Inheritance diagram for PLMD::NormalizedEuclideanDistance:

[legend]

Public Member Functions
	NormalizedEuclideanDistance (const ReferenceConfigurationOptions &ro)

double	calc (const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &myder, const bool &squared) const override
	Calculate the distance from the reference configuration. More...

double	calculate (const std::vector< Value * > &vals, ReferenceValuePack &myder, const bool &squared) const

double	calculate (const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value * > &vals, ReferenceValuePack &myder, const bool &squared=false) const
	Calculate the distance from the reference configuration. More...

virtual double	calculateArgumentDistance (const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &myder, const bool &squared) const
	Calculate the euclidean/malanobius distance the atoms have moved from the reference configuration in CV space. More...

void	copyDerivatives (const ReferenceConfiguration *)
	Parse something from the pdb remarks Copy derivatives from one frame to this frame. More...

void	displaceReferenceArguments (const double &weight, const std::vector< double > &displace)
	Displace the positions of the reference atoms. More...

void	displaceReferenceConfiguration (const double &weight, Direction &dir)
	Move the reference configuration by an amount specified using a Direction. More...

virtual void	extractArgumentDisplacement (const std::vector< Value * > &vals, const std::vector< double > &arg, std::vector< double > &dirout) const
	Extract the displacement from a position in a space. More...

void	extractDisplacementVector (const std::vector< Vector > &pos, const std::vector< Value * > &vals, const std::vector< double > &arg, const bool &nflag, Direction &mydir) const
	Extract a Direction giving you the displacement from some position. More...

virtual const std::vector< AtomNumber > &	getAbsoluteIndexes ()
	These are overwritten in ReferenceArguments and ReferenceAtoms to make frame copying work. More...

const std::vector< std::string > &	getArgumentNames () override
	Return names. More...

void	getArgumentRequests (std::vector< std::string > &, bool disable_checks=false) override
	Get the arguments required. More...

virtual void	getAtomRequests (std::vector< AtomNumber > &, bool disable_checks=false)
	Retrieve the atoms that are required for this guy. More...

std::string	getName () const
	Return the name of this metric. More...

unsigned	getNumberOfReferenceArguments () const override
	Get the number of reference arguments. More...

virtual unsigned	getNumberOfReferencePositions () const

double	getReferenceArgument (const unsigned &i) const override
	Get the value of the ith reference argument. More...

const std::vector< double > &	getReferenceArguments () const override
	Return all the reference arguments. More...

const std::vector< double > &	getReferenceMetric () override

virtual const std::vector< Vector > &	getReferencePositions () const
	These are overwritten in ReferenceArguments and ReferenceAtoms but are required here to make PLMD::distance work. More...

void	moveReferenceArguments (const std::vector< double > &arg_vals)
	Set the positions of the reference arguments. More...

bool	pcaIsEnabledForThisReference () override
	Stuff for pca. More...

double	projectArgDisplacementOnVector (const std::vector< double > &eigv, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const
	Project the displacement of the arguments on a vector. More...

double	projectDisplacementOnVector (const Direction &mydir, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const

void	read (const PDB &pdb) override
	Do all local business for setting the configuration. More...

void	setReferenceArguments (const std::vector< double > &arg_vals, const std::vector< double > &sigma)
	Set the positions of the reference arguments. More...

void	setupPCAStorage (ReferenceValuePack &mypack) override
	Stuff to setup pca. More...

Protected Member Functions
void	error (const std::string &msg)
	Crash with an error. More...

void	readArgumentsFromPDB (const PDB &pdb)
	Read in the atoms from the pdb file. More...

void	setReferenceArguments ()
	Set the values of the colvars based on their current instantanous values (used in Analysis) More...

Protected Attributes
bool	hasmetric
	Are we calculating a Malanobius distance. More...

bool	hasweights
	Are we reading weights from input. More...

