gmx::anonymous_namespace{grid.cpp} Namespace Reference

Functions
void	centerPeriodicValueAroundZero (double *x, double period)
	Modify x so that it is periodic in [-period/2, +period/2). More...
int	indexWithinPeriod (int x, int period)
	If period>0, retrun x so that it is periodic in [0, period), else return x. More...
double	getIntervalLengthPeriodic (double origin, double end, double period)
	Get the length of the interval (origin, end). More...
double	getDeviationPeriodic (double x, double x0, double period)
	Get the deviation x - x0. More...
int	multiDimGridIndexToLinear (const std::vector< GridAxis > &axis, const awh_ivec indexMulti)
	Convert a multidimensional grid point index to a linear one. More...
bool	stepInMultiDimArray (int numDim, const awh_ivec numPoints, awh_ivec indexDim)
	Take a step in a multidimensional array. More...
void	gridToSubgridIndex (const Grid &grid, const awh_ivec subgridOrigin, const awh_ivec subgridNpoints, int point, awh_ivec subgridIndex)
	Transforms a grid point index to to the multidimensional index of a subgrid. More...
bool	subgridToGridIndex (const Grid &grid, const awh_ivec subgridOrigin, const awh_ivec subgridIndex, int *gridIndex)
	Transform a multidimensional subgrid index to a grid point index. More...
void	setNeighborsOfGridPoint (int pointIndex, const Grid &grid, std::vector< int > *neighborIndexArray)
	Find and set the neighbors of a grid point. More...

Function Documentation

void gmx::anonymous_namespace{grid.cpp}::centerPeriodicValueAroundZero	(	double *	x,
		double	period
	)

Modify x so that it is periodic in [-period/2, +period/2).

x is modified by shifting its value by a +/- a period if needed. Thus, it is assumed that x is at most one period away from this interval. For period = 0, x is not modified.

Parameters

[in,out]	x	Pointer to the value to modify.
[in]	period	The period, or 0 if not periodic.

double gmx::anonymous_namespace{grid.cpp}::getDeviationPeriodic	(	double	x,
		double	x0,
		double	period
	)

Get the deviation x - x0.

For period > 0, the deviation with minimum absolute value is returned, i.e. with a value in the interval [-period/2, +period/2). Also for period > 0, it is assumed that |x - x0| < period.

Parameters

[in]	x	From value.
[in]	x0	To value.
[in]	period	The period, or 0 if not periodic.

Returns

the deviation from x to x0.

double gmx::anonymous_namespace{grid.cpp}::getIntervalLengthPeriodic	(	double	origin,
		double	end,
		double	period
	)

Get the length of the interval (origin, end).

This returns the distance obtained by connecting the origin point to the end point in the positive direction. Note that this is generally not the shortest distance. For period > 0, both origin and end are expected to take values in the same periodic interval, ie. |origin - end| < period.

Parameters

[in]	origin	Start value of the interval.
[in]	end	End value of the interval.
[in]	period	The period, or 0 if not periodic.

Returns

the interval length from origin to end.

void gmx::anonymous_namespace{grid.cpp}::gridToSubgridIndex	(	const Grid &	grid,
		const awh_ivec	subgridOrigin,
		const awh_ivec	subgridNpoints,
		int	point,
		awh_ivec	subgridIndex
	)

Transforms a grid point index to to the multidimensional index of a subgrid.

The subgrid is defined by the location of its origin and the number of points along each dimension. The index transformation thus consists of a projection of the linear index onto each dimension, followed by a translation of the origin. The subgrid may have parts that don't overlap with the grid. E.g. the origin vector can have negative components meaning the origin lies outside of the grid. However, the given point needs to be both a grid and subgrid point.

Periodic boundaries are taken care of by wrapping the subgrid around the grid. Thus, for periodic dimensions the number of subgrid points need to be less than the number of points in a period to prevent problems of wrapping around.

Parameters

[in]	grid	The grid.
[in]	subgridOrigin	Vector locating the subgrid origin relative to the grid origin.
[in]	subgridNpoints	The number of subgrid points in each dimension.
[in]	point	Grid point to get subgrid index for.
[in,out]	subgridIndex	Subgrid multidimensional index.

int gmx::anonymous_namespace{grid.cpp}::indexWithinPeriod	(	int	x,
		int	period
	)

If period>0, retrun x so that it is periodic in [0, period), else return x.

Return x is shifted its value by a +/- a period, if needed. Thus, it is assumed that x is at most one period away from this interval. For this domain and period > 0 this is equivalent to x = x % period. For period = 0, x is not modified.

Parameters

[in,out]	x	Pointer to the value to modify, should be >= 0.
[in]	period	The period, or 0 if not periodic.

Returns

for period>0: index value witin [0, period), otherwise: x.

int gmx::anonymous_namespace{grid.cpp}::multiDimGridIndexToLinear	(	const std::vector< GridAxis > &	axis,
		const awh_ivec	indexMulti
	)

Convert a multidimensional grid point index to a linear one.

Parameters

[in]	axis	The grid axes.
[in]	indexMulti	Multidimensional grid point index to convert to a linear one.

Returns

the linear index.

void gmx::anonymous_namespace{grid.cpp}::setNeighborsOfGridPoint	(	int	pointIndex,
		const Grid &	grid,
		std::vector< int > *	neighborIndexArray
	)

Find and set the neighbors of a grid point.

The search space for neighbors is a subgrid with size set by a scope cutoff. In general not all point within scope will be valid grid points.

Parameters

[in]	pointIndex	Grid point index.
[in]	grid	The grid.
[in,out]	neighborIndexArray	Array to fill with neighbor indices.

bool gmx::anonymous_namespace{grid.cpp}::stepInMultiDimArray	(	int	numDim,
		const awh_ivec	numPoints,
		awh_ivec	indexDim
	)

Take a step in a multidimensional array.

The multidimensional index gives the starting point to step from. Dimensions are stepped through in order of decreasing dimensional index such that the index is incremented in the highest dimension possible. If the starting point is the end of the array, a step cannot be taken and the index is not modified.

Parameters

[in]	numDim	Number of dimensions of the array.
[in]	numPoints	Vector with the number of points along each dimension.
[in,out]	indexDim	Multidimensional index, each with values in [0, numPoints[d] - 1].

Returns

true if a step was taken, false if not.

bool gmx::anonymous_namespace{grid.cpp}::subgridToGridIndex	(	const Grid &	grid,
		const awh_ivec	subgridOrigin,
		const awh_ivec	subgridIndex,
		int *	gridIndex
	)

Transform a multidimensional subgrid index to a grid point index.

If the given subgrid point is not a grid point the transformation will not be successful and the grid point index will not be set. Periodic boundaries are taken care of by wrapping the subgrid around the grid.

Parameters

[in]	grid	The grid.
[in]	subgridOrigin	Vector locating the subgrid origin relative to the grid origin.
[in]	subgridIndex	Subgrid multidimensional index to get grid point index for.
[in,out]	gridIndex	Grid point index.

Returns

true if the transformation was successful.