src/gromacs/modularsimulator/forceelement.cpp

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  35 /*! \internal \file
  36  * \brief Defines the force 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 "forceelement.h"
  45
  46 #include "gromacs/domdec/mdsetup.h"
  47 #include "gromacs/math/vectypes.h"
  48 #include "gromacs/mdlib/constr.h"
  49 #include "gromacs/mdlib/force.h"
  50 #include "gromacs/mdlib/force_flags.h"
  51 #include "gromacs/mdlib/mdatoms.h"
  52 #include "gromacs/mdrun/shellfc.h"
  53 #include "gromacs/mdtypes/forcebuffers.h"
  54 #include "gromacs/mdtypes/forcerec.h"
  55 #include "gromacs/mdtypes/inputrec.h"
  56 #include "gromacs/mdtypes/interaction_const.h"
  57 #include "gromacs/mdtypes/mdatom.h"
  58 #include "gromacs/mdtypes/mdrunoptions.h"
  59 #include "gromacs/mdtypes/simulation_workload.h"
  60 #include "gromacs/pbcutil/pbc.h"
  61
  62 #include "energydata.h"
  63 #include "freeenergyperturbationdata.h"
  64 #include "modularsimulator.h"
  65 #include "simulatoralgorithm.h"
  66 #include "statepropagatordata.h"
  67
  68 struct gmx_edsam;
  69 struct gmx_enfrot;
  70 struct gmx_multisim_t;
  71 class history_t;
  72
  73 namespace gmx
  74 {
  75 ForceElement::ForceElement(StatePropagatorData*        statePropagatorData,
  76                            EnergyData*                 energyData,
  77                            FreeEnergyPerturbationData* freeEnergyPerturbationData,
  78                            bool                        isVerbose,
  79                            bool                        isDynamicBox,
  80                            FILE*                       fplog,
  81                            const t_commrec*            cr,
  82                            const t_inputrec*           inputrec,
  83                            const MDAtoms*              mdAtoms,
  84                            t_nrnb*                     nrnb,
  85                            t_forcerec*                 fr,
  86                            gmx_wallcycle*              wcycle,
  87                            MdrunScheduleWorkload*      runScheduleWork,
  88                            VirtualSitesHandler*        vsite,
  89                            ImdSession*                 imdSession,
  90                            pull_t*                     pull_work,
  91                            Constraints*                constr,
  92                            const gmx_mtop_t&           globalTopology,
  93                            gmx_enfrot*                 enforcedRotation) :
  94     shellfc_(init_shell_flexcon(fplog,
  95                                 globalTopology,
  96                                 constr ? constr->numFlexibleConstraints() : 0,
  97                                 inputrec->nstcalcenergy,
  98                                 haveDDAtomOrdering(*cr),
  99                                 runScheduleWork->simulationWork.useGpuPme)),
 100     doShellFC_(shellfc_ != nullptr),
 101     nextNSStep_(-1),
 102     nextEnergyCalculationStep_(-1),
 103     nextVirialCalculationStep_(-1),
 104     nextFreeEnergyCalculationStep_(-1),
 105     statePropagatorData_(statePropagatorData),
 106     energyData_(energyData),
 107     freeEnergyPerturbationData_(freeEnergyPerturbationData),
 108     localTopology_(nullptr),
 109     isDynamicBox_(isDynamicBox),
 110     isVerbose_(isVerbose),
 111     nShellRelaxationSteps_(0),
 112     ddBalanceRegionHandler_(cr),
 113     longRangeNonbondeds_(std::make_unique<CpuPpLongRangeNonbondeds>(fr->n_tpi,
 114                                                                     fr->ic->ewaldcoeff_q,
 115                                                                     fr->ic->epsilon_r,
 116                                                                     fr->qsum,
 117                                                                     fr->ic->eeltype,
 118                                                                     fr->ic->vdwtype,
 119                                                                     *inputrec,
 120                                                                     nrnb,
 121                                                                     wcycle,
 122                                                                     fplog)),
 123     lambda_(),
 124     fplog_(fplog),
 125     cr_(cr),
 126     inputrec_(inputrec),
 127     mdAtoms_(mdAtoms),
 128     nrnb_(nrnb),
 129     wcycle_(wcycle),
 130     fr_(fr),
 131     vsite_(vsite),
 132     imdSession_(imdSession),
 133     pull_work_(pull_work),
 134     runScheduleWork_(runScheduleWork),
 135     constr_(constr),
 136     enforcedRotation_(enforcedRotation)
 137 {
 138     std::fill(lambda_.begin(), lambda_.end(), 0);
 139
 140     if (doShellFC_ && !haveDDAtomOrdering(*cr))
 141     {
 142         // This was done in mdAlgorithmsSetupAtomData(), but shellfc
 143         // won't be available outside this element.