Private Attributes
std::vector< unsigned >	arg_der_index
	The indices for setting derivatives. More...

std::vector< std::string >	arg_names
	The names of the arguments. More...

std::vector< std::string >	fake_arg_names

std::vector< AtomNumber >	fake_atom_numbers
	These are used to do fake things when we copy frames. More...

std::vector< double >	fake_metric

std::vector< double >	fake_refargs

std::vector< Vector >	fake_refatoms
	These are use by the distance function above. More...

std::vector< std::string >	line
	A vector containing all the remarks from the pdb input. More...

Matrix< double >	metric
	The N X N matrix we are using to calculate our Malanobius distance. More...

std::string	name
	The name of this particular config. More...

std::vector< double >	reference_args
	The values of the colvars in the reference configuration. More...

std::vector< double >	sqrtweight

std::vector< double >	trig_metric

std::vector< double >	weights
	The weights for normed euclidean distance. More...

Constructor & Destructor Documentation

◆ NormalizedEuclideanDistance()

PLMD::NormalizedEuclideanDistance::NormalizedEuclideanDistance ( const ReferenceConfigurationOptions & ro )

explicit

Member Function Documentation

◆ calc()

double PLMD::ArgumentOnlyDistance::calc	(	const std::vector< Vector > &	pos,
		const Pbc &	pbc,
		const std::vector< Value * > &	vals,
		const std::vector< double > &	args,
		ReferenceValuePack &	myder,
		const bool &	squared
	)		const

overridevirtualinherited

Calculate the distance from the reference configuration.

Implements PLMD::ReferenceConfiguration.

◆ calculate() [1/2]

double PLMD::ArgumentOnlyDistance::calculate	(	const std::vector< Value * > &	vals,
		ReferenceValuePack &	myder,
		const bool &	squared
	)		const

inherited

◆ calculate() [2/2]

double PLMD::ReferenceConfiguration::calculate	(	const std::vector< Vector > &	pos,
		const Pbc &	pbc,
		const std::vector< Value * > &	vals,
		ReferenceValuePack &	myder,
		const bool &	squared = `false`
	)		const

inherited

Calculate the distance from the reference configuration.

◆ calculateArgumentDistance()

double PLMD::ReferenceArguments::calculateArgumentDistance	(	const std::vector< Value * > &	vals,
		const std::vector< double > &	arg,
		ReferenceValuePack &	myder,
		const bool &	squared
	)		const

virtualinherited

Calculate the euclidean/malanobius distance the atoms have moved from the reference configuration in CV space.

Reimplemented in PLMD::DotProductDistance.

◆ copyDerivatives()

void PLMD::ReferenceConfiguration::copyDerivatives ( const ReferenceConfiguration * )

inherited

Parse something from the pdb remarks Copy derivatives from one frame to this frame.

◆ displaceReferenceArguments()

void PLMD::ReferenceArguments::displaceReferenceArguments	(	const double &	weight,
		const std::vector< double > &	displace
	)

inherited

Displace the positions of the reference atoms.

◆ displaceReferenceConfiguration()

void PLMD::ReferenceConfiguration::displaceReferenceConfiguration	(	const double &	weight,
		Direction &	dir
	)

inherited

Move the reference configuration by an amount specified using a Direction.

◆ error()

void PLMD::ReferenceConfiguration::error ( const std::string & msg )

protectedinherited

Crash with an error.

◆ extractArgumentDisplacement()

void PLMD::ReferenceArguments::extractArgumentDisplacement	(	const std::vector< Value * > &	vals,
		const std::vector< double > &	arg,
		std::vector< double > &	dirout
	)		const

virtualinherited

Extract the displacement from a position in a space.

Reimplemented in PLMD::Direction.

◆ extractDisplacementVector()

void PLMD::ReferenceConfiguration::extractDisplacementVector	(	const std::vector< Vector > &	pos,
		const std::vector< Value * > &	vals,
		const std::vector< double > &	arg,
		const bool &	nflag,
		Direction &	mydir
	)		const

inherited

Extract a Direction giving you the displacement from some position.

◆ getAbsoluteIndexes()

const std::vector< AtomNumber > & PLMD::ReferenceConfiguration::getAbsoluteIndexes ( )

inlinevirtualinherited

These are overwritten in ReferenceArguments and ReferenceAtoms to make frame copying work.

Reimplemented in PLMD::ReferenceAtoms.

◆ getArgumentNames()

const std::vector< std::string > & PLMD::ReferenceArguments::getArgumentNames ( )

inlineoverridevirtualinherited

Return names.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getArgumentRequests()

void PLMD::ReferenceArguments::getArgumentRequests	(	std::vector< std::string > &	argout,
		bool	disable_checks = `false`
	)

overridevirtualinherited

Get the arguments required.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getAtomRequests()

virtual void PLMD::ReferenceConfiguration::getAtomRequests	(	std::vector< AtomNumber > &	,
		bool	disable_checks = `false`
	)

inlinevirtualinherited

Retrieve the atoms that are required for this guy.

Reimplemented in PLMD::ReferenceAtoms.

◆ getName()

std::string PLMD::ReferenceConfiguration::getName ( ) const

inherited

Return the name of this metric.

◆ getNumberOfReferenceArguments()

unsigned PLMD::ReferenceArguments::getNumberOfReferenceArguments ( ) const

inlineoverridevirtualinherited

Get the number of reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getNumberOfReferencePositions()

unsigned PLMD::ReferenceConfiguration::getNumberOfReferencePositions ( ) const

inlinevirtualinherited

Reimplemented in PLMD::ReferenceAtoms.

◆ getReferenceArgument()

double PLMD::ReferenceArguments::getReferenceArgument ( const unsigned & i ) const

inlineoverridevirtualinherited

Get the value of the ith reference argument.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArguments()

const std::vector< double > & PLMD::ReferenceArguments::getReferenceArguments ( ) const

inlineoverridevirtualinherited

Return all the reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceMetric()

const std::vector< double > & PLMD::ReferenceArguments::getReferenceMetric ( )

overridevirtualinherited

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferencePositions()

const std::vector< Vector > & PLMD::ReferenceConfiguration::getReferencePositions ( ) const

inlinevirtualinherited

These are overwritten in ReferenceArguments and ReferenceAtoms but are required here to make PLMD::distance work.

Reimplemented in PLMD::ReferenceAtoms.

◆ moveReferenceArguments()

void PLMD::ReferenceArguments::moveReferenceArguments ( const std::vector< double > & arg_vals )

inherited

Set the positions of the reference arguments.

◆ pcaIsEnabledForThisReference()

bool PLMD::ArgumentOnlyDistance::pcaIsEnabledForThisReference ( )

inlineoverridevirtualinherited

Stuff for pca.

Reimplemented from PLMD::ReferenceConfiguration.

◆ projectArgDisplacementOnVector()

double PLMD::ReferenceArguments::projectArgDisplacementOnVector	(	const std::vector< double > &	eigv,
		const std::vector< Value * > &	vals,
		const std::vector< double > &	arg,
		ReferenceValuePack &	mypack
	)		const

inherited

Project the displacement of the arguments on a vector.

◆ projectDisplacementOnVector()

double PLMD::ReferenceConfiguration::projectDisplacementOnVector	(	const Direction &	mydir,
		const std::vector< Value * > &	vals,
		const std::vector< double > &	arg,
		ReferenceValuePack &	mypack
	)		const

inherited

◆ read()

void PLMD::ArgumentOnlyDistance::read ( const PDB & )

overridevirtualinherited

Do all local business for setting the configuration.

Implements PLMD::ReferenceConfiguration.

Reimplemented in PLMD::DotProductDistance.

◆ readArgumentsFromPDB()

void PLMD::ReferenceArguments::readArgumentsFromPDB ( const PDB & pdb )

protectedinherited

Read in the atoms from the pdb file.

◆ setReferenceArguments() [1/2]

void PLMD::ReferenceArguments::setReferenceArguments ( )

protectedinherited

Set the values of the colvars based on their current instantanous values (used in Analysis)

◆ setReferenceArguments() [2/2]

void PLMD::ReferenceArguments::setReferenceArguments	(	const std::vector< double > &	arg_vals,
		const std::vector< double > &	sigma
	)

inherited

Set the positions of the reference arguments.

◆ setupPCAStorage()

void PLMD::ArgumentOnlyDistance::setupPCAStorage ( ReferenceValuePack & mypack )

inlineoverridevirtualinherited

Stuff to setup pca.

Reimplemented from PLMD::ReferenceConfiguration.

Member Data Documentation

◆ arg_der_index

std::vector<unsigned> PLMD::ReferenceArguments::arg_der_index

privateinherited

The indices for setting derivatives.

◆ arg_names

std::vector<std::string> PLMD::ReferenceArguments::arg_names

privateinherited

The names of the arguments.

◆ fake_arg_names

std::vector<std::string> PLMD::ReferenceConfiguration::fake_arg_names

privateinherited

◆ fake_atom_numbers

std::vector<AtomNumber> PLMD::ReferenceConfiguration::fake_atom_numbers

privateinherited

These are used to do fake things when we copy frames.

◆ fake_metric

std::vector<double> PLMD::ReferenceConfiguration::fake_metric

privateinherited

◆ fake_refargs

std::vector<double> PLMD::ReferenceConfiguration::fake_refargs

privateinherited

◆ fake_refatoms

std::vector<Vector> PLMD::ReferenceConfiguration::fake_refatoms

privateinherited

These are use by the distance function above.

◆ hasmetric

bool PLMD::ReferenceArguments::hasmetric

protectedinherited

Are we calculating a Malanobius distance.

◆ hasweights

bool PLMD::ReferenceArguments::hasweights

protectedinherited

Are we reading weights from input.

◆ line

std::vector<std::string> PLMD::ReferenceConfiguration::line

privateinherited

A vector containing all the remarks from the pdb input.

◆ metric

Matrix<double> PLMD::ReferenceArguments::metric

privateinherited

The N X N matrix we are using to calculate our Malanobius distance.

◆ name

std::string PLMD::ReferenceConfiguration::name

privateinherited

The name of this particular config.

◆ reference_args

std::vector<double> PLMD::ReferenceArguments::reference_args

privateinherited

The values of the colvars in the reference configuration.

◆ sqrtweight

std::vector<double> PLMD::ReferenceArguments::sqrtweight

privateinherited

◆ trig_metric

std::vector<double> PLMD::ReferenceArguments::trig_metric

privateinherited

◆ weights

std::vector<double> PLMD::ReferenceArguments::weights

privateinherited

The weights for normed euclidean distance.

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

reference/NormalizedEuclideanDistance.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Constructor & Destructor Documentation

◆ NormalizedEuclideanDistance()

Member Function Documentation

◆ calc()

◆ calculate() [1/2]

◆ calculate() [2/2]

◆ calculateArgumentDistance()

◆ copyDerivatives()

◆ displaceReferenceArguments()

◆ displaceReferenceConfiguration()

◆ error()

◆ extractArgumentDisplacement()

◆ extractDisplacementVector()

◆ getAbsoluteIndexes()

◆ getArgumentNames()

◆ getArgumentRequests()

◆ getAtomRequests()

◆ getName()

◆ getNumberOfReferenceArguments()

◆ getNumberOfReferencePositions()

◆ getReferenceArgument()

◆ getReferenceArguments()

◆ getReferenceMetric()

◆ getReferencePositions()

◆ moveReferenceArguments()

◆ pcaIsEnabledForThisReference()

◆ projectArgDisplacementOnVector()

◆ projectDisplacementOnVector()

◆ read()

◆ readArgumentsFromPDB()

◆ setReferenceArguments() [1/2]

◆ setReferenceArguments() [2/2]

◆ setupPCAStorage()

Member Data Documentation

◆ arg_der_index

◆ arg_names

◆ fake_arg_names

◆ fake_atom_numbers

◆ fake_metric

◆ fake_refargs

◆ fake_refatoms

◆ hasmetric

◆ hasweights

◆ line

◆ metric

◆ name

◆ reference_args

◆ sqrtweight

◆ trig_metric

◆ weights