struct Corner
{
//! Returns a corner with the minimum coordinates along each dimension
- static Corner min(const Corner &c1,
- const Corner &c2)
+ static Corner min(const Corner& c1, const Corner& c2)
{
Corner cMin;
- cMin.x = std::min(c1.x, c2.x);
- cMin.y = std::min(c1.y, c2.y);
- cMin.z = std::min(c1.z, c2.z);
+ cMin.x = std::min(c1.x, c2.x);
+ cMin.y = std::min(c1.y, c2.y);
+ cMin.z = std::min(c1.z, c2.z);
/* This value of the padding is irrelevant, as long as it
* is initialized. We use min to allow auto-vectorization.
*/
}
//! Returns a corner with the maximum coordinates along each dimension
- static Corner max(const Corner &c1,
- const Corner &c2)
+ static Corner max(const Corner& c1, const Corner& c2)
{
Corner cMax;
}
//! Returns a pointer for SIMD loading of a Corner object
- const float *ptr() const
- {
- return &x;
- }
+ const float* ptr() const { return &x; }
//! Returns a pointer for SIMD storing of a Corner object
- float *ptr()
- {
- return &x;
- }
+ float* ptr() { return &x; }
float x; //!< x coordinate
float y; //!< y coordinate
*/
class Grid
{
- public:
- /*! \internal
- * \brief The cluster and cell geometry of a grid
- */
- struct Geometry
- {
- //! Constructs the cluster/cell geometry given the type of pairlist
- Geometry(PairlistType pairlistType);
-
- bool isSimple; //!< Is this grid simple (CPU) or hierarchical (GPU)
- int numAtomsICluster; //!< Number of atoms per cluster
- int numAtomsJCluster; //!< Number of atoms for list j-clusters
- int numAtomsPerCell; //!< Number of atoms per cell
- int numAtomsICluster2Log; //!< 2log of na_c
- };
-
- // The physical dimensions of a grid
- struct Dimensions
- {
- //! The lower corner of the (local) grid
- rvec lowerCorner;
- //! The upper corner of the (local) grid
- rvec upperCorner;
- //! The physical grid size: upperCorner - lowerCorner
- rvec gridSize;
- //! An estimate for the atom number density of the region targeted by the grid
- real atomDensity;
- //! The maximum distance an atom can be outside of a cell and outside of the grid
- real maxAtomGroupRadius;
- //! Size of cell along dimension x and y
- real cellSize[DIM - 1];
- //! 1/size of a cell along dimensions x and y
- real invCellSize[DIM - 1];
- //! The number of grid cells along dimensions x and y
- int numCells[DIM - 1];
- };
-
- //! Constructs a grid given the type of pairlist
- Grid(PairlistType pairlistType,
- const bool &haveFep);
-
- //! Returns the geometry of the grid cells
- const Geometry &geometry() const
- {
- return geometry_;
- }
-
- //! Returns the dimensions of the grid
- const Dimensions &dimensions() const
- {
- return dimensions_;
- }
+public:
+ /*! \internal
+ * \brief The cluster and cell geometry of a grid
+ */
+ struct Geometry
+ {
+ //! Constructs the cluster/cell geometry given the type of pairlist
+ Geometry(PairlistType pairlistType);
+
+ bool isSimple; //!< Is this grid simple (CPU) or hierarchical (GPU)
+ int numAtomsICluster; //!< Number of atoms per cluster
+ int numAtomsJCluster; //!< Number of atoms for list j-clusters
+ int numAtomsPerCell; //!< Number of atoms per cell
+ int numAtomsICluster2Log; //!< 2log of na_c
+ };
- //! Returns the total number of grid columns
- int numColumns() const
- {
- return dimensions_.numCells[XX]*dimensions_.numCells[YY];
- }
+ // The physical dimensions of a grid
