gmx::DomainCommBackward Class Reference

#include <gromacs/domdec/domainpaircomm.h>

Description

Setup for selecting halo atoms to be sent and sending coordinates to another domain.

Also used for receiving forces.

This object is used for communicating with a domain that resides in backward direction along the domain decomposition grid. This object holds the NBNxM grid cluster indices that needs to be sent and does the packing of coordinates into a buffer in this object. It also does the reverse indexing for the halo force reduction of forces received.

Classes
struct	GridClusterRange
	Struct for storing a cluster range for a grid column. More...

Public Member Functions
	DomainCommBackward (int rank, int zone, const IVec &domainShift, PbcType pbcType, bool commOverPbc, const IVec &pbcCoordinateShift, MPI_Comm mpiCommAll)
	Constructor. More...
void	clear ()
	Clears this communication, set no columns and atoms to send.
void	getTargetZoneCorners (const gmx_domdec_t &dd, const matrix box, const DomainPairComm &domainPairComm)
	Determines the corner for 2-body, corner_2b, and multi-body, corner_mb, communication distances. More...
void	selectHaloAtoms (const gmx_domdec_t &dd, const Grid &grid, const real cutoffTwoBody, const real cutoffMultiBody, const ivec dimensionIsTriclinic, ArrayRef< const RVec > normal, const std::vector< bool > &isCellMissingLinks)
	Determine which NBNxM grid clusters (and atoms) we need to send. More...
FastVector< std::pair< int, int > >	makeColumnsSendBuffer () const
	Creates and returns a buffer with column indices and cluster counts to be sent.
void	packCoordinateSendBuffer (const matrix box, ArrayRef< const RVec > x, ArrayRef< RVec > sendBuffer) const
	Copies the coordinates to commnicate to the send buffer.
void	accumulateReceivedForces (ArrayRef< RVec > forces, ArrayRef< RVec > shiftForces) const
	Accumulates the received forces to the force buffer and shift force buffer, when not empty.
int	rank () const
	Returns the rank we communicate with.
int	zone () const
	Return the zone this domain pair resides in.
int	domainShift (int dim) const
	Returns the shift in domains in Cartesian coordinates between the communicating domains.
bool	shiftMultipleDomains () const
	Returns whether the domain shift is more than one domain along at least one dimension.
int	numAtomsPerCluster () const
	Returns the number of atoms per cluster.
ArrayRef< const GridClusterRange >	clusterRangesToSend () const
	Returns the list of all columns to send with column information.
int	numAtoms () const
	Returns the number of atoms to send.
ArrayRef< const int >	globalAtomIndices () const
	Returns the buffer with global atom indices to communicate.
ArrayRef< RVec >	rvecBuffer ()
	Returns the buffer for sending coordinates and receiving forces.
ArrayRef< const RVec >	rvecBuffer () const
	Returns the buffer for sending coordinates and receiving forces.
MPI_Comm	mpiCommAll () const
	The MPI communication for halo exchange.

Constructor & Destructor Documentation

gmx::DomainCommBackward::DomainCommBackward	(	int	rank,
		int	zone,
		const IVec &	domainShift,
		PbcType	pbcType,
		bool	commOverPbc,
		const IVec &	pbcCoordinateShift,
		MPI_Comm	mpiCommAll
	)

Constructor.

Parameters

[in]	rank	The MPI rank we communicate with
[in]	zone	The domain decomposition zone this pair of domains belongs to
[in]	domainShift	The shift >=0 in domain indices between the two domains
[in]	pbcType	The type of PBC
[in]	commOverPbc	Whether we are communicating over a periodic boundary
[in]	pbcCoordinateShift	The PBC coordinate shift, 0 or 1 for each dimension
[in]	mpiCommAll	MPI communicator for all PP ranks

Member Function Documentation

void gmx::DomainCommBackward::getTargetZoneCorners	(	const gmx_domdec_t &	dd,
		const matrix	box,
		const DomainPairComm &	domainPairComm
	)

Determines the corner for 2-body, corner_2b, and multi-body, corner_mb, communication distances.

Communicates the computed corners between domain pairs

Note that the column bounding boxes are computed for the centers of update groups. Atoms in update groups can stick out by at most grid.dimensions().maxAtomGroupRadius.

Parameters

[in]	dd	The domain decomposition struct
[in]	box	The system unit cell
[in]	domainPairComm	Communication setup for a domain pair

void gmx::DomainCommBackward::selectHaloAtoms	(	const gmx_domdec_t &	dd,
		const Grid &	grid,
		const real	cutoffTwoBody,
		const real	cutoffMultiBody,
		const ivec	dimensionIsTriclinic,
		ArrayRef< const RVec >	normal,
		const std::vector< bool > &	isCellMissingLinks
	)

Determine which NBNxM grid clusters (and atoms) we need to send.

Should be called after calling getTargetZoneCorners().

Parameters

[in]	dd	The domain decomposition struct
[in]	grid	The local NBNxM pair-search grid
[in]	cutoffTwoBody	The cutoff for two-body interactions, includes 2 maxAtomGroupRadius
[in]	cutoffMultiBody	The cutoff for multi-body interactions includes 2 maxAtomGroupRadius
[in]	dimensionIsTriclinic	Tells whether the dimensions require triclinic distance checks
[in]	normal	The normal vectors to planes separating domains along the triclinic dimensions
[in]	isCellMissingLinks	Tells whether cells are missing bonded interactions, only used when filtering bonded communication

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

• src/gromacs/domdec/domainpaircomm.h
• src/gromacs/domdec/domainpaircomm.cpp
• src/gromacs/domdec/haloexchange.cpp