#include <ReferenceArguments.h>

Inheritance diagram for PLMD::ReferenceArguments:

[legend]

Public Member Functions
	ReferenceArguments (const ReferenceConfigurationOptions &ro)

virtual double	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 =0
	Calculate the distance from the reference configuration. More...

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...

virtual bool	pcaIsEnabledForThisReference ()
	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

virtual void	read (const PDB &)=0
	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...

virtual void	setupPCAStorage (ReferenceValuePack &mypack)
	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...

Friends
class	Direction

class	ReferenceConfiguration

Detailed Description

In many applications (e.g. paths, fields, property maps) it is necessary to calculate the distance between two configurations. These distances can be calculated in a variety of different ways. For instance, one can assert that the distance between the two configuration is the distance one would have to move all the atoms to transform configuration 1 into configuration

Alternatively, one could calculate the values of a large set of collective coordinates in the two configurations and then calculate the Euclidean distances between these two points in the resulting high-dimensional vector space. Lastly, one can combine these two forms of distance calculation to calculate a hybrid distance. Plumed allows one to use all these forms of distance calculations and also to implement new forms of distance. You should inherit from this class if your distance involves reference colvar values. This class and PLMD::ReferenceAtoms mirror the functionalities in PLMD::ActionWithArguments and PLMD::ActionAtomistic respectively but for distances.

Constructor & Destructor Documentation

◆ ReferenceArguments()

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

explicit

Member Function Documentation

◆ calc()

virtual double PLMD::ReferenceConfiguration::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

pure virtualinherited

Calculate the distance from the reference configuration.

Implemented in PLMD::Direction, PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::SingleDomainRMSD, and PLMD::FakeFrame.

◆ calculate()

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

virtual

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
	)

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

virtual

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 ( )

inlineoverridevirtual

Return names.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getArgumentRequests()

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

overridevirtual

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

inlineoverridevirtual

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

inlineoverridevirtual

Get the value of the ith reference argument.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArguments()

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

inlineoverridevirtual

Return all the reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceMetric()

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

overridevirtual

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 )

Set the positions of the reference arguments.

◆ pcaIsEnabledForThisReference()

virtual bool PLMD::ReferenceConfiguration::pcaIsEnabledForThisReference ( )

inlinevirtualinherited

Stuff for pca.

Reimplemented in PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.

◆ projectArgDisplacementOnVector()

double PLMD::ReferenceArguments::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.

◆ projectDisplacementOnVector()

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

inherited

◆ read()

virtual void PLMD::ReferenceConfiguration::read ( const PDB & )

pure virtualinherited

Do all local business for setting the configuration.

Implemented in PLMD::ArgumentOnlyDistance, PLMD::IntermolecularDRMSD, PLMD::IntramolecularDRMSD, PLMD::DRMSD, PLMD::MultiDomainRMSD, PLMD::Direction, PLMD::OptimalRMSD, PLMD::FakeFrame, PLMD::SimpleRMSD, and PLMD::DotProductDistance.

◆ readArgumentsFromPDB()

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

protected

Read in the atoms from the pdb file.

◆ setReferenceArguments() [1/2]

void PLMD::ReferenceArguments::setReferenceArguments ( )

protected

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
	)

Set the positions of the reference arguments.

◆ setupPCAStorage()

virtual void PLMD::ReferenceConfiguration::setupPCAStorage ( ReferenceValuePack & mypack )

inlinevirtualinherited

Stuff to setup pca.

Reimplemented in PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.

Friends And Related Function Documentation

◆ Direction

friend class Direction

friend

◆ ReferenceConfiguration

friend class ReferenceConfiguration

friend

Member Data Documentation

◆ arg_der_index

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

private

The indices for setting derivatives.

◆ arg_names

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

private

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

protected

Are we calculating a Malanobius distance.

◆ hasweights

bool PLMD::ReferenceArguments::hasweights

protected

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

private

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

private

The values of the colvars in the reference configuration.

◆ sqrtweight

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

private

◆ trig_metric

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

private

◆ weights

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

private

The weights for normed euclidean distance.

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

reference/ReferenceArguments.h
reference/ReferenceArguments.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ ReferenceArguments()

Member Function Documentation

◆ calc()

◆ calculate()

◆ 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()

Friends And Related Function Documentation

◆ Direction

◆ ReferenceConfiguration

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