grid.cpp File Reference

#include "gmxpre.h"
#include "grid.h"
#include <cmath>
#include <cstring>
#include <algorithm>
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/updategroupscog.h"
#include "gromacs/mdtypes/atominfo.h"
#include "gromacs/nbnxm/atomdata.h"
#include "gromacs/simd/simd.h"
#include "gromacs/simd/vector_operations.h"
#include "boundingboxes.h"
#include "gridsetdata.h"
#include "nbnxm_geometry.h"
#include "pairlistparams.h"

Include dependency graph for grid.cpp:

Description

Implements the Grid class.

Author

Berk Hess hess@.nosp@m.kth..nosp@m.se

Functions
static real	Nbnxm::gridAtomDensity (int numAtoms, const rvec lowerCorner, const rvec upperCorner)
	Returns the atom density (> 0) of a rectangular grid.
static std::array< real, DIM-1 >	Nbnxm::getTargetCellLength (const Grid::Geometry &geometry, const real atomDensity)
	Get approximate dimensions of each cell. Returns the length along X and Y.
static int	Nbnxm::getMaxNumCells (const Grid::Geometry &geometry, const int numAtoms, const int numColumns)
static void	Nbnxm::sort_atoms (int dim, gmx_bool Backwards, int gmx_unused dd_zone, bool gmx_unused relevantAtomsAreWithinGridBounds, int *a, int n, gmx::ArrayRef< const gmx::RVec > x, real h0, real invh, int n_per_h, gmx::ArrayRef< int > sort)
	Sorts particle index a on coordinates x along dim. More...
static float	Nbnxm::R2F_D (const float x)
	Returns x.
static float	Nbnxm::R2F_U (const float x)
	Returns x.
static void	Nbnxm::calc_bounding_box (int na, int stride, const real *x, BoundingBox *bb)
	Computes the bounding box for na coordinates in order x,y,z, bb order xyz0.
static void	Nbnxm::calc_bounding_box_x_x4 (int na, const real *x, BoundingBox *bb)
	Computes the bounding box for na packed coordinates, bb order xyz0.
static void	Nbnxm::calc_bounding_box_x_x8 (int na, const real *x, BoundingBox *bb)
	Computes the bounding box for na coordinates, bb order xyz0.
static gmx_unused void	Nbnxm::calc_bounding_box_x_x4_halves (int na, const real *x, BoundingBox *bb, BoundingBox *bbj)
	Computes the bounding box for na packed coordinates, bb order xyz0.
static void	Nbnxm::combine_bounding_box_pairs (const Grid &grid, gmx::ArrayRef< const BoundingBox > bb, gmx::ArrayRef< BoundingBox > bbj)
	Combines pairs of consecutive bounding boxes.
static void	Nbnxm::print_bbsizes_simple (FILE *fp, const Grid &grid)
	Prints the average bb size, used for debug output.
static void	Nbnxm::print_bbsizes_supersub (FILE *fp, const Grid &grid)
	Prints the average bb size, used for debug output.
static void	Nbnxm::sort_cluster_on_flag (int numAtomsInCluster, int atomStart, int atomEnd, gmx::ArrayRef< const int64_t > atomInfo, gmx::ArrayRef< int > order, int *flags)
	Set non-bonded interaction flags for the current cluster. More...
static void	Nbnxm::setCellAndAtomCount (gmx::ArrayRef< int > cell, int cellIndex, gmx::ArrayRef< int > cxy_na, int atomIndex)
	Sets the cell index in the cell array for atom atomIndex and increments the atom count for the grid column.
static void	Nbnxm::resizeForNumberOfCells (const int numNbnxnAtoms, const int numAtomsMoved, GridSetData *gridSetData, nbnxn_atomdata_t *nbat)
	Resizes grid and atom data which depend on the number of cells.
real	Nbnxm::generateAndFill2DGrid (Grid *grid, gmx::ArrayRef< GridWork > gridWork, gmx::HostVector< int > *cells, const rvec lowerCorner, const rvec upperCorner, const gmx::UpdateGroupsCog *updateGroupsCog, gmx::Range< int > atomRange, real *atomDensity, real maxAtomGroupRadius, bool haveFep, gmx::ArrayRef< const gmx::RVec > x, int ddZone, const int *move, int numAtomsMoved, bool computeGridDensityRatio)
	Sets the 2D search grid dimensions puts the atoms on the 2D grid. More...

Variables
static constexpr int	Nbnxm::c_sortGridRatio = 4
	Ratio of grid cells to atoms.
static constexpr int	Nbnxm::c_sortGridMaxSizeFactor = c_sortGridRatio + 1
	Maximum ratio of holes used, in the worst case all particles end up in the last hole and we need num. atoms extra holes at the end.