#include <PointWiseMapping.h>

Inheritance diagram for PLMD::PointWiseMapping:

Public Member Functions
	PointWiseMapping (const std::string &type, const bool &checksoff)

void	setPropertyNames (const std::vector< std::string > &prop, const bool isp)
	Set the names of the low dimensional properties. More...

bool	mappingNeedsSetup () const
	Check if setup was completed. More...

void	clearRestOfData ()
	Delete the low dimensional projections. More...

void	readRestOfFrame ()
	Read in the data from a file. More...

void	resizeRestOfFrame ()
	Resize everything else from a file. More...

void	getAtomAndArgumentRequirements (std::vector< AtomNumber > &atoms, std::vector< std::string > &args)
	Find what is required of us from the reference frames. More...

void	duplicateFrameList ()
	Make a second copy of the frame list. More...

unsigned	getNumberOfMappedPoints () const
	Get the number of points we are mapping into the lower dimensional space. More...

unsigned	getNumberOfProperties () const
	Get the number of properties. More...

std::string	getPropertyName (const unsigned &i) const
	Get the name of the ith property. More...

unsigned	getPropertyIndex (const std::string &name) const
	Get the index of the property with name. More...

double	getPropertyValue (const unsigned &iframe, const unsigned &jprop) const
	Get the value of the ith property for th jth frame. More...

void	setNumberOfAtomsAndArguments (const unsigned &natoms, const unsigned &nargs)
	Finish setup of frames. More...

Vector	getAtomDerivatives (const unsigned &iframe, const unsigned &jatom)
	Get the derivatives wrt to the position of an atom. More...

bool	getVirial (const unsigned &iframe, Tensor &vir)
	Get the derivatives wrt to the box. More...

double	getArgumentDerivative (const unsigned &iframe, const unsigned &jarg)
	Ge the derivatives wrt to one of the arguments. More...

void	copyFrameDerivatives (const unsigned &from, const unsigned &to)
	Copy derivative information from frame number from to frame number to. More...

Matrix< double > &	modifyDmat ()
	Get a pointer to the matrix of pairwise distances. More...

void	print (const std::string &method, const double &time, OFile &afile, const std::string &fmt)
	Print out the low dimensional mapping. More...

double	getProjectionCoordinate (const unsigned &iframe, const unsigned &jcoord) const
	Get the low dimensional embedding coordinate. More...

void	setProjectionCoordinate (const unsigned &iframe, const unsigned &jcoord, const double &coord)
	Set the value of the projection coordinate. More...

void	clearFrames ()
	Delete all the data in the reference object. More...

void	readFrame (PDB &pdb)
	Read a frame from the input. More...

unsigned	getNumberOfReferenceFrames () const
	Return the size of the frames vector. More...

double	calcDistanceFromConfiguration (const unsigned &ifunc, const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value * > &arg, const bool &squared)
	Calculate the distance from one of the reference points. More...

ReferenceConfiguration *	getFrame (const unsigned &iframe)
	Return the ith reference frame. More...

void	copyFrame (ReferenceConfiguration *frameToCopy)
	Copy a reference configuration into the multi reference object. More...

void	setWeights (const std::vector< double > &ww)
	Set the weight of the ith frame. More...

double	getWeight (const unsigned &ifram) const
	Retrieve the weight of one of the frames. More...

void	calculateAllDistances (const Pbc &pbc, const std::vector< Value * > &vals, Communicator &comm, Matrix< double > &distances, const bool &squared)
	Calculate the distances between all the frames and store in a matrix. More...

Protected Member Functions
template<class T >
void	parse (const std::string &key, T &val)
	Read something from the last frame. More...

Protected Attributes
std::vector < ReferenceConfiguration * >	frames
	These are the configurations that serve as references. More...

Private Attributes
bool	ispath
	This is a path. More...

Matrix< double >	dmat
	The matrix of interframe distances. More...

std::vector< std::string >	property
	The names of the projection coordinates. More...

std::vector< std::vector < double > >	low_dim
	These are where the reference configurations should be projected. More...

Constructor & Destructor Documentation

PLMD::PointWiseMapping::PointWiseMapping	(	const std::string &	type,
		const bool &	checksoff
	)

Member Function Documentation

double PLMD::MultiReferenceBase::calcDistanceFromConfiguration	(	const unsigned &	ifunc,
		const std::vector< Vector > &	pos,
		const Pbc &	pbc,
		const std::vector< Value * > &	arg,
		const bool &	squared
	)

inlineinherited

Calculate the distance from one of the reference points.

void PLMD::MultiReferenceBase::calculateAllDistances	(	const Pbc &	pbc,
		const std::vector< Value * > &	vals,
		Communicator &	comm,
		Matrix< double > &	distances,
		const bool &	squared
	)

inherited

Calculate the distances between all the frames and store in a matrix.

void PLMD::MultiReferenceBase::clearFrames ( )

inherited

Delete all the data in the reference object.

void PLMD::PointWiseMapping::clearRestOfData ( )

virtual

Delete the low dimensional projections.

