src/gromacs/nbnxm/nbnxm.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
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   4  * Copyright (c) 2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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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 "pairlistsets.h"
  53 #include "pairsearch.h"
  54
  55 /*! \cond INTERNAL */
  56
  57 void nbnxn_put_on_grid(nonbonded_verlet_t             *nb_verlet,
  58                        const matrix                    box,
  59                        int                             ddZone,
  60                        const rvec                      lowerCorner,
  61                        const rvec                      upperCorner,
  62                        const gmx::UpdateGroupsCog     *updateGroupsCog,
  63                        int                             atomStart,
  64                        int                             atomEnd,
  65                        real                            atomDensity,
  66                        const int                      *atinfo,
  67                        gmx::ArrayRef<const gmx::RVec>  x,
  68                        int                             numAtomsMoved,
  69                        const int                      *move)
  70 {
  71     nb_verlet->pairSearch_->putOnGrid(box, ddZone, lowerCorner, upperCorner,
  72                                       updateGroupsCog, atomStart, atomEnd, atomDensity,
  73                                       atinfo, x, numAtomsMoved, move,
  74                                       nb_verlet->nbat.get());
  75 }
  76
  77 /* Calls nbnxn_put_on_grid for all non-local domains */
  78 void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t              *nbv,
  79                                 const struct gmx_domdec_zones_t *zones,
  80                                 const int                       *atinfo,
  81                                 gmx::ArrayRef<const gmx::RVec>   x)
  82 {
  83     for (int zone = 1; zone < zones->n; zone++)
  84     {
  85         rvec c0, c1;
  86         for (int d = 0; d < DIM; d++)
  87         {
  88             c0[d] = zones->size[zone].bb_x0[d];
  89             c1[d] = zones->size[zone].bb_x1[d];
  90         }
  91
  92         nbnxn_put_on_grid(nbv, nullptr,
  93                           zone, c0, c1,
  94                           nullptr,
  95                           zones->cg_range[zone],
  96                           zones->cg_range[zone+1],
  97                           -1,
  98                           atinfo,
  99                           x,
 100                           0, nullptr);
 101     }
 102 }
 103
 104 bool nonbonded_verlet_t::isDynamicPruningStepCpu(int64_t step) const
 105 {
 106     return pairlistSets_->isDynamicPruningStepCpu(step);
 107 }
 108
 109 bool nonbonded_verlet_t::isDynamicPruningStepGpu(int64_t step) const
 110 {
 111     return pairlistSets_->isDynamicPruningStepGpu(step);
 112 }
 113
 114 gmx::ArrayRef<const int> nonbonded_verlet_t::getLocalAtomOrder() const
 115 {
 116     /* Return the atom order for the home cell (index 0) */
 117     const Nbnxm::Grid &grid       = pairSearch_->gridSet().grids()[0];
 118
 119     const int          numIndices = grid.atomIndexEnd() - grid.firstAtomInColumn(0);
 120
 121     return gmx::constArrayRefFromArray(pairSearch_->gridSet().atomIndices().data(), numIndices);
 122 }
 123
 124 void nonbonded_verlet_t::setLocalAtomOrder()
 125 {
 126     pairSearch_->setLocalAtomOrder();
 127 }
 128
 129 void nonbonded_verlet_t::setAtomProperties(const t_mdatoms &mdatoms,
 130                                            const int       &atinfo)
 131 {
 132     nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), &mdatoms, &atinfo);
 133 }
 134
 135 void nonbonded_verlet_t::setCoordinates(const Nbnxm::AtomLocality       locality,
 136                                         const bool                      fillLocal,
 137                                         gmx::ArrayRef<const gmx::RVec>  x,
 138                                         gmx_wallcycle                  *wcycle)
 139 {
 140     wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
 141     wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
 142
 143     nbnxn_atomdata_copy_x_to_nbat_x(pairSearch_->gridSet(), locality, fillLocal,
 144                                     as_rvec_array(x.data()),
 145                                     nbat.get());
 146
 147     wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
 148     wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
 149 }
 150
 151 gmx::ArrayRef<const int> nonbonded_verlet_t::getGridIndices() const
 152 {
 153     return pairSearch_->gridSet().cells();
 154 }
 155
 156 void
 157 nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const Nbnxm::AtomLocality  locality,
 158                                              rvec                      *f,
 159                                              gmx_wallcycle             *wcycle)
 160 {
 161     wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
 162     wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
 163
 164     reduceForces(nbat.get(), locality, pairSearch_->gridSet(), f);
 165
 166     wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
 167     wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
 168 }
 169
 170 real nonbonded_verlet_t::pairlistInnerRadius() const
 171 {
 172     return pairlistSets_->params().rlistInner;
 173 }
 174
 175 real nonbonded_verlet_t::pairlistOuterRadius() const
 176 {
 177     return pairlistSets_->params().rlistOuter;
 178 }
 179
 180 void nonbonded_verlet_t::changePairlistRadii(real rlistOuter,
 181                                              real rlistInner)
 182 {
 183     pairlistSets_->changePairlistRadii(rlistOuter, rlistInner);
 184 }
 185
 186 /*! \endcond */