src/gromacs/mdlib/force.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
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  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
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  36  */
  37 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include <math.h>
  42 #include <string.h>
  43 #include <assert.h>
  44 #include "sysstuff.h"
  45 #include "typedefs.h"
  46 #include "macros.h"
  47 #include "smalloc.h"
  48 #include "macros.h"
  49 #include "physics.h"
  50 #include "force.h"
  51 #include "nonbonded.h"
  52 #include "names.h"
  53 #include "network.h"
  54 #include "pbc.h"
  55 #include "ns.h"
  56 #include "nrnb.h"
  57 #include "bondf.h"
  58 #include "mshift.h"
  59 #include "txtdump.h"
  60 #include "coulomb.h"
  61 #include "pme.h"
  62 #include "mdrun.h"
  63 #include "domdec.h"
  64 #include "partdec.h"
  65 #include "qmmm.h"
  66 #include "gmx_omp_nthreads.h"
  67
  68 #include "gromacs/timing/wallcycle.h"
  69
  70 void ns(FILE              *fp,
  71         t_forcerec        *fr,
  72         matrix             box,
  73         gmx_groups_t      *groups,
  74         gmx_localtop_t    *top,
  75         t_mdatoms         *md,
  76         t_commrec         *cr,
  77         t_nrnb            *nrnb,
  78         gmx_bool           bFillGrid,
  79         gmx_bool           bDoLongRangeNS)
  80 {
  81     char   *ptr;
  82     int     nsearch;
  83
  84
  85     if (!fr->ns.nblist_initialized)
  86     {
  87         init_neighbor_list(fp, fr, md->homenr);
  88     }
  89
  90     if (fr->bTwinRange)
  91     {
  92         fr->nlr = 0;
  93     }
  94
  95     nsearch = search_neighbours(fp, fr, box, top, groups, cr, nrnb, md,
  96                                 bFillGrid, bDoLongRangeNS);
  97     if (debug)
  98     {
  99         fprintf(debug, "nsearch = %d\n", nsearch);
 100     }
 101
 102     /* Check whether we have to do dynamic load balancing */
 103     /*if ((nsb->nstDlb > 0) && (mod(step,nsb->nstDlb) == 0))
 104        count_nb(cr,nsb,&(top->blocks[ebCGS]),nns,fr->nlr,
 105        &(top->idef),opts->ngener);
 106      */
 107     if (fr->ns.dump_nl > 0)
 108     {
 109         dump_nblist(fp, cr, fr, fr->ns.dump_nl);
 110     }
 111 }
 112
 113 static void reduce_thread_forces(int n, rvec *f,
 114                                  tensor vir_q, tensor vir_lj,
 115                                  real *Vcorr_q, real *Vcorr_lj,
 116                                  real *dvdl_q, real *dvdl_lj,
 117                                  int nthreads, f_thread_t *f_t)
 118 {
 119     int t, i;
 120
 121     /* This reduction can run over any number of threads */
 122 #pragma omp parallel for num_threads(gmx_omp_nthreads_get(emntBonded)) private(t) schedule(static)
 123     for (i = 0; i < n; i++)
 124     {
 125         for (t = 1; t < nthreads; t++)
 126         {
 127             rvec_inc(f[i], f_t[t].f[i]);
 128         }
 129     }
 130     for (t = 1; t < nthreads; t++)
 131     {
 132         *Vcorr_q  += f_t[t].Vcorr_q;
 133         *Vcorr_lj += f_t[t].Vcorr_lj;
 134         *dvdl_q   += f_t[t].dvdl[efptCOUL];
 135         *dvdl_lj  += f_t[t].dvdl[efptVDW];
 136         m_add(vir_q, f_t[t].vir_q, vir_q);
 137         m_add(vir_lj, f_t[t].vir_lj, vir_lj);
 138     }
 139 }
 140
 141 void gmx_print_sepdvdl(FILE *fplog, const char *s, real v, real dvdlambda)
 142 {
 143     fprintf(fplog, "  %-30s V %12.5e  dVdl %12.5e\n", s, v, dvdlambda);
 144 }
 145
 146 void do_force_lowlevel(FILE       *fplog,   gmx_int64_t step,
 147                        t_forcerec *fr,      t_inputrec *ir,
 148                        t_idef     *idef,    t_commrec  *cr,
 149                        t_nrnb     *nrnb,    gmx_wallcycle_t wcycle,
 150                        t_mdatoms  *md,
 151                        rvec       x[],      history_t  *hist,
 152                        rvec       f[],
 153                        rvec       f_longrange[],
 154                        gmx_enerdata_t *enerd,
 155                        t_fcdata   *fcd,
 156                        gmx_localtop_t *top,
 157                        gmx_genborn_t *born,
 158                        t_atomtypes *atype,
 159                        gmx_bool       bBornRadii,
 160                        matrix     box,
 161                        t_lambda   *fepvals,
 162                        real       *lambda,
 163                        t_graph    *graph,
 164                        t_blocka   *excl,
 165                        rvec       mu_tot[],
 166                        int        flags,
 167                        float      *cycles_pme)
 168 {
 169     int         i, j;
 170     int         donb_flags;
 171     gmx_bool    bDoEpot, bSepDVDL, bSB;
 172     int         pme_flags;
 173     matrix      boxs;
 174     rvec        box_size;
 175     t_pbc       pbc;
 176     char        buf[22];
 177     double      clam_i, vlam_i;
 178     real        dvdl_dum[efptNR], dvdl_nb[efptNR], lam_i[efptNR];
 179     real        dvdl_q, dvdl_lj;
 180
 181 #ifdef GMX_MPI
 182     double  t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
 183 #endif
 184
 185 #define PRINT_SEPDVDL(s, v, dvdlambda) if (bSepDVDL) { gmx_print_sepdvdl(fplog, s, v, dvdlambda); }
 186
 187     set_pbc(&pbc, fr->ePBC, box);
 188
 189     /* reset free energy components */
 190     for (i = 0; i < efptNR; i++)
 191     {
 192         dvdl_nb[i]  = 0;
 193         dvdl_dum[i] = 0;
 194     }
 195
 196     /* Reset box */
 197     for (i = 0; (i < DIM); i++)
 198     {
 199         box_size[i] = box[i][i];
 200     }
 201
 202     bSepDVDL = (fr->bSepDVDL && do_per_step(step, ir->nstlog));
 203     debug_gmx();
 204
 205     /* do QMMM first if requested */
 206     if (fr->bQMMM)
 207     {
 208         enerd->term[F_EQM] = calculate_QMMM(cr, x, f, fr);
 209     }
 210
 211     if (bSepDVDL)
 212     {
 213         fprintf(fplog, "Step %s: non-bonded V and dVdl for node %d:\n",
 214                 gmx_step_str(step, buf), cr->nodeid);
 215     }
 216
 217     /* Call the short range functions all in one go. */
 218
 219 #ifdef GMX_MPI
 220     /*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
 221 #define TAKETIME FALSE
 222     if (TAKETIME)
 223     {
 224         MPI_Barrier(cr->mpi_comm_mygroup);
 225         t0 = MPI_Wtime();
 226     }
 227 #endif
 228
 229     if (ir->nwall)
 230     {
 231         /* foreign lambda component for walls */
 232         real dvdl_walls = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
 233                                    enerd->grpp.ener[egLJSR], nrnb);
 234         PRINT_SEPDVDL("Walls", 0.0, dvdl_walls);
 235         enerd->dvdl_lin[efptVDW] += dvdl_walls;
 236     }
 237
 238     /* If doing GB, reset dvda and calculate the Born radii */
 239     if (ir->implicit_solvent)
 240     {
 241         wallcycle_sub_start(wcycle, ewcsNONBONDED);
 242
 243         for (i = 0; i < born->nr; i++)
 244         {
 245             fr->dvda[i] = 0;
 246         }
 247
 248         if (bBornRadii)
 249         {
 250             calc_gb_rad(cr, fr, ir, top, x, &(fr->gblist), born, md, nrnb);
 251         }
 252
 253         wallcycle_sub_stop(wcycle, ewcsNONBONDED);
 254     }
 255
 256     where();
 257     /* We only do non-bonded calculation with group scheme here, the verlet
 258      * calls are done from do_force_cutsVERLET(). */
 259     if (fr->cutoff_scheme == ecutsGROUP && (flags & GMX_FORCE_NONBONDED))
 260     {
 261         donb_flags = 0;
 262         /* Add short-range interactions */
 263         donb_flags |= GMX_NONBONDED_DO_SR;
 264
 265         if (flags & GMX_FORCE_FORCES)
 266         {
 267             donb_flags |= GMX_NONBONDED_DO_FORCE;
 268         }
 269         if (flags & GMX_FORCE_ENERGY)
 270         {
 271             donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
 272         }
 273         if (flags & GMX_FORCE_DO_LR)
 274         {
 275             donb_flags |= GMX_NONBONDED_DO_LR;
 276         }
 277
 278         wallcycle_sub_start(wcycle, ewcsNONBONDED);
 279         do_nonbonded(fr, x, f, f_longrange, md, excl,
 280                      &enerd->grpp, nrnb,
 281                      lambda, dvdl_nb, -1, -1, donb_flags);
 282
 283         /* If we do foreign lambda and we have soft-core interactions
 284          * we have to recalculate the (non-linear) energies contributions.
 285          */
 286         if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) && fepvals->sc_alpha != 0)
 287         {
 288             for (i = 0; i < enerd->n_lambda; i++)
 289             {
 290                 for (j = 0; j < efptNR; j++)
 291                 {
 292                     lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
 293                 }
 294                 reset_foreign_enerdata(enerd);
 295                 do_nonbonded(fr, x, f, f_longrange, md, excl,
 296                              &(enerd->foreign_grpp), nrnb,
 297                              lam_i, dvdl_dum, -1, -1,
 298                              (donb_flags & ~GMX_NONBONDED_DO_FORCE) | GMX_NONBONDED_DO_FOREIGNLAMBDA);
 299                 sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
 300                 enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
 301             }
 302         }
 303         wallcycle_sub_stop(wcycle, ewcsNONBONDED);
 304         where();
 305     }
 306
 307     /* If we are doing GB, calculate bonded forces and apply corrections
 308      * to the solvation forces */
 309     /* MRS: Eventually, many need to include free energy contribution here! */
 310     if (ir->implicit_solvent)
 311     {
 312         wallcycle_sub_start(wcycle, ewcsBONDED);
 313         calc_gb_forces(cr, md, born, top, x, f, fr, idef,
 314                        ir->gb_algorithm, ir->sa_algorithm, nrnb, &pbc, graph, enerd);
 315         wallcycle_sub_stop(wcycle, ewcsBONDED);
 316     }
 317
 318 #ifdef GMX_MPI
 319     if (TAKETIME)
 320     {
 321         t1          = MPI_Wtime();
 322         fr->t_fnbf += t1-t0;
 323     }
 324 #endif
 325
 326     if (fepvals->sc_alpha != 0)
 327     {
 328         enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
 329     }
 330     else
 331     {
 332         enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
 333     }
 334
 335     if (fepvals->sc_alpha != 0)
 336
 337     /* even though coulomb part is linear, we already added it, beacuse we
 338        need to go through the vdw calculation anyway */
 339     {
 340         enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
 341     }
 342     else
 343     {
 344         enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
 345     }
 346
 347     if (bSepDVDL)
 348     {
 349         real V_short_range    = 0;
 350         real dvdl_short_range = 0;
 351
 352         for (i = 0; i < enerd->grpp.nener; i++)
 353         {
 354             V_short_range +=
 355                 (fr->bBHAM ?
 356                  enerd->grpp.ener[egBHAMSR][i] :
 357                  enerd->grpp.ener[egLJSR][i])
 358                 + enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
 359         }
 360         dvdl_short_range = dvdl_nb[efptVDW] + dvdl_nb[efptCOUL];
 361         PRINT_SEPDVDL("VdW and Coulomb SR particle-p.",
 362                       V_short_range,
 363                       dvdl_short_range);
 364     }
 365     debug_gmx();
 366
 367
 368     if (debug)
 369     {
 370         pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
 371     }
 372
 373     /* Shift the coordinates. Must be done before bonded forces and PPPM,
 374      * but is also necessary for SHAKE and update, therefore it can NOT
 375      * go when no bonded forces have to be evaluated.
 376      */
 377
 378     /* Here sometimes we would not need to shift with NBFonly,
 379      * but we do so anyhow for consistency of the returned coordinates.
 380      */
 381     if (graph)
 382     {
 383         shift_self(graph, box, x);
 384         if (TRICLINIC(box))
 385         {
 386             inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
 387         }
 388         else
 389         {
 390             inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
 391         }
 392     }
 393     /* Check whether we need to do bondeds or correct for exclusions */
 394     if (fr->bMolPBC &&
 395         ((flags & GMX_FORCE_BONDED)
 396          || EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype)))
 397     {
 398         /* Since all atoms are in the rectangular or triclinic unit-cell,
 399          * only single box vector shifts (2 in x) are required.
 400          */
 401         set_pbc_dd(&pbc, fr->ePBC, cr->dd, TRUE, box);
 402     }
 403     debug_gmx();
 404
 405     if (flags & GMX_FORCE_BONDED)
 406     {
 407         wallcycle_sub_start(wcycle, ewcsBONDED);
 408         calc_bonds(fplog, cr->ms,
 409                    idef, x, hist, f, fr, &pbc, graph, enerd, nrnb, lambda, md, fcd,
 410                    DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL, atype, born,
 411                    flags,
 412                    fr->bSepDVDL && do_per_step(step, ir->nstlog), step);
 413
 414         /* Check if we have to determine energy differences
 415          * at foreign lambda's.
 416          */
 417         if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) &&
 418             idef->ilsort != ilsortNO_FE)
 419         {
 420             if (idef->ilsort != ilsortFE_SORTED)
 421             {
 422                 gmx_incons("The bonded interactions are not sorted for free energy");
 423             }
 424             for (i = 0; i < enerd->n_lambda; i++)
 425             {
 426                 reset_foreign_enerdata(enerd);
 427                 for (j = 0; j < efptNR; j++)
 428                 {
 429                     lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
 430                 }
 431                 calc_bonds_lambda(fplog, idef, x, fr, &pbc, graph, &(enerd->foreign_grpp), enerd->foreign_term, nrnb, lam_i, md,
 432                                   fcd, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
 433                 sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
 434                 enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
 435             }
 436         }
 437         debug_gmx();
 438
 439         wallcycle_sub_stop(wcycle, ewcsBONDED);
 440     }
 441
 442     where();
 443
 444     *cycles_pme = 0;
 445     if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
 446     {
 447         real Vlr             = 0, Vcorr = 0;
 448         real dvdl_long_range = 0;
 449         int  status          = 0;
 450
 451         bSB = (ir->nwall == 2);
 452         if (bSB)
 453         {
 454             copy_mat(box, boxs);
 455             svmul(ir->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
 456             box_size[ZZ] *= ir->wall_ewald_zfac;
 457         }
 458     }
 459
 460     /* Do long-range electrostatics and/or LJ-PME, including related short-range
 461      * corrections.
 462      */
 463
 464     clear_mat(fr->vir_el_recip);
 465     clear_mat(fr->vir_lj_recip);
 466
 467     if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
 468     {
 469         real Vlr_q             = 0, Vlr_lj = 0, Vcorr_q = 0, Vcorr_lj = 0;
 470         real dvdl_long_range_q = 0, dvdl_long_range_lj = 0;
 471         int  status            = 0;
 472
 473         if (EEL_EWALD(fr->eeltype) || EVDW_PME(fr->vdwtype))
 474         {
 475             real dvdl_long_range_correction_q   = 0;
 476             real dvdl_long_range_correction_lj  = 0;
 477             /* With the Verlet scheme exclusion forces are calculated
 478              * in the non-bonded kernel.
 479              */
 480             /* The TPI molecule does not have exclusions with the rest
 481              * of the system and no intra-molecular PME grid
 482              * contributions will be calculated in
 483              * gmx_pme_calc_energy.
 484              */
 485             if ((ir->cutoff_scheme == ecutsGROUP && fr->n_tpi == 0) ||
 486                 ir->ewald_geometry != eewg3D ||
 487                 ir->epsilon_surface != 0)
 488             {
 489                 int nthreads, t;
 490
 491                 wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
 492
 493                 if (fr->n_tpi > 0)
 494                 {
 495                     gmx_fatal(FARGS, "TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
 496                 }
 497
 498                 nthreads = gmx_omp_nthreads_get(emntBonded);
 499 #pragma omp parallel for num_threads(nthreads) schedule(static)
 500                 for (t = 0; t < nthreads; t++)
 501                 {
 502                     int     s, e, i;
 503                     rvec   *fnv;
 504                     tensor *vir_q, *vir_lj;
 505                     real   *Vcorrt_q, *Vcorrt_lj, *dvdlt_q, *dvdlt_lj;
 506                     if (t == 0)
 507                     {
 508                         fnv       = fr->f_novirsum;
 509                         vir_q     = &fr->vir_el_recip;
 510                         vir_lj    = &fr->vir_lj_recip;
 511                         Vcorrt_q  = &Vcorr_q;
 512                         Vcorrt_lj = &Vcorr_lj;
 513                         dvdlt_q   = &dvdl_long_range_correction_q;
 514                         dvdlt_lj  = &dvdl_long_range_correction_lj;
 515                     }
 516                     else
 517                     {
 518                         fnv       = fr->f_t[t].f;
 519                         vir_q     = &fr->f_t[t].vir_q;
 520                         vir_lj    = &fr->f_t[t].vir_lj;
 521                         Vcorrt_q  = &fr->f_t[t].Vcorr_q;
 522                         Vcorrt_lj = &fr->f_t[t].Vcorr_lj;
 523                         dvdlt_q   = &fr->f_t[t].dvdl[efptCOUL];
 524                         dvdlt_lj  = &fr->f_t[t].dvdl[efptVDW];
 525                         for (i = 0; i < fr->natoms_force; i++)
 526                         {
 527                             clear_rvec(fnv[i]);
 528                         }
 529                         clear_mat(*vir_q);
 530                         clear_mat(*vir_lj);
 531                     }
 532                     *dvdlt_q  = 0;
 533                     *dvdlt_lj = 0;
 534                     ewald_LRcorrection(fr->excl_load[t], fr->excl_load[t+1],
 535                                        cr, t, fr,
 536                                        md->chargeA,
 537                                        md->nChargePerturbed ? md->chargeB : NULL,
 538                                        md->c6A,
 539                                        md->nChargePerturbed ? md->c6B : NULL,
 540                                        md->sigmaA,
 541                                        md->nChargePerturbed ? md->sigmaB : NULL,
 542                                        md->sigma3A,
 543                                        md->nChargePerturbed ? md->sigma3B : NULL,
 544                                        ir->cutoff_scheme != ecutsVERLET,
 545                                        excl, x, bSB ? boxs : box, mu_tot,
 546                                        ir->ewald_geometry,
 547                                        ir->epsilon_surface,
 548                                        fnv, *vir_q, *vir_lj,
 549                                        Vcorrt_q, Vcorrt_lj,
 550                                        lambda[efptCOUL], lambda[efptVDW],
 551                                        dvdlt_q, dvdlt_lj);
 552                 }
 553                 if (nthreads > 1)
 554                 {
 555                     reduce_thread_forces(fr->natoms_force, fr->f_novirsum,
 556                                          fr->vir_el_recip, fr->vir_lj_recip,
 557                                          &Vcorr_q, &Vcorr_lj,
 558                                          &dvdl_long_range_correction_q,
 559                                          &dvdl_long_range_correction_lj,
 560                                          nthreads, fr->f_t);
 561                 }
 562                 wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
 563             }
 564
 565             if (fr->n_tpi == 0)
 566             {
 567                 Vcorr_q += ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
 568                                                    &dvdl_long_range_correction_q,
 569                                                    fr->vir_el_recip);
 570             }
 571
 572             PRINT_SEPDVDL("Ewald excl./charge/dip. corr.", Vcorr_q, dvdl_long_range_correction_q);
 573             PRINT_SEPDVDL("Ewald excl. corr. LJ", Vcorr_lj, dvdl_long_range_correction_lj);
 574             enerd->dvdl_lin[efptCOUL] += dvdl_long_range_correction_q;
 575             enerd->dvdl_lin[efptVDW]  += dvdl_long_range_correction_lj;
 576         }
 577
 578         if ((EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype)))
 579         {
 580             if (cr->duty & DUTY_PME)
 581             {
 582                 /* Do reciprocal PME for Coulomb and/or LJ. */
 583                 assert(fr->n_tpi >= 0);
 584                 if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
 585                 {
 586                     pme_flags = GMX_PME_SPREAD_Q | GMX_PME_SOLVE;
 587                     if (EEL_PME(fr->eeltype))
 588                     {
 589                         pme_flags     |= GMX_PME_DO_COULOMB;
 590                     }
 591                     if (EVDW_PME(fr->vdwtype))
 592                     {
 593                         pme_flags |= GMX_PME_DO_LJ;
 594                         if (fr->ljpme_combination_rule == eljpmeLB)
 595                         {
 596                             /*Lorentz-Berthelot Comb. Rules in LJ-PME*/
 597                             pme_flags |= GMX_PME_LJ_LB;
 598                         }
 599                     }
 600                     if (flags & GMX_FORCE_FORCES)
 601                     {
 602                         pme_flags |= GMX_PME_CALC_F;
 603                     }
 604                     if (flags & GMX_FORCE_VIRIAL)
 605                     {
 606                         pme_flags |= GMX_PME_CALC_ENER_VIR;
 607                     }
 608                     if (fr->n_tpi > 0)
 609                     {
 610                         /* We don't calculate f, but we do want the potential */
 611                         pme_flags |= GMX_PME_CALC_POT;
 612                     }
 613                     wallcycle_start(wcycle, ewcPMEMESH);
 614                     status = gmx_pme_do(fr->pmedata,
 615                                         md->start, md->homenr - fr->n_tpi,
 616                                         x, fr->f_novirsum,
 617                                         md->chargeA, md->chargeB,
 618                                         md->c6A, md->c6B,
 619                                         md->sigmaA, md->sigmaB,
 620                                         bSB ? boxs : box, cr,
 621                                         DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
 622                                         DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
 623                                         nrnb, wcycle,
 624                                         fr->vir_el_recip, fr->ewaldcoeff_q,
 625                                         fr->vir_lj_recip, fr->ewaldcoeff_lj,
 626                                         &Vlr_q, &Vlr_lj,
 627                                         lambda[efptCOUL], lambda[efptVDW],
 628                                         &dvdl_long_range_q, &dvdl_long_range_lj, pme_flags);
 629                     *cycles_pme = wallcycle_stop(wcycle, ewcPMEMESH);
 630                     if (status != 0)
 631                     {
 632                         gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
 633                     }
 634                     /* We should try to do as little computation after
 635                      * this as possible, because parallel PME synchronizes
 636                      * the nodes, so we want all load imbalance of the
 637                      * rest of the force calculation to be before the PME
 638                      * call.  DD load balancing is done on the whole time
 639                      * of the force call (without PME).
 640                      */
 641                 }
 642                 if (fr->n_tpi > 0)
 643                 {
 644                     if (EVDW_PME(ir->vdwtype))
 645                     {
 646
 647                         gmx_fatal(FARGS, "Test particle insertion not implemented with LJ-PME");
 648                     }
 649                     /* Determine the PME grid energy of the test molecule
 650                      * with the PME grid potential of the other charges.
 651                      */
 652                     gmx_pme_calc_energy(fr->pmedata, fr->n_tpi,
 653                                         x + md->homenr - fr->n_tpi,
 654                                         md->chargeA + md->homenr - fr->n_tpi,
 655                                         &Vlr_q);
 656                 }
 657                 PRINT_SEPDVDL("PME mesh", Vlr_q + Vlr_lj, dvdl_long_range_q+dvdl_long_range_lj);
 658             }
 659         }
 660
 661         if (!EEL_PME(fr->eeltype) && EEL_EWALD(fr->eeltype))
 662         {
 663             Vlr_q = do_ewald(ir, x, fr->f_novirsum,
 664                              md->chargeA, md->chargeB,
 665                              box_size, cr, md->homenr,
 666                              fr->vir_el_recip, fr->ewaldcoeff_q,
 667                              lambda[efptCOUL], &dvdl_long_range_q, fr->ewald_table);
 668             PRINT_SEPDVDL("Ewald long-range", Vlr_q, dvdl_long_range_q);
 669         }
 670         else if (!EEL_EWALD(fr->eeltype))
 671         {
 672             gmx_fatal(FARGS, "No such electrostatics method implemented %s",
 673                       eel_names[fr->eeltype]);
 674         }
 675         /* Note that with separate PME nodes we get the real energies later */
 676         enerd->dvdl_lin[efptCOUL] += dvdl_long_range_q;
 677         enerd->dvdl_lin[efptVDW]  += dvdl_long_range_lj;
 678         enerd->term[F_COUL_RECIP]  = Vlr_q + Vcorr_q;
 679         enerd->term[F_LJ_RECIP]    = Vlr_lj + Vcorr_lj;
 680         if (debug)
 681         {
 682             fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n",
 683                     Vlr_q, Vcorr_q, enerd->term[F_COUL_RECIP]);
 684             pr_rvecs(debug, 0, "vir_el_recip after corr", fr->vir_el_recip, DIM);
 685             pr_rvecs(debug, 0, "fshift after LR Corrections", fr->fshift, SHIFTS);
 686             fprintf(debug, "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n",
 687                     Vlr_lj, Vcorr_lj, enerd->term[F_LJ_RECIP]);
 688             pr_rvecs(debug, 0, "vir_lj_recip after corr", fr->vir_lj_recip, DIM);
 689         }
 690     }
 691     else
 692     {
 693         /* Is there a reaction-field exclusion correction needed? */
 694         if (EEL_RF(fr->eeltype) && eelRF_NEC != fr->eeltype)
 695         {
 696             /* With the Verlet scheme, exclusion forces are calculated
 697              * in the non-bonded kernel.
 698              */
 699             if (ir->cutoff_scheme != ecutsVERLET)
 700             {
 701                 real dvdl_rf_excl      = 0;
 702                 enerd->term[F_RF_EXCL] =
 703                     RF_excl_correction(fr, graph, md, excl, x, f,
 704                                        fr->fshift, &pbc, lambda[efptCOUL], &dvdl_rf_excl);
 705
 706                 enerd->dvdl_lin[efptCOUL] += dvdl_rf_excl;
 707                 PRINT_SEPDVDL("RF exclusion correction",
 708                               enerd->term[F_RF_EXCL], dvdl_rf_excl);
 709             }
 710         }
 711     }
 712     where();
 713     debug_gmx();
 714
 715     if (debug)
 716     {
 717         print_nrnb(debug, nrnb);
 718     }
 719     debug_gmx();
 720
 721 #ifdef GMX_MPI
 722     if (TAKETIME)
 723     {
 724         t2 = MPI_Wtime();
 725         MPI_Barrier(cr->mpi_comm_mygroup);
 726         t3          = MPI_Wtime();
 727         fr->t_wait += t3-t2;
 728         if (fr->timesteps == 11)
 729         {
 730             fprintf(stderr, "* PP load balancing info: node %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
 731                     cr->nodeid, gmx_step_str(fr->timesteps, buf),
 732                     100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
 733                     (fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
 734         }
 735         fr->timesteps++;
 736     }
 737 #endif
 738
 739     if (debug)
 740     {
 741         pr_rvecs(debug, 0, "fshift after bondeds", fr->fshift, SHIFTS);
 742     }
 743
 744 }
 745
 746 void init_enerdata(int ngener, int n_lambda, gmx_enerdata_t *enerd)
 747 {
 748     int i, n2;
 749
 750     for (i = 0; i < F_NRE; i++)
 751     {
 752         enerd->term[i]         = 0;
 753         enerd->foreign_term[i] = 0;
 754     }
 755
 756
 757     for (i = 0; i < efptNR; i++)
 758     {
 759         enerd->dvdl_lin[i]     = 0;
 760         enerd->dvdl_nonlin[i]  = 0;
 761     }
 762
 763     n2 = ngener*ngener;
 764     if (debug)
 765     {
 766         fprintf(debug, "Creating %d sized group matrix for energies\n", n2);
 767     }
 768     enerd->grpp.nener         = n2;
 769     enerd->foreign_grpp.nener = n2;
 770     for (i = 0; (i < egNR); i++)
 771     {
 772         snew(enerd->grpp.ener[i], n2);
 773         snew(enerd->foreign_grpp.ener[i], n2);
 774     }
 775
 776     if (n_lambda)
 777     {
 778         enerd->n_lambda = 1 + n_lambda;
 779         snew(enerd->enerpart_lambda, enerd->n_lambda);
 780     }
 781     else
 782     {
 783         enerd->n_lambda = 0;
 784     }
 785 }
 786
 787 void destroy_enerdata(gmx_enerdata_t *enerd)
 788 {
 789     int i;
 790
 791     for (i = 0; (i < egNR); i++)
 792     {
 793         sfree(enerd->grpp.ener[i]);
 794     }
 795
 796     for (i = 0; (i < egNR); i++)
 797     {
 798         sfree(enerd->foreign_grpp.ener[i]);
 799     }
 800
 801     if (enerd->n_lambda)
 802     {
 803         sfree(enerd->enerpart_lambda);
 804     }
 805 }
 806
 807 static real sum_v(int n, real v[])
 808 {
 809     real t;
 810     int  i;
 811
 812     t = 0.0;
 813     for (i = 0; (i < n); i++)
 814     {
 815         t = t + v[i];
 816     }
 817
 818     return t;
 819 }
 820
 821 void sum_epot(gmx_grppairener_t *grpp, real *epot)
 822 {
 823     int i;
 824
 825     /* Accumulate energies */
 826     epot[F_COUL_SR]  = sum_v(grpp->nener, grpp->ener[egCOULSR]);
 827     epot[F_LJ]       = sum_v(grpp->nener, grpp->ener[egLJSR]);
 828     epot[F_LJ14]     = sum_v(grpp->nener, grpp->ener[egLJ14]);
 829     epot[F_COUL14]   = sum_v(grpp->nener, grpp->ener[egCOUL14]);
 830     epot[F_COUL_LR]  = sum_v(grpp->nener, grpp->ener[egCOULLR]);
 831     epot[F_LJ_LR]    = sum_v(grpp->nener, grpp->ener[egLJLR]);
 832     /* We have already added 1-2,1-3, and 1-4 terms to F_GBPOL */
 833     epot[F_GBPOL]   += sum_v(grpp->nener, grpp->ener[egGB]);
 834
 835 /* lattice part of LR doesnt belong to any group
 836  * and has been added earlier
 837  */
 838     epot[F_BHAM]     = sum_v(grpp->nener, grpp->ener[egBHAMSR]);
 839     epot[F_BHAM_LR]  = sum_v(grpp->nener, grpp->ener[egBHAMLR]);
 840
 841     epot[F_EPOT] = 0;
 842     for (i = 0; (i < F_EPOT); i++)
 843     {
 844         if (i != F_DISRESVIOL && i != F_ORIRESDEV)
 845         {
 846             epot[F_EPOT] += epot[i];
 847         }
 848     }
 849 }
 850
 851 void sum_dhdl(gmx_enerdata_t *enerd, real *lambda, t_lambda *fepvals)
 852 {
 853     int    i, j, index;
 854     double dlam;
 855
 856     enerd->dvdl_lin[efptVDW] += enerd->term[F_DVDL_VDW];  /* include dispersion correction */
 857     enerd->term[F_DVDL]       = 0.0;
 858     for (i = 0; i < efptNR; i++)
 859     {
 860         if (fepvals->separate_dvdl[i])
 861         {
 862             /* could this be done more readably/compactly? */
 863             switch (i)
 864             {
 865                 case (efptMASS):
 866                     index = F_DKDL;
 867                     break;
 868                 case (efptCOUL):
 869                     index = F_DVDL_COUL;
 870                     break;
 871                 case (efptVDW):
 872                     index = F_DVDL_VDW;
 873                     break;
 874                 case (efptBONDED):
 875                     index = F_DVDL_BONDED;
 876                     break;
 877                 case (efptRESTRAINT):
 878                     index = F_DVDL_RESTRAINT;
 879                     break;
 880                 default:
 881                     index = F_DVDL;
 882                     break;
 883             }
 884             enerd->term[index] = enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
 885             if (debug)
 886             {
 887                 fprintf(debug, "dvdl-%s[%2d]: %f: non-linear %f + linear %f\n",
 888                         efpt_names[i], i, enerd->term[index], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
 889             }
 890         }
 891         else
 892         {
 893             enerd->term[F_DVDL] += enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
 894             if (debug)
 895             {
 896                 fprintf(debug, "dvd-%sl[%2d]: %f: non-linear %f + linear %f\n",
 897                         efpt_names[0], i, enerd->term[F_DVDL], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
 898             }
 899         }
 900     }
 901
 902     /* Notes on the foreign lambda free energy difference evaluation:
 903      * Adding the potential and ekin terms that depend linearly on lambda
 904      * as delta lam * dvdl to the energy differences is exact.