Reimplemented from PLMD::MultiReferenceBase.

void PLMD::MultiReferenceBase::copyFrame ( ReferenceConfiguration * frameToCopy )

inherited

Copy a reference configuration into the multi reference object.

void PLMD::PointWiseMapping::copyFrameDerivatives	(	const unsigned &	from,
		const unsigned &	to
	)

inline

Copy derivative information from frame number from to frame number to.

void PLMD::PointWiseMapping::duplicateFrameList ( )

Make a second copy of the frame list.

double PLMD::PointWiseMapping::getArgumentDerivative	(	const unsigned &	iframe,
		const unsigned &	jarg
	)

inline

Ge the derivatives wrt to one of the arguments.

void PLMD::PointWiseMapping::getAtomAndArgumentRequirements	(	std::vector< AtomNumber > &	atoms,
		std::vector< std::string > &	args
	)

Find what is required of us from the reference frames.

Vector PLMD::PointWiseMapping::getAtomDerivatives	(	const unsigned &	iframe,
		const unsigned &	jatom
	)

inline

Get the derivatives wrt to the position of an atom.

ReferenceConfiguration * PLMD::MultiReferenceBase::getFrame ( const unsigned & iframe )

inlineinherited

Return the ith reference frame.

unsigned PLMD::PointWiseMapping::getNumberOfMappedPoints ( ) const

inline

Get the number of points we are mapping into the lower dimensional space.

unsigned PLMD::PointWiseMapping::getNumberOfProperties ( ) const

inline

Get the number of properties.

unsigned PLMD::MultiReferenceBase::getNumberOfReferenceFrames ( ) const

inlineinherited

Return the size of the frames vector.

double PLMD::PointWiseMapping::getProjectionCoordinate	(	const unsigned &	iframe,
		const unsigned &	jcoord
	)		const

inline

Get the low dimensional embedding coordinate.

unsigned PLMD::PointWiseMapping::getPropertyIndex ( const std::string & name ) const

Get the index of the property with name.

std::string PLMD::PointWiseMapping::getPropertyName ( const unsigned & i ) const

inline

Get the name of the ith property.

double PLMD::PointWiseMapping::getPropertyValue	(	const unsigned &	iframe,
		const unsigned &	jprop
	)		const

inline

Get the value of the ith property for th jth frame.

bool PLMD::PointWiseMapping::getVirial	(	const unsigned &	iframe,
		Tensor &	vir
	)

inline

Get the derivatives wrt to the box.

double PLMD::MultiReferenceBase::getWeight ( const unsigned & ifram ) const

inlineinherited

Retrieve the weight of one of the frames.

bool PLMD::PointWiseMapping::mappingNeedsSetup ( ) const

inline

Check if setup was completed.

Matrix< double > & PLMD::PointWiseMapping::modifyDmat ( )

inline

Get a pointer to the matrix of pairwise distances.

template<class T >

void PLMD::MultiReferenceBase::parse	(	const std::string &	key,
		T &	val
	)

protectedinherited

Read something from the last frame.

void PLMD::PointWiseMapping::print	(	const std::string &	method,
		const double &	time,
		OFile &	afile,
		const std::string &	fmt
	)

Print out the low dimensional mapping.

void PLMD::MultiReferenceBase::readFrame ( PDB & pdb )

inherited

Read a frame from the input.

void PLMD::PointWiseMapping::readRestOfFrame ( )

virtual

Read in the data from a file.

Reimplemented from PLMD::MultiReferenceBase.

void PLMD::PointWiseMapping::resizeRestOfFrame ( )

virtual

Resize everything else from a file.

Reimplemented from PLMD::MultiReferenceBase.

void PLMD::PointWiseMapping::setNumberOfAtomsAndArguments	(	const unsigned &	natoms,
		const unsigned &	nargs
	)

Finish setup of frames.

void PLMD::PointWiseMapping::setProjectionCoordinate	(	const unsigned &	iframe,
		const unsigned &	jcoord,
		const double &	coord
	)

inline

Set the value of the projection coordinate.

void PLMD::PointWiseMapping::setPropertyNames	(	const std::vector< std::string > &	prop,
		const bool	isp
	)

Set the names of the low dimensional properties.

void PLMD::MultiReferenceBase::setWeights ( const std::vector< double > & ww )

inherited

Set the weight of the ith frame.

Member Data Documentation

Matrix<double> PLMD::PointWiseMapping::dmat

private

The matrix of interframe distances.

std::vector<ReferenceConfiguration*> PLMD::MultiReferenceBase::frames

protectedinherited

These are the configurations that serve as references.

bool PLMD::PointWiseMapping::ispath

private

This is a path.

std::vector< std::vector<double> > PLMD::PointWiseMapping::low_dim

private

These are where the reference configurations should be projected.

std::vector<std::string> PLMD::PointWiseMapping::property

private

The names of the projection coordinates.

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

reference/PointWiseMapping.h
reference/PointWiseMapping.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation