text: /*
   * This file is part of the GROMACS molecular simulation package.
   *
   * Copyright 2019- The GROMACS Authors
   * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
   * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
   *
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  /*! \internal \file
   * \brief
   * Implements the Nbnxm class
   *
   * \author Berk Hess <hess@kth.se>
   * \ingroup module_nbnxm
   */
  
  #include "gmxpre.h"
  
  #include "nbnxm.h"
  
  #include "gromacs/domdec/domdec_struct.h"
  #include "gromacs/nbnxm/atomdata.h"
  #include "gromacs/timing/wallcycle.h"
  #include "gromacs/utility/message_string_collector.h"
  
  #include "nbnxm_gpu.h"
  #include "pairlistsets.h"
  #include "pairsearch.h"
  
  /*! \cond INTERNAL */
  
  void nbnxn_put_on_grid(nonbonded_verlet_t*            nb_verlet,
                         const matrix                   box,
                         int                            gridIndex,
                         const rvec                     lowerCorner,
                         const rvec                     upperCorner,
                         const gmx::UpdateGroupsCog*    updateGroupsCog,
                         gmx::Range<int>                atomRange,
                         real                           atomDensity,
                         gmx::ArrayRef<const int64_t>   atomInfo,
                         gmx::ArrayRef<const gmx::RVec> x,
                         int                            numAtomsMoved,
                         const int*                     move)
  {
      nb_verlet->pairSearch_->putOnGrid(box,
                                        gridIndex,
                                        lowerCorner,
                                        upperCorner,
                                        updateGroupsCog,
                                        atomRange,
                                        atomDensity,
                                        atomInfo,
                                        x,
                                        numAtomsMoved,
                                        move,
                                        nb_verlet->nbat.get());
  }
  
  /* Calls nbnxn_put_on_grid for all non-local domains */
  void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*              nbv,
                                  const struct gmx_domdec_zones_t* zones,
                                  gmx::ArrayRef<const int64_t>     atomInfo,
                                  gmx::ArrayRef<const gmx::RVec>   x)
  {
      for (int zone = 1; zone < zones->n; zone++)
      {
          rvec c0, c1;
          for (int d = 0; d < DIM; d++)
          {
              c0[d] = zones->size[zone].bb_x0[d];
              c1[d] = zones->size[zone].bb_x1[d];
          }
  
          nbnxn_put_on_grid(nbv,
                            nullptr,
                            zone,
                            c0,
                            c1,
                            nullptr,
                            { zones->cg_range[zone], zones->cg_range[zone + 1] },
                            -1,
                            atomInfo,
                            x,
                            0,
                            nullptr);
      }
  }
  
  bool nonbonded_verlet_t::isDynamicPruningStepCpu(int64_t step) const
  {
      return pairlistSets_->isDynamicPruningStepCpu(step);
  }
  
  bool nonbonded_verlet_t::isDynamicPruningStepGpu(int64_t step) const
  {
      return pairlistSets_->isDynamicPruningStepGpu(step);
  }
  
  gmx::ArrayRef<const int> nonbonded_verlet_t::getLocalAtomOrder() const
  {
      /* Return the atom order for the home cell (index 0) */
      const Nbnxm::Grid& grid = pairSearch_->gridSet().grids()[0];
  
      const int numIndices = grid.atomIndexEnd() - grid.firstAtomInColumn(0);
  
      return gmx::constArrayRefFromArray(pairSearch_->gridSet().atomIndices().data(), numIndices);
  }
  
  void nonbonded_verlet_t::setLocalAtomOrder() const
  {
      pairSearch_->setLocalAtomOrder();
  }
  
  void nonbonded_verlet_t::setAtomProperties(gmx::ArrayRef<const int>     atomTypes,
                                             gmx::ArrayRef<const real>    atomCharges,
                                             gmx::ArrayRef<const int64_t> atomInfo) const
  {
      nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), atomTypes, atomCharges, atomInfo);
  }
  
  void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality        locality,
                                              gmx::ArrayRef<const gmx::RVec> coordinates)
  {
      wallcycle_start(wcycle_, WallCycleCounter::NbXFBufOps);
      wallcycle_sub_start(wcycle_, WallCycleSubCounter::NBXBufOps);
  
      nbnxn_atomdata_copy_x_to_nbat_x(
              pairSearch_->gridSet(), locality, as_rvec_array(coordinates.data()), nbat.get());
  
      wallcycle_sub_stop(wcycle_, WallCycleSubCounter::NBXBufOps);
      wallcycle_stop(wcycle_, WallCycleCounter::NbXFBufOps);
  }
  
