#include <gromacs/nbnxm/grid.h>

Description

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).

Classes
struct	Geometry
	The cluster and cell geometry of a grid. More...

Public Member Functions
	Grid (PairlistType pairlistType, int ddZone, const bool &haveFep, PinningPolicy pinningPolicy)
	Constructs a grid given the type of pairlist.

const Geometry &	geometry () const
	Returns the geometry of the grid cells.

int	ddZone () const
	Returns the zone this grid belong to.

const GridDimensions &	dimensions () const
	Returns the dimensions of the grid.

int	numColumns () const
	Returns the total number of grid columns.

int	numCells () const
	Returns the total number of grid cells.

int	cellOffset () const
	Returns the cell offset of (the first cell of) this grid in the list of cells combined over all grids.

int	numCellsColumnMax () const
	Returns the maximum number of grid cells in a column.

int	srcAtomBegin () const
	Returns the start of the source atom range mapped to this grid.

int	srcAtomEnd () const
	Returns the end of the source atom range mapped to this grid.

int	firstCellInColumn (int columnIndex) const
	Returns the first cell index in the grid, starting at 0 in this grid.

int	numCellsInColumn (int columnIndex) const
	Returns the number of cells in the column.

int	firstAtomInColumn (int columnIndex) const
	Returns the index of the first atom in the column.

int	numAtomsInColumn (int columnIndex) const
	Returns the number of real atoms in the column.

ArrayRef< const int >	cxy_na () const
	Returns a view of the number of non-filler, atoms for each grid column. More...

ArrayRef< const int >	cxy_ind () const
	Returns a view of the grid-local cell index for each grid column. More...

int	numAtomsPerCell () const
	Returns the number of real atoms in the column.

int	paddedNumAtomsInColumn (int columnIndex) const
	Returns the number of atoms in the column including padding.

int	atomIndexEnd () const
	Returns the end of the atom index range on the grid, including padding.

bool	clusterIsPerturbed (int clusterIndex) const
	Returns whether any atom in the cluster is perturbed.

bool	atomIsPerturbed (int clusterIndex, int atomIndexInCluster) const
	Returns whether the given atom in the cluster is perturbed.

unsigned int	fepBits (int clusterIndex) const
	Returns the free-energy perturbation bits for the cluster.

ArrayRef< const BoundingBox >	iBoundingBoxes () const
	Returns the i-bounding boxes for all clusters on the grid.

ArrayRef< const BoundingBox >	jBoundingBoxes () const
	Returns the j-bounding boxes for all clusters on the grid.

ArrayRef< const float >	packedBoundingBoxes () const
	Returns the packed bounding boxes for all clusters on the grid, empty with a CPU list.

ArrayRef< const BoundingBox1D >	zBoundingBoxes () const
	Returns the bounding boxes along z for all i-cells on the grid.

ArrayRef< const int >	clusterFlags () const
	Returns the flags for all clusters on the grid.

ArrayRef< const int >	numClustersPerCell () const
	Returns the number of clusters for all cells on the grid, empty with a CPU geometry.

int	atomToCluster (int atomIndex) const
	Returns the cluster index for an atom.

int	numClusters () const
	Returns the total number of clusters on the grid.

void	resizeBoundingBoxesAndFlags (const int maxNumCells)
	Resizes the bouding box and FEP flag lists for at most `maxNumCells`.

void	setDimensions (int ddZone, int numAtomsTotal, int numAtomsWithoutFillers, const RVec &lowerCorner, const RVec &upperCorner, real *atomDensity, real maxAtomGroupRadius)
	Sets the grid dimensions. More...

void	setCellIndices (int ddZone, int cellOffset, GridSetData gridSetData, ArrayRef< GridWork > gridWork, Range< int > atomRange, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t nbat)
	Sets the cell indices using indices in `gridSetData` and `gridWork`.

void	setNonLocalGrid (int ddZone, const GridDimensions &dimensions, ArrayRef< const std::pair< int, int >> columns, int cellOffset, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, GridSetData gridSetData, nbnxn_atomdata_t nbat)
	Sets a non-local grid using data communicated from a different domain. More...

Static Public Member Functions
static void	calcColumnIndices (const GridDimensions &gridDims, const UpdateGroupsCog updateGroupsCog, Range< int > atomRange, ArrayRef< const RVec > x, int dd_zone, const int move, int thread, int nthread, ArrayRef< int > cell, ArrayRef< int > cxy_na)
	Determine in which grid columns atoms should go, store cells and atom counts in `cell` and `cxy_na`.

Member Function Documentation

ArrayRef<const int> gmx::Grid::cxy_ind ( ) const

inline

Returns a view of the grid-local cell index for each grid column.

Todo:: Needs a useful name.

ArrayRef<const int> gmx::Grid::cxy_na ( ) const

inline

Returns a view of the number of non-filler, atoms for each grid column.

Todo:: Needs a useful name.

void gmx::Grid::setDimensions	(	int	ddZone,
		int	numAtomsTotal,
		int	numAtomsWithoutFillers,
		const RVec &	lowerCorner,
		const RVec &	upperCorner,
		real *	atomDensity,
		real	maxAtomGroupRadius
	)

Sets the grid dimensions.

Parameters

[in]	ddZone	The domain decomposition zone index
[in]	numAtomsTotal	The total number of atoms to put onto this grid
[in]	numAtomsWithoutFillers	The number of atoms that are not filler particles
[in]	lowerCorner	The minimum Cartesian coordinates of the grid
[in]	upperCorner	The maximum Cartesian coordinates of the grid
[in,out]	atomDensity	The atom density, will be computed when <= 0
[in]	maxAtomGroupRadius	The maximum radius of atom groups

void gmx::Grid::setNonLocalGrid	(	int	ddZone,
		const GridDimensions &	dimensions,
		ArrayRef< const std::pair< int, int >>	columns,
		int	cellOffset,
		ArrayRef< const int32_t >	atomInfo,
		ArrayRef< const RVec >	x,
		GridSetData *	gridSetData,
		nbnxn_atomdata_t *	nbat
	)

Sets a non-local grid using data communicated from a different domain.

Parameters

[in]	ddZone	The domain decomposition zone this grid belongs to
[in]	dimensions	The dimensions of the grid
[in]	columns	A list of column indices and number of cells for a column, the list should be ordered on column index
[in]	cellOffset	The offset of this grid in the list of cells over all grids
[in]	atomInfo	A list of information for all local and non-local atoms
[in]	x	The coordinates for all local and non-local atoms
[in,out]	gridSetData	The data shared over all grids
[in,out]	nbat	The NBNxM atom data, used here for storing the atom coordinates

The documentation for this class was generated from the following files:

src/gromacs/nbnxm/grid.h
src/gromacs/nbnxm/grid.cpp

Description

Classes

Public Member Functions

Static Public Member Functions

Member Function Documentation