src/gromacs/modularsimulator/computeglobalselement.cpp

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  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/gmxlib/network.h"
  48 #include "gromacs/gmxlib/nrnb.h"
  49 #include "gromacs/math/vec.h"
  50 #include "gromacs/mdlib/constr.h"
  51 #include "gromacs/mdlib/md_support.h"
  52 #include "gromacs/mdlib/mdatoms.h"
  53 #include "gromacs/mdlib/stat.h"
  54 #include "gromacs/mdlib/update.h"
  55 #include "gromacs/mdlib/vcm.h"
  56 #include "gromacs/mdtypes/commrec.h"
  57 #include "gromacs/mdtypes/group.h"
  58 #include "gromacs/mdtypes/inputrec.h"
  59 #include "gromacs/mdtypes/mdatom.h"
  60 #include "gromacs/topology/topology.h"
  61
  62 #include "freeenergyperturbationdata.h"
  63 #include "modularsimulator.h"
  64 #include "simulatoralgorithm.h"
  65
  66 namespace gmx
  67 {
  68 template<ComputeGlobalsAlgorithm algorithm>
  69 ComputeGlobalsElement<algorithm>::ComputeGlobalsElement(StatePropagatorData* statePropagatorData,
  70                                                         EnergyData*          energyData,
  71                                                         FreeEnergyPerturbationData* freeEnergyPerturbationData,
  72                                                         SimulationSignals* signals,
  73                                                         int                nstglobalcomm,
  74                                                         FILE*              fplog,
  75                                                         const MDLogger&    mdlog,
  76                                                         t_commrec*         cr,
  77                                                         const t_inputrec*  inputrec,
  78                                                         const MDAtoms*     mdAtoms,
  79                                                         t_nrnb*            nrnb,
  80                                                         gmx_wallcycle*     wcycle,
  81                                                         t_forcerec*        fr,
  82                                                         const gmx_mtop_t&  global_top,
  83                                                         Constraints*       constr) :
  84     energyReductionStep_(-1),
  85     virialReductionStep_(-1),
  86     vvSchedulingStep_(-1),
  87     doStopCM_(inputrec->comm_mode != ComRemovalAlgorithm::No),
  88     nstcomm_(inputrec->nstcomm),
  89     nstglobalcomm_(nstglobalcomm),
  90     lastStep_(inputrec->nsteps + inputrec->init_step),
  91     initStep_(inputrec->init_step),
  92     nullSignaller_(std::make_unique<SimulationSignaller>(nullptr, nullptr, nullptr, false, false)),
  93     statePropagatorData_(statePropagatorData),
  94     energyData_(energyData),
  95     localTopology_(nullptr),
  96     freeEnergyPerturbationData_(freeEnergyPerturbationData),
  97     vcm_(global_top.groups, *inputrec),
  98     signals_(signals),
  99     fplog_(fplog),
 100     mdlog_(mdlog),
 101     cr_(cr),
 102     inputrec_(inputrec),
 103     top_global_(global_top),
 104     mdAtoms_(mdAtoms),
 105     constr_(constr),
 106     nrnb_(nrnb),
 107     wcycle_(wcycle),
 108     fr_(fr)
 109 {
 110     reportComRemovalInfo(fplog, vcm_);
 111     gstat_ = global_stat_init(inputrec_);
 112 }
 113
 114 template<ComputeGlobalsAlgorithm algorithm>
 115 ComputeGlobalsElement<algorithm>::~ComputeGlobalsElement()
 116 {
 117     global_stat_destroy(gstat_);
 118 }
 119
 120 template<ComputeGlobalsAlgorithm algorithm>
 121 void ComputeGlobalsElement<algorithm>::elementSetup()
 122 {
 123     GMX_ASSERT(localTopology_, "Setup called before local topology was set.");
 124
 125     if (doStopCM_ && !inputrec_->bContinuation)
 126     {
 127         // To minimize communication, compute_globals computes the COM velocity
 128         // and the kinetic energy for the velocities without COM motion removed.
 129         // Thus to get the kinetic energy without the COM contribution, we need
 130         // to call compute_globals twice.
 131
 132         compute(-1, CGLO_GSTAT | CGLO_STOPCM, nullSignaller_.get(), false, true);
 133
 134         auto v = statePropagatorData_->velocitiesView();
 135         // At initialization, do not pass x with acceleration-correction mode
 136         // to avoid (incorrect) correction of the initial coordinates.
 137         auto x = vcm_.mode == ComRemovalAlgorithm::LinearAccelerationCorrection
 138                          ? ArrayRefWithPadding<RVec>()
 139                          : statePropagatorData_->positionsView();
 140         process_and_stopcm_grp(
 141                 fplog_, &vcm_, *mdAtoms_->mdatoms(), x.unpaddedArrayRef(), v.unpaddedArrayRef());
 142         inc_nrnb(nrnb_, eNR_STOPCM, mdAtoms_->mdatoms()->homenr);
 143     }
 144
 145     unsigned int cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
 146                                | (energyData_->hasReadEkinFromCheckpoint() ? CGLO_READEKIN : 0));
 147
 148     if (algorithm == ComputeGlobalsAlgorithm::VelocityVerlet)
 149     {
 150         cglo_flags |= CGLO_PRESSURE | CGLO_CONSTRAINT;
 151     }
 152
 153     compute(-1, cglo_flags, nullSignaller_.get(), false, true);
 154
 155     // Calculate the initial half step temperature, and save the ekinh_old
 156     for (int i = 0; (i < inputrec_->opts.ngtc); i++)
 157     {
 158         copy_mat(energyData_->ekindata()->tcstat[i].ekinh, energyData_->ekindata()->tcstat[i].ekinh_old);
 159     }
 160 }
 161
 162 template<ComputeGlobalsAlgorithm algorithm>
 163 void ComputeGlobalsElement<algorithm>::scheduleTask(Step                       step,
 164                                                     Time gmx_unused            time,
 165                                                     const RegisterRunFunction& registerRunFunction)
 166 {
 167     const bool needComReduction    = doStopCM_ && do_per_step(step, nstcomm_);
 168     const bool needGlobalReduction = step == energyReductionStep_ || step == virialReductionStep_
 169                                      || needComReduction || do_per_step(step, nstglobalcomm_);
 170
 171     // TODO: CGLO_GSTAT is only used for needToSumEkinhOld_, i.e. to signal that we do or do not
 172     //       sum the previous kinetic energy. We should simplify / clarify this.
 173
 174     if (algorithm == ComputeGlobalsAlgorithm::LeapFrog)
 175     {
 176         // With Leap-Frog we can skip compute_globals at
 177         // non-communication steps, but we need to calculate
 178         // the kinetic energy one step before communication.
 179
 180         // With leap-frog we also need to compute the half-step
 181         // kinetic energy at the step before we need to write
 182         // the full-step kinetic energy
 183         const bool needEkinAtNextStep = (do_per_step(step + 1, nstglobalcomm_) || step + 1 == lastStep_);
 184
 185         if (!needGlobalReduction && !needEkinAtNextStep)
 186         {
 187             return;
 188         }
 189
 190         const bool doEnergy = step == energyReductionStep_;
 191         int        flags    = (needGlobalReduction ? CGLO_GSTAT : 0) | (doEnergy ? CGLO_ENERGY : 0)
 192                     | (needComReduction ? CGLO_STOPCM : 0) | CGLO_TEMPERATURE | CGLO_PRESSURE
 193                     | CGLO_CONSTRAINT;
 194
 195         // Since we're already communicating at this step, we
 196         // can propagate intra-simulation signals. Note that
 197         // check_nstglobalcomm has the responsibility for
 198         // choosing the value of nstglobalcomm which satisfies
 199         // the need of the different signallers.
 200         const bool doIntraSimSignal = true;
 201         // Disable functionality
 202         const bool doInterSimSignal = false;
 203
 204         // Make signaller to signal stop / reset / checkpointing signals
 205         auto signaller = std::make_shared<SimulationSignaller>(
 206                 signals_, cr_, nullptr, doInterSimSignal, doIntraSimSignal);
 207
 208         registerRunFunction([this, step, flags, signaller = std::move(signaller)]() {
 209             compute(step, flags, signaller.get(), true);
 210         });
 211     }
 212     else if (algorithm == ComputeGlobalsAlgorithm::VelocityVerlet)
 213     {
 214         // For VV, we schedule two calls to compute globals per step.
 215         if (step != vvSchedulingStep_)
 216         {
 217             // This is the first scheduling call for this step (positions & velocities at full time
 218             // step) Set this as the current scheduling step
 219             vvSchedulingStep_ = step;
 220
 221             // For vv, the state at the beginning of the step is positions at time t, velocities at time t - dt/2
 222             // The first velocity propagation (+dt/2) therefore actually corresponds to the previous step.
 223             // So we need information from the last step in the first half of the integration
 224             if (!needGlobalReduction && !do_per_step(step - 1, nstglobalcomm_))
 225             {
 226                 return;
 227             }
 228
 229             const bool doTemperature = step != initStep_ || inputrec_->bContinuation;
 230             const bool doEnergy      = step == energyReductionStep_;
 231
 232             int flags = (needGlobalReduction ? CGLO_GSTAT : 0) | (doEnergy ? CGLO_ENERGY : 0)
 233                         | (doTemperature ? CGLO_TEMPERATURE : 0) | CGLO_PRESSURE | CGLO_CONSTRAINT
 234                         | (needComReduction ? CGLO_STOPCM : 0) | CGLO_SCALEEKIN;
 235
 236             registerRunFunction(
 237                     [this, step, flags]() { compute(step, flags, nullSignaller_.get(), false); });
 238         }
 239         else
 240         {
 241             // second call to compute_globals for this step
 242             // Reset the scheduling step to avoid confusion if scheduling needs
 243             // to be repeated (in case of unexpected simulation termination)
 244             vvSchedulingStep_ = -1;
 245
 246             if (!needGlobalReduction)
 247             {
 248                 return;
 249             }
 250             int flags = CGLO_GSTAT | CGLO_CONSTRAINT;
 251
 252             // Since we're already communicating at this step, we
 253             // can propagate intra-simulation signals. Note that
 254             // check_nstglobalcomm has the responsibility for
 255             // choosing the value of nstglobalcomm which satisfies
 256             // the need of the different signallers.
 257             const bool doIntraSimSignal = true;
 258             // Disable functionality
 259             const bool doInterSimSignal = false;
 260
 261             auto signaller = std::make_shared<SimulationSignaller>(
 262                     signals_, cr_, nullptr, doInterSimSignal, doIntraSimSignal);
 263
 264             registerRunFunction([this, step, flags, signaller = std::move(signaller)]() {
 265                 compute(step, flags, signaller.get(), true);
 266             });
 267         }
 268     }
 269 }
 270
 271 template<ComputeGlobalsAlgorithm algorithm>
 272 void ComputeGlobalsElement<algorithm>::compute(gmx::Step            step,
 273                                                unsigned int         flags,
 274                                                SimulationSignaller* signaller,
 275                                                bool                 useLastBox,
 276                                                bool                 isInit)
 277 {
 278     auto        x       = statePropagatorData_->positionsView().unpaddedArrayRef();
 279     auto        v       = statePropagatorData_->velocitiesView().unpaddedArrayRef();
 280     const auto* box     = statePropagatorData_->constBox();
 281     const auto* lastbox = useLastBox ? statePropagatorData_->constPreviousBox()
 282                                      : statePropagatorData_->constBox();
 283
 284     if (DOMAINDECOMP(cr_) && shouldCheckNumberOfBondedInteractions(*cr_->dd))
 285     {
 286         flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 287     }
 288     compute_globals(gstat_,
 289                     cr_,
 290                     inputrec_,
 291                     fr_,
 292                     energyData_->ekindata(),
 293                     x,
 294                     v,
 295                     box,
 296                     mdAtoms_->mdatoms(),
 297                     nrnb_,
 298                     &vcm_,
 299                     step != -1 ? wcycle_ : nullptr,
 300                     energyData_->enerdata(),
 301                     energyData_->forceVirial(step),
 302                     energyData_->constraintVirial(step),
 303                     energyData_->totalVirial(step),
 304                     energyData_->pressure(step),
 305                     (((flags & CGLO_ENERGY) != 0) && constr_ != nullptr) ? constr_->rmsdData()
 306                                                                          : gmx::ArrayRef<real>{},
 307                     signaller,
 308                     lastbox,
 309                     energyData_->needToSumEkinhOld(),
 310                     flags);
 311     if (DOMAINDECOMP(cr_))
 312     {
 313         checkNumberOfBondedInteractions(mdlog_, cr_, top_global_, localTopology_, x, box);
 314     }
 315     if (flags & CGLO_STOPCM && !isInit)
 316     {
 317         process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x, v);
 318         inc_nrnb(nrnb_, eNR_STOPCM, mdAtoms_->mdatoms()->homenr);
 319     }
 320 }
 321
 322 template<ComputeGlobalsAlgorithm algorithm>
 323 void ComputeGlobalsElement<algorithm>::setTopology(const gmx_localtop_t* top)
 324 {
 325     localTopology_ = top;
 326 }
 327
 328 template<ComputeGlobalsAlgorithm algorithm>
 329 std::optional<SignallerCallback> ComputeGlobalsElement<algorithm>::registerEnergyCallback(EnergySignallerEvent event)
 330 {
 331     if (event == EnergySignallerEvent::EnergyCalculationStep)
 332     {
 333         return [this](Step step, Time /*unused*/) { energyReductionStep_ = step; };
 334     }
 335     if (event == EnergySignallerEvent::VirialCalculationStep)
 336     {
 337         return [this](Step step, Time /*unused*/) { virialReductionStep_ = step; };
 338     }
 339     return std::nullopt;
 340 }
 341
 342 template<ComputeGlobalsAlgorithm algorithm>
 343 std::optional<SignallerCallback>
 344 ComputeGlobalsElement<algorithm>::registerTrajectorySignallerCallback(TrajectoryEvent event)
 345 {
 346     if (event == TrajectoryEvent::EnergyWritingStep)
 347     {
 348         return [this](Step step, Time /*unused*/) { energyReductionStep_ = step; };
 349     }
 350     return std::nullopt;
 351 }
 352
 353 //! Explicit template instantiation
 354 //! \{
 355 template class ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>;
 356 template class ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>;
 357 //! \}
 358
 359 template<>
 360 ISimulatorElement* ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>::getElementPointerImpl(
 361         LegacySimulatorData*                    legacySimulatorData,
 362         ModularSimulatorAlgorithmBuilderHelper* builderHelper,
 363         StatePropagatorData*                    statePropagatorData,
 364         EnergyData*                             energyData,
 365         FreeEnergyPerturbationData*             freeEnergyPerturbationData,
 366         GlobalCommunicationHelper*              globalCommunicationHelper)
 367 {
 368     auto* element = builderHelper->storeElement(
 369             std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>>(
 370                     statePropagatorData,
 371                     energyData,
 372                     freeEnergyPerturbationData,
 373                     globalCommunicationHelper->simulationSignals(),
 374                     globalCommunicationHelper->nstglobalcomm(),
 375                     legacySimulatorData->fplog,
 376                     legacySimulatorData->mdlog,
 377                     legacySimulatorData->cr,
 378                     legacySimulatorData->inputrec,
 379                     legacySimulatorData->mdAtoms,
 380                     legacySimulatorData->nrnb,
 381                     legacySimulatorData->wcycle,
 382                     legacySimulatorData->fr,
 383                     legacySimulatorData->top_global,
 384                     legacySimulatorData->constr));
 385
 386     return element;
 387 }
 388
 389 template<>
 390 ISimulatorElement* ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>::getElementPointerImpl(
 391         LegacySimulatorData*                    simulator,
 392         ModularSimulatorAlgorithmBuilderHelper* builderHelper,
 393         StatePropagatorData*                    statePropagatorData,
 394         EnergyData*                             energyData,
 395         FreeEnergyPerturbationData*             freeEnergyPerturbationData,
 396         GlobalCommunicationHelper*              globalCommunicationHelper)
 397 {
 398     // We allow this element to be added multiple times to the call list, but we only want one
 399     // actual element built
 400     static const std::string key("vvComputeGlobalsElement");
 401
 402     const std::optional<std::any> cachedValue = builderHelper->builderData(key);
 403
 404     if (cachedValue)
 405     {
 406         return std::any_cast<ISimulatorElement*>(cachedValue.value());
 407     }
 408     else
 409     {
 410         ISimulatorElement* vvComputeGlobalsElement = builderHelper->storeElement(
 411                 std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>(
 412                         statePropagatorData,
 413                         energyData,
 414                         freeEnergyPerturbationData,
 415                         globalCommunicationHelper->simulationSignals(),
 416                         globalCommunicationHelper->nstglobalcomm(),
 417                         simulator->fplog,
 418                         simulator->mdlog,
 419                         simulator->cr,
 420                         simulator->inputrec,
 421                         simulator->mdAtoms,
 422                         simulator->nrnb,
 423                         simulator->wcycle,
 424                         simulator->fr,
 425                         simulator->top_global,
 426                         simulator->constr));
 427         builderHelper->storeBuilderData(key, vvComputeGlobalsElement);
 428         return vvComputeGlobalsElement;
 429     }
 430 }
 431 } // namespace gmx