gmx::UpdateGroupsCog Class Reference

#include <gromacs/mdlib/updategroupscog.h>

Description

Class for managing and computing centers of geometry of update groups.

Public Member Functions
	UpdateGroupsCog (const gmx_mtop_t &mtop, gmx::ArrayRef< const gmx::RangePartitioning > updateGroupingsPerMoleculeType, real temperature)
	Constructor. More...
void	addCogs (ArrayRef< const int > globalAtomIndices, ArrayRef< const RVec > coordinates, ArrayRef< const int > numAtomsPerNbnxmGridColumn)
	Compute centers of geometry for supplied coordinates. More...
int	numCogs () const
	Returns the number of centers of geometry currently stored.
RVec &	cog (int cogIndex)
	Returns a reference to a center of geometry. More...
bool	cogIsFillerParticle (int cogIndex) const
	Returns whether a COG entry consists of a (single) filler particle. More...
int	cogIndex (int atomIndex) const
	Returns the COG index given an atom index. More...
const RVec &	cogForAtom (int atomIndex) const
	Return a reference to a center of geometry given an atom index. More...
void	clear ()
	Clear the lists of stored center of geometry coordinates.
real	maxUpdateGroupRadius () const
	Returns the maximum radius over all update groups.

Constructor & Destructor Documentation

gmx::UpdateGroupsCog::UpdateGroupsCog	(	const gmx_mtop_t &	mtop,
		gmx::ArrayRef< const gmx::RangePartitioning >	updateGroupingsPerMoleculeType,
		real	temperature
	)

Constructor.

The temperature is used for computing the maximum update group radius.

Parameters

[in]	mtop	The global topology
[in]	updateGroupingsPerMoleculeType	List of update groups for each molecule type in mtop
[in]	temperature	The maximum reference temperature, pass -1 when unknown or not applicable

Member Function Documentation

void gmx::UpdateGroupsCog::addCogs	(	ArrayRef< const int >	globalAtomIndices,
		ArrayRef< const RVec >	coordinates,
		ArrayRef< const int >	numAtomsPerNbnxmGridColumn
	)

Compute centers of geometry for supplied coordinates.

Coordinates are processed starting after the last index processed in the previous call to addCogs(), unless clear() was called last, in which case processing starts at 0. Coordinates are processed until globalAtomIndices.size().

Parameters

[in]	globalAtomIndices	List of global atom indices for the atoms belonging to coordinates
[in]	coordinates	List of coordinates to be processed, processing might not start at 0 (see above)
[in]	numAtomsPerNbnxmGridColumn	A list of the number of atoms per NBNxM grid column, used for OpenMP parallelization, as update groups are never split over columns; can be empty

RVec& gmx::UpdateGroupsCog::cog ( int  cogIndex )

inline

Returns a reference to a center of geometry.

Parameters

[in]

cogIndex

The COG requested, should be; 0 <= cogIndex < cogs_.size()

const RVec& gmx::UpdateGroupsCog::cogForAtom ( int  atomIndex ) const

inline

Return a reference to a center of geometry given an atom index.

Parameters

[in]

atomIndex

The atom index that maps to the COG requested

int gmx::UpdateGroupsCog::cogIndex ( int  atomIndex ) const

inline

Returns the COG index given an atom index.

Parameters

[in]

atomIndex

The local atom index that maps to the COG

bool gmx::UpdateGroupsCog::cogIsFillerParticle ( int  cogIndex ) const

inline

Returns whether a COG entry consists of a (single) filler particle.

Parameters

[in]

cogIndex

The COG requested, should be; 0 <= cogIndex < cogs_.size()

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

• src/gromacs/mdlib/updategroupscog.h
• src/gromacs/mdlib/updategroupscog.cpp