src/gromacs/modularsimulator/computeglobalselement.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 /*! \internal \file
  36  * \brief Defines the global reduction element for the modular simulator
  37  *
  38  * \author Pascal Merz <pascal.merz@me.com>
  39  * \ingroup module_modularsimulator
  40  */
  41
  42 #include "gmxpre.h"
  43
  44 #include "computeglobalselement.h"
  45
  46 #include "gromacs/domdec/domdec.h"
  47 #include "gromacs/domdec/localtopologychecker.h"
  48 #include "gromacs/gmxlib/network.h"
  49 #include "gromacs/gmxlib/nrnb.h"
  50 #include "gromacs/math/vec.h"
  51 #include "gromacs/mdlib/constr.h"
  52 #include "gromacs/mdlib/md_support.h"
  53 #include "gromacs/mdlib/mdatoms.h"
  54 #include "gromacs/mdlib/stat.h"
  55 #include "gromacs/mdlib/update.h"
  56 #include "gromacs/mdlib/vcm.h"
  57 #include "gromacs/mdtypes/commrec.h"
  58 #include "gromacs/mdtypes/group.h"
  59 #include "gromacs/mdtypes/inputrec.h"
  60 #include "gromacs/mdtypes/mdatom.h"
  61 #include "gromacs/topology/topology.h"
  62
  63 #include "freeenergyperturbationdata.h"
  64 #include "modularsimulator.h"
  65 #include "simulatoralgorithm.h"
  66
  67 namespace gmx
  68 {
  69 template<ComputeGlobalsAlgorithm algorithm>
  70 ComputeGlobalsElement<algorithm>::ComputeGlobalsElement(StatePropagatorData* statePropagatorData,
  71                                                         EnergyData*          energyData,
  72                                                         FreeEnergyPerturbationData* freeEnergyPerturbationData,
  73                                                         SimulationSignals* signals,
  74                                                         int                nstglobalcomm,
  75                                                         FILE*              fplog,
  76                                                         const MDLogger&    mdlog,
  77                                                         t_commrec*         cr,
  78                                                         const t_inputrec*  inputrec,
  79                                                         const MDAtoms*     mdAtoms,
  80                                                         t_nrnb*            nrnb,
  81                                                         gmx_wallcycle*     wcycle,
  82                                                         t_forcerec*        fr,
  83                                                         const gmx_mtop_t&  global_top,
  84                                                         Constraints*       constr) :
  85     energyReductionStep_(-1),
  86     virialReductionStep_(-1),
  87     vvSchedulingStep_(-1),
  88     doStopCM_(inputrec->comm_mode != ComRemovalAlgorithm::No),
  89     nstcomm_(inputrec->nstcomm),
  90     nstglobalcomm_(nstglobalcomm),
  91     lastStep_(inputrec->nsteps + inputrec->init_step),
  92     initStep_(inputrec->init_step),
  93     nullSignaller_(std::make_unique<SimulationSignaller>(nullptr, nullptr, nullptr, false, false)),
  94     statePropagatorData_(statePropagatorData),
  95     energyData_(energyData),
  96     localTopology_(nullptr),
  97     freeEnergyPerturbationData_(freeEnergyPerturbationData),
  98     vcm_(global_top.groups, *inputrec),
  99     signals_(signals),
 100     fplog_(fplog),
 101     mdlog_(mdlog),
 102     cr_(cr),
 103     inputrec_(inputrec),
 104     top_global_(global_top),
 105     mdAtoms_(mdAtoms),
 106     constr_(constr),
 107     nrnb_(nrnb),
 108     wcycle_(wcycle),
 109     fr_(fr)
 110 {
 111     reportComRemovalInfo(fplog, vcm_);
 112     gstat_ = global_stat_init(inputrec_);
 113 }
 114
 115 template<ComputeGlobalsAlgorithm algorithm>
 116 ComputeGlobalsElement<algorithm>::~ComputeGlobalsElement()
 117 {
 118     global_stat_destroy(gstat_);
 119 }
 120
 121 template<ComputeGlobalsAlgorithm algorithm>
 122 void ComputeGlobalsElement<algorithm>::elementSetup()
 123 {
 124     GMX_ASSERT(localTopology_, "Setup called before local topology was set.");
 125
 126     if (doStopCM_ && !inputrec_->bContinuation)
 127     {
 128         // To minimize communication, compute_globals computes the COM velocity
 129         // and the kinetic energy for the velocities without COM motion removed.
 130         // Thus to get the kinetic energy without the COM contribution, we need
 131         // to call compute_globals twice.
