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)
	Constructor.
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...

Member Function Documentation

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