gmx::CorrelationTensor Class Reference

#include <gromacs/applied_forces/awh/correlationtensor.h>

Description

Correlation data for computing the correlation tensor of one grid point.

The time integrated autocorrelation of the desired quantity is computed using block averages, which is a computationally efficient and low memory method. Most of the work here goes into computing the block averages for weights and the coordinate quantity. This is done for a number of blocks in the range of c_numCorrelationBlocks/2 + 1 to c_numCorrelationBlocks, depending on the current simulation length. As the simulation time progresses, the blocks get longer. This is implemented in an efficient way by keeping track of log2(c_numCorrelationBlocks) BlockData data blocks with block length increasing progressively by a factor of 2. Once c_numCorrelationBlocks are reached, all block lengths are doubled.

Public Member Functions
	CorrelationTensor (int numDim, int numBlockData, double blockLengthInit)
	Constructor. More...
const std::vector < CorrelationBlockData > &	blockDataList () const
	Get a const reference to the list of block data.
double	getWeight () const
	Get the total weight of the data in the correlation matrix. More...
void	restoreFromHistory (const std::vector< CorrelationBlockDataHistory > &blockDataBuffer, size_t *bufferIndex)
	Restore a correlation element from history. More...
void	addData (double weight, gmx::ArrayRef< const double > data, bool blockLengthInWeight, double t)
	Adds a weighted data vector to one point in the correlation grid. More...
double	getTimeIntegral (int tensorIndex, double dtSample) const
	Returns an element of the time integrated correlation tensor at a given point in the grid. More...
double	getVolumeElement (double dtSample) const
	Returns the volume element of the correlation metric. More...

Static Public Attributes
static constexpr int	c_numCorrelationBlocks = 64
	64 blocks is a good trade-off between signal and noise

Constructor & Destructor Documentation

gmx::CorrelationTensor::CorrelationTensor	(	int	numDim,
		int	numBlockData,
		double	blockLengthInit
	)

Constructor.

Parameters

[in]	numDim	The dimensionality.
[in]	numBlockData	The number of data block data structs.
[in]	blockLengthInit	The initial block length.

Member Function Documentation

void gmx::CorrelationTensor::addData	(	double	weight,
		gmx::ArrayRef< const double >	data,
		bool	blockLengthInWeight,
		double	t
	)

Adds a weighted data vector to one point in the correlation grid.

Note

To avoid rounding noise, data with weight smaller than 1e-6 is ignored.

Parameters

[in]	weight	The weight of the data.
[in]	data	One data point for each grid dimension.
[in]	blockLengthInWeight	If true, a block is measured in probability weight, otherwise in time.
[in]	t	The simulation time.

double gmx::CorrelationTensor::getTimeIntegral	(	int	tensorIndex,
		double	dtSample
	)		const

Returns an element of the time integrated correlation tensor at a given point in the grid.

The units of the integral are time*(units of data)^2. This will be friction units time/length^2 if the data unit is 1/length.

The correlation index lists the elements of the upper-triangular correlation matrix row-wise, so e.g. in 3D: 0 (0,0), 1 (1,0), 2 (1,1), 3 (2,0), 4 (2,1), 5 (2,2). (TODO: this should ideally not have to be known by the caller.)

Parameters

[in]	tensorIndex	Index in the tensor.
[in]	dtSample	The sampling interval length.

Returns

the integral.

double gmx::CorrelationTensor::getVolumeElement

(

double

dtSample

)

const

Returns the volume element of the correlation metric.

The matrix of the metric equals the time-integrated correlation matrix. The volume element of the metric therefore equals the square-root of the absolute value of its determinant according to the standard formula for a volume element in a metric space.

Since the units of the metric matrix elements are time*(units of data)^2, the volume element has units of (sqrt(time)*(units of data))^(ndim of data).

Parameters

[in]

dtSample

The sampling interval length.

Returns

the volume element.

double gmx::CorrelationTensor::getWeight ( ) const

inline

Get the total weight of the data in the correlation matrix.

Returns

the weight of the added data.

void gmx::CorrelationTensor::restoreFromHistory	(	const std::vector< CorrelationBlockDataHistory > &	blockDataBuffer,
		size_t *	bufferIndex
	)

Restore a correlation element from history.

Parameters

[in]	blockDataBuffer	The linear correlation grid data history buffer.
[in,out]	bufferIndex	The index in blockDataBuffer to start reading, is increased with the number of blocks read.

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

• src/gromacs/applied_forces/awh/correlationtensor.h
• src/gromacs/applied_forces/awh/correlationhistory.cpp
• src/gromacs/applied_forces/awh/correlationtensor.cpp