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

Description

The state of a bias.

The bias state has the current coordinate state: its value and the grid point it maps to (the grid point of the umbrella potential if needed). It contains a vector with the state for each point on the grid. It also counts the number of updates issued and tracks which points have been sampled since last update. Finally, the convergence state is a global property set ultimately by the histogram size histogramSize in the sub-class HistogramSize, since the update sizes are ~ 1/histogramSize.

Public Member Functions
	BiasState (const AwhBiasParams &awhBiasParams, double histogramSizeInitial, ArrayRef< const DimParams > dimParams, const BiasGrid &grid, const BiasSharing *biasSharing)
	Constructor. More...

void	restoreFromHistory (const AwhBiasHistory &biasHistory, const BiasGrid &grid)
	Restore the bias state from history. More...

void	broadcast (const t_commrec *commRecord)
	Broadcast the bias state over the MPI ranks in this simulation. More...

void	initHistoryFromState (AwhBiasHistory *biasHistory) const
	Allocate and initialize a bias history with the given bias state. More...

void	updateHistory (AwhBiasHistory *biasHistory, const BiasGrid &grid) const
	Update the bias state history with the current state. More...

void	initGridPointState (const AwhBiasParams &awhBiasParams, ArrayRef< const DimParams > dimParams, const BiasGrid &grid, const BiasParams &params, const CorrelationGrid &forceCorrelation, const std::string &filename, int numBias)
	Initialize the state of grid coordinate points. More...

int	warnForHistogramAnomalies (const BiasGrid &grid, int biasIndex, double t, FILE *fplog, int maxNumWarnings) const
	Performs statistical checks on the collected histograms and warns if issues are detected. More...

double	calcUmbrellaForceAndPotential (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, int point, ArrayRef< const double > neighborLambdaDhdl, ArrayRef< double > force) const
	Calculates and sets the force the coordinate experiences from an umbrella centered at the given point. More...

void	calcConvolvedForce (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, ArrayRef< const double > probWeightNeighbor, ArrayRef< const double > neighborLambdaDhdl, ArrayRef< double > forceWorkBuffer, ArrayRef< double > force) const
	Calculates and sets the convolved force acting on the coordinate. More...

double	moveUmbrella (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, ArrayRef< const double > probWeightNeighbor, ArrayRef< const double > neighborLambdaDhdl, ArrayRef< double > biasForce, int64_t step, int64_t seed, int indexSeed, bool onlySampleUmbrellaGridpoint)
	Move the center point of the umbrella potential. More...

void	doSkippedUpdatesForAllPoints (const BiasParams &params)
	Do all previously skipped updates. Public for use by tests. More...

void	doSkippedUpdatesInNeighborhood (const BiasParams &params, const BiasGrid &grid)
	Do previously skipped updates in this neighborhood. More...

void	setCoordValue (const BiasGrid &grid, const awh_dvec coordValue)
	Update the reaction coordinate value. More...

void	updateFreeEnergyAndAddSamplesToHistogram (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, const BiasParams &params, const CorrelationGrid &forceCorrelation, double t, int64_t step, FILE fplog, std::vector< int > updateList)
	Performs an update of the bias. More...

double	updateProbabilityWeightsAndConvolvedBias (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, ArrayRef< const double > neighborLambdaEnergies, std::vector< double, AlignedAllocator< double >> *weight) const
	Update the probability weights and the convolved bias. More...

void	sampleProbabilityWeights (const BiasGrid &grid, ArrayRef< const double > probWeightNeighbor)
	Take samples of the current probability weights for future updates and analysis. More...

void	sampleCoordAndPmf (const std::vector< DimParams > &dimParams, const BiasGrid &grid, ArrayRef< const double > probWeightNeighbor, double convolvedBias)
	Sample the reaction coordinate and PMF for future updates or analysis. More...

double	calcConvolvedBias (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, const awh_dvec &coordValue) const
	Calculates the convolved bias for a given coordinate value. More...

void	getPmf (ArrayRef< float >) const
	Fills the given array with PMF values. More...

const CoordState &	coordState () const
	Returns the current coordinate state.

const std::vector< PointState > &	points () const
	Returns a const reference to the point state.

bool	inInitialStage () const
	Returns true if we are in the initial stage.

HistogramSize	histogramSize () const
	Returns the current histogram size.

void	setUmbrellaGridpointToGridpoint ()
	Sets the umbrella grid point to the current grid point.

void	updateSharedCorrelationTensorTimeIntegral (const BiasParams &biasParams, const CorrelationGrid &forceCorrelation, bool shareAcrossAllRanks)
	Updates sharedCorrelationTensorTimeIntegral_ for all points. More...

double	getSharedCorrelationTensorTimeIntegral (int gridPointIndex, int correlationTensorIndex) const
	Gets the time integral, shared across all ranks, of a tensor of a correlation grid point. More...

const std::vector< double > &	getSharedPointCorrelationIntegral (int gridPointIndex) const
	Gets the time integral (all tensors), shared across all ranks, of a correlation grid point. More...

Constructor & Destructor Documentation

gmx::BiasState::BiasState	(	const AwhBiasParams &	awhBiasParams,
		double	histogramSizeInitial,
		ArrayRef< const DimParams >	dimParams,
		const BiasGrid &	grid,
		const BiasSharing *	biasSharing
	)

Constructor.

Constructs the global state and the point states on a provided geometric grid passed in grid.

Parameters

[in]	awhBiasParams	The Bias parameters from inputrec.
[in]	histogramSizeInitial	The estimated initial histogram size. This is floating-point, since histograms use weighted entries and grow by a floating-point scaling factor.
[in]	dimParams	The dimension parameters.
[in]	grid	The bias grid.
[in]	biasSharing	Multisim bias sharing object, can be nullptrx

Member Function Documentation

void gmx::BiasState::broadcast ( const t_commrec * commRecord )

Broadcast the bias state over the MPI ranks in this simulation.

Parameters

[in] commRecord Struct for communication.

double gmx::BiasState::calcConvolvedBias	(	ArrayRef< const DimParams >	dimParams,
		const BiasGrid &	grid,
		const awh_dvec &	coordValue
	)		const

Calculates the convolved bias for a given coordinate value.

The convolved bias is the effective bias acting on the coordinate. Since the bias here has arbitrary normalization, this only makes sense as a relative, to other coordinate values, measure of the bias.

Note: If it turns out to be costly to calculate this pointwise the convolved bias for the whole grid could be returned instead.

Parameters

[in]	dimParams	The bias dimensions parameters
[in]	grid	The grid.
[in]	coordValue	Coordinate value.

Returns: the convolved bias >= -GMX_FLOAT_MAX.

void gmx::BiasState::calcConvolvedForce	(	ArrayRef< const DimParams >	dimParams,
		const BiasGrid &	grid,
		ArrayRef< const double >	probWeightNeighbor,
		ArrayRef< const double >	neighborLambdaDhdl,
		ArrayRef< double >	forceWorkBuffer,
		ArrayRef< double >	force
	)		const

Calculates and sets the convolved force acting on the coordinate.

The convolved force is the weighted sum of forces from umbrellas located at each point in the grid.

Parameters

[in]	dimParams	The bias dimensions parameters.
[in]	grid	The grid.
[in]	probWeightNeighbor	Probability weights of the neighbors.
[in]	neighborLambdaDhdl	An array containing the dHdL at the neighboring lambda points. The array is of length numLambdas+1, where numLambdas is the number of free energy lambda states. Element 0 in the array is the dHdL of the current state and elements 1..numLambdas contain the dHdL of the system in the neighboring lambda states (also including the current state). When there are no free energy lambda state dimensions this can be empty.
[in]	forceWorkBuffer	Force work buffer, values only used internally.
[in,out]	force	Bias force vector to set.

double gmx::BiasState::calcUmbrellaForceAndPotential	(	ArrayRef< const DimParams >	dimParams,
		const BiasGrid &	grid,
		int	point,
		ArrayRef< const double >	neighborLambdaDhdl,
		ArrayRef< double >	force
	)		const

Calculates and sets the force the coordinate experiences from an umbrella centered at the given point.

The umbrella potential is an harmonic potential given by 0.5k(coord value - point value)^2. This value is also returned.

Parameters

[in]	dimParams	The bias dimensions parameters.
[in]	grid	The grid.
[in]	point	Point for umbrella center.
[in]	neighborLambdaDhdl	An array containing the dHdL at the neighboring lambda points. The array is of length numLambdas+1, where numLambdas is the number of free energy lambda states. Element 0 in the array is the dHdL of the current state and elements 1..numLambdas contain the dHdL of the system in the neighboring lambda states (also including the current state). When there are no free energy lambda state dimensions this can be empty.
[in,out]	force	Force vector to set. Returns the umbrella potential.

void gmx::BiasState::doSkippedUpdatesForAllPoints ( const BiasParams & params )

Do all previously skipped updates. Public for use by tests.

Parameters

[in] params The bias parameters.

void gmx::BiasState::doSkippedUpdatesInNeighborhood	(	const BiasParams &	params,
		const BiasGrid &	grid
	)

Do previously skipped updates in this neighborhood.

Parameters

[in]	params	The bias parameters.
[in]	grid	The grid.

void gmx::BiasState::getPmf ( gmx::ArrayRef< float > pmf ) const

Fills the given array with PMF values.

Points outside of the biasing target region will get PMF = GMX_FLOAT_MAX.

Note: : The PMF is in single precision, because it is a statistical quantity and therefore never reaches full float precision.

Parameters

[out] pmf Array(ref) to be filled with the PMF values, should have the same size as the bias grid.

double gmx::BiasState::getSharedCorrelationTensorTimeIntegral	(	int	gridPointIndex,
		int	correlationTensorIndex
	)		const

Gets the time integral, shared across all ranks, of a tensor of a correlation grid point.

Parameters

[in]	gridPointIndex	The index of the grid point from which to retrieve the tensor volume.
[in]	correlationTensorIndex	The index of the tensor.

const std::vector< double > & gmx::BiasState::getSharedPointCorrelationIntegral ( int gridPointIndex ) const

Gets the time integral (all tensors), shared across all ranks, of a correlation grid point.

Parameters

[in] gridPointIndex The index of the grid point from which to retrieve the tensor volume.

void gmx::BiasState::initGridPointState	(	const AwhBiasParams &	awhBiasParams,
		ArrayRef< const DimParams >	dimParams,
		const BiasGrid &	grid,
		const BiasParams &	params,
		const CorrelationGrid &	forceCorrelation,
		const std::string &	filename,
		int	numBias
	)

Initialize the state of grid coordinate points.

Parameters

[in]	awhBiasParams	Bias parameters from inputrec.
[in]	dimParams	The dimension parameters.
[in]	grid	The grid.
[in]	params	The bias parameters.
[in]	forceCorrelation	The force correlation statistics for every grid point.
[in]	filename	Name of file to read PMF and target from.
[in]	numBias	The number of biases.

void gmx::BiasState::initHistoryFromState ( AwhBiasHistory * biasHistory ) const

Allocate and initialize a bias history with the given bias state.

This function will be called at the start of a new simulation. Note that this only sets the correct size and does produce a valid history object, but with all data set to zero. Actual history data is set by updateHistory.

Parameters

[in,out] biasHistory AWH history to initialize.

double gmx::BiasState::moveUmbrella	(	ArrayRef< const DimParams >	dimParams,
		const BiasGrid &	grid,
		ArrayRef< const double >	probWeightNeighbor,
		ArrayRef< const double >	neighborLambdaDhdl,
		ArrayRef< double >	biasForce,
		int64_t	step,
		int64_t	seed,
		int	indexSeed,
		bool	onlySampleUmbrellaGridpoint
	)

Move the center point of the umbrella potential.

A new umbrella center is sampled from the biased distibution. Also, the bias force is updated and the new potential is return.

This function should only be called when the bias force is not being convolved. It is assumed that the probability distribution has been updated.

Parameters

[in]	dimParams	Bias dimension parameters.
[in]	grid	The grid.
[in]	probWeightNeighbor	Probability weights of the neighbors.
[in]	neighborLambdaDhdl	An array containing the dHdL at the neighboring lambda points. The array is of length numLambdas+1, where numLambdas is the number of free energy lambda states. Element 0 in the array is the dHdL of the current state and elements 1..numLambdas contain the dHdL of the system in the neighboring lambda states (also including the current state). When there are no free energy lambda state dimensions this can be empty.
[in,out]	biasForce	The AWH bias force.
[in]	step	Step number, needed for the random number generator.
[in]	seed	Random seed.
[in]	indexSeed	Second random seed, should be the bias Index.
[in]	onlySampleUmbrellaGridpoint	Only sample the umbrella gridpoint without calculating force and potential.

Returns: the new potential value.

void gmx::BiasState::restoreFromHistory	(	const AwhBiasHistory &	biasHistory,
		const BiasGrid &	grid
	)

Restore the bias state from history.

Parameters

[in]	biasHistory	Bias history struct.
[in]	grid	The bias grid.

void gmx::BiasState::sampleCoordAndPmf	(	const std::vector< DimParams > &	dimParams,
		const BiasGrid &	grid,
		gmx::ArrayRef< const double >	probWeightNeighbor,
		double	convolvedBias
	)

Sample the reaction coordinate and PMF for future updates or analysis.

These samples do not affect the (future) sampling and are thus pure observables. Statisics of these are stored in the energy file.

Parameters

[in]	dimParams	The bias dimensions parameters
[in]	grid	The grid.
[in]	probWeightNeighbor	Probability weights of the neighbors.
[in]	convolvedBias	The convolved bias.

void gmx::BiasState::sampleProbabilityWeights	(	const BiasGrid &	grid,
		gmx::ArrayRef< const double >	probWeightNeighbor
	)

Take samples of the current probability weights for future updates and analysis.

Points in the current neighborhood will now have data meaning they need to be included in the local update list of the next update. Therefore, the local update range is also update here.

Parameters

[in]	grid	The grid.
[in]	probWeightNeighbor	Probability weights of the neighbors.

void gmx::BiasState::setCoordValue	(	const BiasGrid &	grid,
		const awh_dvec	coordValue
	)

inline

Update the reaction coordinate value.

Parameters

[in]	grid	The bias grid.
[in]	coordValue	The current reaction coordinate value (there are no limits on allowed values).

void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram	(	ArrayRef< const DimParams >	dimParams,
		const BiasGrid &	grid,
		const BiasParams &	params,
		const CorrelationGrid &	forceCorrelation,
		double	t,
		int64_t	step,
		FILE *	fplog,
		std::vector< int > *	updateList
	)

Performs an update of the bias.

The objective of the update is to use collected samples (probability weights) to improve the free energy estimate. For sake of efficiency, the update is local whenever possible, meaning that only points that have actually been sampled are accessed and updated here. For certain AWH settings or at certain steps however, global need to be performed. Besides the actual free energy update, this function takes care of ensuring future convergence of the free energy. Convergence is obtained by increasing the size of the reference weight histogram in a controlled (sometimes dynamic) manner. Also, there are AWH variables that are direct functions of the free energy or sampling history that need to be updated here, namely the target distribution and the bias function.

Parameters

[in]	dimParams	The dimension parameters.
[in]	grid	The grid.
[in]	params	The bias parameters.
[in]	forceCorrelation	The force correlation statistics for every grid point.
[in]	t	Time.
[in]	step	Time step.
[in,out]	fplog	Log file.
[in,out]	updateList	Work space to store a temporary list.

void gmx::BiasState::updateHistory	(	AwhBiasHistory *	biasHistory,
		const BiasGrid &	grid
	)		const

Update the bias state history with the current state.

Parameters

[out]	biasHistory	Bias history struct.
[in]	grid	The bias grid.

double gmx::BiasState::updateProbabilityWeightsAndConvolvedBias	(	ArrayRef< const DimParams >	dimParams,
		const BiasGrid &	grid,
		ArrayRef< const double >	neighborLambdaEnergies,
		std::vector< double, AlignedAllocator< double >> *	weight
	)		const

Update the probability weights and the convolved bias.

Given a coordinate value, each grid point is assigned a probability weight, w(point|value), that depends on the current bias function. The sum of these weights is needed for normalizing the probability sum to 1 but also equals the effective, or convolved, biasing weight for this coordinate value. The convolved bias is needed e.g. for extracting the PMF, so we save it here since this saves us from doing extra exponential function evaluations later on.

Parameters

[in]	dimParams	The bias dimensions parameters
[in]	grid	The grid.
[in]	neighborLambdaEnergies	An array containing the energy of the system in neighboring lambdas. The array is of length numLambdas+1, where numLambdas is the number of free energy lambda states. Element 0 in the array is the energy of the current state and elements 1..numLambdas contain the energy of the system in the neighboring lambda states (also including the current state). When there are no free energy lambda state dimensions this can be empty.
[out]	weight	Probability weights of the neighbors, SIMD aligned.

Returns: the convolved bias.

void gmx::BiasState::updateSharedCorrelationTensorTimeIntegral	(	const BiasParams &	biasParams,
		const CorrelationGrid &	forceCorrelation,
		bool	shareAcrossAllRanks
	)

Updates sharedCorrelationTensorTimeIntegral_ for all points.

Parameters

[in]	biasParams	The bias parameters.
[in]	forceCorrelation	The force correlation grid.
[in]	shareAcrossAllRanks	Share the data across all ranks? Otherwise only the main ranks.

int gmx::BiasState::warnForHistogramAnomalies	(	const BiasGrid &	grid,
		int	biasIndex,
		double	t,
		FILE *	fplog,
		int	maxNumWarnings
	)		const

Performs statistical checks on the collected histograms and warns if issues are detected.

Parameters

[in]	grid	The grid.
[in]	biasIndex	The index of the bias we are checking for.
[in]	t	Time.
[in,out]	fplog	Output file for warnings.
[in]	maxNumWarnings	Don't issue more than this number of warnings.

Returns: the number of warnings issued.

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

src/gromacs/applied_forces/awh/biasstate.h
src/gromacs/applied_forces/awh/biasstate.cpp

Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation