Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
PLMD::MultiReferenceBase Class Reference

#include <MultiReferenceBase.h>

Inheritance diagram for PLMD::MultiReferenceBase:
Inheritance graph
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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...
 
ReferenceConfigurationgetFrame (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 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.

◆ 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.


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