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[gromacs.git] / src / gromacs / nbnxm / grid.h

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2019,2020, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
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/*! \internal \file
 *
 * \brief
 * Declares the Grid class.
 *
 * This class provides functionality for setting up and accessing atoms
 * on a grid for one domain decomposition zone. This grid is used for
 * generating cluster pair lists for computing non-bonded pair interactions.
 * The grid consists of a regular array of columns along dimensions x and y.
 * Along z the number of cells and their boundaries vary between the columns.
 * Each cell can hold one or more clusters of atoms, depending on the grid
 * geometry, which is set by the pair-list type.
 *
 * \author Berk Hess <hess@kth.se>
 * \ingroup module_nbnxm
 */

#ifndef GMX_NBNXM_GRID_H
#define GMX_NBNXM_GRID_H

#include <memory>
#include <vector>

#include "gromacs/gpu_utils/hostallocator.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/alignedallocator.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/range.h"

struct gmx_domdec_zones_t;
struct nbnxn_atomdata_t;
struct nbnxn_search;
enum class PairlistType;

namespace gmx
{
class UpdateGroupsCog;
} // namespace gmx

namespace Nbnxm
{

struct GridSetData;
struct GridWork;

/*! \internal
 * \brief Bounding box for a nbnxm atom cluster
 *
 * \note Should be aligned in memory to enable 4-wide SIMD operations.
 */
struct BoundingBox
{
    /*! \internal
     * \brief Corner for the bounding box, padded with one element to enable 4-wide SIMD operations
     */
    struct Corner
    {
        //! Returns a corner with the minimum coordinates along each dimension
        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);
            /* This value of the padding is irrelevant, as long as it
             * is initialized. We use min to allow auto-vectorization.
             */
            cMin.padding = std::min(c1.padding, c2.padding);

            return cMin;
        }

        //! Returns a corner with the maximum coordinates along each dimension
        static Corner max(const Corner& c1, const Corner& c2)
        {
            Corner cMax;

            cMax.x       = std::max(c1.x, c2.x);
            cMax.y       = std::max(c1.y, c2.y);
            cMax.z       = std::max(c1.z, c2.z);
            cMax.padding = std::max(c1.padding, c2.padding);

            return cMax;
        }

        //! Returns a pointer for SIMD loading of a Corner object
        const float* ptr() const { return &x; }

        //! Returns a pointer for SIMD storing of a Corner object
        float* ptr() { return &x; }

        //! x coordinate
        float x;
        //! y coordinate
        float y;
        //! z coordinate
        float z;
        //! padding, unused, but should be set to avoid operations on unitialized data
        float padding;
    };

    //! lower, along x and y and z, corner
    Corner lower;
    //! upper, along x and y and z, corner
    Corner upper;
};

/*! \internal
 * \brief Bounding box for one dimension of a grid cell
 */
struct BoundingBox1D
{
    //! lower bound
    float lower;
    //! upper bound
    float upper;
};

} // namespace Nbnxm

namespace Nbnxm
{

/*! \internal
 * \brief A pair-search grid object for one domain decomposition zone
 *
 * This is a rectangular 3D grid covering a potentially non-rectangular
 * volume which is either the whole unit cell or the local zone or part
 * of a non-local zone when using domain decomposition. The grid cells
 * are even spaced along x/y and irregular along z. Each cell is sub-divided
 * into atom clusters. With a CPU geometry, each cell contains 1 or 2 clusters.
 * With a GPU geometry, each cell contains up to 8 clusters. The geometry is
 * set by the pairlist type which is the only argument of the constructor.
 *
 * When multiple grids are used, i.e. with domain decomposition, we want
 * to avoid the overhead of multiple coordinate arrays or extra indexing.
 * Therefore each grid stores a cell offset, so a contiguous cell index
 * can be used to index atom arrays. All methods returning atom indices
 * return indices which index into a full atom array.
 *
 * Note that when atom groups, instead of individual atoms, are assigned
 * to grid cells, individual atoms can be geometrically outside the cell
 * and grid that they have been assigned to (as determined by the center
 * or geometry of the atom group they belong to).
 */
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);

        //! Is this grid simple (CPU) or hierarchical (GPU)
        bool isSimple;
        //! Number of atoms per cluster
        int numAtomsICluster;
        //! Number of atoms for list j-clusters
        int numAtomsJCluster;
        //! Number of atoms per cell
        int numAtomsPerCell;
        //! 2log of na_c
        int numAtomsICluster2Log;
    };

    //! The physical dimensions of a grid \internal
    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_; }

    //! Returns the total number of grid columns
    int numColumns() const { return dimensions_.numCells[XX] * dimensions_.numCells[YY]; }

    //! Returns the total number of grid cells
    int numCells() const { return numCellsTotal_; }

    //! 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 maximum number of grid cells in a column
    int numCellsColumnMax() const { return numCellsColumnMax_; }

    //! Returns the start of the source atom range mapped to this grid
    int srcAtomBegin() const { return srcAtomBegin_; }

    //! Returns the end of the source atom range mapped to this grid
    int srcAtomEnd() const { return srcAtomEnd_; }

    //! 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 cells in the column
    int numCellsInColumn(int columnIndex) const
    {
        return cxy_ind_[columnIndex + 1LL] - cxy_ind_[columnIndex];
    }

    //! 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 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 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 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 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 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 total number of clusters on the grid
    int numClusters() const
    {
        if (geometry_.isSimple)
        {
            return numCellsTotal_;
        }
        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

#endif