In many applications (e.g. More...

#include <ReferenceArguments.h>

Inheritance diagram for PLMD::ReferenceArguments:

[legend]

Public Member Functions
	ReferenceArguments (const ReferenceConfigurationOptions &ro)

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

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

void	setArgumentNames (const std::vector< std::string > &arg_vals)
	Set the names of the arguments. More...

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

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

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

void	printArguments (OFile &ofile, const std::string &fmt) const
	Print the arguments out. More...

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

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

const std::vector< std::string > &	getArgumentNames ()
	Return names. 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	displaceReferenceArguments (const double &weight, const std::vector< double > &displace)
	Displace the positions of the reference atoms. 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...

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...

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

virtual unsigned	getNumberOfReferencePositions () const

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

virtual void	set (const PDB &)
	Set the final number of arguments. More...

virtual void	read (const PDB &)=0
	Do all local business for setting the configuration. More...

void	setWeight (const double &ww)
	Set the weight for this frame. More...

double	getWeight () const
	Return the weight for this frame. 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	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...

template<class T >
bool	parse (const std::string &key, T &t, bool ignore_missing=false)
	Return the derivatives of the distance wrt the cell vectors. More...

template<class T >
bool	parseVector (const std::string &key, std::vector< T > &t, bool ignore_missing=false)
	Parse vector from the pdb remarks. More...

void	parseFlag (const std::string &key, bool &t)
	Parse a flag. More...

void	checkRead ()
	Check that all the remarks in the pdb have been read in. More...

void	copyDerivatives (const ReferenceConfiguration *)
	Copy derivatives from one frame to this frame. More...

void	setNamesAndAtomNumbers (const std::vector< AtomNumber > &numbers, const std::vector< std::string > &arg)
	Set the atom numbers and the argument names. More...

void	setReferenceConfig (const std::vector< Vector > &pos, const std::vector< double > &arg, const std::vector< double > &metric)
	Set the reference structure (perhaps should also pass the pbc and align and displace ) More...

void	print (OFile &ofile, const double &time, const double &weight, const double &lunits, const double &old_norm)
	Print a pdb file containing the reference configuration. More...

void	print (OFile &ofile, const std::string &fmt, const double &lunits)

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

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

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

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

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

Protected Member Functions
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...

void	error (const std::string &msg)
	Derivatives wrt to the arguments. More...

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

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

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

std::vector< double >	sqrtweight

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

std::vector< double >	trig_metric

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

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

std::vector< unsigned >	arg_der_index
	The indices for setting derivatives. 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::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::SingleDomainRMSD, PLMD::Direction, 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.

◆ checkRead()

void PLMD::ReferenceConfiguration::checkRead ( )

inherited

Check that all the remarks in the pdb have been read in.

◆ copyDerivatives()

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

inherited

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 ammount specified using a Direction.

◆ error()

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

protectedinherited

Derivatives wrt to the arguments.

The virial contribution has to be stored Derivatives wrt to the atoms 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 ( )

inlinevirtual

Return names.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getArgumentRequests()

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

virtual

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

inlinevirtual

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

inlinevirtual

Get the value of the ith reference argument.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArguments()

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

inlinevirtual

Return all the reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceMetric()

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

virtual

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.

◆ getWeight()

double PLMD::ReferenceConfiguration::getWeight ( ) const

inlineinherited

Return the weight for this frame.

◆ moveReferenceArguments()

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

Set the positions of the reference arguments.

◆ parse()

template<class T >

bool PLMD::ReferenceConfiguration::parse	(	const std::string &	key,
		T &	t,
		bool	ignore_missing = `false`
	)

inherited

Return the derivatives of the distance wrt the cell vectors.

This returns false for everything other than DRMSD as these sort of calculations have to be done separately when you use RMSD Parse something from the pdb remarks

◆ parseFlag()

void PLMD::ReferenceConfiguration::parseFlag	(	const std::string &	key,
		bool &	t
	)

inherited

Parse a flag.

◆ parseVector()

template<class T >

bool PLMD::ReferenceConfiguration::parseVector	(	const std::string &	key,
		std::vector< T > &	t,
		bool	ignore_missing = `false`
	)

inherited

Parse vector from the pdb remarks.

