#include <gromacs/awh/pointstate.h>

Description

The state of a coordinate point.

This class contains all the state variables of a coordinate point (on the bias grid) and methods to update the state of a point.

Public Member Functions
	PointState ()
	Constructs a point state with default values.

void	setFromHistory (const AwhPointStateHistory &psh)
	Set all values in the state to those from a history. More...

void	storeState (AwhPointStateHistory *psh) const
	Store the state of a point in a history struct. More...

bool	inTargetRegion () const
	Query if the point is in the target region. More...

double	bias () const
	Return the bias function estimate.

void	setTargetToZero ()
	Set the target to zero and the bias to minus infinity.

double	freeEnergy () const
	Return the free energy.

void	setFreeEnergy (double freeEnergy)
	Set the free energy, only to be used at initialization. More...

double	target () const
	Return the target distribution value.

double	weightSumIteration () const
	Return the weight accumulated since the last update.

void	increaseWeightSumIteration (double weight)
	Increases the weight accumulated since the last update. More...

double	weightSumTot () const
	Returns the accumulated weight.

double	weightSumRef () const
	Return the reference weight histogram.

double	logPmfSum () const
	Return log(PmfSum).

void	setLogPmfSum (double logPmfSum)
	Set log(PmfSum). More...

double	numVisitsIteration () const
	Return the number of visits since the last update.

double	numVisitsTot () const
	Return the total number of visits.

void	setTargetConstantWeight (double targetConstantWeight)
	Set the constant target weight factor. More...

void	updateBias ()
	Updates the bias of a point.

void	setInitialReferenceWeightHistogram (double histogramSize)
	Set the initial reference weighthistogram. More...

void	normalizeFreeEnergyAndPmfSum (double minimumFreeEnergy)
	Correct free energy and PMF sum for the change in minimum. More...

bool	performPreviouslySkippedUpdates (const BiasParams &params, gmx_int64_t numUpdates, double weighthistScaling, double logPmfSumScaling)
	Apply previous updates that were skipped. More...

void	updateWithNewSampling (const BiasParams &params, gmx_int64_t numUpdates, double weighthistScaling, double logPmfSumScaling)
	Apply a point update with new sampling. More...

void	samplePmf (double convolvedBias)
	Update the PMF histogram with the current coordinate value. More...

double	updateTargetWeight (const BiasParams &params, double freeEnergyCutoff)
	Update the target weight of a point. More...

void	setPartialWeightAndCount (double weightSum, double numVisits)
	Set the weight and count accumulated since the last update. More...

void	addPartialWeightAndCount ()
	Add the weights and counts accumulated between updates.

void	scaleTarget (double scaleFactor)
	Scale the target weight of the point. More...

Member Function Documentation

void gmx::PointState::increaseWeightSumIteration ( double weight )

inline

Increases the weight accumulated since the last update.

Parameters

[in] weight The amount to add to the weight

bool gmx::PointState::inTargetRegion ( ) const

inline

Query if the point is in the target region.

Returns: true if the point is in the target region.

void gmx::PointState::normalizeFreeEnergyAndPmfSum ( double minimumFreeEnergy )

inline

Correct free energy and PMF sum for the change in minimum.

Parameters

[in] minimumFreeEnergy The free energy at the minimum;

bool gmx::PointState::performPreviouslySkippedUpdates	(	const BiasParams &	params,
		gmx_int64_t	numUpdates,
		double	weighthistScaling,
		double	logPmfSumScaling
	)

inline

Apply previous updates that were skipped.

An update can only be skipped if the parameters needed for the update are constant or deterministic so that the same update can be performed at a later time. Here, the necessary parameters are the sampled weight and scaling factors for the histograms. The scaling factors are provided as arguments only to avoid recalculating them for each point

The last update index is also updated here.

Parameters

[in]	params	The AWH bias parameters.
[in]	numUpdates	The global number of updates.
[in]	weighthistScaling	Scale factor for the reference weight histogram.
[in]	logPmfSumScaling	Scale factor for the reference PMF histogram.

Returns: true if at least one update was applied.

void gmx::PointState::samplePmf ( double convolvedBias )

Update the PMF histogram with the current coordinate value.

Parameters

[in] convolvedBias The convolved bias.

void gmx::PointState::scaleTarget ( double scaleFactor )

inline

Scale the target weight of the point.

Parameters

[in] scaleFactor Factor to scale with.

void gmx::PointState::setFreeEnergy ( double freeEnergy )

inline

Set the free energy, only to be used at initialization.

Parameters

[in] freeEnergy The free energy.

void gmx::PointState::setFromHistory ( const AwhPointStateHistory & psh )

inline

Set all values in the state to those from a history.

Parameters

[in] psh Coordinate point history to copy from.

void gmx::PointState::setInitialReferenceWeightHistogram ( double histogramSize )

inline

Set the initial reference weighthistogram.

Parameters

[in] histogramSize The weight histogram size.

void gmx::PointState::setLogPmfSum ( double logPmfSum )

inline

Set log(PmfSum).

TODO: Replace this setter function with a more elegant solution.

Parameters

[in] logPmfSum The log(PmfSum).

void gmx::PointState::setPartialWeightAndCount	(	double	weightSum,
		double	numVisits
	)

inline

Set the weight and count accumulated since the last update.

Parameters

[in]	weightSum	The weight-sum value
[in]	numVisits	The number of visits

void gmx::PointState::setTargetConstantWeight ( double targetConstantWeight )

inline

Set the constant target weight factor.

Parameters

[in] targetConstantWeight The target weight factor.

void gmx::PointState::storeState ( AwhPointStateHistory * psh ) const

inline

Store the state of a point in a history struct.

Parameters

[in,out] psh Coordinate point history to copy to.

double gmx::PointState::updateTargetWeight	(	const BiasParams &	params,
		double	freeEnergyCutoff
	)

inline

Update the target weight of a point.

Note that renormalization over all points is needed after the update.

Parameters

[in]	params	The AWH bias parameters.
[in]	freeEnergyCutoff	The cut-off for the free energy for target type "cutoff".

Returns: the updated value of the target.

void gmx::PointState::updateWithNewSampling	(	const BiasParams &	params,
		gmx_int64_t	numUpdates,
		double	weighthistScaling,
		double	logPmfSumScaling
	)

inline

Apply a point update with new sampling.

Note: The last update index is also updated here.; The new sampling containers are cleared here.

Parameters

[in]	params	The AWH bias parameters.
[in]	numUpdates	The global number of updates.
[in]	weighthistScaling	Scaling factor for the reference weight histogram.
[in]	logPmfSumScaling	Log of the scaling factor for the PMF histogram.

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

src/gromacs/awh/pointstate.h
src/gromacs/awh/pointstate.cpp

Description

Public Member Functions

Member Function Documentation