
  17  * modify it under the terms of the GNU General Public License
  18  * as published by the Free Software Foundation; either version 2
  19  * of the License, or (at your option) any later version.
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  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <math.h>
  41 #include <string.h>
  42 #include "sysstuff.h"
  43 #include "typedefs.h"
  44 #include "macros.h"
  45 #include "smalloc.h"
  46 #include "macros.h"
  47 #include "physics.h"
  48 #include "force.h"
  49 #include "nonbonded.h"
  50 #include "names.h"
  51 #include "network.h"
  52 #include "pbc.h"
  53 #include "ns.h"
  54 #include "nrnb.h"
  55 #include "bondf.h"
  56 #include "mshift.h"
  57 #include "txtdump.h"
  58 #include "coulomb.h"
  59 #include "pme.h"
  60 #include "mdrun.h"
  61 #include "domdec.h"
  62 #include "partdec.h"
  63 #include "qmmm.h"
  64
  65
  66 void ns(FILE *fp,
  67         t_forcerec *fr,
  68         rvec       x[],
  69         matrix     box,
  70         gmx_groups_t *groups,
  71         t_grpopts  *opts,
  72         gmx_localtop_t *top,
  73         t_mdatoms  *md,
  74         t_commrec  *cr,
  75         t_nrnb     *nrnb,
  76         real       lambda,
  77         real       *dvdlambda,
  78         gmx_grppairener_t *grppener,
  79         gmx_bool       bFillGrid,
  80         gmx_bool       bDoLongRange,
  81         gmx_bool       bDoForces,
  82         rvec       *f)
  83 {
  84   char   *ptr;
  85   int    nsearch;
  86
  87
  88   if (!fr->ns.nblist_initialized)
  89   {
  90       init_neighbor_list(fp, fr, md->homenr);
  91   }
  92
  93   if (fr->bTwinRange)
  94     fr->nlr=0;
  95
  96     nsearch = search_neighbours(fp,fr,x,box,top,groups,cr,nrnb,md,
  97                                 lambda,dvdlambda,grppener,
  98                                 bFillGrid,bDoLongRange,
  99                                 bDoForces,f);
 100   if (debug)
 101     fprintf(debug,"nsearch = %d\n",nsearch);
 102
 103   /* Check whether we have to do dynamic load balancing */
 104   /*if ((nsb->nstDlb > 0) && (mod(step,nsb->nstDlb) == 0))
 105     count_nb(cr,nsb,&(top->blocks[ebCGS]),nns,fr->nlr,
 106     &(top->idef),opts->ngener);
 107   */
 108   if (fr->ns.dump_nl > 0)
 109     dump_nblist(fp,cr,fr,fr->ns.dump_nl);
 110 }
 111
 112 void do_force_lowlevel(FILE       *fplog,   gmx_large_int_t step,
 113                        t_forcerec *fr,      t_inputrec *ir,
 114                        t_idef     *idef,    t_commrec  *cr,
 115                        t_nrnb     *nrnb,    gmx_wallcycle_t wcycle,
 116                        t_mdatoms  *md,
 117                        t_grpopts  *opts,
 118                        rvec       x[],      history_t  *hist,
 119                        rvec       f[],
 120                        gmx_enerdata_t *enerd,
 121                        t_fcdata   *fcd,
 122                        gmx_mtop_t     *mtop,
 123                        gmx_localtop_t *top,
 124                        gmx_genborn_t *born,
 125                        t_atomtypes *atype,
 126                        gmx_bool       bBornRadii,
 127                        matrix     box,
 128                        real       lambda,
 129                        t_graph    *graph,
 130                        t_blocka   *excl,
 131                        rvec       mu_tot[],
 132                        int        flags,
 133                        float      *cycles_pme)
 134 {
 135     int     i,status;
