gmx::GridSet Class Reference

#include <gromacs/nbnxm/gridset.h>

Description

Holds a set of search grids for the local + non-local DD zones.

The are three different possible setups:

• a single grid, this is the standard case without domain decomposition
• one grid for each domain decomposition zone
• with test particle insertion there are two grids, one for the system to insert in and one for the molecule that is inserted

Classes
struct	DomainSetup
	Description of the domain setup: PBC and the connections between domains. More...

Public Member Functions
	GridSet (PbcType pbcType, bool doTestParticleInsertion, const IVec *numDDCells, const DomdecZones *ddZones, PairlistType pairlistType, bool haveFep, bool localAtomOrderMatchesNbnxmOrder, int numThreads, PinningPolicy pinningPolicy)
	Constructs a grid set for 1 or multiple DD zones, when numDDCells!=nullptr.
void	putOnGrid (const matrix box, int gridIndex, const rvec lowerCorner, const rvec upperCorner, const UpdateGroupsCog *updateGroupsCog, Range< int > atomRange, int numGridAtoms, real atomDensity, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, const int *move, nbnxn_atomdata_t *nbat)
	Puts the atoms on the grid with index gridIndex and copies the coordinates to nbat.
DomainSetup	domainSetup () const
	Returns the domain setup.
bool	localAtomOrderMatchesNbnxmOrder () const
	Returns whether the local atom order matches the NBNxM atom order.
int	numGridAtomsLocal () const
	Returns the number of atoms in the local grid, including padding.
int	numGridAtomsTotal () const
	Returns the total number of atoms in the grid set, including padding.
int	numRealAtomsLocal () const
	Returns the number of local real atoms, i.e. without padded atoms.
int	numRealAtomsTotal () const
	Returns the number of total real atoms, i.e. without padded atoms.
ArrayRef< const int >	getLocalAtomorder () const
	Returns the atom order on the grid for the local atoms.
void	setLocalAtomOrder ()
	Sets the order of the local atoms to the order grid atom ordering.
const Grid &	grid (size_t idx) const
	Return a single grid.
ArrayRef< const Grid >	grids () const
	Returns the list of grids.
ArrayRef< const int >	cells () const
	Returns the grid atom indices covering all grids.
ArrayRef< const int >	atomIndices () const
	Returns the grid atom indices covering all grids.
bool	haveFep () const
	Returns whether we have perturbed non-bonded interactions.
void	getBox (matrix box) const
	Returns the unit cell in box.
int	numColumnsMax () const
	Returns the maximum number of columns across all grids.
void	setNumColumnsMax (int numColumnsMax)
	Sets the maximum number of columns across all grids.

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

• src/gromacs/nbnxm/gridset.h
• src/gromacs/nbnxm/gridset.cpp