src/gromacs/mdlib/force.cpp

   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) 2013,2014,2015,2016,2017,2018,2019, 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
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  37 #include "gmxpre.h"
  38
  39 #include "force.h"
  40
  41 #include <cassert>
  42 #include <cmath>
  43 #include <cstring>
  44
  45 #include "gromacs/domdec/dlbtiming.h"
  46 #include "gromacs/domdec/domdec.h"
  47 #include "gromacs/domdec/domdec_struct.h"
  48 #include "gromacs/ewald/ewald.h"
  49 #include "gromacs/ewald/long_range_correction.h"
  50 #include "gromacs/ewald/pme.h"
  51 #include "gromacs/gmxlib/network.h"
  52 #include "gromacs/gmxlib/nrnb.h"
  53 #include "gromacs/listed_forces/listed_forces.h"
  54 #include "gromacs/math/vec.h"
  55 #include "gromacs/math/vecdump.h"
  56 #include "gromacs/mdlib/forcerec_threading.h"
  57 #include "gromacs/mdlib/qmmm.h"
  58 #include "gromacs/mdlib/rf_util.h"
  59 #include "gromacs/mdlib/wall.h"
  60 #include "gromacs/mdtypes/commrec.h"
  61 #include "gromacs/mdtypes/enerdata.h"
  62 #include "gromacs/mdtypes/forceoutput.h"
  63 #include "gromacs/mdtypes/forcerec.h"
  64 #include "gromacs/mdtypes/inputrec.h"
  65 #include "gromacs/mdtypes/md_enums.h"
  66 #include "gromacs/mdtypes/mdatom.h"
  67 #include "gromacs/mdtypes/simulation_workload.h"
  68 #include "gromacs/pbcutil/ishift.h"
  69 #include "gromacs/pbcutil/mshift.h"
  70 #include "gromacs/pbcutil/pbc.h"
  71 #include "gromacs/timing/wallcycle.h"
  72 #include "gromacs/utility/exceptions.h"
  73 #include "gromacs/utility/fatalerror.h"
  74 #include "gromacs/utility/smalloc.h"
  75
  76 static void clearEwaldThreadOutput(ewald_corr_thread_t* ewc_t)
  77 {
  78     ewc_t->Vcorr_q        = 0;
  79     ewc_t->Vcorr_lj       = 0;
  80     ewc_t->dvdl[efptCOUL] = 0;
  81     ewc_t->dvdl[efptVDW]  = 0;
  82     clear_mat(ewc_t->vir_q);
  83     clear_mat(ewc_t->vir_lj);
  84 }
  85
  86 static void reduceEwaldThreadOuput(int nthreads, ewald_corr_thread_t* ewc_t)
  87 {
  88     ewald_corr_thread_t& dest = ewc_t[0];
  89
  90     for (int t = 1; t < nthreads; t++)
  91     {
  92         dest.Vcorr_q += ewc_t[t].Vcorr_q;
  93         dest.Vcorr_lj += ewc_t[t].Vcorr_lj;
  94         dest.dvdl[efptCOUL] += ewc_t[t].dvdl[efptCOUL];
  95         dest.dvdl[efptVDW] += ewc_t[t].dvdl[efptVDW];
  96         m_add(dest.vir_q, ewc_t[t].vir_q, dest.vir_q);
  97         m_add(dest.vir_lj, ewc_t[t].vir_lj, dest.vir_lj);
  98     }
  99 }
 100
 101 void do_force_lowlevel(t_forcerec*                         fr,
 102                        const t_inputrec*                   ir,
 103                        const t_idef*                       idef,
 104                        const t_commrec*                    cr,
 105                        const gmx_multisim_t*               ms,
 106                        t_nrnb*                             nrnb,
 107                        gmx_wallcycle_t                     wcycle,
 108                        const t_mdatoms*                    md,
 109                        gmx::ArrayRefWithPadding<gmx::RVec> coordinates,
 110                        history_t*                          hist,
 111                        gmx::ForceOutputs*                  forceOutputs,
 112                        gmx_enerdata_t*                     enerd,
 113                        t_fcdata*                           fcd,
 114                        const matrix                        box,
 115                        const real*                         lambda,
 116                        const t_graph*                      graph,
 117                        const rvec*                         mu_tot,
 118                        const gmx::StepWorkload&            stepWork,
 119                        const DDBalanceRegionHandler&       ddBalanceRegionHandler)
 120 {
 121     // TODO: Replace all uses of x by const coordinates
 122     rvec* x = as_rvec_array(coordinates.paddedArrayRef().data());
 123
 124     auto& forceWithVirial = forceOutputs->forceWithVirial();
 125
 126     /* do QMMM first if requested */
 127     if (fr->bQMMM)
 128     {
 129         enerd->term[F_EQM] = calculate_QMMM(cr, &forceOutputs->forceWithShiftForces(), fr->qr);
 130     }
 131
 132     /* Call the short range functions all in one go. */
 133
 134     if (ir->nwall)
 135     {
 136         /* foreign lambda component for walls */
 137         real dvdl_walls = do_walls(*ir, *fr, box, *md, x, &forceWithVirial, lambda[efptVDW],
 138                                    enerd->grpp.ener[egLJSR].data(), nrnb);
 139         enerd->dvdl_lin[efptVDW] += dvdl_walls;
 140     }
 141
 142     /* Shift the coordinates. Must be done before listed forces and PPPM,
 143      * but is also necessary for SHAKE and update, therefore it can NOT
 144      * go when no listed forces have to be evaluated.
 145      *
 146      * The shifting and PBC code is deliberately not timed, since with
 147      * the Verlet scheme it only takes non-zero time with triclinic
 148      * boxes, and even then the time is around a factor of 100 less
 149      * than the next smallest counter.
 150      */
 151
 152
 153     /* Here sometimes we would not need to shift with NBFonly,
 154      * but we do so anyhow for consistency of the returned coordinates.
 155      */
 156     if (graph)
 157     {
 158         shift_self(graph, box, x);
 159         if (TRICLINIC(box))
 160         {
 161             inc_nrnb(nrnb, eNR_SHIFTX, 2 * graph->nnodes);
 162         }
 163         else
 164         {
 165             inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
 166         }
 167     }
 168
 169     {
 170         t_pbc pbc;
 171
 172         /* Check whether we need to take into account PBC in listed interactions. */
 173         const auto needPbcForListedForces =
 174                 fr->bMolPBC && stepWork.computeListedForces && haveCpuListedForces(*fr, *idef, *fcd);
 175         if (needPbcForListedForces)
 176         {
 177             /* Since all atoms are in the rectangular or triclinic unit-cell,
 178              * only single box vector shifts (2 in x) are required.
 179              */
 180             set_pbc_dd(&pbc, fr->ePBC, DOMAINDECOMP(cr) ? cr->dd->numCells : nullptr, TRUE, box);
 181         }
 182
 183         do_force_listed(wcycle, box, ir->fepvals, cr, ms, idef, x, hist, forceOutputs, fr, &pbc,
 184                         graph, enerd, nrnb, lambda, md, fcd,
 185                         DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr, stepWork);
 186     }
 187
 188     const bool computePmeOnCpu = (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
 189                                  && thisRankHasDuty(cr, DUTY_PME)
 190                                  && (pme_run_mode(fr->pmedata) == PmeRunMode::CPU);
 191
 192     const bool haveEwaldSurfaceTerm = haveEwaldSurfaceContribution(*ir);
 193
 194     /* Do long-range electrostatics and/or LJ-PME
 195      * and compute PME surface terms when necessary.
 196      */
 197     if (computePmeOnCpu || fr->ic->eeltype == eelEWALD || haveEwaldSurfaceTerm)
 198     {
 199         int  status = 0;
 200         real Vlr_q = 0, Vlr_lj = 0;
 201
 202         /* We reduce all virial, dV/dlambda and energy contributions, except
 203          * for the reciprocal energies (Vlr_q, Vlr_lj) into the same struct.
 204          */
 205         ewald_corr_thread_t& ewaldOutput = fr->ewc_t[0];
 206         clearEwaldThreadOutput(&ewaldOutput);
 207
 208         if (EEL_PME_EWALD(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
 209         {
 210             /* Calculate the Ewald surface force and energy contributions, when necessary */
 211             if (haveEwaldSurfaceTerm)
 212             {
 213                 wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
 214
 215                 if (fr->n_tpi > 0)
 216                 {
 217                     gmx_fatal(FARGS,
 218                               "TPI with PME currently only works in a 3D geometry with tin-foil "
 219                               "boundary conditions");
 220                 }
 221
 222                 int nthreads = fr->nthread_ewc;
 223 #pragma omp parallel for num_threads(nthreads) schedule(static)
 224                 for (int t = 0; t < nthreads; t++)
 225                 {
 226                     try
 227                     {
 228                         ewald_corr_thread_t& ewc_t = fr->ewc_t[t];
 229                         if (t > 0)
 230                         {
 231                             clearEwaldThreadOutput(&ewc_t);
 232                         }
 233
 234                         /* Threading is only supported with the Verlet cut-off
 235                          * scheme and then only single particle forces (no
 236                          * exclusion forces) are calculated, so we can store
 237                          * the forces in the normal, single forceWithVirial->force_ array.
 238                          */
 239                         ewald_LRcorrection(md->homenr, cr, nthreads, t, *fr, *ir, md->chargeA,
 240                                            md->chargeB, (md->nChargePerturbed != 0), x, box, mu_tot,
 241                                            as_rvec_array(forceWithVirial.force_.data()),
 242                                            &ewc_t.Vcorr_q, lambda[efptCOUL], &ewc_t.dvdl[efptCOUL]);
 243                     }
 244                     GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
 245                 }
 246                 if (nthreads > 1)
 247                 {
 248                     reduceEwaldThreadOuput(nthreads, fr->ewc_t);
 249                 }
 250                 wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
 251             }
 252
 253             if (EEL_PME_EWALD(fr->ic->eeltype) && fr->n_tpi == 0)
 254             {
 255                 /* This is not in a subcounter because it takes a
 256                    negligible and constant-sized amount of time */
 257                 ewaldOutput.Vcorr_q += ewald_charge_correction(
 258                         cr, fr, lambda[efptCOUL], box, &ewaldOutput.dvdl[efptCOUL], ewaldOutput.vir_q);
 259             }
 260
 261             if (computePmeOnCpu)
 262             {
 263                 /* Do reciprocal PME for Coulomb and/or LJ. */
 264                 assert(fr->n_tpi >= 0);
 265                 if (fr->n_tpi == 0 || stepWork.stateChanged)
 266                 {
 267                     int pme_flags = GMX_PME_SPREAD | GMX_PME_SOLVE;
 268
 269                     if (stepWork.computeForces)
 270                     {
 271                         pme_flags |= GMX_PME_CALC_F;
 272                     }
 273                     if (stepWork.computeVirial)
 274                     {
 275                         pme_flags |= GMX_PME_CALC_ENER_VIR;
 276                     }
 277                     if (fr->n_tpi > 0)
 278                     {
 279                         /* We don't calculate f, but we do want the potential */
 280                         pme_flags |= GMX_PME_CALC_POT;
 281                     }
 282
 283                     /* With domain decomposition we close the CPU side load
 284                      * balancing region here, because PME does global
 285                      * communication that acts as a global barrier.
 286                      */
 287                     ddBalanceRegionHandler.closeAfterForceComputationCpu();
 288
 289                     wallcycle_start(wcycle, ewcPMEMESH);
 290                     status = gmx_pme_do(
 291                             fr->pmedata,
 292                             gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(),
 293                                                         md->homenr - fr->n_tpi),
 294                             forceWithVirial.force_, md->chargeA, md->chargeB, md->sqrt_c6A,
 295                             md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
 296                             DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
 297                             DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
 298                             ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
 299                             lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
 300                             &ewaldOutput.dvdl[efptVDW], pme_flags);
 301                     wallcycle_stop(wcycle, ewcPMEMESH);
 302                     if (status != 0)
 303                     {
 304                         gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
 305                     }
 306
 307                     /* We should try to do as little computation after
 308                      * this as possible, because parallel PME synchronizes
 309                      * the nodes, so we want all load imbalance of the
 310                      * rest of the force calculation to be before the PME
 311                      * call.  DD load balancing is done on the whole time
 312                      * of the force call (without PME).
 313                      */
 314                 }
 315                 if (fr->n_tpi > 0)
 316                 {
 317                     if (EVDW_PME(ir->vdwtype))
 318                     {
 319
 320                         gmx_fatal(FARGS, "Test particle insertion not implemented with LJ-PME");
 321                     }
 322                     /* Determine the PME grid energy of the test molecule
 323                      * with the PME grid potential of the other charges.
 324                      */
 325                     gmx_pme_calc_energy(
 326                             fr->pmedata,
 327                             coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
 328                             gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
 329                             &Vlr_q);
 330                 }
 331             }
 332         }
 333
 334         if (fr->ic->eeltype == eelEWALD)
 335         {
 336             Vlr_q = do_ewald(ir, x, as_rvec_array(forceWithVirial.force_.data()), md->chargeA,
 337                              md->chargeB, box, cr, md->homenr, ewaldOutput.vir_q, fr->ic->ewaldcoeff_q,
 338                              lambda[efptCOUL], &ewaldOutput.dvdl[efptCOUL], fr->ewald_table);
 339         }
 340
 341         /* Note that with separate PME nodes we get the real energies later */
 342         // TODO it would be simpler if we just accumulated a single
 343         // long-range virial contribution.
 344         forceWithVirial.addVirialContribution(ewaldOutput.vir_q);
 345         forceWithVirial.addVirialContribution(ewaldOutput.vir_lj);
 346         enerd->dvdl_lin[efptCOUL] += ewaldOutput.dvdl[efptCOUL];
 347         enerd->dvdl_lin[efptVDW] += ewaldOutput.dvdl[efptVDW];
 348         enerd->term[F_COUL_RECIP] = Vlr_q + ewaldOutput.Vcorr_q;
 349         enerd->term[F_LJ_RECIP]   = Vlr_lj + ewaldOutput.Vcorr_lj;
 350
 351         if (debug)
 352         {
 353             fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n", Vlr_q,
 354                     ewaldOutput.Vcorr_q, enerd->term[F_COUL_RECIP]);
 355             pr_rvecs(debug, 0, "vir_el_recip after corr", ewaldOutput.vir_q, DIM);
 356             rvec* fshift = as_rvec_array(forceOutputs->forceWithShiftForces().shiftForces().data());
 357             pr_rvecs(debug, 0, "fshift after LR Corrections", fshift, SHIFTS);
 358             fprintf(debug, "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n", Vlr_lj,
 359                     ewaldOutput.Vcorr_lj, enerd->term[F_LJ_RECIP]);
 360             pr_rvecs(debug, 0, "vir_lj_recip after corr", ewaldOutput.vir_lj, DIM);
 361         }
 362     }
 363
 364     if (debug)
 365     {
 366         print_nrnb(debug, nrnb);
 367     }
 368
 369     if (debug)
 370     {
 371         rvec* fshift = as_rvec_array(forceOutputs->forceWithShiftForces().shiftForces().data());
 372         pr_rvecs(debug, 0, "fshift after bondeds", fshift, SHIFTS);
 373     }
 374 }