src/gromacs/mdlib/sim_util.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
   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,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  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
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 #include "gmxpre.h"
  38
  39 #include "sim_util.h"
  40
  41 #include "config.h"
  42
  43 #include <cmath>
  44 #include <cstdint>
  45 #include <cstdio>
  46 #include <cstring>
  47
  48 #include <array>
  49
  50 #include "gromacs/awh/awh.h"
  51 #include "gromacs/domdec/dlbtiming.h"
  52 #include "gromacs/domdec/domdec.h"
  53 #include "gromacs/domdec/domdec_struct.h"
  54 #include "gromacs/domdec/partition.h"
  55 #include "gromacs/essentialdynamics/edsam.h"
  56 #include "gromacs/ewald/pme.h"
  57 #include "gromacs/gmxlib/chargegroup.h"
  58 #include "gromacs/gmxlib/network.h"
  59 #include "gromacs/gmxlib/nrnb.h"
  60 #include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
  61 #include "gromacs/gmxlib/nonbonded/nb_kernel.h"
  62 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
  63 #include "gromacs/gpu_utils/gpu_utils.h"
  64 #include "gromacs/imd/imd.h"
  65 #include "gromacs/listed_forces/bonded.h"
  66 #include "gromacs/listed_forces/disre.h"
  67 #include "gromacs/listed_forces/gpubonded.h"
  68 #include "gromacs/listed_forces/manage_threading.h"
  69 #include "gromacs/listed_forces/orires.h"
  70 #include "gromacs/math/arrayrefwithpadding.h"
  71 #include "gromacs/math/functions.h"
  72 #include "gromacs/math/units.h"
  73 #include "gromacs/math/vec.h"
  74 #include "gromacs/math/vecdump.h"
  75 #include "gromacs/mdlib/calcmu.h"
  76 #include "gromacs/mdlib/calcvir.h"
  77 #include "gromacs/mdlib/constr.h"
  78 #include "gromacs/mdlib/force.h"
  79 #include "gromacs/mdlib/forcerec.h"
  80 #include "gromacs/mdlib/gmx_omp_nthreads.h"
  81 #include "gromacs/mdlib/mdrun.h"
  82 #include "gromacs/mdlib/ppforceworkload.h"
  83 #include "gromacs/mdlib/qmmm.h"
  84 #include "gromacs/mdlib/update.h"
  85 #include "gromacs/mdtypes/commrec.h"
  86 #include "gromacs/mdtypes/enerdata.h"
  87 #include "gromacs/mdtypes/forceoutput.h"
  88 #include "gromacs/mdtypes/iforceprovider.h"
  89 #include "gromacs/mdtypes/inputrec.h"
  90 #include "gromacs/mdtypes/md_enums.h"
  91 #include "gromacs/mdtypes/state.h"
  92 #include "gromacs/nbnxm/atomdata.h"
  93 #include "gromacs/nbnxm/gpu_data_mgmt.h"
  94 #include "gromacs/nbnxm/nbnxm.h"
  95 #include "gromacs/pbcutil/ishift.h"
  96 #include "gromacs/pbcutil/mshift.h"
  97 #include "gromacs/pbcutil/pbc.h"
  98 #include "gromacs/pulling/pull.h"
  99 #include "gromacs/pulling/pull_rotation.h"
 100 #include "gromacs/timing/cyclecounter.h"
 101 #include "gromacs/timing/gpu_timing.h"
 102 #include "gromacs/timing/wallcycle.h"
 103 #include "gromacs/timing/wallcyclereporting.h"
 104 #include "gromacs/timing/walltime_accounting.h"
 105 #include "gromacs/topology/topology.h"
 106 #include "gromacs/utility/arrayref.h"
 107 #include "gromacs/utility/basedefinitions.h"
 108 #include "gromacs/utility/cstringutil.h"
 109 #include "gromacs/utility/exceptions.h"
 110 #include "gromacs/utility/fatalerror.h"
 111 #include "gromacs/utility/gmxassert.h"
 112 #include "gromacs/utility/gmxmpi.h"
 113 #include "gromacs/utility/logger.h"
 114 #include "gromacs/utility/smalloc.h"
 115 #include "gromacs/utility/strconvert.h"
 116 #include "gromacs/utility/sysinfo.h"
 117
 118 // TODO: this environment variable allows us to verify before release
 119 // that on less common architectures the total cost of polling is not larger than
 120 // a blocking wait (so polling does not introduce overhead when the static
 121 // PME-first ordering would suffice).
 122 static const bool c_disableAlternatingWait = (getenv("GMX_DISABLE_ALTERNATING_GPU_WAIT") != nullptr);
 123
 124
 125 static void sum_forces(rvec f[], gmx::ArrayRef<const gmx::RVec> forceToAdd)
 126 {
 127     const int      end = forceToAdd.size();
 128
 129     int gmx_unused nt = gmx_omp_nthreads_get(emntDefault);
 130 #pragma omp parallel for num_threads(nt) schedule(static)
 131     for (int i = 0; i < end; i++)
 132     {
 133         rvec_inc(f[i], forceToAdd[i]);
 134     }
 135 }
 136
 137 static void calc_virial(int start, int homenr, const rvec x[], const rvec f[],
 138                         tensor vir_part, const t_graph *graph, const matrix box,
 139                         t_nrnb *nrnb, const t_forcerec *fr, int ePBC)
 140 {
 141     /* The short-range virial from surrounding boxes */
 142     calc_vir(SHIFTS, fr->shift_vec, fr->fshift, vir_part, ePBC == epbcSCREW, box);
 143     inc_nrnb(nrnb, eNR_VIRIAL, SHIFTS);
 144
 145     /* Calculate partial virial, for local atoms only, based on short range.
 146      * Total virial is computed in global_stat, called from do_md
 147      */
 148     f_calc_vir(start, start+homenr, x, f, vir_part, graph, box);
 149     inc_nrnb(nrnb, eNR_VIRIAL, homenr);
 150
 151     if (debug)
 152     {
 153         pr_rvecs(debug, 0, "vir_part", vir_part, DIM);
 154     }
 155 }
 156
 157 static void pull_potential_wrapper(const t_commrec *cr,
 158                                    const t_inputrec *ir,
 159                                    const matrix box, gmx::ArrayRef<const gmx::RVec> x,
 160                                    gmx::ForceWithVirial *force,
 161                                    const t_mdatoms *mdatoms,
 162                                    gmx_enerdata_t *enerd,
 163                                    const real *lambda,
 164                                    double t,
 165                                    gmx_wallcycle_t wcycle)
 166 {
 167     t_pbc  pbc;
 168     real   dvdl;
 169
 170     /* Calculate the center of mass forces, this requires communication,
 171      * which is why pull_potential is called close to other communication.
 172      */
 173     wallcycle_start(wcycle, ewcPULLPOT);
 174     set_pbc(&pbc, ir->ePBC, box);
 175     dvdl                     = 0;
 176     enerd->term[F_COM_PULL] +=
 177         pull_potential(ir->pull_work, mdatoms, &pbc,
 178                        cr, t, lambda[efptRESTRAINT], as_rvec_array(x.data()), force, &dvdl);
 179     enerd->dvdl_lin[efptRESTRAINT] += dvdl;
 180     wallcycle_stop(wcycle, ewcPULLPOT);
 181 }
 182
 183 static void pme_receive_force_ener(const t_commrec      *cr,
 184                                    gmx::ForceWithVirial *forceWithVirial,
 185                                    gmx_enerdata_t       *enerd,
 186                                    gmx_wallcycle_t       wcycle)
 187 {
 188     real   e_q, e_lj, dvdl_q, dvdl_lj;
 189     float  cycles_ppdpme, cycles_seppme;
 190
 191     cycles_ppdpme = wallcycle_stop(wcycle, ewcPPDURINGPME);
 192     dd_cycles_add(cr->dd, cycles_ppdpme, ddCyclPPduringPME);
 193
 194     /* In case of node-splitting, the PP nodes receive the long-range
 195      * forces, virial and energy from the PME nodes here.
 196      */
 197     wallcycle_start(wcycle, ewcPP_PMEWAITRECVF);
 198     dvdl_q  = 0;
 199     dvdl_lj = 0;
 200     gmx_pme_receive_f(cr, forceWithVirial, &e_q, &e_lj, &dvdl_q, &dvdl_lj,
 201                       &cycles_seppme);
 202     enerd->term[F_COUL_RECIP] += e_q;
 203     enerd->term[F_LJ_RECIP]   += e_lj;
 204     enerd->dvdl_lin[efptCOUL] += dvdl_q;
 205     enerd->dvdl_lin[efptVDW]  += dvdl_lj;
 206
 207     if (wcycle)
 208     {
 209         dd_cycles_add(cr->dd, cycles_seppme, ddCyclPME);
 210     }
 211     wallcycle_stop(wcycle, ewcPP_PMEWAITRECVF);
 212 }
 213
 214 static void print_large_forces(FILE            *fp,
 215                                const t_mdatoms *md,
 216                                const t_commrec *cr,
 217                                int64_t          step,
 218                                real             forceTolerance,
 219                                const rvec      *x,
 220                                const rvec      *f)
 221 {
 222     real           force2Tolerance = gmx::square(forceTolerance);
 223     gmx::index     numNonFinite    = 0;
 224     for (int i = 0; i < md->homenr; i++)
 225     {
 226         real force2    = norm2(f[i]);
 227         bool nonFinite = !std::isfinite(force2);
 228         if (force2 >= force2Tolerance || nonFinite)
 229         {
 230             fprintf(fp, "step %" PRId64 " atom %6d  x %8.3f %8.3f %8.3f  force %12.5e\n",
 231                     step,
 232                     ddglatnr(cr->dd, i), x[i][XX], x[i][YY], x[i][ZZ], std::sqrt(force2));
 233         }
 234         if (nonFinite)
 235         {
 236             numNonFinite++;
 237         }
 238     }
 239     if (numNonFinite > 0)
 240     {
 241         /* Note that with MPI this fatal call on one rank might interrupt
 242          * the printing on other ranks. But we can only avoid that with
 243          * an expensive MPI barrier that we would need at each step.
