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