Functions
void	sumPmf (gmx::ArrayRef< PointState > pointState, int numSharedUpdate, const BiasSharing *biasSharing, const int biasIndex)
	Sum PMF over multiple simulations, when requested. More...

double	freeEnergyMinimumValue (gmx::ArrayRef< const PointState > pointState)
	Find the minimum free energy value. More...

double	biasedLogWeightFromPoint (ArrayRef< const DimParams > dimParams, ArrayRef< const PointState > points, const BiasGrid &grid, int pointIndex, double pointBias, const awh_dvec value, ArrayRef< const double > neighborLambdaEnergies, int gridpointIndex)
	Find and return the log of the probability weight of a point given a coordinate value. More...

std::vector< double >	calculateFELambdaMarginalDistribution (const BiasGrid &grid, ArrayRef< const int > neighbors, ArrayRef< const double > probWeightNeighbor)
	Calculates the marginal distribution (marginal probability) for each value along a free energy lambda axis. The marginal distribution of one coordinate dimension value is the sum of the probability distribution of all values (herein all neighbor values) with the same value in the dimension of interest. More...

std::string	gridPointValueString (const BiasGrid &grid, int point)
	Puts together a string describing a grid point. More...

void	setHistogramUpdateScaleFactors (const BiasParams &params, double newHistogramSize, double oldHistogramSize, double weightHistScaling, double logPmfSumScaling)
	Sets the histogram rescaling factors needed to control the histogram size. More...

void	mergeSharedUpdateLists (std::vector< int > *updateList, int numPoints, const BiasSharing &biasSharing, const int biasIndex)
	Merge update lists from multiple sharing simulations. More...

void	makeLocalUpdateList (const BiasGrid &grid, ArrayRef< const PointState > points, const awh_ivec originUpdatelist, const awh_ivec endUpdatelist, std::vector< int > *updateList)
	Generate an update list of points sampled since the last update. More...

void	sumHistograms (gmx::ArrayRef< PointState > pointState, gmx::ArrayRef< double > weightSumCovering, int numSharedUpdate, const BiasSharing *biasSharing, const int biasIndex, const std::vector< int > &localUpdateList)
	Add partial histograms (accumulating between updates) to accumulating histograms. More...

void	labelCoveredPoints (const std::vector< bool > &visited, const std::vector< bool > &checkCovering, int numPoints, int period, int coverRadius, gmx::ArrayRef< int > covered)
	Label points along an axis as covered or not. More...

Function Documentation

double gmx::anonymous_namespace{biasstate.cpp}::biasedLogWeightFromPoint	(	ArrayRef< const DimParams >	dimParams,
		ArrayRef< const PointState >	points,
		const BiasGrid &	grid,
		int	pointIndex,
		double	pointBias,
		const awh_dvec	value,
		ArrayRef< const double >	neighborLambdaEnergies,
		int	gridpointIndex
	)

Find and return the log of the probability weight of a point given a coordinate value.

The unnormalized weight is given by w(point|value) = exp(bias(point) - U(value,point)), where U is a harmonic umbrella potential.

Parameters

[in]	dimParams	The bias dimensions parameters
[in]	points	The point state.
[in]	grid	The grid.
[in]	pointIndex	Point to evaluate probability weight for.
[in]	pointBias	Bias for the point (as a log weight).
[in]	value	Coordinate value.
[in]	neighborLambdaEnergies	The energy of the system in neighboring lambdas states. Can be empty when there are no free energy lambda state dimensions.
[in]	gridpointIndex	The index of the current grid point.

Returns: the log of the biased probability weight.

std::vector<double> gmx::anonymous_namespace{biasstate.cpp}::calculateFELambdaMarginalDistribution	(	const BiasGrid &	grid,
		ArrayRef< const int >	neighbors,
		ArrayRef< const double >	probWeightNeighbor
	)

Calculates the marginal distribution (marginal probability) for each value along a free energy lambda axis. The marginal distribution of one coordinate dimension value is the sum of the probability distribution of all values (herein all neighbor values) with the same value in the dimension of interest.

Parameters

[in]	grid	The bias grid.
[in]	neighbors	The points to use for the calculation of the marginal distribution.
[in]	probWeightNeighbor	Probability weights of the neighbors.

Returns: The calculated marginal distribution in a 1D array with as many elements as there are points along the axis of interest.

double gmx::anonymous_namespace{biasstate.cpp}::freeEnergyMinimumValue ( gmx::ArrayRef< const PointState > pointState )

Find the minimum free energy value.

Parameters

[in] pointState The state of the points.

Returns: the minimum free energy value.

std::string gmx::anonymous_namespace{biasstate.cpp}::gridPointValueString	(	const BiasGrid &	grid,
		int	point
	)

Puts together a string describing a grid point.

Parameters

[in]	grid	The grid.
[in]	point	BiasGrid point index.

Returns: a string for the point.

void gmx::anonymous_namespace{biasstate.cpp}::labelCoveredPoints	(	const std::vector< bool > &	visited,
		const std::vector< bool > &	checkCovering,
		int	numPoints,
		int	period,
		int	coverRadius,
		gmx::ArrayRef< int >	covered
	)

Label points along an axis as covered or not.

A point is covered if it is surrounded by visited points up to a radius = coverRadius.

Parameters

[in]	visited	Visited? For each point.
[in]	checkCovering	Check for covering? For each point.
[in]	numPoints	The number of grid points along this dimension.
[in]	period	Period in number of points.
[in]	coverRadius	Cover radius, in points, needed for defining a point as covered.
[in,out]	covered	In this array elements are 1 for covered points and 0 for non-covered points, this routine assumes that `covered` has at least size `numPoints`.

void gmx::anonymous_namespace{biasstate.cpp}::makeLocalUpdateList	(	const BiasGrid &	grid,
		ArrayRef< const PointState >	points,
		const awh_ivec	originUpdatelist,
		const awh_ivec	endUpdatelist,
		std::vector< int > *	updateList
	)

Generate an update list of points sampled since the last update.

Parameters

[in]	grid	The AWH bias.
[in]	points	The point state.
[in]	originUpdatelist	The origin of the rectangular region that has been sampled since last update.
[in]	endUpdatelist	The end of the rectangular that has been sampled since last update.
[in,out]	updateList	Local update list to set (assumed >= npoints long).

void gmx::anonymous_namespace{biasstate.cpp}::mergeSharedUpdateLists	(	std::vector< int > *	updateList,
		int	numPoints,
		const BiasSharing &	biasSharing,
		const int	biasIndex
	)

Merge update lists from multiple sharing simulations.

Parameters

[in,out]	updateList	Update list for this simulation (assumed >= npoints long).
[in]	numPoints	Total number of points.
[in]	biasSharing	Object for sharing bias data over multiple simulations
[in]	biasIndex	Index of this bias in the total list of biases in this simulation

void gmx::anonymous_namespace{biasstate.cpp}::setHistogramUpdateScaleFactors	(	const BiasParams &	params,
		double	newHistogramSize,
		double	oldHistogramSize,
		double *	weightHistScaling,
		double *	logPmfSumScaling
	)

Sets the histogram rescaling factors needed to control the histogram size.

For sake of robustness, the reference weight histogram can grow at a rate different from the actual sampling rate. Typically this happens for a limited initial time, alternatively growth is scaled down by a constant factor for all times. Since the size of the reference histogram sets the size of the free energy update this should be reflected also in the PMF. Thus the PMF histogram needs to be rescaled too.

This function should only be called by the bias update function or wrapped by a function that knows what scale factors should be applied when, e.g, getSkippedUpdateHistogramScaleFactors().

Parameters

[in]	params	The bias parameters.
[in]	newHistogramSize	New reference weight histogram size.
[in]	oldHistogramSize	Previous reference weight histogram size (before adding new samples).
[out]	weightHistScaling	Scaling factor for the reference weight histogram.
[out]	logPmfSumScaling	Log of the scaling factor for the PMF histogram.

void gmx::anonymous_namespace{biasstate.cpp}::sumHistograms	(	gmx::ArrayRef< PointState >	pointState,
		gmx::ArrayRef< double >	weightSumCovering,
		int	numSharedUpdate,
		const BiasSharing *	biasSharing,
		const int	biasIndex,
		const std::vector< int > &	localUpdateList
	)

Add partial histograms (accumulating between updates) to accumulating histograms.

Parameters

[in,out]	pointState	The state of the points in the bias.
[in,out]	weightSumCovering	The weights for checking covering.
[in]	numSharedUpdate	The number of biases sharing the histrogram.
[in]	biasSharing	Object for sharing bias data over multiple simulations
[in]	biasIndex	Index of this bias in the total list of biases in this simulation
[in]	localUpdateList	List of points with data.

void gmx::anonymous_namespace{biasstate.cpp}::sumPmf	(	gmx::ArrayRef< PointState >	pointState,
		int	numSharedUpdate,
		const BiasSharing *	biasSharing,
		const int	biasIndex
	)

Sum PMF over multiple simulations, when requested.

Parameters

[in,out]	pointState	The state of the points in the bias.
[in]	numSharedUpdate	The number of biases sharing the histogram.
[in]	biasSharing	Object for sharing bias data over multiple simulations
[in]	biasIndex	Index of this bias in the total list of biases in this simulation

Functions

Function Documentation