 244          */
 245         gmx_fatal(FARGS, "At step %" PRId64 " detected non-finite forces on %td atoms", step, numNonFinite);
 246     }
 247 }
 248
 249 static void post_process_forces(const t_commrec           *cr,
 250                                 int64_t                    step,
 251                                 t_nrnb                    *nrnb,
 252                                 gmx_wallcycle_t            wcycle,
 253                                 const gmx_localtop_t      *top,
 254                                 const matrix               box,
 255                                 const rvec                 x[],
 256                                 rvec                       f[],
 257                                 gmx::ForceWithVirial      *forceWithVirial,
 258                                 tensor                     vir_force,
 259                                 const t_mdatoms           *mdatoms,
 260                                 const t_graph             *graph,
 261                                 const t_forcerec          *fr,
 262                                 const gmx_vsite_t         *vsite,
 263                                 int                        flags)
 264 {
 265     if (fr->haveDirectVirialContributions)
 266     {
 267         rvec *fDirectVir = as_rvec_array(forceWithVirial->force_.data());
 268
 269         if (vsite)
 270         {
 271             /* Spread the mesh force on virtual sites to the other particles...
 272              * This is parallellized. MPI communication is performed
 273              * if the constructing atoms aren't local.
 274              */
 275             matrix virial = { { 0 } };
 276             spread_vsite_f(vsite, x, fDirectVir, nullptr,
 277                            (flags & GMX_FORCE_VIRIAL) != 0, virial,
 278                            nrnb,
 279                            &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr, wcycle);
 280             forceWithVirial->addVirialContribution(virial);
 281         }
 282
 283         if (flags & GMX_FORCE_VIRIAL)
 284         {
 285             /* Now add the forces, this is local */
 286             sum_forces(f, forceWithVirial->force_);
 287
 288             /* Add the direct virial contributions */
 289             GMX_ASSERT(forceWithVirial->computeVirial_, "forceWithVirial should request virial computation when we request the virial");
 290             m_add(vir_force, forceWithVirial->getVirial(), vir_force);
 291
 292             if (debug)
 293             {
 294                 pr_rvecs(debug, 0, "vir_force", vir_force, DIM);
 295             }
 296         }
 297     }
 298
 299     if (fr->print_force >= 0)
 300     {
 301         print_large_forces(stderr, mdatoms, cr, step, fr->print_force, x, f);
 302     }
 303 }
 304
 305 static void do_nb_verlet(t_forcerec                       *fr,
 306                          const interaction_const_t        *ic,
 307                          gmx_enerdata_t                   *enerd,
 308                          const int                         flags,
 309                          const Nbnxm::InteractionLocality  ilocality,
 310                          const int                         clearF,
 311                          const int64_t                     step,
 312                          t_nrnb                           *nrnb,
 313                          gmx_wallcycle_t                   wcycle)
 314 {
 315     if (!(flags & GMX_FORCE_NONBONDED))
 316     {
 317         /* skip non-bonded calculation */
 318         return;
 319     }
 320
 321     nonbonded_verlet_t *nbv  = fr->nbv.get();
 322
 323     /* GPU kernel launch overhead is already timed separately */
 324     if (fr->cutoff_scheme != ecutsVERLET)
 325     {
 326         gmx_incons("Invalid cut-off scheme passed!");
 327     }
 328
 329     if (!nbv->useGpu())
 330     {
 331         /* When dynamic pair-list  pruning is requested, we need to prune
 332          * at nstlistPrune steps.
 333          */
 334         if (nbv->pairlistSets().isDynamicPruningStepCpu(step))
 335         {
 336             /* Prune the pair-list beyond fr->ic->rlistPrune using
 337              * the current coordinates of the atoms.
 338              */
 339             wallcycle_sub_start(wcycle, ewcsNONBONDED_PRUNING);
 340             nbv->dispatchPruneKernelCpu(ilocality, fr->shift_vec);
 341             wallcycle_sub_stop(wcycle, ewcsNONBONDED_PRUNING);
 342         }
 343
 344         wallcycle_sub_start(wcycle, ewcsNONBONDED);
 345     }
 346
 347     nbv->dispatchNonbondedKernel(ilocality, *ic, flags, clearF, fr, enerd, nrnb);
 348
 349     if (!nbv->useGpu())
 350     {
 351         wallcycle_sub_stop(wcycle, ewcsNONBONDED);
 352     }
 353 }
 354
 355 gmx_bool use_GPU(const nonbonded_verlet_t *nbv)
 356 {
 357     return nbv != nullptr && nbv->useGpu();
 358 }
 359
 360 static inline void clear_rvecs_omp(int n, rvec v[])
 361 {
 362     int nth = gmx_omp_nthreads_get_simple_rvec_task(emntDefault, n);
 363
 364     /* Note that we would like to avoid this conditional by putting it
 365      * into the omp pragma instead, but then we still take the full
 366      * omp parallel for overhead (at least with gcc5).
 367      */
 368     if (nth == 1)
 369     {
 370         for (int i = 0; i < n; i++)
 371         {
 372             clear_rvec(v[i]);
 373         }
 374     }
 375     else
 376     {
 377 #pragma omp parallel for num_threads(nth) schedule(static)
 378         for (int i = 0; i < n; i++)
 379         {
 380             clear_rvec(v[i]);
 381         }
 382     }
 383 }
 384
 385 /*! \brief Return an estimate of the average kinetic energy or 0 when unreliable
 386  *
 387  * \param groupOptions  Group options, containing T-coupling options
 388  */
 389 static real averageKineticEnergyEstimate(const t_grpopts &groupOptions)
 390 {
 391     real nrdfCoupled   = 0;
 392     real nrdfUncoupled = 0;
 393     real kineticEnergy = 0;
 394     for (int g = 0; g < groupOptions.ngtc; g++)
 395     {
 396         if (groupOptions.tau_t[g] >= 0)
 397         {
 398             nrdfCoupled   += groupOptions.nrdf[g];
 399             kineticEnergy += groupOptions.nrdf[g]*0.5*groupOptions.ref_t[g]*BOLTZ;
 400         }
 401         else
 402         {
 403             nrdfUncoupled += groupOptions.nrdf[g];
 404         }
 405     }
 406
 407     /* This conditional with > also catches nrdf=0 */
 408     if (nrdfCoupled > nrdfUncoupled)
 409     {
 410         return kineticEnergy*(nrdfCoupled + nrdfUncoupled)/nrdfCoupled;
 411     }
 412     else
 413     {
 414         return 0;
 415     }
 416 }
 417
 418 /*! \brief This routine checks that the potential energy is finite.
 419  *
 420  * Always checks that the potential energy is finite. If step equals
 421  * inputrec.init_step also checks that the magnitude of the potential energy
 422  * is reasonable. Terminates with a fatal error when a check fails.
 423  * Note that passing this check does not guarantee finite forces,
 424  * since those use slightly different arithmetics. But in most cases
 425  * there is just a narrow coordinate range where forces are not finite
 426  * and energies are finite.
 427  *
 428  * \param[in] step      The step number, used for checking and printing
 429  * \param[in] enerd     The energy data; the non-bonded group energies need to be added to enerd.term[F_EPOT] before calling this routine
 430  * \param[in] inputrec  The input record
 431  */
 432 static void checkPotentialEnergyValidity(int64_t               step,
 433                                          const gmx_enerdata_t &enerd,
 434                                          const t_inputrec     &inputrec)
 435 {
 436     /* Threshold valid for comparing absolute potential energy against
 437      * the kinetic energy. Normally one should not consider absolute
 438      * potential energy values, but with a factor of one million
 439      * we should never get false positives.
 440      */
 441     constexpr real c_thresholdFactor = 1e6;
 442
 443     bool           energyIsNotFinite    = !std::isfinite(enerd.term[F_EPOT]);
 444     real           averageKineticEnergy = 0;
 445     /* We only check for large potential energy at the initial step,
 446      * because that is by far the most likely step for this too occur
 447      * and because computing the average kinetic energy is not free.
 448      * Note: nstcalcenergy >> 1 often does not allow to catch large energies
 449      * before they become NaN.
 450      */
 451     if (step == inputrec.init_step && EI_DYNAMICS(inputrec.eI))
 452     {
 453         averageKineticEnergy = averageKineticEnergyEstimate(inputrec.opts);
 454     }
 455
 456     if (energyIsNotFinite || (averageKineticEnergy > 0 &&
 457                               enerd.term[F_EPOT] > c_thresholdFactor*averageKineticEnergy))
 458     {
 459         gmx_fatal(FARGS, "Step %" PRId64 ": The total potential energy is %g, which is %s. The LJ and electrostatic contributions to the energy are %g and %g, respectively. A %s potential energy can be caused by overlapping interactions in bonded interactions or very large%s coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology.",
 460                   step,
 461                   enerd.term[F_EPOT],
 462                   energyIsNotFinite ? "not finite" : "extremely high",
 463                   enerd.term[F_LJ],
 464                   enerd.term[F_COUL_SR],
 465                   energyIsNotFinite ? "non-finite" : "very high",
 466                   energyIsNotFinite ? " or Nan" : "");
 467     }
 468 }
 469
 470 /*! \brief Compute forces and/or energies for special algorithms
 471  *
 472  * The intention is to collect all calls to algorithms that compute
 473  * forces on local atoms only and that do not contribute to the local
 474  * virial sum (but add their virial contribution separately).
 475  * Eventually these should likely all become ForceProviders.
 476  * Within this function the intention is to have algorithms that do
 477  * global communication at the end, so global barriers within the MD loop
 478  * are as close together as possible.
 479  *
 480  * \param[in]     fplog            The log file
 481  * \param[in]     cr               The communication record
 482  * \param[in]     inputrec         The input record
 483  * \param[in]     awh              The Awh module (nullptr if none in use).
 484  * \param[in]     enforcedRotation Enforced rotation module.
 485  * \param[in]     step             The current MD step
 486  * \param[in]     t                The current time
 487  * \param[in,out] wcycle           Wallcycle accounting struct
 488  * \param[in,out] forceProviders   Pointer to a list of force providers
 489  * \param[in]     box              The unit cell
 490  * \param[in]     x                The coordinates
 491  * \param[in]     mdatoms          Per atom properties
 492  * \param[in]     lambda           Array of free-energy lambda values
 493  * \param[in]     forceFlags       Flags that tell whether we should compute forces/energies/virial
 494  * \param[in,out] forceWithVirial  Force and virial buffers
 495  * \param[in,out] enerd            Energy buffer
 496  * \param[in,out] ed               Essential dynamics pointer
 497  * \param[in]     bNS              Tells if we did neighbor searching this step, used for ED sampling
 498  *
 499  * \todo Remove bNS, which is used incorrectly.
 500  * \todo Convert all other algorithms called here to ForceProviders.
