ForeignLambdaTerms Class Reference

#include <gromacs/mdtypes/enerdata.h>

Description

Accumulates free-energy foreign lambda energies and dH/dlamba.

Public Member Functions
	ForeignLambdaTerms (const gmx::EnumerationArray< FreeEnergyPerturbationCouplingType, std::vector< double >> *allLambdas)
	Constructor. More...
int	numLambdas () const
	Returns the number of foreign lambda values.
gmx::ArrayRef< const double >	foreignLambdas (FreeEnergyPerturbationCouplingType couplingType)
	Returns the foreign lambda values for the given perturbation type.
double	deltaH (int lambdaIndex) const
	Returns the H(lambdaIndex) - H(lambda_current)
gmx::ArrayRef< double >	energies ()
	Returns a list of partial energies, the part which depends on lambda), current lambda in entry 0, foreign lambda i in entry 1+i. More...
gmx::ArrayRef< const double >	energies () const
	Returns a list of partial energies, the part which depends on lambda), current lambda in entry 0, foreign lambda i in entry 1+i. More...
void	accumulate (int listIndex, FreeEnergyPerturbationCouplingType couplingType, double energy, real dvdl)
	Adds an energy and dV/dl constribution to lambda list index listIndex. More...
void	accumulate (int listIndex, double energy, const gmx::EnumerationArray< FreeEnergyPerturbationCouplingType, real > &dvdl)
	Adds an energy and dV/dl constribution to lambda list index listIndex. More...
void	finalizePotentialContributions (const gmx::EnumerationArray< FreeEnergyPerturbationCouplingType, double > &dvdlLinear, gmx::ArrayRef< const real > lambda, const t_lambda &fepvals)
	Finalizes the potential (non-kinetic) terms. More...
void	finalizeKineticContributions (const gmx::EnumerationArray< InteractionFunction, real > &energyTerms, double dhdlMass, gmx::ArrayRef< const real > lambda, const t_lambda &fepvals)
	Accumulates the kinetic and constraint free-energy contributions. More...
std::pair< std::vector< double > , std::vector< double > >	getTerms (const gmx::MpiComm &mpiComm) const
	Returns a pair of lists of deltaH and dH/dlambda. More...
void	zeroAllTerms ()
	Sets all terms to 0.

Constructor & Destructor Documentation

ForeignLambdaTerms::ForeignLambdaTerms

(

const gmx::EnumerationArray< FreeEnergyPerturbationCouplingType, std::vector< double >> *

allLambdas

)

Constructor.

Parameters

[in]

allLambdas

The list of lambda values for all lambda components, can be nullptr

Member Function Documentation

void ForeignLambdaTerms::accumulate ( int  listIndex, FreeEnergyPerturbationCouplingType  couplingType, double  energy, real  dvdl  )

inline

Adds an energy and dV/dl constribution to lambda list index listIndex.

This should only be used for terms with non-linear dependence on lambda The value passed as listIndex should be 0 for the current lambda and 1+i for foreign lambda index i.

void ForeignLambdaTerms::accumulate ( int  listIndex, double  energy, const gmx::EnumerationArray< FreeEnergyPerturbationCouplingType, real > &  dvdl  )

inline

Adds an energy and dV/dl constribution to lambda list index listIndex.

This should only be used for terms with non-linear dependence on lambda The value passed as listIndex should be 0 for the current lambda and 1+i for foreign lambda index i.

gmx::ArrayRef<double> ForeignLambdaTerms::energies ( )

inline

Returns a list of partial energies, the part which depends on lambda), current lambda in entry 0, foreign lambda i in entry 1+i.

Note: the potential terms needs to be finalized before calling this method.

gmx::ArrayRef<const double> ForeignLambdaTerms::energies ( ) const

inline

Returns a list of partial energies, the part which depends on lambda), current lambda in entry 0, foreign lambda i in entry 1+i.

Note: the potential terms needs to be finalized before calling this method.

void ForeignLambdaTerms::finalizeKineticContributions	(	const gmx::EnumerationArray< InteractionFunction, real > &	energyTerms,
		double	dhdlMass,
		gmx::ArrayRef< const real >	lambda,
		const t_lambda &	fepvals
	)

Accumulates the kinetic and constraint free-energy contributions.

Parameters

[in]	energyTerms	List of energy terms, pass term in gmx_enerdata_t
[in]	dhdlMass	The mass dependent contribution to dH/dlambda
[in]	lambda	Lambda values for the efptNR contribution types
[in]	fepvals	Free-energy parameters

void ForeignLambdaTerms::finalizePotentialContributions	(	const gmx::EnumerationArray< FreeEnergyPerturbationCouplingType, double > &	dvdlLinear,
		gmx::ArrayRef< const real >	lambda,
		const t_lambda &	fepvals
	)

Finalizes the potential (non-kinetic) terms.

Note: This can be called multiple times during the same force calculations without affecting the results.

Parameters

[in]	dvdlLinear	List of dV/dlambda contributions of size efptNR with depend linearly on lambda
[in]	lambda	Lambda values for the efptNR contribution types
[in]	fepvals	Free-energy parameters

std::pair< std::vector< double >, std::vector< double > > ForeignLambdaTerms::getTerms

(

const gmx::MpiComm &

mpiComm

)

const

Returns a pair of lists of deltaH and dH/dlambda.

Both lists are of size numLambdas() and are indexed with the lambda index.

Note: should only be called after the object has been finalized by a call to accumulateLinearPotentialComponents() (is asserted).

Parameters

[in]

mpiComm

Communication object for my group

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

• src/gromacs/mdtypes/enerdata.h
• src/gromacs/mdlib/enerdata_utils.cpp