+ struct Dimensions
+ {
+ //! The lower corner of the (local) grid
+ rvec lowerCorner;
+ //! The upper corner of the (local) grid
+ rvec upperCorner;
+ //! The physical grid size: upperCorner - lowerCorner
+ rvec gridSize;
+ //! An estimate for the atom number density of the region targeted by the grid
+ real atomDensity;
+ //! The maximum distance an atom can be outside of a cell and outside of the grid
+ real maxAtomGroupRadius;
+ //! Size of cell along dimension x and y
+ real cellSize[DIM - 1];
+ //! 1/size of a cell along dimensions x and y
+ real invCellSize[DIM - 1];
+ //! The number of grid cells along dimensions x and y
+ int numCells[DIM - 1];
+ };
- //! Returns the total number of grid cells
- int numCells() const
- {
- return numCellsTotal_;
- }
+ //! Constructs a grid given the type of pairlist
+ Grid(PairlistType pairlistType, const bool& haveFep);
- //! Returns the cell offset of (the first cell of) this grid in the list of cells combined over all grids
- int cellOffset() const
- {
- return cellOffset_;
- }
+ //! Returns the geometry of the grid cells
+ const Geometry& geometry() const { return geometry_; }
- //! Returns the maximum number of grid cells in a column
- int numCellsColumnMax() const
- {
- return numCellsColumnMax_;
- }
+ //! Returns the dimensions of the grid
+ const Dimensions& dimensions() const { return dimensions_; }
- //! Returns the start of the source atom range mapped to this grid
- int srcAtomBegin() const
- {
- return srcAtomBegin_;
- }
+ //! Returns the total number of grid columns
+ int numColumns() const { return dimensions_.numCells[XX] * dimensions_.numCells[YY]; }
- //! Returns the end of the source atom range mapped to this grid
- int srcAtomEnd() const
- {
- return srcAtomEnd_;
- }
+ //! Returns the total number of grid cells
+ int numCells() const { return numCellsTotal_; }
- //! Returns the first cell index in the grid, starting at 0 in this grid
- int firstCellInColumn(int columnIndex) const
- {
- return cxy_ind_[columnIndex];
- }
+ //! Returns the cell offset of (the first cell of) this grid in the list of cells combined over all grids
+ int cellOffset() const { return cellOffset_; }
- //! Returns the number of cells in the column
- int numCellsInColumn(int columnIndex) const
- {
- return cxy_ind_[columnIndex + 1] - cxy_ind_[columnIndex];
- }
+ //! Returns the maximum number of grid cells in a column
+ int numCellsColumnMax() const { return numCellsColumnMax_; }
- //! Returns the index of the first atom in the column
- int firstAtomInColumn(int columnIndex) const
- {
- return (cellOffset_ + cxy_ind_[columnIndex])*geometry_.numAtomsPerCell;
- }
+ //! Returns the start of the source atom range mapped to this grid
+ int srcAtomBegin() const { return srcAtomBegin_; }
- //! Returns the number of real atoms in the column
- int numAtomsInColumn(int columnIndex) const
- {
- return cxy_na_[columnIndex];
- }
+ //! Returns the end of the source atom range mapped to this grid
+ int srcAtomEnd() const { return srcAtomEnd_; }
- /*! \brief Returns a view of the number of non-filler, atoms for each grid column
- *
- * \todo Needs a useful name. */
- gmx::ArrayRef<const int> cxy_na() const
- {
- return cxy_na_;
- }
- /*! \brief Returns a view of the grid-local cell index for each grid column
- *
- * \todo Needs a useful name. */
- gmx::ArrayRef<const int> cxy_ind() const
- {
- return cxy_ind_;
- }
+ //! Returns the first cell index in the grid, starting at 0 in this grid
+ int firstCellInColumn(int columnIndex) const { return cxy_ind_[columnIndex]; }
- //! Returns the number of real atoms in the column
- int numAtomsPerCell() const
- {
- return geometry_.numAtomsPerCell;
- }
+ //! Returns the number of cells in the column
+ int numCellsInColumn(int columnIndex) const
+ {
+ return cxy_ind_[columnIndex + 1] - cxy_ind_[columnIndex];
+ }
- //! Returns the number of atoms in the column including padding
- int paddedNumAtomsInColumn(int columnIndex) const
- {
- return numCellsInColumn(columnIndex)*geometry_.numAtomsPerCell;
- }
+ //! Returns the index of the first atom in the column
+ int firstAtomInColumn(int columnIndex) const
+ {
+ return (cellOffset_ + cxy_ind_[columnIndex]) * geometry_.numAtomsPerCell;
+ }
+
+ //! Returns the number of real atoms in the column
+ int numAtomsInColumn(int columnIndex) const { return cxy_na_[columnIndex]; }
+
+ /*! \brief Returns a view of the number of non-filler, atoms for each grid column
+ *
+ * \todo Needs a useful name. */
+ gmx::ArrayRef<const int> cxy_na() const { return cxy_na_; }
+ /*! \brief Returns a view of the grid-local cell index for each grid column
+ *
+ * \todo Needs a useful name. */
+ gmx::ArrayRef<const int> cxy_ind() const { return cxy_ind_; }
+
+ //! Returns the number of real atoms in the column
+ int numAtomsPerCell() const { return geometry_.numAtomsPerCell; }
+
+ //! Returns the number of atoms in the column including padding
+ int paddedNumAtomsInColumn(int columnIndex) const
+ {
+ return numCellsInColumn(columnIndex) * geometry_.numAtomsPerCell;
+ }
- //! Returns the end of the atom index range on the grid, including padding
- int atomIndexEnd() const
- {
- return (cellOffset_ + numCellsTotal_)*geometry_.numAtomsPerCell;
- }
+ //! Returns the end of the atom index range on the grid, including padding
+ int atomIndexEnd() const { return (cellOffset_ + numCellsTotal_) * geometry_.numAtomsPerCell; }
- //! Returns whether any atom in the cluster is perturbed
- bool clusterIsPerturbed(int clusterIndex) const
- {
- return fep_[clusterIndex] != 0U;
- }
+ //! Returns whether any atom in the cluster is perturbed
+ bool clusterIsPerturbed(int clusterIndex) const { return fep_[clusterIndex] != 0U; }
- //! Returns whether the given atom in the cluster is perturbed
- bool atomIsPerturbed(int clusterIndex,
- int atomIndexInCluster) const
- {
- return (fep_[clusterIndex] & (1 << atomIndexInCluster)) != 0U;
- }
+ //! Returns whether the given atom in the cluster is perturbed
+ bool atomIsPerturbed(int clusterIndex, int atomIndexInCluster) const
+ {
+ return (fep_[clusterIndex] & (1 << atomIndexInCluster)) != 0U;
+ }
- //! Returns the free-energy perturbation bits for the cluster
- unsigned int fepBits(int clusterIndex) const
- {
- return fep_[clusterIndex];
- }
+ //! Returns the free-energy perturbation bits for the cluster
+ unsigned int fepBits(int clusterIndex) const { return fep_[clusterIndex]; }
- //! Returns the i-bounding boxes for all clusters on the grid
- gmx::ArrayRef<const BoundingBox> iBoundingBoxes() const
- {
- return bb_;
- }
+ //! Returns the i-bounding boxes for all clusters on the grid
+ gmx::ArrayRef<const BoundingBox> iBoundingBoxes() const { return bb_; }
- //! Returns the j-bounding boxes for all clusters on the grid
- gmx::ArrayRef<const BoundingBox> jBoundingBoxes() const
- {
- return bbj_;
- }
+ //! Returns the j-bounding boxes for all clusters on the grid
+ gmx::ArrayRef<const BoundingBox> jBoundingBoxes() const { return bbj_; }
- //! Returns the packed bounding boxes for all clusters on the grid, empty with a CPU list
- gmx::ArrayRef<const float> packedBoundingBoxes() const
- {
- return pbb_;
- }
+ //! Returns the packed bounding boxes for all clusters on the grid, empty with a CPU list
+ gmx::ArrayRef<const float> packedBoundingBoxes() const { return pbb_; }
- //! Returns the bounding boxes along z for all cells on the grid
- gmx::ArrayRef<const BoundingBox1D> zBoundingBoxes() const
- {
- return bbcz_;
- }
+ //! Returns the bounding boxes along z for all cells on the grid
+ gmx::ArrayRef<const BoundingBox1D> zBoundingBoxes() const { return bbcz_; }
- //! Returns the flags for all clusters on the grid
- gmx::ArrayRef<const int> clusterFlags() const
- {
- return flags_;
- }
+ //! Returns the flags for all clusters on the grid
+ gmx::ArrayRef<const int> clusterFlags() const { return flags_; }
- //! Returns the number of clusters for all cells on the grid, empty with a CPU geometry
- gmx::ArrayRef<const int> numClustersPerCell() const
- {
- return numClusters_;
- }
+ //! Returns the number of clusters for all cells on the grid, empty with a CPU geometry
+ gmx::ArrayRef<const int> numClustersPerCell() const { return numClusters_; }
- //! Returns the cluster index for an atom
- int atomToCluster(int atomIndex) const
- {
- return (atomIndex >> geometry_.numAtomsICluster2Log);
- }
+ //! Returns the cluster index for an atom
+ int atomToCluster(int atomIndex) const { return (atomIndex >> geometry_.numAtomsICluster2Log); }
- //! Returns the total number of clusters on the grid
- int numClusters() const
+ //! Returns the total number of clusters on the grid
+ int numClusters() const
+ {
+ if (geometry_.isSimple)
{
- if (geometry_.isSimple)
- {
- return numCellsTotal_;
- }
- else
- {
- return numClustersTotal_;
- }
+ return numCellsTotal_;
}
-
- //! Sets the grid dimensions
- void setDimensions(int ddZone,
- int numAtoms,
- gmx::RVec lowerCorner,
- gmx::RVec upperCorner,
- real atomDensity,
- real maxAtomGroupRadius,
- bool haveFep,
- gmx::PinningPolicy pinningPolicy);
-
- //! Sets the cell indices using indices in \p gridSetData and \p gridWork
- void setCellIndices(int ddZone,
- int cellOffset,
- GridSetData *gridSetData,
- gmx::ArrayRef<GridWork> gridWork,
- gmx::Range<int> atomRange,
- const int *atinfo,
- gmx::ArrayRef<const gmx::RVec> x,
- int numAtomsMoved,
- nbnxn_atomdata_t *nbat);
-
- //! Determine in which grid columns atoms should go, store cells and atom counts in \p cell and \p cxy_na
- static void calcColumnIndices(const Grid::Dimensions &gridDims,
- const gmx::UpdateGroupsCog *updateGroupsCog,
- gmx::Range<int> atomRange,
- gmx::ArrayRef<const gmx::RVec> x,
- int dd_zone,
- const int *move,
- int thread,
- int nthread,
- gmx::ArrayRef<int> cell,
- gmx::ArrayRef<int> cxy_na);
-
- private:
- /*! \brief Fill a pair search cell with atoms
- *
- * Potentially sorts atoms and sets the interaction flags.
- */
- void fillCell(GridSetData *gridSetData,
- nbnxn_atomdata_t *nbat,
- int atomStart,
- int atomEnd,
- const int *atinfo,
- gmx::ArrayRef<const gmx::RVec> x,
- BoundingBox gmx_unused *bb_work_aligned);
-
- //! Spatially sort the atoms within the given column range, for CPU geometry
- void sortColumnsCpuGeometry(GridSetData *gridSetData,
- int dd_zone,
- const int *atinfo,
- gmx::ArrayRef<const gmx::RVec> x,
- nbnxn_atomdata_t *nbat,
- gmx::Range<int> columnRange,
- gmx::ArrayRef<int> sort_work);
-
- //! Spatially sort the atoms within the given column range, for GPU geometry
- void sortColumnsGpuGeometry(GridSetData *gridSetData,
- int dd_zone,
- const int *atinfo,
- gmx::ArrayRef<const gmx::RVec> x,
- nbnxn_atomdata_t *nbat,
- gmx::Range<int> columnRange,
- gmx::ArrayRef<int> sort_work);
-
- /* Data members */
- //! The geometry of the grid clusters and cells
- Geometry geometry_;
- //! The physical dimensions of the grid
- Dimensions dimensions_;
-
- //! The total number of cells in this grid
- int numCellsTotal_;
- //! Index in nbs->cell corresponding to cell 0
- int cellOffset_;
- //! The maximum number of cells in a column
- int numCellsColumnMax_;
-
- //! The start of the source atom range mapped to this grid
- int srcAtomBegin_;
- //! The end of the source atom range mapped to this grid
- int srcAtomEnd_;
-
- /* Grid data */
- /*! \brief The number of, non-filler, atoms for each grid column.
- *
- * \todo Needs a useful name. */
- gmx::HostVector<int> cxy_na_;
- /*! \brief The grid-local cell index for each grid column
- *
- * \todo Needs a useful name. */
- gmx::HostVector<int> cxy_ind_;
-
- //! The number of cluster for each cell
- std::vector<int> numClusters_;
-
- /* Bounding boxes */
- //! Bounding boxes in z for the cells
- std::vector<BoundingBox1D> bbcz_;
- //! 3D bounding boxes for the sub cells
- std::vector < BoundingBox, gmx::AlignedAllocator < BoundingBox>> bb_;
- //! 3D j-bounding boxes for the case where the i- and j-cluster sizes are different
- std::vector < BoundingBox, gmx::AlignedAllocator < BoundingBox>> bbjStorage_;
- //! 3D j-bounding boxes
- gmx::ArrayRef<BoundingBox> bbj_;
- //! 3D bounding boxes in packed xxxx format per cell
- std::vector < float, gmx::AlignedAllocator < float>> pbb_;
-
- //! Tells whether we have perturbed interactions, authorative source is in GridSet (never modified)
- const bool &haveFep_;
-
- /* Bit-flag information */
- //! Flags for properties of clusters in each cell
- std::vector<int> flags_;
- //! Signal bits for atoms in each cell that tell whether an atom is perturbed
- std::vector<unsigned int> fep_;
-
- /* Statistics */
- //! Total number of clusters, used for printing
- int numClustersTotal_;
+ else
+ {
+ return numClustersTotal_;
+ }
+ }
+
+ //! Sets the grid dimensions
+ void setDimensions(int ddZone,
+ int numAtoms,
+ gmx::RVec lowerCorner,
+ gmx::RVec upperCorner,
+ real atomDensity,
+ real maxAtomGroupRadius,
+ bool haveFep,
+ gmx::PinningPolicy pinningPolicy);
+
+ //! Sets the cell indices using indices in \p gridSetData and \p gridWork
+ void setCellIndices(int ddZone,
+ int cellOffset,
+ GridSetData* gridSetData,
+ gmx::ArrayRef<GridWork> gridWork,
+ gmx::Range<int> atomRange,
+ const int* atinfo,
+ gmx::ArrayRef<const gmx::RVec> x,
+ int numAtomsMoved,
+ nbnxn_atomdata_t* nbat);
+
+ //! Determine in which grid columns atoms should go, store cells and atom counts in \p cell and \p cxy_na
+ static void calcColumnIndices(const Grid::Dimensions& gridDims,
+ const gmx::UpdateGroupsCog* updateGroupsCog,
+ gmx::Range<int> atomRange,
+ gmx::ArrayRef<const gmx::RVec> x,
+ int dd_zone,
+ const int* move,
+ int thread,
+ int nthread,
+ gmx::ArrayRef<int> cell,
+ gmx::ArrayRef<int> cxy_na);
+
+private:
+ /*! \brief Fill a pair search cell with atoms
+ *
+ * Potentially sorts atoms and sets the interaction flags.
+ */
+ void fillCell(GridSetData* gridSetData,
+ nbnxn_atomdata_t* nbat,
+ int atomStart,
+ int atomEnd,
+ const int* atinfo,
+ gmx::ArrayRef<const gmx::RVec> x,
+ BoundingBox gmx_unused* bb_work_aligned);
+
+ //! Spatially sort the atoms within the given column range, for CPU geometry
+ void sortColumnsCpuGeometry(GridSetData* gridSetData,
+ int dd_zone,
+ const int* atinfo,
+ gmx::ArrayRef<const gmx::RVec> x,
+ nbnxn_atomdata_t* nbat,
+ gmx::Range<int> columnRange,
+ gmx::ArrayRef<int> sort_work);
+
+ //! Spatially sort the atoms within the given column range, for GPU geometry
+ void sortColumnsGpuGeometry(GridSetData* gridSetData,
+ int dd_zone,
+ const int* atinfo,
+ gmx::ArrayRef<const gmx::RVec> x,
+ nbnxn_atomdata_t* nbat,
+ gmx::Range<int> columnRange,
+ gmx::ArrayRef<int> sort_work);
+
+ /* Data members */
+ //! The geometry of the grid clusters and cells
+ Geometry geometry_;
+ //! The physical dimensions of the grid
+ Dimensions dimensions_;
+
+ //! The total number of cells in this grid
+ int numCellsTotal_;
+ //! Index in nbs->cell corresponding to cell 0
+ int cellOffset_;
+ //! The maximum number of cells in a column
+ int numCellsColumnMax_;
+
+ //! The start of the source atom range mapped to this grid
+ int srcAtomBegin_;
+ //! The end of the source atom range mapped to this grid
+ int srcAtomEnd_;
+
+ /* Grid data */
+ /*! \brief The number of, non-filler, atoms for each grid column.
+ *
+ * \todo Needs a useful name. */
+ gmx::HostVector<int> cxy_na_;
+ /*! \brief The grid-local cell index for each grid column
+ *
+ * \todo Needs a useful name. */
+ gmx::HostVector<int> cxy_ind_;
+
+ //! The number of cluster for each cell
+ std::vector<int> numClusters_;
+
+ /* Bounding boxes */
+ //! Bounding boxes in z for the cells
+ std::vector<BoundingBox1D> bbcz_;
+ //! 3D bounding boxes for the sub cells
+ std::vector<BoundingBox, gmx::AlignedAllocator<BoundingBox>> bb_;
+ //! 3D j-bounding boxes for the case where the i- and j-cluster sizes are different
+ std::vector<BoundingBox, gmx::AlignedAllocator<BoundingBox>> bbjStorage_;
+ //! 3D j-bounding boxes
+ gmx::ArrayRef<BoundingBox> bbj_;
+ //! 3D bounding boxes in packed xxxx format per cell
+ std::vector<float, gmx::AlignedAllocator<float>> pbb_;
+
+ //! Tells whether we have perturbed interactions, authorative source is in GridSet (never modified)
+ const bool& haveFep_;
+
+ /* Bit-flag information */
+ //! Flags for properties of clusters in each cell
+ std::vector<int> flags_;
+ //! Signal bits for atoms in each cell that tell whether an atom is perturbed
+ std::vector<unsigned int> fep_;
+
+ /* Statistics */
+ //! Total number of clusters, used for printing
+ int numClustersTotal_;
};
} // namespace Nbnxm
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff