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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  26  * files - if they are missing, get the official version at www.gromacs.org.
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  28  * To help us fund GROMACS development, we humbly ask that you cite
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  35  */
  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 "pppm.h"
  60 #include "pme.h"
  61 #include "mdrun.h"
  62 #include "domdec.h"
  63 #include "partdec.h"
  64 #include "qmmm.h"
  65
  66
  67 void ns(FILE *fp,
  68         t_forcerec *fr,
  69         rvec       x[],
  70         matrix     box,
  71         gmx_groups_t *groups,
  72         t_grpopts  *opts,
  73         gmx_localtop_t *top,
  74         t_mdatoms  *md,
  75         t_commrec  *cr,
  76         t_nrnb     *nrnb,
  77         real       lambda,
  78         real       *dvdlambda,
  79         gmx_grppairener_t *grppener,
  80         gmx_bool       bFillGrid,
  81         gmx_bool       bDoLongRange,
  82         gmx_bool       bDoForces,
  83         rvec       *f)
  84 {
  85   char   *ptr;
  86   int    nsearch;
  87
  88
  89   if (!fr->ns.nblist_initialized)
  90   {
  91       init_neighbor_list(fp, fr, md->homenr);
  92   }
  93
  94   if (fr->bTwinRange)
  95     fr->nlr=0;
  96
  97     nsearch = search_neighbours(fp,fr,x,box,top,groups,cr,nrnb,md,
  98                                 lambda,dvdlambda,grppener,
  99                                 bFillGrid,bDoLongRange,
 100                                 bDoForces,f);
 101   if (debug)
 102     fprintf(debug,"nsearch = %d\n",nsearch);
 103
 104   /* Check whether we have to do dynamic load balancing */
 105   /*if ((nsb->nstDlb > 0) && (mod(step,nsb->nstDlb) == 0))
 106     count_nb(cr,nsb,&(top->blocks[ebCGS]),nns,fr->nlr,
 107     &(top->idef),opts->ngener);
 108   */
 109   if (fr->ns.dump_nl > 0)
 110     dump_nblist(fp,cr,fr,fr->ns.dump_nl);
 111 }
 112
 113 void do_force_lowlevel(FILE       *fplog,   gmx_large_int_t step,
 114                        t_forcerec *fr,      t_inputrec *ir,
 115                        t_idef     *idef,    t_commrec  *cr,
 116                        t_nrnb     *nrnb,    gmx_wallcycle_t wcycle,
 117                        t_mdatoms  *md,
 118                        t_grpopts  *opts,
 119                        rvec       x[],      history_t  *hist,
 120                        rvec       f[],
 121                        gmx_enerdata_t *enerd,
 122                        t_fcdata   *fcd,
 123                        gmx_mtop_t     *mtop,
 124                        gmx_localtop_t *top,
 125                        gmx_genborn_t *born,
 126                        t_atomtypes *atype,
 127                        gmx_bool       bBornRadii,
 128                        matrix     box,
 129                        real       lambda,
 130                        t_graph    *graph,
 131                        t_blocka   *excl,
 132                        rvec       mu_tot[],
 133                        int        flags,
 134                        float      *cycles_pme)
 135 {
 136     int     i,status;
 137     int     donb_flags;
 138     gmx_bool    bDoEpot,bSepDVDL,bSB;
 139     int     pme_flags;
 140     matrix  boxs;
 141     rvec    box_size;
 142     real    dvdlambda,Vsr,Vlr,Vcorr=0,vdip,vcharge;
 143     t_pbc   pbc;
 144     real    dvdgb;
 145     char    buf[22];
 146     gmx_enerdata_t ed_lam;
 147     double  lam_i;
 148     real    dvdl_dum;
 149
 150 #ifdef GMX_MPI
 151     double  t0=0.0,t1,t2,t3; /* time measurement for coarse load balancing */
 152 #endif
 153
 154 #define PRINT_SEPDVDL(s,v,dvdl) if (bSepDVDL) fprintf(fplog,sepdvdlformat,s,v,dvdl);
 155
 156
 157     set_pbc(&pbc,fr->ePBC,box);
 158
 159     /* Reset box */
 160     for(i=0; (i<DIM); i++)
 161     {
 162         box_size[i]=box[i][i];
 163     }
 164
 165     bSepDVDL=(fr->bSepDVDL && do_per_step(step,ir->nstlog));
 166     debug_gmx();
 167
 168     /* do QMMM first if requested */
 169     if(fr->bQMMM)
 170     {
 171         enerd->term[F_EQM] = calculate_QMMM(cr,x,f,fr,md);
 172     }
 173
 174     if (bSepDVDL)
 175     {
 176         fprintf(fplog,"Step %s: non-bonded V and dVdl for node %d:\n",
 177                 gmx_step_str(step,buf),cr->nodeid);
 178     }
 179
 180     /* Call the short range functions all in one go. */
 181
 182     dvdlambda = 0;
 183
 184 #ifdef GMX_MPI
 185     /*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
 186 #define TAKETIME FALSE
 187     if (TAKETIME)
 188     {
 189         MPI_Barrier(cr->mpi_comm_mygroup);
 190         t0=MPI_Wtime();
 191     }
 192 #endif
 193
 194     if (ir->nwall)
 195     {
 196         dvdlambda = do_walls(ir,fr,box,md,x,f,lambda,
 197                              enerd->grpp.ener[egLJSR],nrnb);
 198         PRINT_SEPDVDL("Walls",0.0,dvdlambda);
 199         enerd->dvdl_lin += dvdlambda;
 200     }
 201
 202         /* If doing GB, reset dvda and calculate the Born radii */
 203         if (ir->implicit_solvent)
 204         {
 205                 /* wallcycle_start(wcycle,ewcGB); */
 206
 207                 for(i=0;i<born->nr;i++)
 208                 {
 209                         fr->dvda[i]=0;
 210                 }
 211
 212                 if(bBornRadii)
 213                 {
 214                         calc_gb_rad(cr,fr,ir,top,atype,x,&(fr->gblist),born,md,nrnb);
 215                 }
 216
 217                 /* wallcycle_stop(wcycle, ewcGB); */
 218         }
 219
 220     where();
 221     donb_flags = 0;
 222     if (flags & GMX_FORCE_FORCES)
 223     {
 224         donb_flags |= GMX_DONB_FORCES;
 225     }
 226     do_nonbonded(cr,fr,x,f,md,excl,
 227                  fr->bBHAM ?
 228                  enerd->grpp.ener[egBHAMSR] :
 229                  enerd->grpp.ener[egLJSR],
 230                  enerd->grpp.ener[egCOULSR],
 231                                  enerd->grpp.ener[egGB],box_size,nrnb,
 232                  lambda,&dvdlambda,-1,-1,donb_flags);
 233     /* If we do foreign lambda and we have soft-core interactions
 234      * we have to recalculate the (non-linear) energies contributions.
 235      */
 236     if (ir->n_flambda > 0 && (flags & GMX_FORCE_DHDL) && ir->sc_alpha != 0)
 237     {
 238         init_enerdata(mtop->groups.grps[egcENER].nr,ir->n_flambda,&ed_lam);
 239
 240         for(i=0; i<enerd->n_lambda; i++)
 241         {
 242             lam_i = (i==0 ? lambda : ir->flambda[i-1]);
 243             dvdl_dum = 0;
 244             reset_enerdata(&ir->opts,fr,TRUE,&ed_lam,FALSE);
 245             do_nonbonded(cr,fr,x,f,md,excl,
 246                          fr->bBHAM ?
 247                          ed_lam.grpp.ener[egBHAMSR] :
 248                          ed_lam.grpp.ener[egLJSR],
 249                          ed_lam.grpp.ener[egCOULSR],
 250                          enerd->grpp.ener[egGB], box_size,nrnb,
 251                          lam_i,&dvdl_dum,-1,-1,
 252                          GMX_DONB_FOREIGNLAMBDA);
 253             sum_epot(&ir->opts,&ed_lam);
 254             enerd->enerpart_lambda[i] += ed_lam.term[F_EPOT];
 255         }
 256         destroy_enerdata(&ed_lam);
 257     }
 258     where();
 259
 260         /* If we are doing GB, calculate bonded forces and apply corrections
 261          * to the solvation forces */
 262         if (ir->implicit_solvent)  {
 263                 calc_gb_forces(cr,md,born,top,atype,x,f,fr,idef,
 264                        ir->gb_algorithm,ir->sa_algorithm,nrnb,bBornRadii,&pbc,graph,enerd);
 265     }
 266
 267 #ifdef GMX_MPI
 268     if (TAKETIME)
 269     {
 270         t1=MPI_Wtime();
 271         fr->t_fnbf += t1-t0;
 272     }
 273 #endif
 274
 275     if (ir->sc_alpha != 0)
 276     {
 277         enerd->dvdl_nonlin += dvdlambda;
 278     }
 279     else
 280     {
 281         enerd->dvdl_lin    += dvdlambda;
 282     }
 283     Vsr = 0;
 284     if (bSepDVDL)
 285     {
 286         for(i=0; i<enerd->grpp.nener; i++)
 287         {
 288             Vsr +=
 289                 (fr->bBHAM ?
 290                  enerd->grpp.ener[egBHAMSR][i] :
 291                  enerd->grpp.ener[egLJSR][i])
 292                 + enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
 293         }
 294     }
 295     PRINT_SEPDVDL("VdW and Coulomb SR particle-p.",Vsr,dvdlambda);
 296     debug_gmx();
 297
 298     if (debug)
 299     {
 300         pr_rvecs(debug,0,"fshift after SR",fr->fshift,SHIFTS);
 301     }
 302
 303     /* Shift the coordinates. Must be done before bonded forces and PPPM,
 304      * but is also necessary for SHAKE and update, therefore it can NOT
 305      * go when no bonded forces have to be evaluated.
 306      */
 307
 308     /* Here sometimes we would not need to shift with NBFonly,
 309      * but we do so anyhow for consistency of the returned coordinates.
 310      */
 311     if (graph)
 312     {
 313         shift_self(graph,box,x);
 314         if (TRICLINIC(box))
 315         {
 316             inc_nrnb(nrnb,eNR_SHIFTX,2*graph->nnodes);
 317         }
 318         else
 319         {
 320             inc_nrnb(nrnb,eNR_SHIFTX,graph->nnodes);
 321         }
 322     }
 323     /* Check whether we need to do bondeds or correct for exclusions */
 324     if (fr->bMolPBC &&
 325         ((flags & GMX_FORCE_BONDED)
 326          || EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype)))
 327     {
 328         /* Since all atoms are in the rectangular or triclinic unit-cell,
 329          * only single box vector shifts (2 in x) are required.
 330          */
 331         set_pbc_dd(&pbc,fr->ePBC,cr->dd,TRUE,box);
 332     }
 333     debug_gmx();
 334
 335     if (flags & GMX_FORCE_BONDED)
 336     {
 337         calc_bonds(fplog,cr->ms,
 338                    idef,x,hist,f,fr,&pbc,graph,enerd,nrnb,lambda,md,fcd,
 339                    DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL, atype, born,
 340                    fr->bSepDVDL && do_per_step(step,ir->nstlog),step);
 341
 342         /* Check if we have to determine energy differences
 343          * at foreign lambda's.
 344          */
 345         if (ir->n_flambda > 0 && (flags & GMX_FORCE_DHDL) &&
 346             idef->ilsort != ilsortNO_FE)
 347         {
 348             if (idef->ilsort != ilsortFE_SORTED)
 349             {
 350                 gmx_incons("The bonded interactions are not sorted for free energy");
 351             }
 352             init_enerdata(mtop->groups.grps[egcENER].nr,ir->n_flambda,&ed_lam);
 353
 354             for(i=0; i<enerd->n_lambda; i++)
 355             {
 356                 lam_i = (i==0 ? lambda : ir->flambda[i-1]);
 357                 dvdl_dum = 0;
 358                 reset_enerdata(&ir->opts,fr,TRUE,&ed_lam,FALSE);
 359                 calc_bonds_lambda(fplog,
 360                                   idef,x,fr,&pbc,graph,&ed_lam,nrnb,lam_i,md,
 361                                   fcd,
 362                                   DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
 363                 sum_epot(&ir->opts,&ed_lam);
 364                 enerd->enerpart_lambda[i] += ed_lam.term[F_EPOT];
 365             }
 366             destroy_enerdata(&ed_lam);
 367         }
 368         debug_gmx();
 369     }
 370
 371     where();
 372
 373     *cycles_pme = 0;
 374     if (EEL_FULL(fr->eeltype))
 375     {
 376         bSB = (ir->nwall == 2);
 377         if (bSB)
 378         {
 379             copy_mat(box,boxs);
 380             svmul(ir->wall_ewald_zfac,boxs[ZZ],boxs[ZZ]);
 381             box_size[ZZ] *= ir->wall_ewald_zfac;
 382         }
 383
 384         clear_mat(fr->vir_el_recip);
 385
 386         if (fr->bEwald)
 387         {
 388             if (fr->n_tpi == 0)
 389             {
 390                 dvdlambda = 0;
 391                 Vcorr = ewald_LRcorrection(fplog,md->start,md->start+md->homenr,
 392                                            cr,fr,
 393                                            md->chargeA,
 394                                            md->nChargePerturbed ? md->chargeB : NULL,
 395                                            excl,x,bSB ? boxs : box,mu_tot,
 396                                            ir->ewald_geometry,
 397                                            ir->epsilon_surface,
 398                                            lambda,&dvdlambda,&vdip,&vcharge);
 399                 PRINT_SEPDVDL("Ewald excl./charge/dip. corr.",Vcorr,dvdlambda);
 400                 enerd->dvdl_lin += dvdlambda;
 401             }
 402             else
 403             {
 404                 if (ir->ewald_geometry != eewg3D || ir->epsilon_surface != 0)
 405                 {
 406                     gmx_fatal(FARGS,"TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
 407                 }
 408                 /* The TPI molecule does not have exclusions with the rest
 409                  * of the system and no intra-molecular PME grid contributions
 410                  * will be calculated in gmx_pme_calc_energy.
 411                  */
 412                 Vcorr = 0;
 413             }
 414         }
 415         else
 416         {
 417             Vcorr = shift_LRcorrection(fplog,md->start,md->homenr,cr,fr,
 418                                        md->chargeA,excl,x,TRUE,box,
 419                                        fr->vir_el_recip);
 420         }
 421
 422         dvdlambda = 0;
 423         status = 0;
 424         switch (fr->eeltype)
 425         {
 426         case eelPPPM:
 427             status = gmx_pppm_do(fplog,fr->pmedata,FALSE,x,fr->f_novirsum,
 428                                  md->chargeA,
 429                                  box_size,fr->phi,cr,md->start,md->homenr,
 430                                  nrnb,ir->pme_order,&Vlr);
 431             break;
 432         case eelPME:
 433         case eelPMESWITCH:
 434         case eelPMEUSER:
 435         case eelPMEUSERSWITCH:
 436             if (cr->duty & DUTY_PME)
 437             {
 438                 if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
 439                 {
 440                     pme_flags = GMX_PME_SPREAD_Q | GMX_PME_SOLVE;
 441                     if (flags & GMX_FORCE_FORCES)
 442                     {
 443                         pme_flags |= GMX_PME_CALC_F;
 444                     }
 445                     if (flags & GMX_FORCE_VIRIAL)
 446                     {
 447                         pme_flags |= GMX_PME_CALC_ENER_VIR;
 448                     }
 449                     if (fr->n_tpi > 0)
 450                     {
 451                         /* We don't calculate f, but we do want the potential */
 452                         pme_flags |= GMX_PME_CALC_POT;
 453                     }
 454                     wallcycle_start(wcycle,ewcPMEMESH);
 455                     status = gmx_pme_do(fr->pmedata,
 456                                         md->start,md->homenr - fr->n_tpi,
 457                                         x,fr->f_novirsum,
 458                                         md->chargeA,md->chargeB,
 459                                         bSB ? boxs : box,cr,
 460                                         DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
 461                                         DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
 462                                         nrnb,wcycle,
 463                                         fr->vir_el_recip,fr->ewaldcoeff,
 464                                         &Vlr,lambda,&dvdlambda,
 465                                         pme_flags);
 466                     *cycles_pme = wallcycle_stop(wcycle,ewcPMEMESH);
 467
 468                     /* We should try to do as little computation after
 469                      * this as possible, because parallel PME synchronizes
 470                      * the nodes, so we want all load imbalance of the rest
 471                      * of the force calculation to be before the PME call.
 472                      * DD load balancing is done on the whole time of
 473                      * the force call (without PME).
 474                      */
 475                 }
 476                 if (fr->n_tpi > 0)
 477                 {
 478                     /* Determine the PME grid energy of the test molecule
 479                      * with the PME grid potential of the other charges.
 480                      */
 481                     gmx_pme_calc_energy(fr->pmedata,fr->n_tpi,
 482                                         x + md->homenr - fr->n_tpi,
 483                                         md->chargeA + md->homenr - fr->n_tpi,
 484                                         &Vlr);
 485                 }
 486                 PRINT_SEPDVDL("PME mesh",Vlr,dvdlambda);
 487             }
 488             else
 489             {
 490                 /* Energies and virial are obtained later from the PME nodes */
 491                 /* but values have to be zeroed out here */
 492                 Vlr=0.0;
 493             }
 494             break;
 495         case eelEWALD:
 496             Vlr = do_ewald(fplog,FALSE,ir,x,fr->f_novirsum,
 497                            md->chargeA,md->chargeB,
 498                            box_size,cr,md->homenr,
 499                            fr->vir_el_recip,fr->ewaldcoeff,
 500                            lambda,&dvdlambda,fr->ewald_table);
 501             PRINT_SEPDVDL("Ewald long-range",Vlr,dvdlambda);
 502             break;
 503         default:
 504             Vlr = 0;
 505             gmx_fatal(FARGS,"No such electrostatics method implemented %s",
 506                       eel_names[fr->eeltype]);
 507         }
 508         if (status != 0)
 509         {
 510             gmx_fatal(FARGS,"Error %d in long range electrostatics routine %s",
 511                       status,EELTYPE(fr->eeltype));
 512                 }
 513         enerd->dvdl_lin += dvdlambda;
 514         enerd->term[F_COUL_RECIP] = Vlr + Vcorr;
 515         if (debug)
 516         {
 517             fprintf(debug,"Vlr = %g, Vcorr = %g, Vlr_corr = %g\n",
 518                     Vlr,Vcorr,enerd->term[F_COUL_RECIP]);
 519             pr_rvecs(debug,0,"vir_el_recip after corr",fr->vir_el_recip,DIM);
 520             pr_rvecs(debug,0,"fshift after LR Corrections",fr->fshift,SHIFTS);
 521         }
 522     }
 523     else
 524     {
 525         if (EEL_RF(fr->eeltype))
 526         {
 527             dvdlambda = 0;
 528
 529             if (fr->eeltype != eelRF_NEC)
 530             {
 531                 enerd->term[F_RF_EXCL] =
 532                     RF_excl_correction(fplog,fr,graph,md,excl,x,f,
 533                                        fr->fshift,&pbc,lambda,&dvdlambda);
 534             }
 535
 536             enerd->dvdl_lin += dvdlambda;
 537             PRINT_SEPDVDL("RF exclusion correction",
 538                           enerd->term[F_RF_EXCL],dvdlambda);
 539         }
 540     }
 541     where();
 542     debug_gmx();
 543
 544     if (debug)
 545     {
 546         print_nrnb(debug,nrnb);
 547     }
 548     debug_gmx();
 549
 550 #ifdef GMX_MPI
 551     if (TAKETIME)
 552     {
 553         t2=MPI_Wtime();
 554         MPI_Barrier(cr->mpi_comm_mygroup);
 555         t3=MPI_Wtime();
 556         fr->t_wait += t3-t2;
 557         if (fr->timesteps == 11)
 558         {
 559             fprintf(stderr,"* PP load balancing info: node %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
 560                     cr->nodeid, gmx_step_str(fr->timesteps,buf),
 561                     100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
 562                     (fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
 563         }
 564         fr->timesteps++;
 565     }
 566 #endif
 567
 568     if (debug)
 569     {
 570         pr_rvecs(debug,0,"fshift after bondeds",fr->fshift,SHIFTS);
 571     }
 572
 573 }
 574
 575 void init_enerdata(int ngener,int n_flambda,gmx_enerdata_t *enerd)
 576 {
 577     int i,n2;
 578
 579     for(i=0; i<F_NRE; i++)
 580     {
 581         enerd->term[i] = 0;
 582     }
 583
 584     n2=ngener*ngener;
 585     if (debug)
 586     {
 587         fprintf(debug,"Creating %d sized group matrix for energies\n",n2);
 588     }
 589     enerd->grpp.nener = n2;
 590     for(i=0; (i<egNR); i++)
 591     {
 592         snew(enerd->grpp.ener[i],n2);
 593     }
 594
 595     if (n_flambda)
 596     {
 597         enerd->n_lambda = 1 + n_flambda;
 598         snew(enerd->enerpart_lambda,enerd->n_lambda);
 599     }
 600     else
 601     {
 602         enerd->n_lambda = 0;
 603     }
 604 }
 605
 606 void destroy_enerdata(gmx_enerdata_t *enerd)
 607 {
 608     int i;
 609
 610     for(i=0; (i<egNR); i++)
 611     {
 612         sfree(enerd->grpp.ener[i]);
 613     }
 614
 615     if (enerd->n_lambda)
 616     {
 617         sfree(enerd->enerpart_lambda);
 618     }
 619 }
 620
 621 static real sum_v(int n,real v[])
 622 {
 623   real t;
 624   int  i;
 625
 626   t = 0.0;
 627   for(i=0; (i<n); i++)
 628     t = t + v[i];
 629
 630   return t;
 631 }
 632
 633 void sum_epot(t_grpopts *opts,gmx_enerdata_t *enerd)
 634 {
 635   gmx_grppairener_t *grpp;
 636   real *epot;
 637   int i;
 638
 639   grpp = &enerd->grpp;
 640   epot = enerd->term;
 641
 642   /* Accumulate energies */
 643   epot[F_COUL_SR]  = sum_v(grpp->nener,grpp->ener[egCOULSR]);
 644   epot[F_LJ]       = sum_v(grpp->nener,grpp->ener[egLJSR]);
 645   epot[F_LJ14]     = sum_v(grpp->nener,grpp->ener[egLJ14]);
 646   epot[F_COUL14]   = sum_v(grpp->nener,grpp->ener[egCOUL14]);
 647   epot[F_COUL_LR]  = sum_v(grpp->nener,grpp->ener[egCOULLR]);
 648   epot[F_LJ_LR]    = sum_v(grpp->nener,grpp->ener[egLJLR]);
 649   /* We have already added 1-2,1-3, and 1-4 terms to F_GBPOL */
 650   epot[F_GBPOL]   += sum_v(grpp->nener,grpp->ener[egGB]);
 651
 652 /* lattice part of LR doesnt belong to any group
 653  * and has been added earlier
 654  */
 655   epot[F_BHAM]     = sum_v(grpp->nener,grpp->ener[egBHAMSR]);
 656   epot[F_BHAM_LR]  = sum_v(grpp->nener,grpp->ener[egBHAMLR]);
