src/gromacs/modularsimulator/domdechelper.cpp

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  35 /*! \internal \file
  36  * \brief Defines the domain decomposition helper 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 "domdechelper.h"
  45
  46 #include "gromacs/domdec/collect.h"
  47 #include "gromacs/domdec/partition.h"
  48 #include "gromacs/mdtypes/commrec.h"
  49 #include "gromacs/mdtypes/inputrec.h"
  50 #include "gromacs/mdtypes/state.h"
  51 #include "gromacs/pbcutil/pbc.h"
  52
  53 #include "freeenergyperturbationdata.h"
  54 #include "statepropagatordata.h"
  55 #include "topologyholder.h"
  56
  57 namespace gmx
  58 {
  59 DomDecHelper::DomDecHelper(bool                        isVerbose,
  60                            int                         verbosePrintInterval,
  61                            StatePropagatorData*        statePropagatorData,
  62                            FreeEnergyPerturbationData* freeEnergyPerturbationData,
  63                            TopologyHolder*             topologyHolder,
  64                            int                         nstglobalcomm,
  65                            FILE*                       fplog,
  66                            t_commrec*                  cr,
  67                            const MDLogger&             mdlog,
  68                            Constraints*                constr,
  69                            const t_inputrec*           inputrec,
  70                            MDAtoms*                    mdAtoms,
  71                            t_nrnb*                     nrnb,
  72                            gmx_wallcycle*              wcycle,
  73                            t_forcerec*                 fr,
  74                            VirtualSitesHandler*        vsite,
  75                            ImdSession*                 imdSession,
  76                            pull_t*                     pull_work) :
  77     nextNSStep_(-1),
  78     isVerbose_(isVerbose),
  79     verbosePrintInterval_(verbosePrintInterval),
  80     nstglobalcomm_(nstglobalcomm),
  81     statePropagatorData_(statePropagatorData),
  82     freeEnergyPerturbationData_(freeEnergyPerturbationData),
  83     topologyHolder_(topologyHolder),
  84     fplog_(fplog),
  85     cr_(cr),
  86     mdlog_(mdlog),
  87     constr_(constr),
  88     inputrec_(inputrec),
  89     mdAtoms_(mdAtoms),
  90     nrnb_(nrnb),
  91     wcycle_(wcycle),
  92     fr_(fr),
  93     vsite_(vsite),
  94     imdSession_(imdSession),
  95     pull_work_(pull_work)
  96 {
  97     GMX_ASSERT(DOMAINDECOMP(cr), "Domain decomposition Helper constructed in non-DD simulation");
  98 }
  99
 100 void DomDecHelper::setup()
 101 {
 102     // constant choices for this call to dd_partition_system
 103     const bool     verbose       = false;
 104     const bool     isMasterState = true;
 105     const int      nstglobalcomm = 1;
 106     gmx_wallcycle* wcycle        = nullptr;
 107
 108     // Distribute the charge groups over the nodes from the master node
 109     partitionSystem(verbose,
 110                     isMasterState,
 111                     nstglobalcomm,
 112                     wcycle,
 113                     statePropagatorData_->localState(),
 114                     statePropagatorData_->globalState());
 115 }
 116
 117 void DomDecHelper::run(Step step, Time gmx_unused time)
 118 {
 119     if (step != nextNSStep_ || (step == inputrec_->init_step && inputrec_->bContinuation))
 120     {
 121         return;
 122     }
 123     std::unique_ptr<t_state> localState  = statePropagatorData_->localState();
 124     t_state*                 globalState = statePropagatorData_->globalState();
 125
 126     // constant choices for this call to dd_partition_system
 127     const bool verbose = isVerbose_ && (step % verbosePrintInterval_ == 0 || step == inputrec_->init_step);
 128     bool isMasterState = false;
 129
 130     // Correct the new box if it is too skewed
 131     if (inputrecDynamicBox(inputrec_))
 132     {
 133         // TODO: Correcting the box is done here (if using DD) or in ForceElement (non-DD simulations).
 134         //       Think about unifying this responsibility, could this be done in one place?
 135         if (correct_box(fplog_, step, localState->box))
 136         {
 137             isMasterState = true;
 138         }
 139     }
 140     if (isMasterState)
 141     {
 142         dd_collect_state(cr_->dd, localState.get(), globalState);
 143     }
 144
 145     // Distribute the charge groups over the nodes from the master node
 146     partitionSystem(verbose, isMasterState, nstglobalcomm_, wcycle_, std::move(localState), globalState);
 147 }
 148
 149 void DomDecHelper::partitionSystem(bool                     verbose,
 150                                    bool                     isMasterState,
 151                                    int                      nstglobalcomm,
 152                                    gmx_wallcycle*           wcycle,
 153                                    std::unique_ptr<t_state> localState,
 154                                    t_state*                 globalState)
 155 {
 156     ForceBuffers* forcePointer = statePropagatorData_->forcePointer();
 157
 158     // Distribute the charge groups over the nodes from the master node
 159     dd_partition_system(fplog_,
 160                         mdlog_,
 161                         inputrec_->init_step,
 162                         cr_,
 163                         isMasterState,
 164                         nstglobalcomm,
 165                         globalState,
 166                         topologyHolder_->globalTopology(),
 167                         *inputrec_,
 168                         imdSession_,
 169                         pull_work_,
 170                         localState.get(),
 171                         forcePointer,
 172                         mdAtoms_,
 173                         topologyHolder_->localTopology_.get(),
 174                         fr_,
 175                         vsite_,
 176                         constr_,
 177                         nrnb_,
 178                         wcycle,
 179                         verbose);
 180     topologyHolder_->updateLocalTopology();
 181     statePropagatorData_->setLocalState(std::move(localState));
 182     if (freeEnergyPerturbationData_)
 183     {
 184         freeEnergyPerturbationData_->updateMDAtoms();
 185     }
 186 }
 187
 188 std::optional<SignallerCallback> DomDecHelper::registerNSCallback()
 189 {
 190     return [this](Step step, Time gmx_unused time) { this->nextNSStep_ = step; };
 191 }
 192
 193 } // namespace gmx