 144         make_local_shells(cr, *mdAtoms->mdatoms(), shellfc_);
 145     }
 146 }
 147
 148 void ForceElement::scheduleTask(Step step, Time time, const RegisterRunFunction& registerRunFunction)
 149 {
 150     unsigned int flags =
 151             (GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | (isDynamicBox_ ? GMX_FORCE_DYNAMICBOX : 0)
 152              | (nextVirialCalculationStep_ == step ? GMX_FORCE_VIRIAL : 0)
 153              | (nextEnergyCalculationStep_ == step ? GMX_FORCE_ENERGY : 0)
 154              | (nextFreeEnergyCalculationStep_ == step ? GMX_FORCE_DHDL : 0)
 155              | (!doShellFC_ && nextNSStep_ == step ? GMX_FORCE_NS : 0));
 156
 157     registerRunFunction([this, step, time, flags]() {
 158         if (doShellFC_)
 159         {
 160             run<true>(step, time, flags);
 161         }
 162         else
 163         {
 164             run<false>(step, time, flags);
 165         }
 166     });
 167 }
 168
 169 void ForceElement::elementSetup()
 170 {
 171     GMX_ASSERT(localTopology_, "Setup called before local topology was set.");
 172 }
 173
 174 template<bool doShellFC>
 175 void ForceElement::run(Step step, Time time, unsigned int flags)
 176 {
 177     // Disabled functionality
 178     gmx_multisim_t* ms = nullptr;
 179
 180
 181     if (!haveDDAtomOrdering(*cr_) && (flags & GMX_FORCE_NS) && inputrecDynamicBox(inputrec_))
 182     {
 183         // TODO: Correcting the box is done in DomDecHelper (if using DD) or here (non-DD simulations).
 184         //       Think about unifying this responsibility, could this be done in one place?
 185         auto* box = statePropagatorData_->box();
 186         correct_box(fplog_, step, box);
 187     }
 188
 189     /* The coordinates (x) are shifted (to get whole molecules)
 190      * in do_force.
 191      * This is parallelized as well, and does communication too.
 192      * Check comments in sim_util.c
 193      */
 194     auto        x      = statePropagatorData_->positionsView();
 195     auto&       forces = statePropagatorData_->forcesView();
 196     const auto* box    = statePropagatorData_->constBox();
 197     history_t*  hist   = nullptr; // disabled
 198
 199     tensor force_vir = { { 0 } };
 200     // TODO: Make lambda const (needs some adjustments in lower force routines)
 201     ArrayRef<real> lambda =
 202             freeEnergyPerturbationData_ ? freeEnergyPerturbationData_->lambdaView() : lambda_;
 203
 204     longRangeNonbondeds_->updateAfterPartition(*mdAtoms_->mdatoms());
 205
 206     if (doShellFC)
 207     {
 208         auto v = statePropagatorData_->velocitiesView();
 209
 210         relax_shell_flexcon(fplog_,
 211                             cr_,
 212                             ms,
 213                             isVerbose_,
 214                             enforcedRotation_,
 215                             step,
 216                             inputrec_,
 217                             imdSession_,
 218                             pull_work_,
 219                             step == nextNSStep_,
 220                             static_cast<int>(flags),
 221                             localTopology_,
 222                             constr_,
 223                             energyData_->enerdata(),
 224                             statePropagatorData_->localNumAtoms(),
 225                             x,
 226                             v,
 227                             box,
 228                             lambda,
 229                             hist,
 230                             &forces,
 231                             force_vir,
 232                             *mdAtoms_->mdatoms(),
 233                             longRangeNonbondeds_.get(),
 234                             nrnb_,
 235                             wcycle_,
 236                             shellfc_,
 237                             fr_,
 238                             runScheduleWork_,
 239                             time,
 240                             energyData_->muTot(),
 241                             vsite_,
 242                             ddBalanceRegionHandler_);
 243         nShellRelaxationSteps_++;
 244     }
 245     else
 246     {
 247         // Disabled functionality
 248         Awh*       awh = nullptr;
 249         gmx_edsam* ed  = nullptr;
 250
 251         do_force(fplog_,
 252                  cr_,
 253                  ms,
 254                  *inputrec_,
 255                  awh,
 256                  enforcedRotation_,
 257                  imdSession_,