 501  */
 502 static void
 503 computeSpecialForces(FILE                          *fplog,
 504                      const t_commrec               *cr,
 505                      const t_inputrec              *inputrec,
 506                      gmx::Awh                      *awh,
 507                      gmx_enfrot                    *enforcedRotation,
 508                      int64_t                        step,
 509                      double                         t,
 510                      gmx_wallcycle_t                wcycle,
 511                      ForceProviders                *forceProviders,
 512                      matrix                         box,
 513                      gmx::ArrayRef<const gmx::RVec> x,
 514                      const t_mdatoms               *mdatoms,
 515                      real                          *lambda,
 516                      int                            forceFlags,
 517                      gmx::ForceWithVirial          *forceWithVirial,
 518                      gmx_enerdata_t                *enerd,
 519                      gmx_edsam                     *ed,
 520                      gmx_bool                       bNS)
 521 {
 522     const bool computeForces = (forceFlags & GMX_FORCE_FORCES) != 0;
 523
 524     /* NOTE: Currently all ForceProviders only provide forces.
 525      *       When they also provide energies, remove this conditional.
 526      */
 527     if (computeForces)
 528     {
 529         gmx::ForceProviderInput  forceProviderInput(x, *mdatoms, t, box, *cr);
 530         gmx::ForceProviderOutput forceProviderOutput(forceWithVirial, enerd);
 531
 532         /* Collect forces from modules */
 533         forceProviders->calculateForces(forceProviderInput, &forceProviderOutput);
 534     }
 535
 536     if (inputrec->bPull && pull_have_potential(inputrec->pull_work))
 537     {
 538         pull_potential_wrapper(cr, inputrec, box, x,
 539                                forceWithVirial,
 540                                mdatoms, enerd, lambda, t,
 541                                wcycle);
 542
 543         if (awh)
 544         {
 545             enerd->term[F_COM_PULL] +=
 546                 awh->applyBiasForcesAndUpdateBias(inputrec->ePBC, *mdatoms, box,
 547                                                   forceWithVirial,
 548                                                   t, step, wcycle, fplog);
 549         }
 550     }
 551
 552     rvec *f = as_rvec_array(forceWithVirial->force_.data());
 553
 554     /* Add the forces from enforced rotation potentials (if any) */
 555     if (inputrec->bRot)
 556     {
 557         wallcycle_start(wcycle, ewcROTadd);
 558         enerd->term[F_COM_PULL] += add_rot_forces(enforcedRotation, f, cr, step, t);
 559         wallcycle_stop(wcycle, ewcROTadd);
 560     }
 561
 562     if (ed)
 563     {
 564         /* Note that since init_edsam() is called after the initialization
 565          * of forcerec, edsam doesn't request the noVirSum force buffer.
 566          * Thus if no other algorithm (e.g. PME) requires it, the forces
 567          * here will contribute to the virial.
 568          */
 569         do_flood(cr, inputrec, as_rvec_array(x.data()), f, ed, box, step, bNS);
 570     }
 571
 572     /* Add forces from interactive molecular dynamics (IMD), if bIMD == TRUE. */
 573     if (inputrec->bIMD && computeForces)
 574     {
 575         IMD_apply_forces(inputrec->bIMD, inputrec->imd, cr, f, wcycle);
 576     }
 577 }
 578
 579 /*! \brief Launch the prepare_step and spread stages of PME GPU.
 580  *
 581  * \param[in]  pmedata       The PME structure
 582  * \param[in]  box           The box matrix
 583  * \param[in]  x             Coordinate array
 584  * \param[in]  flags         Force flags
 585  * \param[in]  pmeFlags      PME flags
 586  * \param[in]  wcycle        The wallcycle structure
 587  */
 588 static inline void launchPmeGpuSpread(gmx_pme_t      *pmedata,
 589                                       matrix          box,
 590                                       rvec            x[],
 591                                       int             flags,
 592                                       int             pmeFlags,
 593                                       gmx_wallcycle_t wcycle)
 594 {
 595     pme_gpu_prepare_computation(pmedata, (flags & GMX_FORCE_DYNAMICBOX) != 0, box, wcycle, pmeFlags);
 596     pme_gpu_launch_spread(pmedata, x, wcycle);
 597 }
 598
 599 /*! \brief Launch the FFT and gather stages of PME GPU
 600  *
 601  * This function only implements setting the output forces (no accumulation).
 602  *
 603  * \param[in]  pmedata        The PME structure
 604  * \param[in]  wcycle         The wallcycle structure
 605  */
 606 static void launchPmeGpuFftAndGather(gmx_pme_t        *pmedata,
 607                                      gmx_wallcycle_t   wcycle)
 608 {
 609     pme_gpu_launch_complex_transforms(pmedata, wcycle);
 610     pme_gpu_launch_gather(pmedata, wcycle, PmeForceOutputHandling::Set);
 611 }
 612
 613 /*! \brief
 614  *  Polling wait for either of the PME or nonbonded GPU tasks.
 615  *
 616  * Instead of a static order in waiting for GPU tasks, this function
 617  * polls checking which of the two tasks completes first, and does the
 618  * associated force buffer reduction overlapped with the other task.
 619  * By doing that, unlike static scheduling order, it can always overlap
 620  * one of the reductions, regardless of the GPU task completion order.
 621  *
 622  * \param[in]     nbv              Nonbonded verlet structure
 623  * \param[in,out] pmedata          PME module data
 624  * \param[in,out] force            Force array to reduce task outputs into.
 625  * \param[in,out] forceWithVirial  Force and virial buffers
 626  * \param[in,out] fshift           Shift force output vector results are reduced into
 627  * \param[in,out] enerd            Energy data structure results are reduced into
 628  * \param[in]     flags            Force flags
 629  * \param[in]     pmeFlags         PME flags
 630  * \param[in]     haveOtherWork    Tells whether there is other work than non-bonded in the stream(s)
 631  * \param[in]     wcycle           The wallcycle structure
 632  */
 633 static void alternatePmeNbGpuWaitReduce(nonbonded_verlet_t                  *nbv,
 634                                         gmx_pme_t                           *pmedata,
 635                                         gmx::ArrayRefWithPadding<gmx::RVec> *force,
 636                                         gmx::ForceWithVirial                *forceWithVirial,
 637                                         rvec                                 fshift[],
 638                                         gmx_enerdata_t                      *enerd,
 639                                         int                                  flags,
 640                                         int                                  pmeFlags,
 641                                         bool                                 haveOtherWork,
 642                                         gmx_wallcycle_t                      wcycle)
 643 {
 644     bool isPmeGpuDone = false;
 645     bool isNbGpuDone  = false;
 646
 647
 648     gmx::ArrayRef<const gmx::RVec> pmeGpuForces;
 649
 650     while (!isPmeGpuDone || !isNbGpuDone)
 651     {
 652         if (!isPmeGpuDone)
 653         {
 654             GpuTaskCompletion completionType = (isNbGpuDone) ? GpuTaskCompletion::Wait : GpuTaskCompletion::Check;
 655             isPmeGpuDone = pme_gpu_try_finish_task(pmedata, pmeFlags, wcycle, forceWithVirial, enerd, completionType);
 656         }
 657
 658         if (!isNbGpuDone)
 659         {
 660             GpuTaskCompletion completionType = (isPmeGpuDone) ? GpuTaskCompletion::Wait : GpuTaskCompletion::Check;
 661             wallcycle_start_nocount(wcycle, ewcWAIT_GPU_NB_L);
 662             isNbGpuDone = Nbnxm::gpu_try_finish_task(nbv->gpu_nbv,
 663                                                      flags,
 664                                                      Nbnxm::AtomLocality::Local,
 665                                                      haveOtherWork,
 666                                                      enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
 667                                                      fshift, completionType);
 668             wallcycle_stop(wcycle, ewcWAIT_GPU_NB_L);
 669             // To get the call count right, when the task finished we
 670             // issue a start/stop.
 671             // TODO: move the ewcWAIT_GPU_NB_L cycle counting into nbnxn_gpu_try_finish_task()
 672             // and ewcNB_XF_BUF_OPS counting into nbnxn_atomdata_add_nbat_f_to_f().
 673             if (isNbGpuDone)
 674             {
 675                 wallcycle_start(wcycle, ewcWAIT_GPU_NB_L);
 676                 wallcycle_stop(wcycle, ewcWAIT_GPU_NB_L);
 677
 678                 nbv->atomdata_add_nbat_f_to_f(Nbnxm::AtomLocality::Local,
 679                                               as_rvec_array(force->unpaddedArrayRef().data()), wcycle);
 680             }
 681         }
 682     }
 683 }
 684
 685 static void do_force_cutsVERLET(FILE *fplog,
 686                                 const t_commrec *cr,
 687                                 const gmx_multisim_t *ms,
 688                                 const t_inputrec *inputrec,
 689                                 gmx::Awh *awh,
 690                                 gmx_enfrot *enforcedRotation,
 691                                 int64_t step,
 692                                 t_nrnb *nrnb,
 693                                 gmx_wallcycle_t wcycle,
 694                                 const gmx_localtop_t *top,
 695                                 const gmx_groups_t * /* groups */,
 696                                 matrix box, gmx::ArrayRefWithPadding<gmx::RVec> x,
 697                                 history_t *hist,
 698                                 gmx::ArrayRefWithPadding<gmx::RVec> force,
 699                                 tensor vir_force,
 700                                 const t_mdatoms *mdatoms,
 701                                 gmx_enerdata_t *enerd, t_fcdata *fcd,
 702                                 real *lambda,
 703                                 t_graph *graph,
 704                                 t_forcerec *fr,
 705                                 gmx::PpForceWorkload *ppForceWorkload,
 706                                 interaction_const_t *ic,
 707                                 const gmx_vsite_t *vsite,
 708                                 rvec mu_tot,
 709                                 double t,
 710                                 gmx_edsam *ed,
 711                                 const int flags,
 712                                 const DDBalanceRegionHandler &ddBalanceRegionHandler)
 713 {
 714     int                 cg1, i, j;
 715     double              mu[2*DIM];
 716     gmx_bool            bStateChanged, bNS, bFillGrid, bCalcCGCM;
 717     gmx_bool            bDoForces, bUseGPU, bUseOrEmulGPU;
 718     rvec                vzero, box_diag;
 719     float               cycles_pme, cycles_wait_gpu;
 720     nonbonded_verlet_t *nbv = fr->nbv.get();
 721
 722     bStateChanged = ((flags & GMX_FORCE_STATECHANGED) != 0);
 723     bNS           = ((flags & GMX_FORCE_NS) != 0);
 724     bFillGrid     = (bNS && bStateChanged);
 725     bCalcCGCM     = (bFillGrid && !DOMAINDECOMP(cr));
 726     bDoForces     = ((flags & GMX_FORCE_FORCES) != 0);
 727     bUseGPU       = fr->nbv->useGpu();
 728     bUseOrEmulGPU = bUseGPU || fr->nbv->emulateGpu();
 729
 730     const auto pmeRunMode = fr->pmedata ? pme_run_mode(fr->pmedata) : PmeRunMode::CPU;
 731     // TODO slim this conditional down - inputrec and duty checks should mean the same in proper code!