 132
 133         compute(-1, CGLO_GSTAT | CGLO_STOPCM, nullSignaller_.get(), false, true);
 134
 135         auto v = statePropagatorData_->velocitiesView();
 136         // At initialization, do not pass x with acceleration-correction mode
 137         // to avoid (incorrect) correction of the initial coordinates.
 138         auto x = vcm_.mode == ComRemovalAlgorithm::LinearAccelerationCorrection
 139                          ? ArrayRefWithPadding<RVec>()
 140                          : statePropagatorData_->positionsView();
 141         process_and_stopcm_grp(
 142                 fplog_, &vcm_, *mdAtoms_->mdatoms(), x.unpaddedArrayRef(), v.unpaddedArrayRef());
 143         inc_nrnb(nrnb_, eNR_STOPCM, mdAtoms_->mdatoms()->homenr);
 144     }
 145
 146     unsigned int cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
 147                                | (energyData_->hasReadEkinFromCheckpoint() ? CGLO_READEKIN : 0));
 148
 149     if (algorithm == ComputeGlobalsAlgorithm::VelocityVerlet)
 150     {
 151         cglo_flags |= CGLO_PRESSURE | CGLO_CONSTRAINT;
 152     }
 153
 154     compute(-1, cglo_flags, nullSignaller_.get(), false, true);
 155
 156     // Calculate the initial half step temperature, and save the ekinh_old
 157     for (int i = 0; (i < inputrec_->opts.ngtc); i++)
 158     {
 159         copy_mat(energyData_->ekindata()->tcstat[i].ekinh, energyData_->ekindata()->tcstat[i].ekinh_old);
 160     }
 161 }
 162
 163 template<ComputeGlobalsAlgorithm algorithm>
 164 void ComputeGlobalsElement<algorithm>::scheduleTask(Step                       step,
 165                                                     Time gmx_unused            time,
 166                                                     const RegisterRunFunction& registerRunFunction)
 167 {
 168     const bool needComReduction    = doStopCM_ && do_per_step(step, nstcomm_);
 169     const bool needGlobalReduction = step == energyReductionStep_ || step == virialReductionStep_
 170                                      || needComReduction || do_per_step(step, nstglobalcomm_);
 171
 172     // TODO: CGLO_GSTAT is only used for needToSumEkinhOld_, i.e. to signal that we do or do not
 173     //       sum the previous kinetic energy. We should simplify / clarify this.
 174
 175     if (algorithm == ComputeGlobalsAlgorithm::LeapFrog)
 176     {
 177         // With Leap-Frog we can skip compute_globals at
 178         // non-communication steps, but we need to calculate
 179         // the kinetic energy one step before communication.
 180
 181         // With leap-frog we also need to compute the half-step
 182         // kinetic energy at the step before we need to write
 183         // the full-step kinetic energy
 184         const bool needEkinAtNextStep = (do_per_step(step + 1, nstglobalcomm_) || step + 1 == lastStep_);
 185
 186         if (!needGlobalReduction && !needEkinAtNextStep)
 187         {
 188             return;
 189         }
 190
 191         const bool doEnergy = step == energyReductionStep_;
 192         int        flags    = (needGlobalReduction ? CGLO_GSTAT : 0) | (doEnergy ? CGLO_ENERGY : 0)
 193                     | (needComReduction ? CGLO_STOPCM : 0) | CGLO_TEMPERATURE | CGLO_PRESSURE
 194                     | CGLO_CONSTRAINT;
 195
 196         // Since we're already communicating at this step, we
 197         // can propagate intra-simulation signals. Note that
 198         // check_nstglobalcomm has the responsibility for
 199         // choosing the value of nstglobalcomm which satisfies
 200         // the need of the different signallers.
 201         const bool doIntraSimSignal = true;
 202         // Disable functionality
 203         const bool doInterSimSignal = false;
 204
 205         // Make signaller to signal stop / reset / checkpointing signals
 206         auto signaller = std::make_shared<SimulationSignaller>(
 207                 signals_, cr_, nullptr, doInterSimSignal, doIntraSimSignal);
 208
 209         registerRunFunction([this, step, flags, signaller = std::move(signaller)]() {
 210             compute(step, flags, signaller.get(), true);
 211         });
 212     }
 213     else if (algorithm == ComputeGlobalsAlgorithm::VelocityVerlet)
 214     {
 215         // For VV, we schedule two calls to compute globals per step.
 216         if (step != vvSchedulingStep_)
 217         {
 218             // This is the first scheduling call for this step (positions & velocities at full time
 219             // step) Set this as the current scheduling step
 220             vvSchedulingStep_ = step;
 221
 222             // For vv, the state at the beginning of the step is positions at time t, velocities at time t - dt/2
 223             // The first velocity propagation (+dt/2) therefore actually corresponds to the previous step.
 224             // So we need information from the last step in the first half of the integration
 225             if (!needGlobalReduction && !do_per_step(step - 1, nstglobalcomm_))
 226             {
 227                 return;
 228             }
 229
 230             const bool doTemperature = step != initStep_ || inputrec_->bContinuation;
 231             const bool doEnergy      = step == energyReductionStep_;
 232
 233             int flags = (needGlobalReduction ? CGLO_GSTAT : 0) | (doEnergy ? CGLO_ENERGY : 0)
 234                         | (doTemperature ? CGLO_TEMPERATURE : 0) | CGLO_PRESSURE | CGLO_CONSTRAINT
 235                         | (needComReduction ? CGLO_STOPCM : 0) | CGLO_SCALEEKIN;
 236
 237             registerRunFunction(
 238                     [this, step, flags]() { compute(step, flags, nullSignaller_.get(), false); });
 239         }
 240         else
 241         {
 242             // second call to compute_globals for this step
 243             // Reset the scheduling step to avoid confusion if scheduling needs
 244             // to be repeated (in case of unexpected simulation termination)
 245             vvSchedulingStep_ = -1;
 246
 247             if (!needGlobalReduction)
 248             {
 249                 return;
 250             }
 251             int flags = CGLO_GSTAT | CGLO_CONSTRAINT;
 252
 253             // Since we're already communicating at this step, we
 254             // can propagate intra-simulation signals. Note that
 255             // check_nstglobalcomm has the responsibility for
 256             // choosing the value of nstglobalcomm which satisfies
 257             // the need of the different signallers.
 258             const bool doIntraSimSignal = true;
 259             // Disable functionality
 260             const bool doInterSimSignal = false;
 261
 262             auto signaller = std::make_shared<SimulationSignaller>(
 263                     signals_, cr_, nullptr, doInterSimSignal, doIntraSimSignal);
 264
 265             registerRunFunction([this, step, flags, signaller = std::move(signaller)]() {
 266                 compute(step, flags, signaller.get(), true);
 267             });
 268         }
 269     }
 270 }
 271
 272 template<ComputeGlobalsAlgorithm algorithm>
 273 void ComputeGlobalsElement<algorithm>::compute(gmx::Step            step,
 274                                                unsigned int         flags,
 275                                                SimulationSignaller* signaller,
 276                                                bool                 useLastBox,
 277                                                bool                 isInit)
 278 {
 279     auto        x       = statePropagatorData_->positionsView().unpaddedArrayRef();
 280     auto        v       = statePropagatorData_->velocitiesView().unpaddedArrayRef();
 281     const auto* box     = statePropagatorData_->constBox();
 282     const auto* lastbox = useLastBox ? statePropagatorData_->constPreviousBox()
 283                                      : statePropagatorData_->constBox();
 284
 285     if (DOMAINDECOMP(cr_) && shouldCheckNumberOfBondedInteractions(*cr_->dd))
 286     {
 287         flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 288     }
 289     compute_globals(gstat_,
 290                     cr_,
 291                     inputrec_,
 292                     fr_,
 293                     energyData_->ekindata(),
 294                     x,
 295                     v,
 296                     box,
 297                     mdAtoms_->mdatoms(),
 298                     nrnb_,
 299                     &vcm_,
 300                     step != -1 ? wcycle_ : nullptr,
 301                     energyData_->enerdata(),
 302                     energyData_->forceVirial(step),
 303                     energyData_->constraintVirial(step),
 304                     energyData_->totalVirial(step),
 305                     energyData_->pressure(step),
 306                     (((flags & CGLO_ENERGY) != 0) && constr_ != nullptr) ? constr_->rmsdData()
 307                                                                          : gmx::ArrayRef<real>{},
 308                     signaller,
 309                     lastbox,
 310                     energyData_->needToSumEkinhOld(),
 311                     flags);
 312     if (DOMAINDECOMP(cr_))
 313     {
 314         checkNumberOfBondedInteractions(mdlog_, cr_, top_global_, localTopology_, x, box);
 315     }
 316     if (flags & CGLO_STOPCM && !isInit)
 317     {
 318         process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x, v);
 319         inc_nrnb(nrnb_, eNR_STOPCM, mdAtoms_->mdatoms()->homenr);
 320     }
 321 }
 322
 323 template<ComputeGlobalsAlgorithm algorithm>
 324 void ComputeGlobalsElement<algorithm>::setTopology(const gmx_localtop_t* top)
 325 {
 326     localTopology_ = top;
 327 }
 328
 329 template<ComputeGlobalsAlgorithm algorithm>
 330 std::optional<SignallerCallback> ComputeGlobalsElement<algorithm>::registerEnergyCallback(EnergySignallerEvent event)
 331 {
 332     if (event == EnergySignallerEvent::EnergyCalculationStep)
 333     {
 334         return [this](Step step, Time /*unused*/) { energyReductionStep_ = step; };
 335     }
 336     if (event == EnergySignallerEvent::VirialCalculationStep)
 337     {
 338         return [this](Step step, Time /*unused*/) { virialReductionStep_ = step; };
 339     }
 340     return std::nullopt;
 341 }
 342
 343 template<ComputeGlobalsAlgorithm algorithm>
 344 std::optional<SignallerCallback>
 345 ComputeGlobalsElement<algorithm>::registerTrajectorySignallerCallback(TrajectoryEvent event)
 346 {
 347     if (event == TrajectoryEvent::EnergyWritingStep)
 348     {
 349         return [this](Step step, Time /*unused*/) { energyReductionStep_ = step; };
 350     }
 351     return std::nullopt;
 352 }
 353
 354 //! Explicit template instantiation
 355 //! \{
 356 template class ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>;
 357 template class ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>;
 358 //! \}
 359
 360 template<>
 361 ISimulatorElement* ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>::getElementPointerImpl(
 362         LegacySimulatorData*                    legacySimulatorData,
 363         ModularSimulatorAlgorithmBuilderHelper* builderHelper,
 364         StatePropagatorData*                    statePropagatorData,
 365         EnergyData*                             energyData,
 366         FreeEnergyPerturbationData*             freeEnergyPerturbationData,
 367         GlobalCommunicationHelper*              globalCommunicationHelper)
 368 {
 369     auto* element = builderHelper->storeElement(
 370             std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>>(
 371                     statePropagatorData,
 372                     energyData,
 373                     freeEnergyPerturbationData,
 374                     globalCommunicationHelper->simulationSignals(),
 375                     globalCommunicationHelper->nstglobalcomm(),
 376                     legacySimulatorData->fplog,
 377                     legacySimulatorData->mdlog,
 378                     legacySimulatorData->cr,
 379                     legacySimulatorData->inputrec,
 380                     legacySimulatorData->mdAtoms,
 381                     legacySimulatorData->nrnb,
 382                     legacySimulatorData->wcycle,
 383                     legacySimulatorData->fr,
 384                     legacySimulatorData->top_global,
 385                     legacySimulatorData->constr));
 386
 387     return element;
 388 }
 389
 390 template<>
 391 ISimulatorElement* ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>::getElementPointerImpl(
 392         LegacySimulatorData*                    simulator,
 393         ModularSimulatorAlgorithmBuilderHelper* builderHelper,
 394         StatePropagatorData*                    statePropagatorData,
 395         EnergyData*                             energyData,
 396         FreeEnergyPerturbationData*             freeEnergyPerturbationData,
 397         GlobalCommunicationHelper*              globalCommunicationHelper)
 398 {
 399     // We allow this element to be added multiple times to the call list, but we only want one
 400     // actual element built
 401     static const std::string key("vvComputeGlobalsElement");
 402
 403     const std::optional<std::any> cachedValue = builderHelper->builderData(key);
 404
 405     if (cachedValue)
 406     {
 407         return std::any_cast<ISimulatorElement*>(cachedValue.value());
 408     }
 409     else
 410     {
 411         ISimulatorElement* vvComputeGlobalsElement = builderHelper->storeElement(
 412                 std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>(
 413                         statePropagatorData,
 414                         energyData,
 415                         freeEnergyPerturbationData,
 416                         globalCommunicationHelper->simulationSignals(),
 417                         globalCommunicationHelper->nstglobalcomm(),
 418                         simulator->fplog,
 419                         simulator->mdlog,
 420                         simulator->cr,
 421                         simulator->inputrec,
 422                         simulator->mdAtoms,
 423                         simulator->nrnb,
 424                         simulator->wcycle,
 425                         simulator->fr,
 426                         simulator->top_global,
 427                         simulator->constr));
 428         builderHelper->storeBuilderData(key, vvComputeGlobalsElement);
 429         return vvComputeGlobalsElement;
 430     }
 431 }
 432 } // namespace gmx