 657
 658   epot[F_EPOT] = 0;
 659   for(i=0; (i<F_EPOT); i++)
 660     if (i != F_DISRESVIOL && i != F_ORIRESDEV && i != F_DIHRESVIOL)
 661       epot[F_EPOT] += epot[i];
 662 }
 663
 664 void sum_dhdl(gmx_enerdata_t *enerd,double lambda,t_inputrec *ir)
 665 {
 666     int i;
 667     double dlam,dhdl_lin;
 668
 669     enerd->term[F_DVDL] = enerd->dvdl_lin + enerd->dvdl_nonlin;
 670
 671     if (debug)
 672     {
 673         fprintf(debug,"dvdl: %f, non-linear %f + linear %f\n",
 674                 enerd->term[F_DVDL],enerd->dvdl_nonlin,enerd->dvdl_lin);
 675     }
 676
 677     /* Notes on the foreign lambda free energy difference evaluation:
 678      * Adding the potential and ekin terms that depend linearly on lambda
 679      * as delta lam * dvdl to the energy differences is exact.
 680      * For the constraint dvdl this is not exact, but we have no other option.
 681      * For the non-bonded LR term we assume that the soft-core (if present)
 682      * no longer affects the energy beyond the short-range cut-off,
 683      * which is a very good approximation (except for exotic settings).
 684      */
 685     for(i=1; i<enerd->n_lambda; i++)
 686     {
 687         dlam = (ir->flambda[i-1] - lambda);
 688         dhdl_lin =
 689             enerd->dvdl_lin + enerd->term[F_DKDL] + enerd->term[F_DHDL_CON];
 690         if (debug)
 691         {
 692             fprintf(debug,"enerdiff lam %g: non-linear %f linear %f*%f\n",
 693                     ir->flambda[i-1],
 694                     enerd->enerpart_lambda[i] - enerd->enerpart_lambda[0],
 695                     dlam,dhdl_lin);
 696         }
 697         enerd->enerpart_lambda[i] += dlam*dhdl_lin;
 698
 699     }
 700 }
 701
 702 void reset_enerdata(t_grpopts *opts,
 703                     t_forcerec *fr,gmx_bool bNS,
 704                     gmx_enerdata_t *enerd,
 705                     gmx_bool bMaster)
 706 {
 707   gmx_bool bKeepLR;
 708   int  i,j;
 709
 710   /* First reset all energy components, except for the long range terms
 711    * on the master at non neighbor search steps, since the long range
 712    * terms have already been summed at the last neighbor search step.
 713    */
 714   bKeepLR = (fr->bTwinRange && !bNS);
 715   for(i=0; (i<egNR); i++) {
 716     if (!(bKeepLR && bMaster && (i == egCOULLR || i == egLJLR))) {
 717       for(j=0; (j<enerd->grpp.nener); j++)
 718         enerd->grpp.ener[i][j] = 0.0;
 719     }
 720   }
 721   enerd->dvdl_lin    = 0.0;
 722   enerd->dvdl_nonlin = 0.0;
 723
 724   /* Normal potential energy components */
 725   for(i=0; (i<=F_EPOT); i++) {
 726     enerd->term[i] = 0.0;
 727   }
 728   /* Initialize the dVdlambda term with the long range contribution */
 729   enerd->term[F_DVDL]     = 0.0;
 730   enerd->term[F_DKDL]     = 0.0;
 731   enerd->term[F_DHDL_CON] = 0.0;
 732   if (enerd->n_lambda > 0)
 733   {
 734       for(i=0; i<enerd->n_lambda; i++)
 735       {
 736           enerd->enerpart_lambda[i] = 0.0;
 737       }
 738   }
 739 }