 732     const bool useGpuPme  = EEL_PME(fr->ic->eeltype) && thisRankHasDuty(cr, DUTY_PME) &&
 733         ((pmeRunMode == PmeRunMode::GPU) || (pmeRunMode == PmeRunMode::Mixed));
 734     const int  pmeFlags = GMX_PME_SPREAD | GMX_PME_SOLVE |
 735         ((flags & GMX_FORCE_VIRIAL) ? GMX_PME_CALC_ENER_VIR : 0) |
 736         ((flags & GMX_FORCE_ENERGY) ? GMX_PME_CALC_ENER_VIR : 0) |
 737         ((flags & GMX_FORCE_FORCES) ? GMX_PME_CALC_F : 0);
 738
 739     /* At a search step we need to start the first balancing region
 740      * somewhere early inside the step after communication during domain
 741      * decomposition (and not during the previous step as usual).
 742      */
 743     if (bNS)
 744     {
 745         ddBalanceRegionHandler.openBeforeForceComputationCpu(DdAllowBalanceRegionReopen::yes);
 746     }
 747
 748     cycles_wait_gpu = 0;
 749
 750     const int start  = 0;
 751     const int homenr = mdatoms->homenr;
 752
 753     clear_mat(vir_force);
 754
 755     if (DOMAINDECOMP(cr))
 756     {
 757         cg1 = cr->dd->globalAtomGroupIndices.size();
 758     }
 759     else
 760     {
 761         cg1 = top->cgs.nr;
 762     }
 763     if (fr->n_tpi > 0)
 764     {
 765         cg1--;
 766     }
 767
 768     if (bStateChanged)
 769     {
 770         update_forcerec(fr, box);
 771
 772         if (inputrecNeedMutot(inputrec))
 773         {
 774             /* Calculate total (local) dipole moment in a temporary common array.
 775              * This makes it possible to sum them over nodes faster.
 776              */
 777             calc_mu(start, homenr,
 778                     x.unpaddedArrayRef(), mdatoms->chargeA, mdatoms->chargeB, mdatoms->nChargePerturbed,
 779                     mu, mu+DIM);
 780         }
 781     }
 782
 783     if (fr->ePBC != epbcNONE)
 784     {
 785         /* Compute shift vectors every step,
 786          * because of pressure coupling or box deformation!
 787          */
 788         if ((flags & GMX_FORCE_DYNAMICBOX) && bStateChanged)
 789         {
 790             calc_shifts(box, fr->shift_vec);
 791         }
 792
 793         if (bCalcCGCM)
 794         {
 795             put_atoms_in_box_omp(fr->ePBC, box, x.unpaddedArrayRef().subArray(0, homenr));
 796             inc_nrnb(nrnb, eNR_SHIFTX, homenr);
 797         }
 798         else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph)
 799         {
 800             unshift_self(graph, box, as_rvec_array(x.unpaddedArrayRef().data()));
 801         }
 802     }
 803
 804     nbnxn_atomdata_copy_shiftvec((flags & GMX_FORCE_DYNAMICBOX) != 0,
 805                                  fr->shift_vec, nbv->nbat.get());
 806
 807 #if GMX_MPI
 808     if (!thisRankHasDuty(cr, DUTY_PME))
 809     {
 810         /* Send particle coordinates to the pme nodes.
 811          * Since this is only implemented for domain decomposition
 812          * and domain decomposition does not use the graph,
 813          * we do not need to worry about shifting.
 814          */
 815         gmx_pme_send_coordinates(cr, box, as_rvec_array(x.unpaddedArrayRef().data()),
 816                                  lambda[efptCOUL], lambda[efptVDW],
 817                                  (flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY)) != 0,
 818                                  step, wcycle);
 819     }
 820 #endif /* GMX_MPI */
 821
 822     if (useGpuPme)
 823     {
 824         launchPmeGpuSpread(fr->pmedata, box, as_rvec_array(x.unpaddedArrayRef().data()), flags, pmeFlags, wcycle);
 825     }
 826
 827     /* do gridding for pair search */
 828     if (bNS)
 829     {
 830         if (graph && bStateChanged)
 831         {
 832             /* Calculate intramolecular shift vectors to make molecules whole */
 833             mk_mshift(fplog, graph, fr->ePBC, box, as_rvec_array(x.unpaddedArrayRef().data()));
 834         }
 835
 836         clear_rvec(vzero);
 837         box_diag[XX] = box[XX][XX];
 838         box_diag[YY] = box[YY][YY];
 839         box_diag[ZZ] = box[ZZ][ZZ];
 840
 841         wallcycle_start(wcycle, ewcNS);
 842         if (!DOMAINDECOMP(cr))
 843         {
 844             wallcycle_sub_start(wcycle, ewcsNBS_GRID_LOCAL);
 845             nbnxn_put_on_grid(nbv, box,
 846                               0, vzero, box_diag,
 847                               nullptr, 0, mdatoms->homenr, -1,
 848                               fr->cginfo, x.unpaddedArrayRef(),
 849                               0, nullptr);
 850             wallcycle_sub_stop(wcycle, ewcsNBS_GRID_LOCAL);
 851         }
 852         else
 853         {
 854             wallcycle_sub_start(wcycle, ewcsNBS_GRID_NONLOCAL);
 855             nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd),
 856                                        fr->cginfo, x.unpaddedArrayRef());
 857             wallcycle_sub_stop(wcycle, ewcsNBS_GRID_NONLOCAL);
 858         }
 859
 860         nbnxn_atomdata_set(nbv->nbat.get(), nbv->nbs.get(), mdatoms, fr->cginfo);
 861
 862         wallcycle_stop(wcycle, ewcNS);
 863     }
 864
 865     /* initialize the GPU atom data and copy shift vector */
 866     if (bUseGPU)
 867     {
 868         wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
 869         wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
 870
 871         if (bNS)
 872         {
 873             Nbnxm::gpu_init_atomdata(nbv->gpu_nbv, nbv->nbat.get());
 874         }
 875
 876         Nbnxm::gpu_upload_shiftvec(nbv->gpu_nbv, nbv->nbat.get());
 877
 878         wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
 879
 880         if (bNS && fr->gpuBonded)
 881         {
 882             /* Now we put all atoms on the grid, we can assign bonded
 883              * interactions to the GPU, where the grid order is
 884              * needed. Also the xq, f and fshift device buffers have
 885              * been reallocated if needed, so the bonded code can
 886              * learn about them. */
 887             // TODO the xq, f, and fshift buffers are now shared
 888             // resources, so they should be maintained by a
 889             // higher-level object than the nb module.
 890             fr->gpuBonded->updateInteractionListsAndDeviceBuffers(nbnxn_get_gridindices(fr->nbv->nbs.get()),
 891                                                                   top->idef,
 892                                                                   Nbnxm::gpu_get_xq(nbv->gpu_nbv),
 893                                                                   Nbnxm::gpu_get_f(nbv->gpu_nbv),
 894                                                                   Nbnxm::gpu_get_fshift(nbv->gpu_nbv));
 895             ppForceWorkload->haveGpuBondedWork = fr->gpuBonded->haveInteractions();
 896         }
 897
 898         wallcycle_stop(wcycle, ewcLAUNCH_GPU);
 899     }
 900
 901     /* do local pair search */
 902     if (bNS)
 903     {
 904         wallcycle_start_nocount(wcycle, ewcNS);
 905         wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_LOCAL);
 906         /* Note that with a GPU the launch overhead of the list transfer is not timed separately */
 907         nbv->constructPairlist(Nbnxm::InteractionLocality::Local,
 908                                &top->excls, step, nrnb);
 909         wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_LOCAL);
 910         wallcycle_stop(wcycle, ewcNS);
 911     }
 912     else
 913     {
 914         nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs.get(), Nbnxm::AtomLocality::Local,
 915                                         FALSE, as_rvec_array(x.unpaddedArrayRef().data()),
 916                                         nbv->nbat.get(), wcycle);
 917     }
 918
 919     if (bUseGPU)
 920     {
 921         ddBalanceRegionHandler.openBeforeForceComputationGpu();
 922
 923         wallcycle_start(wcycle, ewcLAUNCH_GPU);
 924
 925         wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
 926         Nbnxm::gpu_copy_xq_to_gpu(nbv->gpu_nbv, nbv->nbat.get(),
 927                                   Nbnxm::AtomLocality::Local,
 928                                   ppForceWorkload->haveGpuBondedWork);
 929         wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
 930
 931         // bonded work not split into separate local and non-local, so with DD
 932         // we can only launch the kernel after non-local coordinates have been received.
 933         if (ppForceWorkload->haveGpuBondedWork && !havePPDomainDecomposition(cr))
 934         {
 935             wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_BONDED);
 936             fr->gpuBonded->launchKernels(fr, flags, box);
 937             wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_BONDED);
 938         }
 939
 940         /* launch local nonbonded work on GPU */
 941         wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
 942         do_nb_verlet(fr, ic, enerd, flags, Nbnxm::InteractionLocality::Local, enbvClearFNo,
 943                      step, nrnb, wcycle);
 944         wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
 945         wallcycle_stop(wcycle, ewcLAUNCH_GPU);
 946     }
 947
 948     if (useGpuPme)
 949     {
 950         // In PME GPU and mixed mode we launch FFT / gather after the
 951         // X copy/transform to allow overlap as well as after the GPU NB
 952         // launch to avoid FFT launch overhead hijacking the CPU and delaying
 953         // the nonbonded kernel.
