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

#include <ReferenceArguments.h>

Inheritance diagram for PLMD::ReferenceArguments:

Public Member Functions
	ReferenceArguments (const ReferenceConfigurationOptions &ro)

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...

double	getReferenceArgument (const unsigned &i)
	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 ()
	Return all the reference arguments. More...

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

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

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

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

virtual void	setNumberOfArguments (const unsigned &)
	Set the final number of arguments. More...

virtual void	setNumberOfAtoms (const unsigned &)
	Set the final number of atoms. More...

virtual void	set (const PDB &)
	Set the reference configuration using a PDB. 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, const bool &squared=false)
	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, const bool &squared)=0
	Calculate the distance from the reference configuration. More...

Vector	getAtomDerivative (const unsigned &) const
	Return the derivative wrt to the ith atom. More...

double	getArgumentDerivative (const unsigned &) const
	Return the derivative wrt to the ith argument. More...

bool	getVirial (Tensor &virout) const
	Return the derivatives of the distance wrt the cell vectors. More...

template<class T >
bool	parse (const std::string &key, T &t, bool ignore_missing=false)
	Parse something from the pdb remarks. 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 &old_norm)
	Print a pdb file containing the reference configuration. More...

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

virtual const std::vector < Vector > &	getReferencePositions ()
	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...

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...

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

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

void	clearDerivatives ()
	Clear the derivatives. More...

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

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

std::vector< double >	arg_ders
	Derivatives wrt to the arguments. More...

bool	virialWasSet
	The virial contribution has to be stored. More...

Tensor	virial

std::vector< Vector >	atom_ders
	Derivatives wrt to the atoms. More...

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

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 >	der_index
	The indices for setting derivatives. More...

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

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

Member Function Documentation

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

pure virtualinherited

Calculate the distance from the reference configuration.

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

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

inherited

Calculate the distance from the reference configuration.

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

protected

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

void PLMD::ReferenceConfiguration::checkRead ( )

inherited

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

void PLMD::ReferenceConfiguration::clearDerivatives ( )

protectedinherited

Clear the derivatives.

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

inherited

Copy derivatives from one frame to this frame.

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

protectedinherited

Crash with an error.

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

inlinevirtualinherited

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

Reimplemented in PLMD::ReferenceAtoms.

double PLMD::ReferenceConfiguration::getArgumentDerivative ( const unsigned & ider ) const

inlineinherited

Return the derivative wrt to the ith argument.

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

inlinevirtual

Return names.

Reimplemented from PLMD::ReferenceConfiguration.

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

virtual

Get the arguments required.

Reimplemented from PLMD::ReferenceConfiguration.

Vector PLMD::ReferenceConfiguration::getAtomDerivative ( const unsigned & ider ) const

inlineinherited

Return the derivative wrt to the ith atom.

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.

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

inherited

Return the name of this metric.

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

inlinevirtual

Get the value of the ith reference argument.

Reimplemented from PLMD::ReferenceConfiguration.

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

inlinevirtual

Return all the reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

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

virtual

Reimplemented from PLMD::ReferenceConfiguration.

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

inlinevirtualinherited

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

Reimplemented in PLMD::ReferenceAtoms.

bool PLMD::ReferenceConfiguration::getVirial ( Tensor & virout ) const

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

double PLMD::ReferenceConfiguration::getWeight ( ) const

inlineinherited

Return the weight for this frame.

template<class T >

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

inherited

Parse something from the pdb remarks.

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

inherited

Parse a flag.

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.

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

inherited

Print a pdb file containing the reference configuration.

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

inherited

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

Print the arguments out.

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

pure virtualinherited

Do all local business for setting the configuration.

Implemented in PLMD::DRMSD, PLMD::MultiDomainRMSD, PLMD::SimpleRMSD, PLMD::OptimalRMSD, PLMD::FakeFrame, PLMD::SimpleRMSD, PLMD::EuclideanDistance, and PLMD::NormalizedEuclideanDistance.

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

protected

Read in the atoms from the pdb file.

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

virtualinherited

Set the reference configuration using a PDB.

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

Set the names of the arguments.

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

inherited

Set the atom numbers and the argument names.

void PLMD::ReferenceConfiguration::setNumberOfArguments ( const unsigned & n )

virtualinherited

Set the final number of arguments.

void PLMD::ReferenceConfiguration::setNumberOfAtoms ( const unsigned & n )

virtualinherited

Set the final number of atoms.

void PLMD::ReferenceArguments::setReferenceArguments ( )

protected

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

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

Set the positions of the refernce arguments.

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 )

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

inlineinherited

Set the weight for this frame.

Member Data Documentation

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

protectedinherited

Derivatives wrt to the arguments.

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

private

The names of the arguments.

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

protectedinherited

Derivatives wrt to the atoms.

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

private

The indices for setting derivatives.

bool PLMD::ReferenceArguments::hasmetric

protected

Are we calculating a Malanobius distance.

bool PLMD::ReferenceArguments::hasweights

protected

Are we reading weights from input.

Matrix<double> PLMD::ReferenceArguments::metric

private

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

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

private

The values of the colvars in the reference configuration.

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

private

Tensor PLMD::ReferenceConfiguration::virial

protectedinherited

bool PLMD::ReferenceConfiguration::virialWasSet

protectedinherited

The virial contribution has to be stored.

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

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation