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                                                         ObservablesReducer* observablesReducer) :
  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     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     observablesReducer_(observablesReducer)
 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     if (doStopCM_ && !inputrec_->bContinuation)
 125     {
 126         // To minimize communication, compute_globals computes the COM velocity
 127         // and the kinetic energy for the velocities without COM motion removed.
 128         // Thus to get the kinetic energy without the COM contribution, we need
 129         // to call compute_globals twice.
 130
 131         compute(-1, CGLO_GSTAT | CGLO_STOPCM, nullSignaller_.get(), false, true);
 132
 133         auto v = statePropagatorData_->velocitiesView();
 134         // At initialization, do not pass x with acceleration-correction mode
 135         // to avoid (incorrect) correction of the initial coordinates.
 136         auto x = vcm_.mode == ComRemovalAlgorithm::LinearAccelerationCorrection
 137                          ? ArrayRefWithPadding<RVec>()
 138                          : statePropagatorData_->positionsView();
 139         process_and_stopcm_grp(
 140                 fplog_, &vcm_, *mdAtoms_->mdatoms(), x.unpaddedArrayRef(), v.unpaddedArrayRef());
 141         inc_nrnb(nrnb_, eNR_STOPCM, mdAtoms_->mdatoms()->homenr);
 142     }
 143
 144     unsigned int cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
 145                                | (energyData_->hasReadEkinFromCheckpoint() ? CGLO_READEKIN : 0));
 146
 147     if (algorithm == ComputeGlobalsAlgorithm::VelocityVerlet)
 148     {
 149         cglo_flags |= CGLO_PRESSURE | CGLO_CONSTRAINT;
 150     }
 151
 152     compute(-1, cglo_flags, nullSignaller_.get(), false, true);
 153
 154     // Calculate the initial half step temperature, and save the ekinh_old
 155     for (int i = 0; (i < inputrec_->opts.ngtc); i++)
 156     {
 157         copy_mat(energyData_->ekindata()->tcstat[i].ekinh, energyData_->ekindata()->tcstat[i].ekinh_old);
 158     }
 159 }
 160
 161 template<ComputeGlobalsAlgorithm algorithm>
 162 void ComputeGlobalsElement<algorithm>::scheduleTask(Step                       step,
 163                                                     Time gmx_unused            time,
 164                                                     const RegisterRunFunction& registerRunFunction)
 165 {
 166     const bool needComReduction    = doStopCM_ && do_per_step(step, nstcomm_);
 167     const bool needGlobalReduction = step == energyReductionStep_ || step == virialReductionStep_
 168                                      || needComReduction || do_per_step(step, nstglobalcomm_)
 169                                      || (EI_VV(inputrec_->eI) && inputrecNvtTrotter(inputrec_)
 170                                          && do_per_step(step - 1, 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     compute_globals(gstat_,
 286                     cr_,
 287                     inputrec_,
 288                     fr_,
 289                     energyData_->ekindata(),
 290                     x,
 291                     v,
 292                     box,
 293                     mdAtoms_->mdatoms(),
 294                     nrnb_,
 295                     &vcm_,
 296                     step != -1 ? wcycle_ : nullptr,
 297                     energyData_->enerdata(),
 298                     energyData_->forceVirial(step),
 299                     energyData_->constraintVirial(step),
 300                     energyData_->totalVirial(step),
 301                     energyData_->pressure(step),
 302                     (((flags & CGLO_ENERGY) != 0) && constr_ != nullptr) ? constr_->rmsdData()
 303                                                                          : gmx::ArrayRef<real>{},
 304                     signaller,
 305                     lastbox,
 306                     energyData_->needToSumEkinhOld(),
 307                     flags,
 308                     step,
 309                     observablesReducer_);
 310     if (flags & CGLO_STOPCM && !isInit)
 311     {
 312         process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x, v);
 313         inc_nrnb(nrnb_, eNR_STOPCM, mdAtoms_->mdatoms()->homenr);
 314     }
 315 }
 316
 317 template<ComputeGlobalsAlgorithm algorithm>
 318 std::optional<SignallerCallback> ComputeGlobalsElement<algorithm>::registerEnergyCallback(EnergySignallerEvent event)
 319 {
 320     if (event == EnergySignallerEvent::EnergyCalculationStep)
 321     {
 322         return [this](Step step, Time /*unused*/) { energyReductionStep_ = step; };
 323     }
 324     if (event == EnergySignallerEvent::VirialCalculationStep)
 325     {
 326         return [this](Step step, Time /*unused*/) { virialReductionStep_ = step; };
 327     }
 328     return std::nullopt;
 329 }
 330
 331 template<ComputeGlobalsAlgorithm algorithm>
 332 std::optional<SignallerCallback>
 333 ComputeGlobalsElement<algorithm>::registerTrajectorySignallerCallback(TrajectoryEvent event)
 334 {
 335     if (event == TrajectoryEvent::EnergyWritingStep)
 336     {
 337         return [this](Step step, Time /*unused*/) { energyReductionStep_ = step; };
 338     }
 339     return std::nullopt;
 340 }
 341
 342 //! Explicit template instantiation
 343 //! \{
 344 template class ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>;
 345 template class ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>;
 346 //! \}
 347
 348 template<>
 349 ISimulatorElement* ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>::getElementPointerImpl(
 350         LegacySimulatorData*                    legacySimulatorData,
 351         ModularSimulatorAlgorithmBuilderHelper* builderHelper,
 352         StatePropagatorData*                    statePropagatorData,
 353         EnergyData*                             energyData,
 354         FreeEnergyPerturbationData*             freeEnergyPerturbationData,
 355         GlobalCommunicationHelper*              globalCommunicationHelper,
 356         ObservablesReducer*                     observablesReducer)
 357 {
 358     auto* element = builderHelper->storeElement(
 359             std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::LeapFrog>>(
 360                     statePropagatorData,
 361                     energyData,
 362                     freeEnergyPerturbationData,
 363                     globalCommunicationHelper->simulationSignals(),
 364                     globalCommunicationHelper->nstglobalcomm(),
 365                     legacySimulatorData->fplog,
 366                     legacySimulatorData->mdlog,
 367                     legacySimulatorData->cr,
 368                     legacySimulatorData->inputrec,
 369                     legacySimulatorData->mdAtoms,
 370                     legacySimulatorData->nrnb,
 371                     legacySimulatorData->wcycle,
 372                     legacySimulatorData->fr,
 373                     legacySimulatorData->top_global,
 374                     legacySimulatorData->constr,
 375                     observablesReducer));
 376
 377     return element;
 378 }
 379
 380 template<>
 381 ISimulatorElement* ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>::getElementPointerImpl(
 382         LegacySimulatorData*                    simulator,
 383         ModularSimulatorAlgorithmBuilderHelper* builderHelper,
 384         StatePropagatorData*                    statePropagatorData,
 385         EnergyData*                             energyData,
 386         FreeEnergyPerturbationData*             freeEnergyPerturbationData,
 387         GlobalCommunicationHelper*              globalCommunicationHelper,
 388         ObservablesReducer*                     observablesReducer)
 389 {
 390     // We allow this element to be added multiple times to the call list, but we only want one
 391     // actual element built
 392     static const std::string key("vvComputeGlobalsElement");
 393
 394     const std::optional<std::any> cachedValue = builderHelper->builderData(key);
 395
 396     if (cachedValue)
 397     {
 398         return std::any_cast<ISimulatorElement*>(cachedValue.value());
 399     }
 400     else
 401     {
 402         ISimulatorElement* vvComputeGlobalsElement = builderHelper->storeElement(
 403                 std::make_unique<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>(
 404                         statePropagatorData,
 405                         energyData,
 406                         freeEnergyPerturbationData,
 407                         globalCommunicationHelper->simulationSignals(),
 408                         globalCommunicationHelper->nstglobalcomm(),
 409                         simulator->fplog,
 410                         simulator->mdlog,
 411                         simulator->cr,
 412                         simulator->inputrec,
 413                         simulator->mdAtoms,
 414                         simulator->nrnb,
 415                         simulator->wcycle,
 416                         simulator->fr,
 417                         simulator->top_global,
 418                         simulator->constr,
 419                         observablesReducer));
 420         builderHelper->storeBuilderData(key, vvComputeGlobalsElement);
 421         return vvComputeGlobalsElement;
 422     }
 423 }
 424 } // namespace gmx