 905      * For the constraints this is not exact, but we have no other option
 906      * without literally changing the lengths and reevaluating the energies at each step.
 907      * (try to remedy this post 4.6 - MRS)
 908      * For the non-bonded LR term we assume that the soft-core (if present)
 909      * no longer affects the energy beyond the short-range cut-off,
 910      * which is a very good approximation (except for exotic settings).
 911      * (investigate how to overcome this post 4.6 - MRS)
 912      */
 913     if (fepvals->separate_dvdl[efptBONDED])
 914     {
 915         enerd->term[F_DVDL_BONDED] += enerd->term[F_DVDL_CONSTR];
 916     }
 917     else
 918     {
 919         enerd->term[F_DVDL] += enerd->term[F_DVDL_CONSTR];
 920     }
 921     enerd->term[F_DVDL_CONSTR] = 0;
 922
 923     for (i = 0; i < fepvals->n_lambda; i++)
 924     {
 925         /* note we are iterating over fepvals here!
 926            For the current lam, dlam = 0 automatically,
 927            so we don't need to add anything to the
 928            enerd->enerpart_lambda[0] */
 929
 930         /* we don't need to worry about dvdl_lin contributions to dE at
 931            current lambda, because the contributions to the current
 932            lambda are automatically zeroed */
 933
 934         for (j = 0; j < efptNR; j++)
 935         {
 936             /* Note that this loop is over all dhdl components, not just the separated ones */
 937             dlam = (fepvals->all_lambda[j][i]-lambda[j]);
 938             enerd->enerpart_lambda[i+1] += dlam*enerd->dvdl_lin[j];
 939             if (debug)
 940             {
 941                 fprintf(debug, "enerdiff lam %g: (%15s), non-linear %f linear %f*%f\n",
 942                         fepvals->all_lambda[j][i], efpt_names[j],
 943                         (enerd->enerpart_lambda[i+1] - enerd->enerpart_lambda[0]),
 944                         dlam, enerd->dvdl_lin[j]);
 945             }
 946         }
 947     }
 948 }
 949
 950
 951 void reset_foreign_enerdata(gmx_enerdata_t *enerd)
 952 {
 953     int  i, j;
 954
 955     /* First reset all foreign energy components.  Foreign energies always called on
 956        neighbor search steps */
 957     for (i = 0; (i < egNR); i++)
 958     {
 959         for (j = 0; (j < enerd->grpp.nener); j++)
 960         {
 961             enerd->foreign_grpp.ener[i][j] = 0.0;
 962         }
 963     }
 964
 965     /* potential energy components */
 966     for (i = 0; (i <= F_EPOT); i++)
 967     {
 968         enerd->foreign_term[i] = 0.0;
 969     }
 970 }
 971
 972 void reset_enerdata(t_forcerec *fr, gmx_bool bNS,
 973                     gmx_enerdata_t *enerd,
 974                     gmx_bool bMaster)
 975 {
 976     gmx_bool bKeepLR;
 977     int      i, j;
 978
 979     /* First reset all energy components, except for the long range terms
 980      * on the master at non neighbor search steps, since the long range
 981      * terms have already been summed at the last neighbor search step.
 982      */
 983     bKeepLR = (fr->bTwinRange && !bNS);
 984     for (i = 0; (i < egNR); i++)
 985     {
 986         if (!(bKeepLR && bMaster && (i == egCOULLR || i == egLJLR)))
 987         {
 988             for (j = 0; (j < enerd->grpp.nener); j++)
 989             {
 990                 enerd->grpp.ener[i][j] = 0.0;
 991             }
 992         }
 993     }
 994     for (i = 0; i < efptNR; i++)
 995     {
 996         enerd->dvdl_lin[i]    = 0.0;
 997         enerd->dvdl_nonlin[i] = 0.0;
 998     }
 999
1000     /* Normal potential energy components */
1001     for (i = 0; (i <= F_EPOT); i++)
1002     {
1003         enerd->term[i] = 0.0;
1004     }
1005     /* Initialize the dVdlambda term with the long range contribution */
1006     /* Initialize the dvdl term with the long range contribution */
1007     enerd->term[F_DVDL]            = 0.0;
1008     enerd->term[F_DVDL_COUL]       = 0.0;
1009     enerd->term[F_DVDL_VDW]        = 0.0;
1010     enerd->term[F_DVDL_BONDED]     = 0.0;
1011     enerd->term[F_DVDL_RESTRAINT]  = 0.0;
1012     enerd->term[F_DKDL]            = 0.0;
1013     if (enerd->n_lambda > 0)
1014     {
1015         for (i = 0; i < enerd->n_lambda; i++)
1016         {
1017             enerd->enerpart_lambda[i] = 0.0;
1018         }
1019     }
1020     /* reset foreign energy data - separate function since we also call it elsewhere */
1021     reset_foreign_enerdata(enerd);
1022 }