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

#include <PointWiseMapping.h>

Inheritance diagram for PLMD::PointWiseMapping:
Inheritance graph
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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...
 
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 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: