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39 * Declares the GridSet class.
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.
44 * \author Berk Hess <hess@kth.se>
45 * \ingroup module_nbnxm
48 #ifndef GMX_NBNXM_GRIDSET_H
49 #define GMX_NBNXM_GRIDSET_H
54 #include "gromacs/math/vec.h"
55 #include "gromacs/math/vectypes.h"
56 #include "gromacs/utility/alignedallocator.h"
57 #include "gromacs/utility/arrayref.h"
60 #include "gridsetdata.h"
63 struct nbnxn_atomdata_t;
64 enum class PairlistType;
68 class UpdateGroupsCog;
75 * \brief Holds a set of search grids for the local + non-local DD zones
81 * \brief Description of the domain setup: PBC and the connections between domains
85 //! Constructor, without DD \p numDDCells and \p ddZones should be nullptr
87 const ivec *numDDCells,
88 const gmx_domdec_zones_t *ddZones);
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;
100 //! Constructs a grid set for 1 or multiple DD zones, when numDDCells!=nullptr
102 const ivec *numDDCells,
103 const gmx_domdec_zones_t *ddZones,
104 PairlistType pairlistType,
107 gmx::PinningPolicy pinningPolicy);
109 //! Puts the atoms in \p ddZone on the grid and copies the coordinates to \p nbat
110 void putOnGrid(const matrix box,
112 const rvec lowerCorner,
113 const rvec upperCorner,
114 const gmx::UpdateGroupsCog *updateGroupsCog,
118 gmx::ArrayRef<const int> atomInfo,
119 gmx::ArrayRef<const gmx::RVec> x,
122 nbnxn_atomdata_t *nbat);
124 //! Returns the domain setup
125 const DomainSetup domainSetup() const
130 //! Returns the total number of atoms in the grid set, including padding
131 int numGridAtomsTotal() const
133 return grids_.back().atomIndexEnd();
136 //! Returns the number of local real atoms, i.e. without padded atoms
137 int numRealAtomsLocal() const
139 return numRealAtomsLocal_;
142 //! Returns the number of total real atoms, i.e. without padded atoms
143 int numRealAtomsTotal() const
145 return numRealAtomsTotal_;
148 //! Returns the atom order on the grid for the local atoms
149 gmx::ArrayRef<const int> getLocalAtomorder() const
151 /* Return the atom order for the home cell (index 0) */
152 const int numIndices = grids_[0].atomIndexEnd() - grids_[0].firstAtomInColumn(0);
154 return gmx::constArrayRefFromArray(atomIndices().data(), numIndices);
157 //! Sets the order of the local atoms to the order grid atom ordering
158 void setLocalAtomOrder();
160 //! Returns the list of grids
161 gmx::ArrayRef<const Grid> grids() const
166 //! Returns the grid atom indices covering all grids
167 gmx::ArrayRef<const int> cells() const
169 return gridSetData_.cells;
172 //! Returns the grid atom indices covering all grids
173 gmx::ArrayRef<const int> atomIndices() const
175 return gridSetData_.atomIndices;
178 //! Returns whether we have perturbed non-bonded interactions
184 //! Returns the unit cell in \p box
185 void getBox(matrix box) const
190 //! Returns the maximum number of columns across all grids
191 int numColumnsMax() const
193 return numColumnsMax_;
196 //! Sets the maximum number of columns across all grids
197 void setNumColumnsMax(int numColumnsMax)
199 numColumnsMax_ = numColumnsMax;
205 DomainSetup domainSetup_;
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
212 //! The periodic unit-cell
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