src/gromacs/nbnxm/nbnxm.cpp

   1 /*
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   3  *
   4  * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
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  35
  36 /*! \internal \file
  37  * \brief
  38  * Implements the Nbnxm class
  39  *
  40  * \author Berk Hess <hess@kth.se>
  41  * \ingroup module_nbnxm
  42  */
  43
  44 #include "gmxpre.h"
  45
  46 #include "nbnxm.h"
  47
  48 #include "gromacs/domdec/domdec_struct.h"
  49 #include "gromacs/nbnxm/atomdata.h"
  50 #include "gromacs/timing/wallcycle.h"
  51
  52 #include "nbnxm_gpu.h"
  53 #include "pairlistsets.h"
  54 #include "pairsearch.h"
  55
  56 /*! \cond INTERNAL */
  57
  58 void nbnxn_put_on_grid(nonbonded_verlet_t*            nb_verlet,
  59                        const matrix                   box,
  60                        int                            gridIndex,
  61                        const rvec                     lowerCorner,
  62                        const rvec                     upperCorner,
  63                        const gmx::UpdateGroupsCog*    updateGroupsCog,
  64                        gmx::Range<int>                atomRange,
  65                        real                           atomDensity,
  66                        gmx::ArrayRef<const int>       atomInfo,
  67                        gmx::ArrayRef<const gmx::RVec> x,
  68                        int                            numAtomsMoved,
  69                        const int*                     move)
  70 {
  71     nb_verlet->pairSearch_->putOnGrid(box,
  72                                       gridIndex,
  73                                       lowerCorner,
  74                                       upperCorner,
  75                                       updateGroupsCog,
  76                                       atomRange,
  77                                       atomDensity,
  78                                       atomInfo,
  79                                       x,
  80                                       numAtomsMoved,
  81                                       move,
  82                                       nb_verlet->nbat.get());
  83 }
  84
  85 /* Calls nbnxn_put_on_grid for all non-local domains */
  86 void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*              nbv,
  87                                 const struct gmx_domdec_zones_t* zones,
  88                                 gmx::ArrayRef<const int>         atomInfo,
  89                                 gmx::ArrayRef<const gmx::RVec>   x)
  90 {
  91     for (int zone = 1; zone < zones->n; zone++)
  92     {
  93         rvec c0, c1;
  94         for (int d = 0; d < DIM; d++)
  95         {
  96             c0[d] = zones->size[zone].bb_x0[d];
  97             c1[d] = zones->size[zone].bb_x1[d];
  98         }
  99
 100         nbnxn_put_on_grid(nbv,
 101                           nullptr,
 102                           zone,
 103                           c0,
 104                           c1,
 105                           nullptr,
 106                           { zones->cg_range[zone], zones->cg_range[zone + 1] },
 107                           -1,
 108                           atomInfo,
 109                           x,
 110                           0,
 111                           nullptr);
 112     }
 113 }
 114
 115 bool nonbonded_verlet_t::isDynamicPruningStepCpu(int64_t step) const
 116 {
 117     return pairlistSets_->isDynamicPruningStepCpu(step);
 118 }
 119
 120 bool nonbonded_verlet_t::isDynamicPruningStepGpu(int64_t step) const
 121 {
 122     return pairlistSets_->isDynamicPruningStepGpu(step);
 123 }
 124
 125 gmx::ArrayRef<const int> nonbonded_verlet_t::getLocalAtomOrder() const
 126 {
 127     /* Return the atom order for the home cell (index 0) */
 128     const Nbnxm::Grid& grid = pairSearch_->gridSet().grids()[0];
 129
 130     const int numIndices = grid.atomIndexEnd() - grid.firstAtomInColumn(0);
 131
 132     return gmx::constArrayRefFromArray(pairSearch_->gridSet().atomIndices().data(), numIndices);
 133 }
 134
 135 void nonbonded_verlet_t::setLocalAtomOrder() const
 136 {
 137     pairSearch_->setLocalAtomOrder();
 138 }
 139
 140 void nonbonded_verlet_t::setAtomProperties(gmx::ArrayRef<const int>  atomTypes,
 141                                            gmx::ArrayRef<const real> atomCharges,
 142                                            gmx::ArrayRef<const int>  atomInfo) const
 143 {
 144     nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), atomTypes, atomCharges, atomInfo);
 145 }
 146
 147 void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality        locality,
 148                                             gmx::ArrayRef<const gmx::RVec> coordinates)
 149 {
 150     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 151     wallcycle_sub_start(wcycle_, ewcsNB_X_BUF_OPS);
 152
 153     nbnxn_atomdata_copy_x_to_nbat_x(
 154             pairSearch_->gridSet(), locality, as_rvec_array(coordinates.data()), nbat.get());
 155
 156     wallcycle_sub_stop(wcycle_, ewcsNB_X_BUF_OPS);
 157     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 158 }
 159
 160 void nonbonded_verlet_t::convertCoordinatesGpu(const gmx::AtomLocality locality,
 161                                                DeviceBuffer<gmx::RVec> d_x,
 162                                                GpuEventSynchronizer*   xReadyOnDevice)
 163 {
 164     wallcycle_start(wcycle_, ewcLAUNCH_GPU);
 165     wallcycle_sub_start(wcycle_, ewcsLAUNCH_GPU_NB_X_BUF_OPS);
 166
 167     nbnxn_atomdata_x_to_nbat_x_gpu(pairSearch_->gridSet(), locality, gpu_nbv, d_x, xReadyOnDevice);
 168
 169     wallcycle_sub_stop(wcycle_, ewcsLAUNCH_GPU_NB_X_BUF_OPS);
 170     wallcycle_stop(wcycle_, ewcLAUNCH_GPU);
 171 }
 172
 173 gmx::ArrayRef<const int> nonbonded_verlet_t::getGridIndices() const
 174 {
 175     return pairSearch_->gridSet().cells();
 176 }
 177
 178 void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality  locality,
 179                                                   gmx::ArrayRef<gmx::RVec> force)
 180 {
 181
 182     /* Skip the reduction if there was no short-range GPU work to do
 183      * (either NB or both NB and bonded work). */
 184     if (!pairlistIsSimple() && !Nbnxm::haveGpuShortRangeWork(gpu_nbv, locality))
 185     {
 186         return;
 187     }
 188
 189     wallcycle_start(wcycle_, ewcNB_XF_BUF_OPS);
 190     wallcycle_sub_start(wcycle_, ewcsNB_F_BUF_OPS);
 191
 192     reduceForces(nbat.get(), locality, pairSearch_->gridSet(), as_rvec_array(force.data()));
 193
 194     wallcycle_sub_stop(wcycle_, ewcsNB_F_BUF_OPS);
 195     wallcycle_stop(wcycle_, ewcNB_XF_BUF_OPS);
 196 }
 197
 198 int nonbonded_verlet_t::getNumAtoms(const gmx::AtomLocality locality) const
 199 {
 200     int numAtoms = 0;
 201     switch (locality)
 202     {
 203         case gmx::AtomLocality::All: numAtoms = pairSearch_->gridSet().numRealAtomsTotal(); break;
 204         case gmx::AtomLocality::Local: numAtoms = pairSearch_->gridSet().numRealAtomsLocal(); break;
 205         case gmx::AtomLocality::NonLocal:
 206             numAtoms = pairSearch_->gridSet().numRealAtomsTotal()
 207                        - pairSearch_->gridSet().numRealAtomsLocal();
 208             break;
 209         case gmx::AtomLocality::Count:
 210             GMX_ASSERT(false, "Count is invalid locality specifier");
 211             break;
 212     }
 213     return numAtoms;
 214 }
 215
 216 DeviceBuffer<gmx::RVec> nonbonded_verlet_t::getGpuForces() const
 217 {
 218     return Nbnxm::getGpuForces(gpu_nbv);
 219 }
 220
 221 real nonbonded_verlet_t::pairlistInnerRadius() const
 222 {
 223     return pairlistSets_->params().rlistInner;
 224 }
 225
 226 real nonbonded_verlet_t::pairlistOuterRadius() const
 227 {
 228     return pairlistSets_->params().rlistOuter;
 229 }
 230
 231 void nonbonded_verlet_t::changePairlistRadii(real rlistOuter, real rlistInner) const
 232 {
 233     pairlistSets_->changePairlistRadii(rlistOuter, rlistInner);
 234 }
 235
 236 void nonbonded_verlet_t::setupGpuShortRangeWork(const gmx::GpuBonded*          gpuBonded,
 237                                                 const gmx::InteractionLocality iLocality) const
 238 {
 239     if (useGpu() && !emulateGpu())
 240     {
 241         Nbnxm::setupGpuShortRangeWork(gpu_nbv, gpuBonded, iLocality);
 242     }
 243 }
 244
 245 void nonbonded_verlet_t::atomdata_init_copy_x_to_nbat_x_gpu() const
 246 {
 247     Nbnxm::nbnxn_gpu_init_x_to_nbat_x(pairSearch_->gridSet(), gpu_nbv);
 248 }
 249
 250 /*! \endcond */