src/gromacs/nbnxm/gridset.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  *
  38  * \brief
  39  * Implements the GridSet class.
  40  *
  41  * \author Berk Hess <hess@kth.se>
  42  * \ingroup module_nbnxm
  43  */
  44
  45 #include "gmxpre.h"
  46
  47 #include "gridset.h"
  48
  49 #include "gromacs/mdlib/gmx_omp_nthreads.h"
  50 #include "gromacs/mdlib/updategroupscog.h"
  51 #include "gromacs/nbnxm/atomdata.h"
  52 #include "gromacs/utility/fatalerror.h"
  53
  54 namespace Nbnxm
  55 {
  56
  57 //! Returns the number of DD zones
  58 static int numDDZones(const std::array<bool, DIM> &haveMultipleDomainsPerDim)
  59 {
  60     int  numDDZones = 1;
  61     for (auto haveDD : haveMultipleDomainsPerDim)
  62     {
  63         if (haveDD)
  64         {
  65             numDDZones *= 2;
  66         }
  67     }
  68
  69     return numDDZones;
  70 }
  71
  72 GridSet::DomainSetup::DomainSetup(const int                 ePBC,
  73                                   const ivec               *numDDCells,
  74                                   const gmx_domdec_zones_t *ddZones) :
  75     ePBC(ePBC),
  76     haveMultipleDomains(numDDCells != nullptr),
  77     zones(ddZones)
  78 {
  79     for (int d = 0; d < DIM; d++)
  80     {
  81         haveMultipleDomainsPerDim[d] = (numDDCells != nullptr && (*numDDCells)[d] > 1);
  82     }
  83 }
  84
  85 GridSet::GridSet(const int                 ePBC,
  86                  const ivec               *numDDCells,
  87                  const gmx_domdec_zones_t *ddZones,
  88                  const PairlistType        pairlistType,
  89                  const bool                haveFep,
  90                  const int                 numThreads,
  91                  gmx::PinningPolicy        pinningPolicy) :
  92     domainSetup_(ePBC, numDDCells, ddZones),
  93     grids_(numDDZones(domainSetup_.haveMultipleDomainsPerDim), Grid(pairlistType, haveFep_)),
  94     haveFep_(haveFep),
  95     numRealAtomsLocal_(0),
  96     numRealAtomsTotal_(0),
  97     gridWork_(numThreads)
  98 {
  99     clear_mat(box_);
 100     changePinningPolicy(&gridSetData_.cells, pinningPolicy);
 101     changePinningPolicy(&gridSetData_.atomIndices, pinningPolicy);
 102 }
 103
 104 void GridSet::setLocalAtomOrder()
 105 {
 106     /* Set the atom order for the home cell (index 0) */
 107     const Nbnxm::Grid &grid = grids_[0];
 108
 109     int                atomIndex = 0;
 110     for (int cxy = 0; cxy < grid.numColumns(); cxy++)
 111     {
 112         const int numAtoms  = grid.numAtomsInColumn(cxy);
 113         int       cellIndex = grid.firstCellInColumn(cxy)*grid.geometry().numAtomsPerCell;
 114         for (int i = 0; i < numAtoms; i++)
 115         {
 116             gridSetData_.atomIndices[cellIndex] = atomIndex;
 117             gridSetData_.cells[atomIndex]       = cellIndex;
 118             atomIndex++;
 119             cellIndex++;
 120         }
 121     }
 122 }
 123
 124 // TODO: Move to gridset.cpp
 125 void GridSet::putOnGrid(const matrix                    box,
 126                         const int                       ddZone,
 127                         const rvec                      lowerCorner,
 128                         const rvec                      upperCorner,
 129                         const gmx::UpdateGroupsCog     *updateGroupsCog,
 130                         const int                       atomStart,
 131                         const int                       atomEnd,
 132                         real                            atomDensity,
 133                         gmx::ArrayRef<const int>        atomInfo,
 134                         gmx::ArrayRef<const gmx::RVec>  x,
 135                         const int                       numAtomsMoved,
 136                         const int                      *move,
 137                         nbnxn_atomdata_t               *nbat)
 138 {
 139     Nbnxm::Grid  &grid = grids_[ddZone];
 140
 141     int           cellOffset;
 142     if (ddZone == 0)
 143     {
 144         cellOffset = 0;
 145     }
 146     else
 147     {
 148         const Nbnxm::Grid &previousGrid = grids_[ddZone - 1];
 149         cellOffset = previousGrid.atomIndexEnd()/previousGrid.geometry().numAtomsPerCell;
 150     }
 151
 152     const int n = atomEnd - atomStart;
 153
 154     real      maxAtomGroupRadius;
 155     if (ddZone == 0)
 156     {
 157         copy_mat(box, box_);
 158
 159         numRealAtomsLocal_ = atomEnd - numAtomsMoved;
 160         /* We assume that nbnxn_put_on_grid is called first
 161          * for the local atoms (ddZone=0).
 162          */
 163         numRealAtomsTotal_ = atomEnd - numAtomsMoved;
 164
 165         maxAtomGroupRadius = (updateGroupsCog ? updateGroupsCog->maxUpdateGroupRadius() : 0);
 166
 167         if (debug)
 168         {
 169             fprintf(debug, "natoms_local = %5d atom_density = %5.1f\n",
 170                     numRealAtomsLocal_, atomDensity);
 171         }
 172     }
 173     else
 174     {
 175         const Nbnxm::Grid::Dimensions &dimsGrid0 = grids_[0].dimensions();
 176         atomDensity        = dimsGrid0.atomDensity;
 177         maxAtomGroupRadius = dimsGrid0.maxAtomGroupRadius;
 178
 179         numRealAtomsTotal_ = std::max(numRealAtomsTotal_, atomEnd);
 180     }
 181
 182     /* We always use the home zone (grid[0]) for setting the cell size,
 183      * since determining densities for non-local zones is difficult.
 184      */
 185     // grid data used in GPU transfers inherits the gridset pinnin policy
 186     auto pinPolicy = gridSetData_.cells.get_allocator().pinningPolicy();
 187     grid.setDimensions(ddZone, n - numAtomsMoved,
 188                        lowerCorner, upperCorner,
 189                        atomDensity,
 190                        maxAtomGroupRadius,
 191                        haveFep_,
 192                        pinPolicy);
 193
 194     for (GridWork &work : gridWork_)
 195     {
 196         work.numAtomsPerColumn.resize(grid.numColumns() + 1);
 197     }
 198
 199     /* Make space for the new cell indices */
 200     gridSetData_.cells.resize(atomEnd);
 201
 202     const int nthread = gmx_omp_nthreads_get(emntPairsearch);
 203
 204 #pragma omp parallel for num_threads(nthread) schedule(static)
 205     for (int thread = 0; thread < nthread; thread++)
 206     {
 207         try
 208         {
 209             Grid::calcColumnIndices(grid.dimensions(),
 210                                     updateGroupsCog,
 211                                     atomStart, atomEnd, x,
 212                                     ddZone, move, thread, nthread,
 213                                     gridSetData_.cells,
 214                                     gridWork_[thread].numAtomsPerColumn);
 215         }
 216         GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
 217     }
 218
 219     /* Copy the already computed cell indices to the grid and sort, when needed */
 220     grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_,
 221                         atomStart, atomEnd, atomInfo.data(), x, numAtomsMoved, nbat);
 222
 223     if (ddZone == 0)
 224     {
 225         nbat->natoms_local = nbat->numAtoms();
 226     }
 227     if (ddZone == gmx::ssize(grids_) - 1)
 228     {
 229         /* We are done setting up all grids, we can resize the force buffers */
 230         nbat->resizeForceBuffers();
 231     }
 232
 233     int maxNumColumns = 0;
 234     for (const auto &grid : grids())
 235     {
 236         maxNumColumns = std::max(maxNumColumns, grid.numColumns());
 237     }
 238     setNumColumnsMax(maxNumColumns);
 239
 240 }
 241
 242 } // namespace Nbnxm