grid.h File Reference

#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"

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Description

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@.nosp@m.kth..nosp@m.se

Classes
struct	Nbnxm::BoundingBox
	Bounding box for a nbnxm atom cluster. More...
struct	Nbnxm::BoundingBox::Corner
	Corner for the bounding box, padded with one element to enable 4-wide SIMD operations. More...
struct	Nbnxm::BoundingBox1D
	Bounding box for one dimension of a grid cell. More...
class	Nbnxm::Grid
	A pair-search grid object for one domain decomposition zone. More...
struct	Nbnxm::Grid::Geometry
	The cluster and cell geometry of a grid. More...
struct	Nbnxm::Grid::Dimensions
	The physical dimensions of a grid. More...

Functions
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...