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
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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 class GridSet
  78 {
  79     public:
  80         /*! \internal
  81          * \brief Description of the domain setup: PBC and the connections between domains
  82          */
  83         struct DomainSetup
  84         {
  85             //! Constructor, without DD \p numDDCells and \p ddZones should be nullptr
  86             DomainSetup(int                       ePBC,
  87                         const ivec               *numDDCells,
  88                         const gmx_domdec_zones_t *ddZones);
  89
  90             //! The type of PBC
  91             int                       ePBC;
  92             //! Are there multiple domains?
  93             bool                      haveMultipleDomains;
  94             //! Are there multiple domains along each dimension?
  95             std::array<bool, DIM>     haveMultipleDomainsPerDim;
  96             //! The domain decomposition zone setup
  97             const gmx_domdec_zones_t *zones;
  98         };
  99
 100         //! Constructs a grid set for 1 or multiple DD zones, when numDDCells!=nullptr
 101         GridSet(int                       ePBC,
 102                 const ivec               *numDDCells,
 103                 const gmx_domdec_zones_t *ddZones,
 104                 PairlistType              pairlistType,
 105                 bool                      haveFep,
 106                 int                       numThreads,
 107                 gmx::PinningPolicy        pinningPolicy);
 108
 109         //! Puts the atoms in \p ddZone on the grid and copies the coordinates to \p nbat
 110         void putOnGrid(const matrix                    box,
 111                        int                             ddZone,
 112                        const rvec                      lowerCorner,
 113                        const rvec                      upperCorner,
 114                        const gmx::UpdateGroupsCog     *updateGroupsCog,
 115                        int                             atomStart,
 116                        int                             atomEnd,
 117                        real                            atomDensity,
 118                        gmx::ArrayRef<const int>        atomInfo,
 119                        gmx::ArrayRef<const gmx::RVec>  x,
 120                        int                             numAtomsMoved,
 121                        const int                      *move,
 122                        nbnxn_atomdata_t               *nbat);
 123
 124         //! Returns the domain setup
 125         const DomainSetup domainSetup() const
 126         {
 127             return domainSetup_;
 128         }
 129
 130         //! Returns the total number of atoms in the grid set, including padding
 131         int numGridAtomsTotal() const
 132         {
 133             return grids_.back().atomIndexEnd();
 134         }
 135
 136         //! Returns the number of local real atoms, i.e. without padded atoms
 137         int numRealAtomsLocal() const
 138         {
 139             return numRealAtomsLocal_;
 140         }
 141
 142         //! Returns the number of total real atoms, i.e. without padded atoms
 143         int numRealAtomsTotal() const
 144         {
 145             return numRealAtomsTotal_;
 146         }
 147
 148         //! Returns the atom order on the grid for the local atoms
 149         gmx::ArrayRef<const int> getLocalAtomorder() const
 150         {
 151             /* Return the atom order for the home cell (index 0) */
 152             const int numIndices = grids_[0].atomIndexEnd() - grids_[0].firstAtomInColumn(0);
 153
 154             return gmx::constArrayRefFromArray(atomIndices().data(), numIndices);
 155         }
 156
 157         //! Sets the order of the local atoms to the order grid atom ordering
 158         void setLocalAtomOrder();
 159
 160         //! Returns the list of grids
 161         gmx::ArrayRef<const Grid> grids() const
 162         {
 163             return grids_;
 164         }
 165
 166         //! Returns the grid atom indices covering all grids
 167         gmx::ArrayRef<const int> cells() const
 168         {
 169             return gridSetData_.cells;
 170         }
 171
 172         //! Returns the grid atom indices covering all grids
 173         gmx::ArrayRef<const int> atomIndices() const
 174         {
 175             return gridSetData_.atomIndices;
 176         }
 177
 178         //! Returns whether we have perturbed non-bonded interactions
 179         bool haveFep() const
 180         {
 181             return haveFep_;
 182         }
 183
 184         //! Returns the unit cell in \p box
 185         void getBox(matrix box) const
 186         {
 187             copy_mat(box_, box);
 188         }
 189
 190         //! Returns the maximum number of columns across all grids
 191         int numColumnsMax() const
 192         {
 193             return numColumnsMax_;
 194         }
 195
 196         //! Sets the maximum number of columns across all grids
 197         void setNumColumnsMax(int numColumnsMax)
 198         {
 199             numColumnsMax_ = numColumnsMax;
 200         }
 201
 202     private:
 203         /* Data members */
 204         //! The domain setup
 205         DomainSetup           domainSetup_;
 206         //! The search grids
 207         std::vector<Grid>     grids_;
 208         //! The cell and atom index data which runs over all grids
 209         GridSetData           gridSetData_;
 210         //! Tells whether we have perturbed non-bonded interactions
 211         bool                  haveFep_;
 212         //! The periodic unit-cell
 213         matrix                box_;
 214         //! The number of local real atoms, i.e. without padded atoms, local atoms: 0 to numAtomsLocal_
 215         int                   numRealAtomsLocal_;
 216         //! The total number of real atoms, i.e. without padded atoms
 217         int                   numRealAtomsTotal_;
 218         //! Working data for constructing a single grid, one entry per thread
 219         std::vector<GridWork> gridWork_;
 220         //! Maximum number of columns across all grids
 221         int                   numColumnsMax_;
 222
 223 };
 224
 225 } // namespace Nbnxm
 226
 227 #endif