 954         launchPmeGpuFftAndGather(fr->pmedata, wcycle);
 955     }
 956
 957     /* Communicate coordinates and sum dipole if necessary +
 958        do non-local pair search */
 959     if (havePPDomainDecomposition(cr))
 960     {
 961         if (bNS)
 962         {
 963             wallcycle_start_nocount(wcycle, ewcNS);
 964             wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_NONLOCAL);
 965             /* Note that with a GPU the launch overhead of the list transfer is not timed separately */
 966             nbv->constructPairlist(Nbnxm::InteractionLocality::NonLocal,
 967                                    &top->excls, step, nrnb);
 968             wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_NONLOCAL);
 969             wallcycle_stop(wcycle, ewcNS);
 970         }
 971         else
 972         {
 973             dd_move_x(cr->dd, box, x.unpaddedArrayRef(), wcycle);
 974
 975             nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs.get(), Nbnxm::AtomLocality::NonLocal,
 976                                             FALSE, as_rvec_array(x.unpaddedArrayRef().data()),
 977                                             nbv->nbat.get(), wcycle);
 978         }
 979
 980         if (bUseGPU)
 981         {
 982             wallcycle_start(wcycle, ewcLAUNCH_GPU);
 983
 984             /* launch non-local nonbonded tasks on GPU */
 985             wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
 986             Nbnxm::gpu_copy_xq_to_gpu(nbv->gpu_nbv, nbv->nbat.get(),
 987                                       Nbnxm::AtomLocality::NonLocal,
 988                                       ppForceWorkload->haveGpuBondedWork);
 989             wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
 990
 991             if (ppForceWorkload->haveGpuBondedWork)
 992             {
 993                 wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_BONDED);
 994                 fr->gpuBonded->launchKernels(fr, flags, box);
 995                 wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_BONDED);
 996             }
 997
 998             wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
 999             do_nb_verlet(fr, ic, enerd, flags, Nbnxm::InteractionLocality::NonLocal, enbvClearFNo,
1000                          step, nrnb, wcycle);
1001             wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1002
1003             wallcycle_stop(wcycle, ewcLAUNCH_GPU);
1004         }
1005     }
1006
1007     if (bUseGPU)
1008     {
1009         /* launch D2H copy-back F */
1010         wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
1011         wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1012         if (havePPDomainDecomposition(cr))
1013         {
1014             Nbnxm::gpu_launch_cpyback(nbv->gpu_nbv, nbv->nbat.get(),
1015                                       flags, Nbnxm::AtomLocality::NonLocal, ppForceWorkload->haveGpuBondedWork);
1016         }
1017         Nbnxm::gpu_launch_cpyback(nbv->gpu_nbv, nbv->nbat.get(),
1018                                   flags, Nbnxm::AtomLocality::Local, ppForceWorkload->haveGpuBondedWork);
1019         wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1020
1021         if (ppForceWorkload->haveGpuBondedWork && (flags & GMX_FORCE_ENERGY))
1022         {
1023             wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_BONDED);
1024             fr->gpuBonded->launchEnergyTransfer();
1025             wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_BONDED);
1026         }
1027         wallcycle_stop(wcycle, ewcLAUNCH_GPU);
1028     }
1029
1030     if (bStateChanged && inputrecNeedMutot(inputrec))
1031     {
1032         if (PAR(cr))
1033         {
1034             gmx_sumd(2*DIM, mu, cr);
1035
1036             ddBalanceRegionHandler.reopenRegionCpu();
1037         }
1038
1039         for (i = 0; i < 2; i++)
1040         {
1041             for (j = 0; j < DIM; j++)
1042             {
1043                 fr->mu_tot[i][j] = mu[i*DIM + j];
1044             }
1045         }
1046     }
1047     if (fr->efep == efepNO)
1048     {
1049         copy_rvec(fr->mu_tot[0], mu_tot);
1050     }
1051     else
1052     {
1053         for (j = 0; j < DIM; j++)
1054         {
1055             mu_tot[j] =
1056                 (1.0 - lambda[efptCOUL])*fr->mu_tot[0][j] +
1057                 lambda[efptCOUL]*fr->mu_tot[1][j];
1058         }
1059     }
1060
1061     /* Reset energies */
1062     reset_enerdata(enerd);
1063     clear_rvecs(SHIFTS, fr->fshift);
1064
1065     if (DOMAINDECOMP(cr) && !thisRankHasDuty(cr, DUTY_PME))
1066     {
1067         wallcycle_start(wcycle, ewcPPDURINGPME);
1068         dd_force_flop_start(cr->dd, nrnb);
1069     }
1070
1071     if (inputrec->bRot)
1072     {
1073         wallcycle_start(wcycle, ewcROT);
1074         do_rotation(cr, enforcedRotation, box, as_rvec_array(x.unpaddedArrayRef().data()), t, step, bNS);
1075         wallcycle_stop(wcycle, ewcROT);
1076     }
1077
1078     /* Temporary solution until all routines take PaddedRVecVector */
1079     rvec *const f = as_rvec_array(force.unpaddedArrayRef().data());
1080
1081     /* Start the force cycle counter.
1082      * Note that a different counter is used for dynamic load balancing.
1083      */
1084     wallcycle_start(wcycle, ewcFORCE);
1085
1086     gmx::ArrayRef<gmx::RVec> forceRef = force.unpaddedArrayRef();
1087     if (bDoForces)
1088     {
1089         /* If we need to compute the virial, we might need a separate
1090          * force buffer for algorithms for which the virial is calculated
1091          * directly, such as PME.
1092          */
1093         if ((flags & GMX_FORCE_VIRIAL) && fr->haveDirectVirialContributions)
1094         {
1095             forceRef = *fr->forceBufferForDirectVirialContributions;
1096
1097             /* TODO: update comment
1098              * We only compute forces on local atoms. Note that vsites can
1099              * spread to non-local atoms, but that part of the buffer is
1100              * cleared separately in the vsite spreading code.
1101              */
1102             clear_rvecs_omp(forceRef.size(), as_rvec_array(forceRef.data()));
1103         }
1104         /* Clear the short- and long-range forces */
1105         clear_rvecs_omp(fr->natoms_force_constr, f);
1106     }
1107
1108     /* forceWithVirial uses the local atom range only */
1109     gmx::ForceWithVirial forceWithVirial(forceRef, (flags & GMX_FORCE_VIRIAL) != 0);
1110
1111     if (inputrec->bPull && pull_have_constraint(inputrec->pull_work))
1112     {
1113         clear_pull_forces(inputrec->pull_work);
1114     }
1115
1116     /* We calculate the non-bonded forces, when done on the CPU, here.
1117      * We do this before calling do_force_lowlevel, because in that
1118      * function, the listed forces are calculated before PME, which
1119      * does communication.  With this order, non-bonded and listed
1120      * force calculation imbalance can be balanced out by the domain
1121      * decomposition load balancing.
1122      */
1123
1124     if (!bUseOrEmulGPU)
1125     {
1126         do_nb_verlet(fr, ic, enerd, flags, Nbnxm::InteractionLocality::Local, enbvClearFYes,
1127                      step, nrnb, wcycle);
1128     }
1129
1130     if (fr->efep != efepNO)
1131     {
1132         /* Calculate the local and non-local free energy interactions here.
1133          * Happens here on the CPU both with and without GPU.
1134          */
1135         wallcycle_sub_start(wcycle, ewcsNONBONDED);
1136         nbv->dispatchFreeEnergyKernel(Nbnxm::InteractionLocality::Local,
1137                                       fr, as_rvec_array(x.unpaddedArrayRef().data()), f, *mdatoms,
1138                                       inputrec->fepvals, lambda,
1139                                       enerd, flags, nrnb);
1140
1141         if (havePPDomainDecomposition(cr))
1142         {
1143             nbv->dispatchFreeEnergyKernel(Nbnxm::InteractionLocality::NonLocal,
1144                                           fr, as_rvec_array(x.unpaddedArrayRef().data()), f, *mdatoms,
1145                                           inputrec->fepvals, lambda,
1146                                           enerd, flags, nrnb);
1147         }
1148         wallcycle_sub_stop(wcycle, ewcsNONBONDED);
1149     }
1150
1151     if (!bUseOrEmulGPU)
1152     {
1153         if (havePPDomainDecomposition(cr))
1154         {
1155             do_nb_verlet(fr, ic, enerd, flags, Nbnxm::InteractionLocality::NonLocal, enbvClearFNo,
1156                          step, nrnb, wcycle);
1157         }
1158
1159         /* Add all the non-bonded force to the normal force array.
1160          * This can be split into a local and a non-local part when overlapping
1161          * communication with calculation with domain decomposition.
1162          */
1163         wallcycle_stop(wcycle, ewcFORCE);
1164
1165         nbv->atomdata_add_nbat_f_to_f(Nbnxm::AtomLocality::All, f, wcycle);
1166
1167         wallcycle_start_nocount(wcycle, ewcFORCE);
1168
1169         /* If there are multiple fshift output buffers we need to reduce them */
1170         if (flags & GMX_FORCE_VIRIAL)
1171         {
1172             /* This is not in a subcounter because it takes a
1173                negligible and constant-sized amount of time */
1174             nbnxn_atomdata_add_nbat_fshift_to_fshift(nbv->nbat.get(),
1175                                                      fr->fshift);
1176         }
1177     }
1178
1179     /* update QMMMrec, if necessary */
1180     if (fr->bQMMM)
1181     {
1182         update_QMMMrec(cr, fr, as_rvec_array(x.unpaddedArrayRef().data()), mdatoms, box);
1183     }
1184
1185     /* Compute the bonded and non-bonded energies and optionally forces */
1186     do_force_lowlevel(fr, inputrec, &(top->idef),
1187                       cr, ms, nrnb, wcycle, mdatoms,
1188                       as_rvec_array(x.unpaddedArrayRef().data()), hist, f, &forceWithVirial, enerd, fcd,
1189                       box, inputrec->fepvals, lambda, graph, &(top->excls), fr->mu_tot,
1190                       flags,
1191                       &cycles_pme, ddBalanceRegionHandler);
1192
1193     wallcycle_stop(wcycle, ewcFORCE);
1194
1195     computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation,
1196                          step, t, wcycle,
1197                          fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda,
1198                          flags, &forceWithVirial, enerd,
1199                          ed, bNS);
1200
1201     if (bUseOrEmulGPU)
1202     {
1203         /* wait for non-local forces (or calculate in emulation mode) */
1204         if (havePPDomainDecomposition(cr))
1205         {
1206             if (bUseGPU)
1207             {
1208                 wallcycle_start(wcycle, ewcWAIT_GPU_NB_NL);
1209                 Nbnxm::gpu_wait_finish_task(nbv->gpu_nbv,
1210                                             flags, Nbnxm::AtomLocality::NonLocal,
1211                                             ppForceWorkload->haveGpuBondedWork,
1212                                             enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
1213                                             fr->fshift);
1214                 cycles_wait_gpu += wallcycle_stop(wcycle, ewcWAIT_GPU_NB_NL);
1215             }
1216             else
1217             {
1218                 wallcycle_start_nocount(wcycle, ewcFORCE);
1219                 do_nb_verlet(fr, ic, enerd, flags, Nbnxm::InteractionLocality::NonLocal, enbvClearFYes,
1220                              step, nrnb, wcycle);
1221                 wallcycle_stop(wcycle, ewcFORCE);
1222             }
1223
1224             nbv->atomdata_add_nbat_f_to_f(Nbnxm::AtomLocality::NonLocal,
1225                                           f, wcycle);
1226         }
1227     }
1228
1229     if (havePPDomainDecomposition(cr))
1230     {
1231         /* We are done with the CPU compute.
