gmx::WholeMoleculeTransform Class Reference

#include <gromacs/mdlib/wholemoleculetransform.h>

Description

This class manages a coordinate buffer with molecules not split over periodic boundary conditions for use in force calculations which require whole molecules.

Note: This class should not be used for computation of forces which have virial contributions through shift forces.

Public Member Functions
	WholeMoleculeTransform (const gmx_mtop_t &mtop, PbcType pbcType, bool useAtomReordering)
	Constructor. More...
void	updateAtomOrder (ArrayRef< const int > globalAtomIndices, const gmx_ga2la_t &ga2la)
	Changes the atom order to the one provided. More...
void	updateForAtomPbcJumps (ArrayRef< const RVec > x, const matrix box)
	Updates the graph when atoms have been shifted by periodic vectors.
ArrayRef< const RVec >	wholeMoleculeCoordinates (ArrayRef< const RVec > x, const matrix box)
	Create and return coordinates with whole molecules for input coordinates x. More...

Constructor & Destructor Documentation

gmx::WholeMoleculeTransform::WholeMoleculeTransform	(	const gmx_mtop_t &	mtop,
		PbcType	pbcType,
		bool	useAtomReordering
	)

Constructor.

Parameters

[in]	mtop	The global topology use for getting the connections between atoms
[in]	pbcType	The type of PBC
[in]	useAtomReordering	Whether we will use atom reordering

Member Function Documentation

void gmx::WholeMoleculeTransform::updateAtomOrder	(	ArrayRef< const int >	globalAtomIndices,
		const gmx_ga2la_t &	ga2la
	)

Changes the atom order to the one provided.

This method is called after domain repartitioning. The object should have been constructed with useAtomReordering set to true.

Parameters

[in]	globalAtomIndices	The global atom indices for the local atoms, size should be the system size
[in]	ga2la	Global to local atom index lookup (the inverse of globalAtomIndices)

ArrayRef< const RVec > gmx::WholeMoleculeTransform::wholeMoleculeCoordinates	(	ArrayRef< const RVec >	x,
		const matrix	box
	)

Create and return coordinates with whole molecules for input coordinates x.

Parameters

[in]	x	Input coordinates, should not have periodic displacement compared with the coordinates passed in the last call to updateForAtomPbcJumps().
[in]	box	The current periodic image vectors

Note: this operation is not free. If you need whole molecules coordinates more than once during the force calculation, store the result and reuse it.

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

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