PLMD::MultiReferenceBase Class Reference

#include <MultiReferenceBase.h>

Inheritance diagram for PLMD::MultiReferenceBase:

Public Member Functions
	MultiReferenceBase (const std::string &type, const bool &checksoff)
virtual	~MultiReferenceBase ()
	Destructor deletes all polymorphic pointers. More...
void	clearFrames ()
	Delete all the data in the reference object. More...
virtual void	clearRestOfData ()
void	readFrame (PDB &pdb)
	Read a frame from the input. More...
void	getAtomAndArgumentRequirements (std::vector< AtomNumber > &atoms, std::vector< std::string > &args)
	Find what is required of us from the reference frames. More...
virtual void	readRestOfFrame ()
	Finish setup of frames. More...
virtual void	resizeRestOfFrame ()
	Do additional resizing required by derived class. 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, ReferenceValuePack &myder, const bool &squared) const
	Calculate the distance from one of the reference points. More...
ReferenceConfiguration *	getFrame (const unsigned &iframe)
	Return the ith reference frame. More...
std::vector< ReferenceConfiguration * > &	getReferenceConfigurations ()
	Return a reference to all the reference frames. 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	wasSet
	Everything has been set. More...
bool	skipchecks
	Skip all checking allows users to do really dodgy stuff :-) More...
std::string	mtype
	The type of metric we are using. More...

Constructor & Destructor Documentation

MultiReferenceBase()

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

~MultiReferenceBase()

PLMD::MultiReferenceBase::~MultiReferenceBase ( )

virtual

Destructor deletes all polymorphic pointers.

Member Function Documentation

calcDistanceFromConfiguration()

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

inline

Calculate the distance from one of the reference points.

calculateAllDistances()

void PLMD::MultiReferenceBase::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.

clearFrames()

void PLMD::MultiReferenceBase::clearFrames

(

)

Delete all the data in the reference object.

clearRestOfData()

virtual void PLMD::MultiReferenceBase::clearRestOfData ( )

inlinevirtual

Reimplemented in PLMD::PointWiseMapping.

copyFrame()

void PLMD::MultiReferenceBase::copyFrame

(

ReferenceConfiguration *

frameToCopy

)

Copy a reference configuration into the multi reference object.

getAtomAndArgumentRequirements()

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

Find what is required of us from the reference frames.

getFrame()

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

inline

Return the ith reference frame.

getNumberOfReferenceFrames()

unsigned PLMD::MultiReferenceBase::getNumberOfReferenceFrames ( ) const

inline

Return the size of the frames vector.

getReferenceConfigurations()

std::vector< ReferenceConfiguration * > & PLMD::MultiReferenceBase::getReferenceConfigurations ( )

inline

Return a reference to all the reference frames.

getWeight()

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

inline

Retrieve the weight of one of the frames.

parse()

template<class T >

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

protected

Read something from the last frame.

readFrame()

void PLMD::MultiReferenceBase::readFrame

(

PDB &

pdb

)

Read a frame from the input.

readRestOfFrame()

virtual void PLMD::MultiReferenceBase::readRestOfFrame ( )

inlinevirtual

Finish setup of frames.

Do additional reading required by derived class

Reimplemented in PLMD::PointWiseMapping.

resizeRestOfFrame()

virtual void PLMD::MultiReferenceBase::resizeRestOfFrame ( )

inlinevirtual

Do additional resizing required by derived class.

Reimplemented in PLMD::PointWiseMapping.

setWeights()

void PLMD::MultiReferenceBase::setWeights

(

const std::vector< double > &

ww

)

Set the weight of the ith frame.

Member Data Documentation

frames

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

protected

These are the configurations that serve as references.

mtype

std::string PLMD::MultiReferenceBase::mtype

private

The type of metric we are using.

skipchecks

bool PLMD::MultiReferenceBase::skipchecks

private

Skip all checking allows users to do really dodgy stuff :-)

wasSet

bool PLMD::MultiReferenceBase::wasSet

private

Everything has been set.

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

• reference/MultiReferenceBase.h
• reference/MultiReferenceBase.cpp