1232          * We will now communicate the non-local forces.
1233          * If we use a GPU this will overlap with GPU work, so in that case
1234          * we do not close the DD force balancing region here.
1235          */
1236         ddBalanceRegionHandler.closeAfterForceComputationCpu();
1237
1238         if (bDoForces)
1239         {
1240             dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle);
1241         }
1242     }
1243
1244     // With both nonbonded and PME offloaded a GPU on the same rank, we use
1245     // an alternating wait/reduction scheme.
1246     bool alternateGpuWait = (!c_disableAlternatingWait && useGpuPme && bUseGPU && !DOMAINDECOMP(cr));
1247     if (alternateGpuWait)
1248     {
1249         alternatePmeNbGpuWaitReduce(fr->nbv.get(), fr->pmedata, &force, &forceWithVirial, fr->fshift, enerd,
1250                                     flags, pmeFlags, ppForceWorkload->haveGpuBondedWork, wcycle);
1251     }
1252
1253     if (!alternateGpuWait && useGpuPme)
1254     {
1255         pme_gpu_wait_and_reduce(fr->pmedata, pmeFlags, wcycle, &forceWithVirial, enerd);
1256     }
1257
1258     /* Wait for local GPU NB outputs on the non-alternating wait path */
1259     if (!alternateGpuWait && bUseGPU)
1260     {
1261         /* Measured overhead on CUDA and OpenCL with(out) GPU sharing
1262          * is between 0.5 and 1.5 Mcycles. So 2 MCycles is an overestimate,
1263          * but even with a step of 0.1 ms the difference is less than 1%
1264          * of the step time.
1265          */
1266         const float gpuWaitApiOverheadMargin = 2e6f; /* cycles */
1267
1268         wallcycle_start(wcycle, ewcWAIT_GPU_NB_L);
1269         Nbnxm::gpu_wait_finish_task(nbv->gpu_nbv,
1270                                     flags, Nbnxm::AtomLocality::Local, ppForceWorkload->haveGpuBondedWork,
1271                                     enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
1272                                     fr->fshift);
1273         float cycles_tmp = wallcycle_stop(wcycle, ewcWAIT_GPU_NB_L);
1274
1275         if (ddBalanceRegionHandler.useBalancingRegion())
1276         {
1277             DdBalanceRegionWaitedForGpu waitedForGpu = DdBalanceRegionWaitedForGpu::yes;
1278             if (bDoForces && cycles_tmp <= gpuWaitApiOverheadMargin)
1279             {
1280                 /* We measured few cycles, it could be that the kernel
1281                  * and transfer finished earlier and there was no actual
1282                  * wait time, only API call overhead.
1283                  * Then the actual time could be anywhere between 0 and
1284                  * cycles_wait_est. We will use half of cycles_wait_est.
1285                  */
1286                 waitedForGpu = DdBalanceRegionWaitedForGpu::no;
1287             }
1288             ddBalanceRegionHandler.closeAfterForceComputationGpu(cycles_wait_gpu, waitedForGpu);
1289         }
1290     }
1291
1292     if (fr->nbv->emulateGpu())
1293     {
1294         // NOTE: emulation kernel is not included in the balancing region,
1295         // but emulation mode does not target performance anyway
1296         wallcycle_start_nocount(wcycle, ewcFORCE);
1297         do_nb_verlet(fr, ic, enerd, flags, Nbnxm::InteractionLocality::Local,
1298                      DOMAINDECOMP(cr) ? enbvClearFNo : enbvClearFYes,
1299                      step, nrnb, wcycle);
1300         wallcycle_stop(wcycle, ewcFORCE);
1301     }
1302
1303     if (useGpuPme)
1304     {
1305         pme_gpu_reinit_computation(fr->pmedata, wcycle);
1306     }
1307
1308     if (bUseGPU)
1309     {
1310         /* now clear the GPU outputs while we finish the step on the CPU */
1311         wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
1312         wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1313         Nbnxm::gpu_clear_outputs(nbv->gpu_nbv, flags);
1314
1315         if (nbv->pairlistSets().isDynamicPruningStepGpu(step))
1316         {
1317             nbv->dispatchPruneKernelGpu(step);
1318         }
1319         wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1320         wallcycle_stop(wcycle, ewcLAUNCH_GPU);
1321     }
1322
1323     if (ppForceWorkload->haveGpuBondedWork && (flags & GMX_FORCE_ENERGY))
1324     {
1325         wallcycle_start(wcycle, ewcWAIT_GPU_BONDED);
1326         // in principle this should be included in the DD balancing region,
1327         // but generally it is infrequent so we'll omit it for the sake of
1328         // simpler code
1329         fr->gpuBonded->accumulateEnergyTerms(enerd);
1330         wallcycle_stop(wcycle, ewcWAIT_GPU_BONDED);
1331
1332         wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
1333         wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_BONDED);
1334         fr->gpuBonded->clearEnergies();
1335         wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_BONDED);
1336         wallcycle_stop(wcycle, ewcLAUNCH_GPU);
1337     }
1338
1339     /* Do the nonbonded GPU (or emulation) force buffer reduction
1340      * on the non-alternating path. */
1341     if (bUseOrEmulGPU && !alternateGpuWait)
1342     {
1343         nbv->atomdata_add_nbat_f_to_f(Nbnxm::AtomLocality::Local,
1344                                       f, wcycle);
1345     }
1346     if (DOMAINDECOMP(cr))
1347     {
1348         dd_force_flop_stop(cr->dd, nrnb);
1349     }
1350
1351     if (bDoForces)
1352     {
1353         /* If we have NoVirSum forces, but we do not calculate the virial,
1354          * we sum fr->f_novirsum=f later.
1355          */
1356         if (vsite && !(fr->haveDirectVirialContributions && !(flags & GMX_FORCE_VIRIAL)))
1357         {
1358             spread_vsite_f(vsite, as_rvec_array(x.unpaddedArrayRef().data()), f, fr->fshift, FALSE, nullptr, nrnb,
1359                            &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr, wcycle);
1360         }
1361
1362         if (flags & GMX_FORCE_VIRIAL)
1363         {
1364             /* Calculation of the virial must be done after vsites! */
1365             calc_virial(0, mdatoms->homenr, as_rvec_array(x.unpaddedArrayRef().data()), f,
1366                         vir_force, graph, box, nrnb, fr, inputrec->ePBC);
1367         }
1368     }
1369
1370     if (PAR(cr) && !thisRankHasDuty(cr, DUTY_PME))
1371     {
1372         /* In case of node-splitting, the PP nodes receive the long-range
1373          * forces, virial and energy from the PME nodes here.
1374          */
1375         pme_receive_force_ener(cr, &forceWithVirial, enerd, wcycle);
1376     }
1377
1378     if (bDoForces)
1379     {
1380         post_process_forces(cr, step, nrnb, wcycle,
1381                             top, box, as_rvec_array(x.unpaddedArrayRef().data()), f, &forceWithVirial,
1382                             vir_force, mdatoms, graph, fr, vsite,
1383                             flags);
1384     }
1385
1386     if (flags & GMX_FORCE_ENERGY)
1387     {
1388         /* Sum the potential energy terms from group contributions */
1389         sum_epot(&(enerd->grpp), enerd->term);
1390
1391         if (!EI_TPI(inputrec->eI))
1392         {
1393             checkPotentialEnergyValidity(step, *enerd, *inputrec);
1394         }
1395     }
1396 }
1397
1398 static void do_force_cutsGROUP(FILE *fplog,
1399                                const t_commrec *cr,
1400                                const gmx_multisim_t *ms,
1401                                const t_inputrec *inputrec,
1402                                gmx::Awh *awh,
1403                                gmx_enfrot *enforcedRotation,
1404                                int64_t step,
1405                                t_nrnb *nrnb,
1406                                gmx_wallcycle_t wcycle,
1407                                gmx_localtop_t *top,
1408                                const gmx_groups_t *groups,
1409                                matrix box, gmx::ArrayRefWithPadding<gmx::RVec> x,
1410                                history_t *hist,
1411                                gmx::ArrayRefWithPadding<gmx::RVec> force,
1412                                tensor vir_force,
1413                                const t_mdatoms *mdatoms,
1414                                gmx_enerdata_t *enerd,
1415                                t_fcdata *fcd,
1416                                real *lambda,
1417                                t_graph *graph,
1418                                t_forcerec *fr,
1419                                const gmx_vsite_t *vsite,
1420                                rvec mu_tot,
1421                                double t,
1422                                gmx_edsam *ed,
1423                                int flags,
1424                                const DDBalanceRegionHandler &ddBalanceRegionHandler)
1425 {
1426     int        cg0, cg1, i, j;
1427     double     mu[2*DIM];
1428     gmx_bool   bStateChanged, bNS, bFillGrid, bCalcCGCM;
1429     gmx_bool   bDoForces;
1430     float      cycles_pme;
1431
1432     const int  start  = 0;
1433     const int  homenr = mdatoms->homenr;
1434
1435     clear_mat(vir_force);
1436
1437     cg0 = 0;
1438     if (DOMAINDECOMP(cr))
1439     {
1440         cg1 = cr->dd->globalAtomGroupIndices.size();
1441     }
1442     else
1443     {
1444         cg1 = top->cgs.nr;
1445     }
1446     if (fr->n_tpi > 0)
1447     {
1448         cg1--;
1449     }
1450
1451     bStateChanged  = ((flags & GMX_FORCE_STATECHANGED) != 0);
1452     bNS            = ((flags & GMX_FORCE_NS) != 0);
1453     /* Should we perform the long-range nonbonded evaluation inside the neighborsearching? */
1454     bFillGrid      = (bNS && bStateChanged);
1455     bCalcCGCM      = (bFillGrid && !DOMAINDECOMP(cr));
1456     bDoForces      = ((flags & GMX_FORCE_FORCES) != 0);
1457
1458     if (bStateChanged)
1459     {
1460         update_forcerec(fr, box);
1461
1462         if (inputrecNeedMutot(inputrec))
1463         {
1464             /* Calculate total (local) dipole moment in a temporary common array.
1465              * This makes it possible to sum them over nodes faster.
1466              */
1467             calc_mu(start, homenr,
1468                     x.unpaddedArrayRef(), mdatoms->chargeA, mdatoms->chargeB, mdatoms->nChargePerturbed,
1469                     mu, mu+DIM);
1470         }
1471     }
1472
1473     if (fr->ePBC != epbcNONE)
1474     {
1475         /* Compute shift vectors every step,
1476          * because of pressure coupling or box deformation!
1477          */
1478         if ((flags & GMX_FORCE_DYNAMICBOX) && bStateChanged)
1479         {
1480             calc_shifts(box, fr->shift_vec);
1481         }
1482
1483         if (bCalcCGCM)
1484         {
1485             put_charge_groups_in_box(fplog, cg0, cg1, fr->ePBC, box,
1486                                      &(top->cgs), as_rvec_array(x.unpaddedArrayRef().data()), fr->cg_cm);
1487             inc_nrnb(nrnb, eNR_CGCM, homenr);
1488             inc_nrnb(nrnb, eNR_RESETX, cg1-cg0);
1489         }
1490         else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph)
1491         {
1492             unshift_self(graph, box, as_rvec_array(x.unpaddedArrayRef().data()));
1493         }
1494     }
1495     else if (bCalcCGCM)
1496     {
1497         calc_cgcm(fplog, cg0, cg1, &(top->cgs), as_rvec_array(x.unpaddedArrayRef().data()), fr->cg_cm);
1498         inc_nrnb(nrnb, eNR_CGCM, homenr);
1499     }
1500
1501     if (bCalcCGCM && gmx_debug_at)
1502     {
1503         pr_rvecs(debug, 0, "cgcm", fr->cg_cm, top->cgs.nr);
1504     }
1505
1506 #if GMX_MPI
1507     if (!thisRankHasDuty(cr, DUTY_PME))
1508     {
1509         /* Send particle coordinates to the pme nodes.
1510          * Since this is only implemented for domain decomposition
1511          * and domain decomposition does not use the graph,
1512          * we do not need to worry about shifting.
1513          */
1514         gmx_pme_send_coordinates(cr, box, as_rvec_array(x.unpaddedArrayRef().data()),
1515                                  lambda[efptCOUL], lambda[efptVDW],
1516                                  (flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY)) != 0,
1517                                  step, wcycle);
1518     }
1519 #endif /* GMX_MPI */
1520
1521     /* Communicate coordinates and sum dipole if necessary */
1522     if (DOMAINDECOMP(cr))
1523     {
1524         dd_move_x(cr->dd, box, x.unpaddedArrayRef(), wcycle);
1525
1526         /* No GPU support, no move_x overlap, so reopen the balance region here */
1527         ddBalanceRegionHandler.reopenRegionCpu();
1528     }
1529
1530     if (inputrecNeedMutot(inputrec))
1531     {
1532         if (bStateChanged)
1533         {
1534             if (PAR(cr))
1535             {
1536                 gmx_sumd(2*DIM, mu, cr);
1537
1538                 ddBalanceRegionHandler.reopenRegionCpu();
1539             }
1540             for (i = 0; i < 2; i++)
1541             {
1542                 for (j = 0; j < DIM; j++)
1543                 {
1544                     fr->mu_tot[i][j] = mu[i*DIM + j];
1545                 }
1546             }
1547         }
1548         if (fr->efep == efepNO)
1549         {
1550             copy_rvec(fr->mu_tot[0], mu_tot);
1551         }
1552         else
1553         {
1554             for (j = 0; j < DIM; j++)
1555             {
1556                 mu_tot[j] =
1557                     (1.0 - lambda[efptCOUL])*fr->mu_tot[0][j] + lambda[efptCOUL]*fr->mu_tot[1][j];
1558             }
1559         }
1560     }
1561
1562     /* Reset energies */
1563     reset_enerdata(enerd);
1564     clear_rvecs(SHIFTS, fr->fshift);
1565
1566     if (bNS)
1567     {
1568         wallcycle_start(wcycle, ewcNS);
1569
1570         if (graph && bStateChanged)
1571         {
1572             /* Calculate intramolecular shift vectors to make molecules whole */
1573             mk_mshift(fplog, graph, fr->ePBC, box, as_rvec_array(x.unpaddedArrayRef().data()));
1574         }
1575
1576         /* Do the actual neighbour searching */
1577         ns(fplog, fr, box,
1578            groups, top, mdatoms,
1579            cr, nrnb, bFillGrid);
1580
1581         wallcycle_stop(wcycle, ewcNS);
1582     }
1583
1584     if (DOMAINDECOMP(cr) && !thisRankHasDuty(cr, DUTY_PME))
1585     {
1586         wallcycle_start(wcycle, ewcPPDURINGPME);
1587         dd_force_flop_start(cr->dd, nrnb);
1588     }
1589
1590     if (inputrec->bRot)
1591     {
1592         wallcycle_start(wcycle, ewcROT);
1593         do_rotation(cr, enforcedRotation, box, as_rvec_array(x.unpaddedArrayRef().data()), t, step, bNS);
1594         wallcycle_stop(wcycle, ewcROT);
1595     }
1596
1597     /* Temporary solution until all routines take PaddedRVecVector */
1598     rvec *f = as_rvec_array(force.unpaddedArrayRef().data());
1599
1600     /* Start the force cycle counter.
1601      * Note that a different counter is used for dynamic load balancing.
1602      */
1603     wallcycle_start(wcycle, ewcFORCE);
1604
1605     gmx::ArrayRef<gmx::RVec> forceRef = force.paddedArrayRef();
1606     if (bDoForces)
1607     {
1608         /* If we need to compute the virial, we might need a separate
1609          * force buffer for algorithms for which the virial is calculated
1610          * separately, such as PME.
1611          */
1612         if ((flags & GMX_FORCE_VIRIAL) && fr->haveDirectVirialContributions)
1613         {
1614             forceRef = *fr->forceBufferForDirectVirialContributions;
1615
1616             clear_rvecs_omp(forceRef.size(), as_rvec_array(forceRef.data()));
1617         }
1618
1619         /* Clear the short- and long-range forces */
1620         clear_rvecs(fr->natoms_force_constr, f);
1621     }
1622
1623     /* forceWithVirial might need the full force atom range */
1624     gmx::ForceWithVirial forceWithVirial(forceRef, (flags & GMX_FORCE_VIRIAL) != 0);
1625
1626     if (inputrec->bPull && pull_have_constraint(inputrec->pull_work))
1627     {
1628         clear_pull_forces(inputrec->pull_work);
1629     }
1630
1631     /* update QMMMrec, if necessary */
1632     if (fr->bQMMM)
1633     {
1634         update_QMMMrec(cr, fr, as_rvec_array(x.unpaddedArrayRef().data()), mdatoms, box);
1635     }
1636
1637     /* Compute the bonded and non-bonded energies and optionally forces */
1638     do_force_lowlevel(fr, inputrec, &(top->idef),
1639                       cr, ms, nrnb, wcycle, mdatoms,
1640                       as_rvec_array(x.unpaddedArrayRef().data()), hist, f, &forceWithVirial, enerd, fcd,
1641                       box, inputrec->fepvals, lambda,
1642                       graph, &(top->excls), fr->mu_tot,
1643                       flags,
1644                       &cycles_pme, ddBalanceRegionHandler);
1645
1646     wallcycle_stop(wcycle, ewcFORCE);
1647
1648     if (DOMAINDECOMP(cr))
1649     {
1650         dd_force_flop_stop(cr->dd, nrnb);
1651
1652         ddBalanceRegionHandler.closeAfterForceComputationCpu();
1653     }
1654
1655     computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation,
1656                          step, t, wcycle,
1657                          fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda,
1658                          flags, &forceWithVirial, enerd,
1659                          ed, bNS);
1660
1661     if (bDoForces)
1662     {
1663         /* Communicate the forces */
1664         if (DOMAINDECOMP(cr))
1665         {
1666             dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle);
1667             /* Do we need to communicate the separate force array
1668              * for terms that do not contribute to the single sum virial?
1669              * Position restraints and electric fields do not introduce
1670              * inter-cg forces, only full electrostatics methods do.
1671              * When we do not calculate the virial, fr->f_novirsum = f,
1672              * so we have already communicated these forces.
1673              */
1674             if (EEL_FULL(fr->ic->eeltype) && cr->dd->n_intercg_excl &&
1675                 (flags & GMX_FORCE_VIRIAL))
1676             {
1677                 dd_move_f(cr->dd, forceWithVirial.force_, nullptr, wcycle);
1678             }
1679         }
1680
1681         /* If we have NoVirSum forces, but we do not calculate the virial,
1682          * we sum fr->f_novirsum=f later.
1683          */
1684         if (vsite && !(fr->haveDirectVirialContributions && !(flags & GMX_FORCE_VIRIAL)))
1685         {
1686             spread_vsite_f(vsite, as_rvec_array(x.unpaddedArrayRef().data()), f, fr->fshift, FALSE, nullptr, nrnb,
1687                            &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr, wcycle);
1688         }
1689
1690         if (flags & GMX_FORCE_VIRIAL)
1691         {
1692             /* Calculation of the virial must be done after vsites! */
1693             calc_virial(0, mdatoms->homenr, as_rvec_array(x.unpaddedArrayRef().data()), f,
1694                         vir_force, graph, box, nrnb, fr, inputrec->ePBC);
1695         }
1696     }
1697
1698     if (PAR(cr) && !thisRankHasDuty(cr, DUTY_PME))
1699     {
1700         /* In case of node-splitting, the PP nodes receive the long-range
1701          * forces, virial and energy from the PME nodes here.
1702          */
1703         pme_receive_force_ener(cr, &forceWithVirial, enerd, wcycle);
1704     }
1705
1706     if (bDoForces)
1707     {
1708         post_process_forces(cr, step, nrnb, wcycle,
1709                             top, box, as_rvec_array(x.unpaddedArrayRef().data()), f, &forceWithVirial,
1710                             vir_force, mdatoms, graph, fr, vsite,
1711                             flags);
1712     }
1713
1714     if (flags & GMX_FORCE_ENERGY)
1715     {
1716         /* Sum the potential energy terms from group contributions */
1717         sum_epot(&(enerd->grpp), enerd->term);
1718
1719         if (!EI_TPI(inputrec->eI))
1720         {
1721             checkPotentialEnergyValidity(step, *enerd, *inputrec);
1722         }
1723     }
1724
1725 }
1726
1727 void do_force(FILE                                     *fplog,
1728               const t_commrec                          *cr,
1729               const gmx_multisim_t                     *ms,
1730               const t_inputrec                         *inputrec,
1731               gmx::Awh                                 *awh,
1732               gmx_enfrot                               *enforcedRotation,
1733               int64_t                                   step,
1734               t_nrnb                                   *nrnb,
1735               gmx_wallcycle_t                           wcycle,
1736               gmx_localtop_t                           *top,
1737               const gmx_groups_t                       *groups,
1738               matrix                                    box,
1739               gmx::ArrayRefWithPadding<gmx::RVec>       x,     //NOLINT(performance-unnecessary-value-param)
1740               history_t                                *hist,
1741               gmx::ArrayRefWithPadding<gmx::RVec>       force, //NOLINT(performance-unnecessary-value-param)
1742               tensor                                    vir_force,
1743               const t_mdatoms                          *mdatoms,
1744               gmx_enerdata_t                           *enerd,
1745               t_fcdata                                 *fcd,
1746               gmx::ArrayRef<real>                       lambda,
1747               t_graph                                  *graph,
1748               t_forcerec                               *fr,
1749               gmx::PpForceWorkload                     *ppForceWorkload,
1750               const gmx_vsite_t                        *vsite,
1751               rvec                                      mu_tot,
1752               double                                    t,
1753               gmx_edsam                                *ed,
1754               int                                       flags,
1755               const DDBalanceRegionHandler             &ddBalanceRegionHandler)
1756 {
1757     /* modify force flag if not doing nonbonded */
1758     if (!fr->bNonbonded)
1759     {
1760         flags &= ~GMX_FORCE_NONBONDED;
1761     }
1762
1763     switch (inputrec->cutoff_scheme)
1764     {
1765         case ecutsVERLET:
1766             do_force_cutsVERLET(fplog, cr, ms, inputrec,
1767                                 awh, enforcedRotation, step, nrnb, wcycle,
1768                                 top,
1769                                 groups,
1770                                 box, x, hist,
1771                                 force, vir_force,
1772                                 mdatoms,
1773                                 enerd, fcd,
1774                                 lambda.data(), graph,
1775                                 fr,
1776                                 ppForceWorkload,
1777                                 fr->ic,
1778                                 vsite, mu_tot,
1779                                 t, ed,
1780                                 flags,
1781                                 ddBalanceRegionHandler);
1782             break;
1783         case ecutsGROUP:
1784             do_force_cutsGROUP(fplog, cr, ms, inputrec,
1785                                awh, enforcedRotation, step, nrnb, wcycle,
1786                                top,
1787                                groups,
1788                                box, x, hist,
1789                                force, vir_force,
1790                                mdatoms,
1791                                enerd, fcd,
1792                                lambda.data(), graph,
1793                                fr, vsite, mu_tot,
1794                                t, ed,
1795                                flags,
1796                                ddBalanceRegionHandler);
1797             break;
1798         default:
1799             gmx_incons("Invalid cut-off scheme passed!");
1800     }
1801
1802     /* In case we don't have constraints and are using GPUs, the next balancing
1803      * region starts here.
1804      * Some "special" work at the end of do_force_cuts?, such as vsite spread,
1805      * virial calculation and COM pulling, is not thus not included in
1806      * the balance timing, which is ok as most tasks do communication.
1807      */
1808     ddBalanceRegionHandler.openBeforeForceComputationCpu(DdAllowBalanceRegionReopen::no);
1809 }
1810
1811
1812 void do_constrain_first(FILE *fplog, gmx::Constraints *constr,
1813                         const t_inputrec *ir, const t_mdatoms *md,
1814                         t_state *state)
1815 {
1816     int             i, m, start, end;
1817     int64_t         step;
1818     real            dt = ir->delta_t;
1819     real            dvdl_dum;
1820     rvec           *savex;
1821
1822     /* We need to allocate one element extra, since we might use
1823      * (unaligned) 4-wide SIMD loads to access rvec entries.
1824      */
1825     snew(savex, state->natoms + 1);
1826
1827     start = 0;
1828     end   = md->homenr;
1829
1830     if (debug)
1831     {
1832         fprintf(debug, "vcm: start=%d, homenr=%d, end=%d\n",
1833                 start, md->homenr, end);
1834     }
1835     /* Do a first constrain to reset particles... */
1836     step = ir->init_step;
1837     if (fplog)
1838     {
1839         char buf[STEPSTRSIZE];
1840         fprintf(fplog, "\nConstraining the starting coordinates (step %s)\n",
1841                 gmx_step_str(step, buf));
1842     }
1843     dvdl_dum = 0;
1844
1845     /* constrain the current position */
1846     constr->apply(TRUE, FALSE,
1847                   step, 0, 1.0,
1848                   state->x.rvec_array(), state->x.rvec_array(), nullptr,
1849                   state->box,
1850                   state->lambda[efptBONDED], &dvdl_dum,
1851                   nullptr, nullptr, gmx::ConstraintVariable::Positions);
1852     if (EI_VV(ir->eI))
1853     {
1854         /* constrain the inital velocity, and save it */
1855         /* also may be useful if we need the ekin from the halfstep for velocity verlet */
1856         constr->apply(TRUE, FALSE,
1857                       step, 0, 1.0,
1858                       state->x.rvec_array(), state->v.rvec_array(), state->v.rvec_array(),
1859                       state->box,
1860                       state->lambda[efptBONDED], &dvdl_dum,
1861                       nullptr, nullptr, gmx::ConstraintVariable::Velocities);
1862     }
1863     /* constrain the inital velocities at t-dt/2 */
1864     if (EI_STATE_VELOCITY(ir->eI) && ir->eI != eiVV)
1865     {
1866         auto x = makeArrayRef(state->x).subArray(start, end);
1867         auto v = makeArrayRef(state->v).subArray(start, end);
1868         for (i = start; (i < end); i++)
1869         {
1870             for (m = 0; (m < DIM); m++)
1871             {
1872                 /* Reverse the velocity */
1873                 v[i][m] = -v[i][m];
1874                 /* Store the position at t-dt in buf */
1875                 savex[i][m] = x[i][m] + dt*v[i][m];
1876             }
1877         }
1878         /* Shake the positions at t=-dt with the positions at t=0
1879          * as reference coordinates.
1880          */
1881         if (fplog)
1882         {
1883             char buf[STEPSTRSIZE];
1884             fprintf(fplog, "\nConstraining the coordinates at t0-dt (step %s)\n",
1885                     gmx_step_str(step, buf));
1886         }
1887         dvdl_dum = 0;
1888         constr->apply(TRUE, FALSE,
1889                       step, -1, 1.0,
1890                       state->x.rvec_array(), savex, nullptr,
1891                       state->box,
1892                       state->lambda[efptBONDED], &dvdl_dum,
1893                       state->v.rvec_array(), nullptr, gmx::ConstraintVariable::Positions);
1894
1895         for (i = start; i < end; i++)
1896         {
1897             for (m = 0; m < DIM; m++)
1898             {
1899                 /* Re-reverse the velocities */
1900                 v[i][m] = -v[i][m];
1901             }
1902         }
1903     }
1904     sfree(savex);
1905 }
1906
1907 void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
1908 {
1909     int t, nth;
1910     nth = gmx_omp_nthreads_get(emntDefault);
1911
1912 #pragma omp parallel for num_threads(nth) schedule(static)
1913     for (t = 0; t < nth; t++)
1914     {
1915         try
1916         {
1917             size_t natoms = x.size();
1918             size_t offset = (natoms*t    )/nth;
1919             size_t len    = (natoms*(t + 1))/nth - offset;
1920             put_atoms_in_box(ePBC, box, x.subArray(offset, len));
1921         }
1922         GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1923     }
1924 }
1925
1926 void initialize_lambdas(FILE               *fplog,
1927                         const t_inputrec   &ir,
1928                         bool                isMaster,
1929                         int                *fep_state,
1930                         gmx::ArrayRef<real> lambda,
1931                         double             *lam0)
1932 {
1933     /* TODO: Clean up initialization of fep_state and lambda in
1934        t_state.  This function works, but could probably use a logic
1935        rewrite to keep all the different types of efep straight. */
1936
1937     if ((ir.efep == efepNO) && (!ir.bSimTemp))
1938     {
1939         return;
1940     }
1941
1942     const t_lambda *fep = ir.fepvals;
1943     if (isMaster)
1944     {
1945         *fep_state = fep->init_fep_state; /* this might overwrite the checkpoint
1946                                              if checkpoint is set -- a kludge is in for now
1947                                              to prevent this.*/
1948     }
1949
1950     for (int i = 0; i < efptNR; i++)
1951     {
1952         double thisLambda;
1953         /* overwrite lambda state with init_lambda for now for backwards compatibility */
1954         if (fep->init_lambda >= 0) /* if it's -1, it was never initialized */
1955         {
1956             thisLambda = fep->init_lambda;
1957         }
1958         else
1959         {
1960             thisLambda = fep->all_lambda[i][fep->init_fep_state];
1961         }
1962         if (isMaster)
1963         {
1964             lambda[i] = thisLambda;
1965         }
1966         if (lam0 != nullptr)
1967         {
1968             lam0[i] = thisLambda;
1969         }
1970     }
1971     if (ir.bSimTemp)
1972     {
1973         /* need to rescale control temperatures to match current state */
1974         for (int i = 0; i < ir.opts.ngtc; i++)
1975         {
1976             if (ir.opts.ref_t[i] > 0)
1977             {
1978                 ir.opts.ref_t[i] = ir.simtempvals->temperatures[fep->init_fep_state];
1979             }
1980         }
1981     }
1982
1983     /* Send to the log the information on the current lambdas */
1984     if (fplog != nullptr)
1985     {
1986         fprintf(fplog, "Initial vector of lambda components:[ ");
1987         for (const auto &l : lambda)
1988         {
1989             fprintf(fplog, "%10.4f ", l);
1990         }
1991         fprintf(fplog, "]\n");
1992     }
1993 }