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39 * Implements the GridSet class.
41 * \author Berk Hess <hess@kth.se>
42 * \ingroup module_nbnxm
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"
57 //! Returns the number of DD zones
58 static int numDDZones(const std::array
<bool, DIM
> &haveMultipleDomainsPerDim
)
61 for (auto haveDD
: haveMultipleDomainsPerDim
)
72 GridSet::DomainSetup::DomainSetup(const int ePBC
,
73 const ivec
*numDDCells
,
74 const gmx_domdec_zones_t
*ddZones
) :
76 haveMultipleDomains(numDDCells
!= nullptr),
79 for (int d
= 0; d
< DIM
; d
++)
81 haveMultipleDomainsPerDim
[d
] = (numDDCells
!= nullptr && (*numDDCells
)[d
] > 1);
85 GridSet::GridSet(const int ePBC
,
86 const ivec
*numDDCells
,
87 const gmx_domdec_zones_t
*ddZones
,
88 const PairlistType pairlistType
,
90 const int numThreads
) :
91 domainSetup_(ePBC
, numDDCells
, ddZones
),
92 grids_(numDDZones(domainSetup_
.haveMultipleDomainsPerDim
), pairlistType
),
94 numRealAtomsLocal_(0),
95 numRealAtomsTotal_(0),
101 void GridSet::setLocalAtomOrder()
103 /* Set the atom order for the home cell (index 0) */
104 const Nbnxm::Grid
&grid
= grids_
[0];
107 for (int cxy
= 0; cxy
< grid
.numColumns(); cxy
++)
109 const int numAtoms
= grid
.numAtomsInColumn(cxy
);
110 int cellIndex
= grid
.firstCellInColumn(cxy
)*grid
.geometry().numAtomsPerCell
;
111 for (int i
= 0; i
< numAtoms
; i
++)
113 atomIndices_
[cellIndex
] = atomIndex
;
114 cells_
[atomIndex
] = cellIndex
;
121 // TODO: Move to gridset.cpp
122 void GridSet::putOnGrid(const matrix box
,
124 const rvec lowerCorner
,
125 const rvec upperCorner
,
126 const gmx::UpdateGroupsCog
*updateGroupsCog
,
130 gmx::ArrayRef
<const int> atomInfo
,
131 gmx::ArrayRef
<const gmx::RVec
> x
,
132 const int numAtomsMoved
,
134 nbnxn_atomdata_t
*nbat
)
136 Nbnxm::Grid
&grid
= grids_
[ddZone
];
145 const Nbnxm::Grid
&previousGrid
= grids_
[ddZone
- 1];
146 cellOffset
= previousGrid
.atomIndexEnd()/previousGrid
.geometry().numAtomsPerCell
;
149 const int n
= atomEnd
- atomStart
;
151 real maxAtomGroupRadius
;
156 numRealAtomsLocal_
= atomEnd
- numAtomsMoved
;
157 /* We assume that nbnxn_put_on_grid is called first
158 * for the local atoms (ddZone=0).
160 numRealAtomsTotal_
= atomEnd
- numAtomsMoved
;
162 maxAtomGroupRadius
= (updateGroupsCog
? updateGroupsCog
->maxUpdateGroupRadius() : 0);
166 fprintf(debug
, "natoms_local = %5d atom_density = %5.1f\n",
167 numRealAtomsLocal_
, atomDensity
);
172 const Nbnxm::Grid::Dimensions
&dimsGrid0
= grids_
[0].dimensions();
173 atomDensity
= dimsGrid0
.atomDensity
;
174 maxAtomGroupRadius
= dimsGrid0
.maxAtomGroupRadius
;
176 numRealAtomsTotal_
= std::max(numRealAtomsTotal_
, atomEnd
);
179 /* We always use the home zone (grid[0]) for setting the cell size,
180 * since determining densities for non-local zones is difficult.
182 grid
.setDimensions(ddZone
, n
- numAtomsMoved
,
183 lowerCorner
, upperCorner
,
188 for (GridWork
&work
: gridWork_
)
190 work
.numAtomsPerColumn
.resize(grid
.numColumns() + 1);
193 /* Make space for the new cell indices */
194 cells_
.resize(atomEnd
);
196 const int nthread
= gmx_omp_nthreads_get(emntPairsearch
);
198 #pragma omp parallel for num_threads(nthread) schedule(static)
199 for (int thread
= 0; thread
< nthread
; thread
++)
203 Grid::calcColumnIndices(grid
.dimensions(),
205 atomStart
, atomEnd
, x
,
206 ddZone
, move
, thread
, nthread
,
207 cells_
, gridWork_
[thread
].numAtomsPerColumn
);
209 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
212 GridSetData gridSetData
= getGridSetData();
214 /* Copy the already computed cell indices to the grid and sort, when needed */
215 grid
.setCellIndices(ddZone
, cellOffset
, &gridSetData
, gridWork_
,
216 atomStart
, atomEnd
, atomInfo
.data(), x
, numAtomsMoved
, nbat
);
220 nbat
->natoms_local
= nbat
->numAtoms();
222 if (ddZone
== gmx::ssize(grids_
) - 1)
224 /* We are done setting up all grids, we can resize the force buffers */
225 nbat
->resizeForceBuffers();
228 int maxNumColumns
= 0;
229 for (const auto &grid
: grids())
231 maxNumColumns
= std::max(maxNumColumns
, grid
.numColumns());
233 setNumColumnsMax(maxNumColumns
);