#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 numAtomsWithoutFillers, 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`.

void	setNonLocalGrid (const int gridIndex, const int ddZone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int >> columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t *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 (int gridIndex) const
	Return a single grid.

ArrayRef< const Grid >	grids () const
	Returns the list of grids.

ArrayRef< const int >	cells () const
	Returns the cell indices for all atoms, the cell indices number contiguously over 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.

ArrayRef< const int >	getLocalGridNumAtomsPerColumn () const
	Returns the number of atoms for each column of the local grid.

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

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

Description

Classes

Public Member Functions