src/gromacs/nbnxm/gridset.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2019, 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
   7  * top-level source directory and at http://www.gromacs.org.
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  35
  36 /*! \internal \file
  37  *
  38  * \brief
  39  * Declares the GridSet class.
  40  *
  41  * This class holds the grids for the local and non-local domain decomposition
  42  * zones, as well as the cell and atom data that covers all grids.
  43  *
  44  * \author Berk Hess <hess@kth.se>
  45  * \ingroup module_nbnxm
  46  */
  47
  48 #ifndef GMX_NBNXM_GRIDSET_H
  49 #define GMX_NBNXM_GRIDSET_H
  50
  51 #include <memory>
  52 #include <vector>
  53
  54 #include "gromacs/math/vec.h"
  55 #include "gromacs/math/vectypes.h"
  56 #include "gromacs/utility/alignedallocator.h"
  57 #include "gromacs/utility/arrayref.h"
  58
  59 #include "grid.h"
  60 #include "gridsetdata.h"
  61
  62
  63 struct nbnxn_atomdata_t;
  64 enum class PairlistType;
  65
  66 namespace gmx
  67 {
  68 class UpdateGroupsCog;
  69 }
  70
  71 namespace Nbnxm
  72 {
  73
  74 /*! \internal
  75  * \brief Holds a set of search grids for the local + non-local DD zones
  76  *
  77  * The are three different possible setups:
  78  * - a single grid, this is the standard case without domain decomposition
  79  * - one grid for each domain decomposition zone
  80  * - with test particle insertion there are two grids, one for the system
  81  *   to insert in and one for the molecule that is inserted
  82  */
  83 class GridSet
  84 {
  85     public:
  86         /*! \internal
  87          * \brief Description of the domain setup: PBC and the connections between domains
  88          */
  89         struct DomainSetup
  90         {
  91             //! Constructor, without DD \p numDDCells and \p ddZones should be nullptr
  92             DomainSetup(int                       ePBC,
  93                         bool                      doTestParticleInsertion,
  94                         const ivec               *numDDCells,
  95                         const gmx_domdec_zones_t *ddZones);
  96
  97             //! The type of PBC
  98             int                       ePBC;
  99             //! Tells whether we are doing test-particle insertion
 100             bool                      doTestParticleInsertion;
 101             //! Are there multiple domains?
 102             bool                      haveMultipleDomains;
 103             //! Are there multiple domains along each dimension?
 104             std::array<bool, DIM>     haveMultipleDomainsPerDim;
 105             //! The domain decomposition zone setup
 106             const gmx_domdec_zones_t *zones;
 107         };
 108
 109         //! Constructs a grid set for 1 or multiple DD zones, when numDDCells!=nullptr
 110         GridSet(int                       ePBC,
 111                 bool                      doTestParticleInsertion,
 112                 const ivec               *numDDCells,
 113                 const gmx_domdec_zones_t *ddZones,
 114                 PairlistType              pairlistType,
 115                 bool                      haveFep,
 116                 int                       numThreads,
 117                 gmx::PinningPolicy        pinningPolicy);
 118
 119         //! Puts the atoms on the grid with index \p gridIndex and copies the coordinates to \p nbat
 120         void putOnGrid(const matrix                    box,
 121                        int                             gridIndex,
 122                        const rvec                      lowerCorner,
 123                        const rvec                      upperCorner,
 124                        const gmx::UpdateGroupsCog     *updateGroupsCog,
 125                        int                             atomStart,
 126                        int                             atomEnd,
 127                        real                            atomDensity,
 128                        gmx::ArrayRef<const int>        atomInfo,
 129                        gmx::ArrayRef<const gmx::RVec>  x,
 130                        int                             numAtomsMoved,
 131                        const int                      *move,
 132                        nbnxn_atomdata_t               *nbat);
 133
 134         //! Returns the domain setup
 135         DomainSetup domainSetup() const
 136         {
 137             return domainSetup_;
 138         }
 139
 140         //! Returns the total number of atoms in the grid set, including padding
 141         int numGridAtomsTotal() const
 142         {
 143             return grids_.back().atomIndexEnd();
 144         }
 145
 146         //! Returns the number of local real atoms, i.e. without padded atoms
 147         int numRealAtomsLocal() const
 148         {
 149             return numRealAtomsLocal_;
 150         }
 151
 152         //! Returns the number of total real atoms, i.e. without padded atoms
 153         int numRealAtomsTotal() const
 154         {
 155             return numRealAtomsTotal_;
 156         }
 157
 158         //! Returns the atom order on the grid for the local atoms
 159         gmx::ArrayRef<const int> getLocalAtomorder() const
 160         {
 161             /* Return the atom order for the home cell (index 0) */
 162             const int numIndices = grids_[0].atomIndexEnd() - grids_[0].firstAtomInColumn(0);
 163
 164             return gmx::constArrayRefFromArray(atomIndices().data(), numIndices);
 165         }
 166
 167         //! Sets the order of the local atoms to the order grid atom ordering
 168         void setLocalAtomOrder();
 169
 170         //! Returns the list of grids
 171         gmx::ArrayRef<const Grid> grids() const
 172         {
 173             return grids_;
 174         }
 175
 176         //! Returns the grid atom indices covering all grids
 177         gmx::ArrayRef<const int> cells() const
 178         {
 179             return gridSetData_.cells;
 180         }
 181
 182         //! Returns the grid atom indices covering all grids
 183         gmx::ArrayRef<const int> atomIndices() const
 184         {
 185             return gridSetData_.atomIndices;
 186         }
 187
 188         //! Returns whether we have perturbed non-bonded interactions
 189         bool haveFep() const
 190         {
 191             return haveFep_;
 192         }
 193
 194         //! Returns the unit cell in \p box
 195         void getBox(matrix box) const
 196         {
 197             copy_mat(box_, box);
 198         }
 199
 200         //! Returns the maximum number of columns across all grids
 201         int numColumnsMax() const
 202         {
 203             return numColumnsMax_;
 204         }
 205
 206         //! Sets the maximum number of columns across all grids
 207         void setNumColumnsMax(int numColumnsMax)
 208         {
 209             numColumnsMax_ = numColumnsMax;
 210         }
 211
 212     private:
 213         /* Data members */
 214         //! The domain setup
 215         DomainSetup           domainSetup_;
 216         //! The search grids
 217         std::vector<Grid>     grids_;
 218         //! The cell and atom index data which runs over all grids
 219         GridSetData           gridSetData_;
 220         //! Tells whether we have perturbed non-bonded interactions
 221         bool                  haveFep_;
 222         //! The periodic unit-cell
 223         matrix                box_;
 224         //! The number of local real atoms, i.e. without padded atoms, local atoms: 0 to numAtomsLocal_
 225         int                   numRealAtomsLocal_;
 226         //! The total number of real atoms, i.e. without padded atoms
 227         int                   numRealAtomsTotal_;
 228         //! Working data for constructing a single grid, one entry per thread
 229         std::vector<GridWork> gridWork_;
 230         //! Maximum number of columns across all grids
 231         int                   numColumnsMax_;
 232
 233 };
 234
 235 } // namespace Nbnxm
 236
 237 #endif