 136     int     donb_flags;
 137     gmx_bool    bDoEpot,bSepDVDL,bSB;
 138     int     pme_flags;
 139     matrix  boxs;
 140     rvec    box_size;
 141     real    dvdlambda,Vsr,Vlr,Vcorr=0,vdip,vcharge;
 142     t_pbc   pbc;
 143     real    dvdgb;
 144     char    buf[22];
 145     gmx_enerdata_t ed_lam;
 146     double  lam_i;
 147     real    dvdl_dum;
 148
 149 #ifdef GMX_MPI
 150     double  t0=0.0,t1,t2,t3; /* time measurement for coarse load balancing */
 151 #endif
 152
 153 #define PRINT_SEPDVDL(s,v,dvdl) if (bSepDVDL) fprintf(fplog,sepdvdlformat,s,v,dvdl);
 154
 155
 156     set_pbc(&pbc,fr->ePBC,box);
 157
 158     /* Reset box */
 159     for(i=0; (i<DIM); i++)
 160     {
 161         box_size[i]=box[i][i];
 162     }
 163
 164     bSepDVDL=(fr->bSepDVDL && do_per_step(step,ir->nstlog));
 165     debug_gmx();
 166
 167     /* do QMMM first if requested */
 168     if(fr->bQMMM)
 169     {
 170         enerd->term[F_EQM] = calculate_QMMM(cr,x,f,fr,md);
 171     }
 172
 173     if (bSepDVDL)
 174     {
 175         fprintf(fplog,"Step %s: non-bonded V and dVdl for node %d:\n",
 176                 gmx_step_str(step,buf),cr->nodeid);
 177     }
 178
 179     /* Call the short range functions all in one go. */
 180
 181     dvdlambda = 0;
 182
 183 #ifdef GMX_MPI
 184     /*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
 185 #define TAKETIME FALSE
 186     if (TAKETIME)
 187     {
 188         MPI_Barrier(cr->mpi_comm_mygroup);
 189         t0=MPI_Wtime();
 190     }
 191 #endif
 192
 193     if (ir->nwall)
 194     {
 195         dvdlambda = do_walls(ir,fr,box,md,x,f,lambda,
 196                              enerd->grpp.ener[egLJSR],nrnb);
 197         PRINT_SEPDVDL("Walls",0.0,dvdlambda);
 198         enerd->dvdl_lin += dvdlambda;
 199     }
 200
 201         /* If doing GB, reset dvda and calculate the Born radii */
 202         if (ir->implicit_solvent)
 203         {
 204                 /* wallcycle_start(wcycle,ewcGB); */
 205
 206                 for(i=0;i<born->nr;i++)
 207                 {
 208                         fr->dvda[i]=0;
 209                 }
 210
 211                 if(bBornRadii)
 212                 {
 213                         calc_gb_rad(cr,fr,ir,top,atype,x,&(fr->gblist),born,md,nrnb);
 214                 }
 215
 216                 /* wallcycle_stop(wcycle, ewcGB); */
 217         }
 218
 219     where();
 220     donb_flags = 0;
 221     if (flags & GMX_FORCE_FORCES)
 222     {
 223         donb_flags |= GMX_DONB_FORCES;
 224     }
 225     do_nonbonded(cr,fr,x,f,md,excl,
 226                  fr->bBHAM ?
 227                  enerd->grpp.ener[egBHAMSR] :
 228                  enerd->grpp.ener[egLJSR],
 229                  enerd->grpp.ener[egCOULSR],
 230                                  enerd->grpp.ener[egGB],box_size,nrnb,
 231                  lambda,&dvdlambda,-1,-1,donb_flags);
 232     /* If we do foreign lambda and we have soft-core interactions
 233      * we have to recalculate the (non-linear) energies contributions.
 234      */
 235     if (ir->n_flambda > 0 && (flags & GMX_FORCE_DHDL) && ir->sc_alpha != 0)
 236     {
 237         init_enerdata(mtop->groups.grps[egcENER].nr,ir->n_flambda,&ed_lam);
 238
 239         for(i=0; i<enerd->n_lambda; i++)
 240         {
 241             lam_i = (i==0 ? lambda : ir->flambda[i-1]);
 242             dvdl_dum = 0;
 243             reset_enerdata(&ir->opts,fr,TRUE,&ed_lam,FALSE);
 244             do_nonbonded(cr,fr,x,f,md,excl,
 245                          fr->bBHAM ?
 246                          ed_lam.grpp.ener[egBHAMSR] :
 247                          ed_lam.grpp.ener[egLJSR],
 248                          ed_lam.grpp.ener[egCOULSR],
 249                          enerd->grpp.ener[egGB], box_size,nrnb,
 250                          lam_i,&dvdl_dum,-1,-1,
 251                          GMX_DONB_FOREIGNLAMBDA);
 252             sum_epot(&ir->opts,&ed_lam);
 253             enerd->enerpart_lambda[i] += ed_lam.term[F_EPOT];
 254         }
 255         destroy_enerdata(&ed_lam);
 256     }
 257     where();
 258
 259         /* If we are doing GB, calculate bonded forces and apply corrections
 260          * to the solvation forces */
 261         if (ir->implicit_solvent)  {
 262                 calc_gb_forces(cr,md,born,top,atype,x,f,fr,idef,
 263                        ir->gb_algorithm,ir->sa_algorithm,nrnb,bBornRadii,&pbc,graph,enerd);
 264     }
 265
 266 #ifdef GMX_MPI
 267     if (TAKETIME)
 268     {
 269         t1=MPI_Wtime();
 270         fr->t_fnbf += t1-t0;
 271     }
 272 #endif
 273
 274     if (ir->sc_alpha != 0)
 275     {
 276         enerd->dvdl_nonlin += dvdlambda;
 277     }
 278     else
 279     {
 280         enerd->dvdl_lin    += dvdlambda;
 281     }
 282     Vsr = 0;
 283     if (bSepDVDL)
 284     {
 285         for(i=0; i<enerd->grpp.nener; i++)
 286         {
 287             Vsr +=
 288                 (fr->bBHAM ?
 289                  enerd->grpp.ener[egBHAMSR][i] :
 290                  enerd->grpp.ener[egLJSR][i])
 291                 + enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
 292         }
 293     }
 294     PRINT_SEPDVDL("VdW and Coulomb SR particle-p.",Vsr,dvdlambda);
 295     debug_gmx();
 296
 297     if (debug)
 298     {
 299         pr_rvecs(debug,0,"fshift after SR",fr->fshift,SHIFTS);
 300     }
 301
 302     /* Shift the coordinates. Must be done before bonded forces and PPPM,
 303      * but is also necessary for SHAKE and update, therefore it can NOT
 304      * go when no bonded forces have to be evaluated.
 305      */
 306
 307     /* Here sometimes we would not need to shift with NBFonly,
 308      * but we do so anyhow for consistency of the returned coordinates.
 309      */
 310     if (graph)
 311     {
 312         shift_self(graph,box,x);
 313         if (TRICLINIC(box))
 314         {
 315             inc_nrnb(nrnb,eNR_SHIFTX,2*graph->nnodes);
 316         }
 317         else
 318         {
 319             inc_nrnb(nrnb,eNR_SHIFTX,graph->nnodes);
 320         }
 321     }
 322     /* Check whether we need to do bondeds or correct for exclusions */
 323     if (fr->bMolPBC &&
 324         ((flags & GMX_FORCE_BONDED)
 325          || EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype)))
 326     {
 327         /* Since all atoms are in the rectangular or triclinic unit-cell,
 328          * only single box vector shifts (2 in x) are required.
 329          */
 330         set_pbc_dd(&pbc,fr->ePBC,cr->dd,TRUE,box);
 331     }
 332     debug_gmx();
 333
 334     if (flags & GMX_FORCE_BONDED)
 335     {
 336         calc_bonds(fplog,cr->ms,
 337                    idef,x,hist,f,fr,&pbc,graph,enerd,nrnb,lambda,md,fcd,
 338                    DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL, atype, born,
 339                    fr->bSepDVDL && do_per_step(step,ir->nstlog),step);
 340
 341         /* Check if we have to determine energy differences
 342          * at foreign lambda's.
 343          */
 344         if (ir->n_flambda > 0 && (flags & GMX_FORCE_DHDL) &&
 345             idef->ilsort != ilsortNO_FE)
 346         {
 347             if (idef->ilsort != ilsortFE_SORTED)
 348             {
 349                 gmx_incons("The bonded interactions are not sorted for free energy");
 350             }
 351             init_enerdata(mtop->groups.grps[egcENER].nr,ir->n_flambda,&ed_lam);
 352
 353             for(i=0; i<enerd->n_lambda; i++)
 354             {
 355                 lam_i = (i==0 ? lambda : ir->flambda[i-1]);
 356                 dvdl_dum = 0;
 357                 reset_enerdata(&ir->opts,fr,TRUE,&ed_lam,FALSE);
 358                 calc_bonds_lambda(fplog,
 359                                   idef,x,fr,&pbc,graph,&ed_lam,nrnb,lam_i,md,
 360                                   fcd,
 361                                   DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
 362                 sum_epot(&ir->opts,&ed_lam);
 363                 enerd->enerpart_lambda[i] += ed_lam.term[F_EPOT];
 364             }
 365             destroy_enerdata(&ed_lam);
 366         }
 367         debug_gmx();
 368     }
 369
 370     where();
 371
 372     *cycles_pme = 0;
 373     if (EEL_FULL(fr->eeltype))
 374     {
 375         bSB = (ir->nwall == 2);
 376         if (bSB)
 377         {
 378             copy_mat(box,boxs);
 379             svmul(ir->wall_ewald_zfac,boxs[ZZ],boxs[ZZ]);
 380             box_size[ZZ] *= ir->wall_ewald_zfac;
 381         }
 382
 383         clear_mat(fr->vir_el_recip);
 384
 385         if (fr->bEwald)
 386         {
 387             if (fr->n_tpi == 0)
 388             {
 389                 dvdlambda = 0;
 390                 Vcorr = ewald_LRcorrection(fplog,md->start,md->start+md->homenr,
 391                                            cr,fr,
 392                                            md->chargeA,
 393                                            md->nChargePerturbed ? md->chargeB : NULL,
 394                                            excl,x,bSB ? boxs : box,mu_tot,
 395                                            ir->ewald_geometry,
 396                                            ir->epsilon_surface,
 397                                            lambda,&dvdlambda,&vdip,&vcharge);
 398                 PRINT_SEPDVDL("Ewald excl./charge/dip. corr.",Vcorr,dvdlambda);
 399                 enerd->dvdl_lin += dvdlambda;
 400             }
 401             else
 402             {
 403                 if (ir->ewald_geometry != eewg3D || ir->epsilon_surface != 0)
 404                 {
 405                     gmx_fatal(FARGS,"TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
 406                 }
 407                 /* The TPI molecule does not have exclusions with the rest
 408                  * of the system and no intra-molecular PME grid contributions
 409                  * will be calculated in gmx_pme_calc_energy.
 410                  */
 411                 Vcorr = 0;
 412             }
 413         }
 414
 415         dvdlambda = 0;
 416         status = 0;
 417         switch (fr->eeltype)
 418         {
 419         case eelPME:
 420         case eelPMESWITCH:
 421         case eelPMEUSER:
 422         case eelPMEUSERSWITCH:
 423         case eelP3M_AD:
 424             if (cr->duty & DUTY_PME)
 425             {
 426                 if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
 427                 {
 428                     pme_flags = GMX_PME_SPREAD_Q | GMX_PME_SOLVE;
 429                     if (flags & GMX_FORCE_FORCES)
 430                     {
 431                         pme_flags |= GMX_PME_CALC_F;
 432                     }
 433                     if (flags & GMX_FORCE_VIRIAL)
 434                     {
 435                         pme_flags |= GMX_PME_CALC_ENER_VIR;
 436                     }
 437                     if (fr->n_tpi > 0)
 438                     {
 439                         /* We don't calculate f, but we do want the potential */
 440                         pme_flags |= GMX_PME_CALC_POT;
 441                     }
 442                     wallcycle_start(wcycle,ewcPMEMESH);
 443                     status = gmx_pme_do(fr->pmedata,
 444                                         md->start,md->homenr - fr->n_tpi,
 445                                         x,fr->f_novirsum,
 446                                         md->chargeA,md->chargeB,
 447                                         bSB ? boxs : box,cr,
 448                                         DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
 449                                         DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
 450                                         nrnb,wcycle,
 451                                         fr->vir_el_recip,fr->ewaldcoeff,
 452                                         &Vlr,lambda,&dvdlambda,
 453                                         pme_flags);
 454                     *cycles_pme = wallcycle_stop(wcycle,ewcPMEMESH);
 455
 456                     /* We should try to do as little computation after
 457                      * this as possible, because parallel PME synchronizes
 458                      * the nodes, so we want all load imbalance of the rest
 459                      * of the force calculation to be before the PME call.
 460                      * DD load balancing is done on the whole time of
 461                      * the force call (without PME).
 462                      */
 463                 }
 464                 if (fr->n_tpi > 0)
 465                 {
 466                     /* Determine the PME grid energy of the test molecule
 467                      * with the PME grid potential of the other charges.
 468                      */
 469                     gmx_pme_calc_energy(fr->pmedata,fr->n_tpi,
 470                                         x + md->homenr - fr->n_tpi,
 471                                         md->chargeA + md->homenr - fr->n_tpi,
 472                                         &Vlr);
 473                 }
 474                 PRINT_SEPDVDL("PME mesh",Vlr,dvdlambda);
 475             }
 476             else
 477             {
 478                 /* Energies and virial are obtained later from the PME nodes */
 479                 /* but values have to be zeroed out here */
 480                 Vlr=0.0;
 481             }
 482             break;
 483         case eelEWALD:
 484             Vlr = do_ewald(fplog,FALSE,ir,x,fr->f_novirsum,
 485                            md->chargeA,md->chargeB,
 486                            box_size,cr,md->homenr,
 487                            fr->vir_el_recip,fr->ewaldcoeff,
 488                            lambda,&dvdlambda,fr->ewald_table);
 489             PRINT_SEPDVDL("Ewald long-range",Vlr,dvdlambda);
 490             break;
 491         default:
 492             Vlr = 0;
 493             gmx_fatal(FARGS,"No such electrostatics method implemented %s",
 494                       eel_names[fr->eeltype]);
 495         }
 496         if (status != 0)
 497         {
 498             gmx_fatal(FARGS,"Error %d in long range electrostatics routine %s",
 499                       status,EELTYPE(fr->eeltype));
 500                 }
 501         enerd->dvdl_lin += dvdlambda;
 502         enerd->term[F_COUL_RECIP] = Vlr + Vcorr;
 503         if (debug)
 504         {
 505             fprintf(debug,"Vlr = %g, Vcorr = %g, Vlr_corr = %g\n",
 506                     Vlr,Vcorr,enerd->term[F_COUL_RECIP]);
 507             pr_rvecs(debug,0,"vir_el_recip after corr",fr->vir_el_recip,DIM);
 508             pr_rvecs(debug,0,"fshift after LR Corrections",fr->fshift,SHIFTS);
 509         }
 510     }
 511     else
 512     {
 513         if (EEL_RF(fr->eeltype))
 514         {
 515             dvdlambda = 0;
 516
 517             if (fr->eeltype != eelRF_NEC)
 518             {
 519                 enerd->term[F_RF_EXCL] =
 520                     RF_excl_correction(fplog,fr,graph,md,excl,x,f,
 521                                        fr->fshift,&pbc,lambda,&dvdlambda);
 522             }
 523
 524             enerd->dvdl_lin += dvdlambda;
 525             PRINT_SEPDVDL("RF exclusion correction",
 526                           enerd->term[F_RF_EXCL],dvdlambda);
 527         }
 528     }
 529     where();
 530     debug_gmx();
 531
 532     if (debug)
 533     {
 534         print_nrnb(debug,nrnb);
 535     }
 536     debug_gmx();
 537
 538 #ifdef GMX_MPI
 539     if (TAKETIME)
 540     {
 541         t2=MPI_Wtime();
 542         MPI_Barrier(cr->mpi_comm_mygroup);
 543         t3=MPI_Wtime();
 544         fr->t_wait += t3-t2;
 545         if (fr->timesteps == 11)
 546         {
 547             fprintf(stderr,"* PP load balancing info: node %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
 548                     cr->nodeid, gmx_step_str(fr->timesteps,buf),
 549                     100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
 550                     (fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
 551         }
 552         fr->timesteps++;
 553     }
 554 #endif
 555
 556     if (debug)
 557     {
 558         pr_rvecs(debug,0,"fshift after bondeds",fr->fshift,SHIFTS);
 559     }
 560
 561 }
 562
 563 void init_enerdata(int ngener,int n_flambda,gmx_enerdata_t *enerd)
 564 {
 565     int i,n2;
 566
 567     for(i=0; i<F_NRE; i++)
 568     {
 569         enerd->term[i] = 0;
 570     }
 571
 572     n2=ngener*ngener;
 573     if (debug)
 574     {
 575         fprintf(debug,"Creating %d sized group matrix for energies\n",n2);
 576     }
 577     enerd->grpp.nener = n2;
 578     for(i=0; (i<egNR); i++)
 579     {
 580         snew(enerd->grpp.ener[i],n2);
 581     }
 582
 583     if (n_flambda)
 584     {
 585         enerd->n_lambda = 1 + n_flambda;
 586         snew(enerd->enerpart_lambda,enerd->n_lambda);
 587     }
 588     else
 589     {
 590         enerd->n_lambda = 0;
 591     }
 592 }
 593
 594 void destroy_enerdata(gmx_enerdata_t *enerd)
 595 {
 596     int i;
 597
 598     for(i=0; (i<egNR); i++)
 599     {
 600         sfree(enerd->grpp.ener[i]);
 601     }
 602
 603     if (enerd->n_lambda)
 604     {
 605         sfree(enerd->enerpart_lambda);
 606     }
 607 }
 608
 609 static real sum_v(int n,real v[])
 610 {
 611   real t;
 612   int  i;
 613
 614   t = 0.0;
 615   for(i=0; (i<n); i++)
 616     t = t + v[i];
 617
 618   return t;
 619 }
 620
 621 void sum_epot(t_grpopts *opts,gmx_enerdata_t *enerd)
 622 {
 623   gmx_grppairener_t *grpp;
 624   real *epot;
 625   int i;
 626
 627   grpp = &enerd->grpp;
 628   epot = enerd->term;
 629
 630   /* Accumulate energies */
 631   epot[F_COUL_SR]  = sum_v(grpp->nener,grpp->ener[egCOULSR]);
 632   epot[F_LJ]       = sum_v(grpp->nener,grpp->ener[egLJSR]);
 633   epot[F_LJ14]     = sum_v(grpp->nener,grpp->ener[egLJ14]);
 634   epot[F_COUL14]   = sum_v(grpp->nener,grpp->ener[egCOUL14]);
 635   epot[F_COUL_LR]  = sum_v(grpp->nener,grpp->ener[egCOULLR]);
 636   epot[F_LJ_LR]    = sum_v(grpp->nener,grpp->ener[egLJLR]);
 637   /* We have already added 1-2,1-3, and 1-4 terms to F_GBPOL */
 638   epot[F_GBPOL]   += sum_v(grpp->nener,grpp->ener[egGB]);
 639
 640 /* lattice part of LR doesnt belong to any group
 641  * and has been added earlier
 642  */
 643   epot[F_BHAM]     = sum_v(grpp->nener,grpp->ener[egBHAMSR]);
 644   epot[F_BHAM_LR]  = sum_v(grpp->nener,grpp->ener[egBHAMLR]);
 645
 646   epot[F_EPOT] = 0;
 647   for(i=0; (i<F_EPOT); i++)
 648     if (i != F_DISRESVIOL && i != F_ORIRESDEV && i != F_DIHRESVIOL)
 649       epot[F_EPOT] += epot[i];
 650 }
 651
 652 void sum_dhdl(gmx_enerdata_t *enerd,double lambda,t_inputrec *ir)
 653 {
 654     int i;
 655     double dlam,dhdl_lin;
 656
 657     enerd->term[F_DVDL] = enerd->dvdl_lin + enerd->dvdl_nonlin;
 658
 659     if (debug)
 660     {
 661         fprintf(debug,"dvdl: %f, non-linear %f + linear %f\n",
 662                 enerd->term[F_DVDL],enerd->dvdl_nonlin,enerd->dvdl_lin);
 663     }
 664
 665     /* Notes on the foreign lambda free energy difference evaluation:
 666      * Adding the potential and ekin terms that depend linearly on lambda
 667      * as delta lam * dvdl to the energy differences is exact.
 668      * For the constraint dvdl this is not exact, but we have no other option.
 669      * For the non-bonded LR term we assume that the soft-core (if present)
 670      * no longer affects the energy beyond the short-range cut-off,
 671      * which is a very good approximation (except for exotic settings).
 672      */
 673     for(i=1; i<enerd->n_lambda; i++)
 674     {
 675         dlam = (ir->flambda[i-1] - lambda);
 676         dhdl_lin =
 677             enerd->dvdl_lin + enerd->term[F_DKDL] + enerd->term[F_DHDL_CON];
 678         if (debug)
 679         {
 680             fprintf(debug,"enerdiff lam %g: non-linear %f linear %f*%f\n",
 681                     ir->flambda[i-1],
 682                     enerd->enerpart_lambda[i] - enerd->enerpart_lambda[0],
 683                     dlam,dhdl_lin);
 684         }
 685         enerd->enerpart_lambda[i] += dlam*dhdl_lin;
 686
 687     }
 688 }
 689
 690 void reset_enerdata(t_grpopts *opts,
 691                     t_forcerec *fr,gmx_bool bNS,
 692                     gmx_enerdata_t *enerd,
 693                     gmx_bool bMaster)
 694 {
 695   gmx_bool bKeepLR;
 696   int  i,j;
 697
 698   /* First reset all energy components, except for the long range terms
 699    * on the master at non neighbor search steps, since the long range
 700    * terms have already been summed at the last neighbor search step.
 701    */
 702   bKeepLR = (fr->bTwinRange && !bNS);
 703   for(i=0; (i<egNR); i++) {
 704     if (!(bKeepLR && bMaster && (i == egCOULLR || i == egLJLR))) {
 705       for(j=0; (j<enerd->grpp.nener); j++)
 706         enerd->grpp.ener[i][j] = 0.0;
 707     }
 708   }
 709   enerd->dvdl_lin    = 0.0;
 710   enerd->dvdl_nonlin = 0.0;
 711
 712   /* Normal potential energy components */
 713   for(i=0; (i<=F_EPOT); i++) {
 714     enerd->term[i] = 0.0;
 715   }
 716   /* Initialize the dVdlambda term with the long range contribution */
 717   enerd->term[F_DVDL]     = 0.0;
 718   enerd->term[F_DKDL]     = 0.0;
 719   enerd->term[F_DHDL_CON] = 0.0;
 720   if (enerd->n_lambda > 0)
 721   {
 722       for(i=0; i<enerd->n_lambda; i++)
 723       {
 724           enerd->enerpart_lambda[i] = 0.0;
 725       }
 726   }
 727 }