◆ pcaIsEnabledForThisReference()

virtual bool PLMD::ReferenceConfiguration::pcaIsEnabledForThisReference ( )

inlinevirtualinherited

Stuff for pca.

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

◆ print() [1/2]

void PLMD::ReferenceConfiguration::print	(	OFile &	ofile,
		const double &	time,
		const double &	weight,
		const double &	lunits,
		const double &	old_norm
	)

inherited

Print a pdb file containing the reference configuration.

◆ print() [2/2]

void PLMD::ReferenceConfiguration::print	(	OFile &	ofile,
		const std::string &	fmt,
		const double &	lunits
	)

inherited

◆ printArguments()

void PLMD::ReferenceArguments::printArguments	(	OFile &	ofile,
		const std::string &	fmt
	)		const

Print the arguments out.

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

◆ readArgumentsFromPDB()

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

protected

Read in the atoms from the pdb file.

◆ set()

void PLMD::ReferenceConfiguration::set ( const PDB & pdb )

virtualinherited

Set the final number of arguments.

Set the final number of atoms Set the reference configuration using a PDB

◆ setArgumentNames()

void PLMD::ReferenceArguments::setArgumentNames ( const std::vector< std::string > & arg_vals )

Set the names of the arguments.

◆ setNamesAndAtomNumbers()

void PLMD::ReferenceConfiguration::setNamesAndAtomNumbers	(	const std::vector< AtomNumber > &	numbers,
		const std::vector< std::string > &	arg
	)

inherited

Set the atom numbers and the argument names.

◆ 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 refernce arguments.

◆ setReferenceConfig()

void PLMD::ReferenceConfiguration::setReferenceConfig	(	const std::vector< Vector > &	pos,
		const std::vector< double > &	arg,
		const std::vector< double > &	metric
	)

inherited

Set the reference structure (perhaps should also pass the pbc and align and displace )

◆ setupPCAStorage()

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

inlinevirtualinherited

Stuff to setup pca.

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

◆ setWeight()

void PLMD::ReferenceConfiguration::setWeight ( const double & ww )

inlineinherited

Set the weight for this frame.

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.

◆ hasmetric

bool PLMD::ReferenceArguments::hasmetric

protected

Are we calculating a Malanobius distance.

◆ hasweights

bool PLMD::ReferenceArguments::hasweights

protected

Are we reading weights from input.

◆ metric

Matrix<double> PLMD::ReferenceArguments::metric

private

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

◆ 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()

◆ checkRead()

◆ copyDerivatives()

◆ displaceReferenceArguments()

◆ displaceReferenceConfiguration()

◆ error()

◆ extractArgumentDisplacement()

◆ extractDisplacementVector()

◆ getAbsoluteIndexes()

◆ getArgumentNames()

◆ getArgumentRequests()

◆ getAtomRequests()

◆ getName()

◆ getNumberOfReferenceArguments()

◆ getNumberOfReferencePositions()

◆ getReferenceArgument()

◆ getReferenceArguments()

◆ getReferenceMetric()

◆ getReferencePositions()

◆ getWeight()

◆ moveReferenceArguments()

◆ parse()

◆ parseFlag()

◆ parseVector()

◆ pcaIsEnabledForThisReference()

◆ print() [1/2]

◆ print() [2/2]

◆ printArguments()

◆ projectArgDisplacementOnVector()

◆ projectDisplacementOnVector()

◆ read()

◆ readArgumentsFromPDB()

◆ set()

◆ setArgumentNames()

◆ setNamesAndAtomNumbers()

◆ setReferenceArguments() [1/2]

◆ setReferenceArguments() [2/2]

◆ setReferenceConfig()

◆ setupPCAStorage()

◆ setWeight()

Friends And Related Function Documentation

◆ Direction

◆ ReferenceConfiguration

Member Data Documentation

◆ arg_der_index

◆ arg_names

◆ hasmetric

◆ hasweights

◆ metric

◆ reference_args

◆ sqrtweight

◆ trig_metric

◆ weights