  void nonbonded_verlet_t::convertCoordinatesGpu(const gmx::AtomLocality locality,
                                                 DeviceBuffer<gmx::RVec> d_x,
                                                 GpuEventSynchronizer*   xReadyOnDevice)
  {
      wallcycle_start(wcycle_, WallCycleCounter::LaunchGpu);
      wallcycle_sub_start(wcycle_, WallCycleSubCounter::LaunchGpuNBXBufOps);
  
      nbnxn_atomdata_x_to_nbat_x_gpu(pairSearch_->gridSet(), locality, gpu_nbv, d_x, xReadyOnDevice);
  
      wallcycle_sub_stop(wcycle_, WallCycleSubCounter::LaunchGpuNBXBufOps);
      wallcycle_stop(wcycle_, WallCycleCounter::LaunchGpu);
  }
  
  gmx::ArrayRef<const int> nonbonded_verlet_t::getGridIndices() const
  {
      return pairSearch_->gridSet().cells();
  }
  
  void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality  locality,
                                                    gmx::ArrayRef<gmx::RVec> force)
  {
  
      /* Skip the reduction if there was no short-range GPU work to do
       * (either NB or both NB and bonded work). */
      if (!pairlistIsSimple() && !Nbnxm::haveGpuShortRangeWork(gpu_nbv, atomToInteractionLocality(locality)))
      {
          return;
      }
  
      wallcycle_start(wcycle_, WallCycleCounter::NbXFBufOps);
      wallcycle_sub_start(wcycle_, WallCycleSubCounter::NBFBufOps);
  
      reduceForces(nbat.get(), locality, pairSearch_->gridSet(), as_rvec_array(force.data()));
  
      wallcycle_sub_stop(wcycle_, WallCycleSubCounter::NBFBufOps);
      wallcycle_stop(wcycle_, WallCycleCounter::NbXFBufOps);
  }
  
  int nonbonded_verlet_t::getNumAtoms(const gmx::AtomLocality locality) const
  {
      int numAtoms = 0;
      switch (locality)
      {
          case gmx::AtomLocality::All: numAtoms = pairSearch_->gridSet().numRealAtomsTotal(); break;
          case gmx::AtomLocality::Local: numAtoms = pairSearch_->gridSet().numRealAtomsLocal(); break;
          case gmx::AtomLocality::NonLocal:
              numAtoms = pairSearch_->gridSet().numRealAtomsTotal()
                         - pairSearch_->gridSet().numRealAtomsLocal();
              break;
          case gmx::AtomLocality::Count:
              GMX_ASSERT(false, "Count is invalid locality specifier");
              break;
      }
      return numAtoms;
  }
  
  real nonbonded_verlet_t::pairlistInnerRadius() const
  {
      return pairlistSets_->params().rlistInner;
  }
  
  real nonbonded_verlet_t::pairlistOuterRadius() const
  {
      return pairlistSets_->params().rlistOuter;
  }
  
  void nonbonded_verlet_t::changePairlistRadii(real rlistOuter, real rlistInner) const
  {
      pairlistSets_->changePairlistRadii(rlistOuter, rlistInner);
  }
  
  void nonbonded_verlet_t::setupGpuShortRangeWork(const gmx::ListedForcesGpu*    listedForcesGpu,
                                                  const gmx::InteractionLocality iLocality) const
  {
      if (useGpu() && !emulateGpu())
      {
          Nbnxm::setupGpuShortRangeWork(gpu_nbv, listedForcesGpu, iLocality);
      }
  }
  
  void nonbonded_verlet_t::atomdata_init_copy_x_to_nbat_x_gpu() const
  {
      Nbnxm::nbnxn_gpu_init_x_to_nbat_x(pairSearch_->gridSet(), gpu_nbv);
  }
  
  bool buildSupportsNonbondedOnGpu(std::string* error)
  {
      gmx::MessageStringCollector errorReasons;
      // Before changing the prefix string, make sure that it is not searched for in regression tests.
      errorReasons.startContext("Nonbonded interactions on GPUs are not supported in:");
      errorReasons.appendIf(GMX_DOUBLE, "Double precision build of GROMACS");
      errorReasons.appendIf(!GMX_GPU, "Non-GPU build of GROMACS.");
      errorReasons.finishContext();
      if (error != nullptr)
      {
          *error = errorReasons.toString();
      }
      return errorReasons.isEmpty();
  }
  
  /*! \endcond */
  