Classes
class	MsdData
	Mean Squared Displacement data accumulator. More...

struct	MoleculeData
	Holds data needed for MSD calculations for a single molecule, if requested. More...

class	MsdCoordinateManager
	Handles coordinate operations for MSD calculations. More...

struct	MsdGroupData
	Holds per-group coordinates, analysis, and results. More...

Enumerations
enum	SingleDimDiffType : int { X = 0, Y, Z, Unused, Count }
	Describes 1D MSDs, in the given dimension.

enum	TwoDimDiffType : int { NormalToX = 0, NormalToY, NormalToZ, Unused, Count }
	Describes 2D MSDs, in the plane normal to the given dimension.

Functions
template<bool x, bool y, bool z>
double	calcSingleSquaredDistance (const DVec &firstCoords, const DVec &secondCoords)
	Calculates 1,2, or 3D distance for two vectors. More...

template<bool x, bool y, bool z>
double	calcAverageDisplacement (ArrayRef< const DVec > c1, ArrayRef< const DVec > c2)
	Calculate average displacement between sets of points. More...

void	removePbcJumps (ArrayRef< DVec > currentCoords, ArrayRef< const DVec > previousCoords, t_pbc *pbc)
	Removes jumps across periodic boundaries for currentFrame, based on the positions in previousFrame. Updates currentCoords in place.

Variables
constexpr double	c_diffusionConversionFactor = 1000.0
	Convert nm^2/ps to 10e-5 cm^2/s.

constexpr double	c_3DdiffusionDimensionFactor = 6.0
	Three dimensional diffusion coefficient multiplication constant.

constexpr double	c_2DdiffusionDimensionFactor = 4.0
	Two dimensional diffusion coefficient multiplication constant.

constexpr double	c_1DdiffusionDimensionFactor = 2.0
	One dimensional diffusion coefficient multiplication constant.

Function Documentation

template<bool x, bool y, bool z>

double gmx::analysismodules::anonymous_namespace{msd.cpp}::calcAverageDisplacement	(	ArrayRef< const DVec >	c1,
		ArrayRef< const DVec >	c2
	)

Calculate average displacement between sets of points.

Each displacement c1[i] - c2[i] is calculated and the distances are averaged.

Template Parameters

x	If true, calculate x dimension of displacement
y	If true, calculate y dimension of displacement
z	If true, calculate z dimension of displacement

Parameters

[in]	c1	First vector
[in]	c2	Second vector

template<bool x, bool y, bool z>

double gmx::analysismodules::anonymous_namespace{msd.cpp}::calcSingleSquaredDistance	(	const DVec &	firstCoords,
		const DVec &	secondCoords
	)

inline

Calculates 1,2, or 3D distance for two vectors.

Template Parameters

x	If true, calculate x dimension of displacement
y	If true, calculate y dimension of displacement
z	If true, calculate z dimension of displacement

Parameters

[in]	firstCoords	First point
[in]	secondCoords	Second point

Classes