 258                  pull_work_,
 259                  step,
 260                  nrnb_,
 261                  wcycle_,
 262                  localTopology_,
 263                  box,
 264                  x,
 265                  hist,
 266                  &forces,
 267                  force_vir,
 268                  mdAtoms_->mdatoms(),
 269                  energyData_->enerdata(),
 270                  lambda,
 271                  fr_,
 272                  runScheduleWork_,
 273                  vsite_,
 274                  energyData_->muTot(),
 275                  time,
 276                  ed,
 277                  longRangeNonbondeds_.get(),
 278                  static_cast<int>(flags),
 279                  ddBalanceRegionHandler_);
 280     }
 281     energyData_->addToForceVirial(force_vir, step);
 282 }
 283
 284 void ForceElement::elementTeardown()
 285 {
 286     if (doShellFC_)
 287     {
 288         done_shellfc(fplog_, shellfc_, nShellRelaxationSteps_);
 289     }
 290 }
 291
 292 void ForceElement::setTopology(const gmx_localtop_t* top)
 293 {
 294     localTopology_ = top;
 295 }
 296
 297 std::optional<SignallerCallback> ForceElement::registerNSCallback()
 298 {
 299     return [this](Step step, Time gmx_unused time) { this->nextNSStep_ = step; };
 300 }
 301
 302 std::optional<SignallerCallback> ForceElement::registerEnergyCallback(EnergySignallerEvent event)
 303 {
 304     if (event == EnergySignallerEvent::EnergyCalculationStep)
 305     {
 306         return [this](Step step, Time /*unused*/) { nextEnergyCalculationStep_ = step; };
 307     }
 308     if (event == EnergySignallerEvent::VirialCalculationStep)
 309     {
 310         return [this](Step step, Time /*unused*/) { nextVirialCalculationStep_ = step; };
 311     }
 312     if (event == EnergySignallerEvent::FreeEnergyCalculationStep)
 313     {
 314         return [this](Step step, Time /*unused*/) { nextFreeEnergyCalculationStep_ = step; };
 315     }
 316     return std::nullopt;
 317 }
 318
 319 DomDecCallback ForceElement::registerDomDecCallback()
 320 {
 321     return [this]() { longRangeNonbondeds_->updateAfterPartition(*mdAtoms_->mdatoms()); };
 322 }
 323
 324 ISimulatorElement*
 325 ForceElement::getElementPointerImpl(LegacySimulatorData*                    legacySimulatorData,
 326                                     ModularSimulatorAlgorithmBuilderHelper* builderHelper,
 327                                     StatePropagatorData*                    statePropagatorData,
 328                                     EnergyData*                             energyData,
 329                                     FreeEnergyPerturbationData* freeEnergyPerturbationData,
 330                                     GlobalCommunicationHelper gmx_unused* globalCommunicationHelper,
 331                                     ObservablesReducer* /*observablesReducer*/)
 332 {
 333     const bool isVerbose    = legacySimulatorData->mdrunOptions.verbose;
 334     const bool isDynamicBox = inputrecDynamicBox(legacySimulatorData->inputrec);
 335     return builderHelper->storeElement(
 336             std::make_unique<ForceElement>(statePropagatorData,
 337                                            energyData,
 338                                            freeEnergyPerturbationData,
 339                                            isVerbose,
 340                                            isDynamicBox,
 341                                            legacySimulatorData->fplog,
 342                                            legacySimulatorData->cr,
 343                                            legacySimulatorData->inputrec,
 344                                            legacySimulatorData->mdAtoms,
 345                                            legacySimulatorData->nrnb,
 346                                            legacySimulatorData->fr,
 347                                            legacySimulatorData->wcycle,
 348                                            legacySimulatorData->runScheduleWork,
 349                                            legacySimulatorData->vsite,
 350                                            legacySimulatorData->imdSession,
 351                                            legacySimulatorData->pull_work,
 352                                            legacySimulatorData->constr,
 353                                            legacySimulatorData->top_global,
 354                                            legacySimulatorData->enforcedRotation));
 355 }
 356 } // namespace gmx