Public Member Functions | Private Member Functions | Private Attributes | List of all members
PLMD::mapping::PathReparameterization Class Reference

This class can be used to make a set of reference configurations equidistant. More...

#include <PathReparameterization.h>

Public Member Functions

 PathReparameterization (const Pbc &ipbc, const std::vector< Value *> &iargs, std::vector< std::unique_ptr< ReferenceConfiguration >> &pp)
 
void reparameterize (const int &istart, const int &iend, const double &TOL)
 Reparameterize the frames of the path between istart and iend so as to make the spacing constant. More...
 

Private Member Functions

void calcCurrentPathSpacings (const int &istart, const int &iend)
 Calculate the current spacings for the frames between istart and iend and return the average spacing. More...
 
bool loopEnd (const int &index, const int &end, const int &inc) const
 This function is used to work out when we are at loop ends as we go through them in positive and negative order. More...
 
void reparameterizePart (const int &istart, const int &iend, const double &target, const double &TOL)
 Reparameterize the frames of the path between istart and iend and make the spacing equal to target. More...
 

Private Attributes

const std::vector< Value * > & args
 The underlying value object for the arguments. More...
 
std::vector< double > len
 These are the current separations and the total length of the path. More...
 
unsigned MAXCYCLES
 Maximum number of cycles in path reparameterization. More...
 
Direction mydir
 Direction that is used to reparameterize configurations. More...
 
MultiValue mydpack
 Packs that we use to store the vectors connecting frames. More...
 
ReferenceValuePack mypack
 
const std::vector< std::unique_ptr< ReferenceConfiguration > > & mypath
 Reference to path that we are reparameterizing. More...
 
PDB mypdb
 This is used when setting up frames. More...
 
const Pbcpbc
 The PBC object that you would like to use to calculate distances. More...
 
std::vector< double > sfrac
 
std::vector< double > sumlen
 

Detailed Description

This class can be used to make a set of reference configurations equidistant.

Constructor & Destructor Documentation

◆ PathReparameterization()

PLMD::mapping::PathReparameterization::PathReparameterization ( const Pbc ipbc,
const std::vector< Value *> &  iargs,
std::vector< std::unique_ptr< ReferenceConfiguration >> &  pp 
)

Member Function Documentation

◆ calcCurrentPathSpacings()

void PLMD::mapping::PathReparameterization::calcCurrentPathSpacings ( const int &  istart,
const int &  iend 
)
private

Calculate the current spacings for the frames between istart and iend and return the average spacing.

◆ loopEnd()

bool PLMD::mapping::PathReparameterization::loopEnd ( const int &  index,
const int &  end,
const int &  inc 
) const
private

This function is used to work out when we are at loop ends as we go through them in positive and negative order.

◆ reparameterize()

void PLMD::mapping::PathReparameterization::reparameterize ( const int &  istart,
const int &  iend,
const double &  TOL 
)

Reparameterize the frames of the path between istart and iend so as to make the spacing constant.

◆ reparameterizePart()

void PLMD::mapping::PathReparameterization::reparameterizePart ( const int &  istart,
const int &  iend,
const double &  target,
const double &  TOL 
)
private

Reparameterize the frames of the path between istart and iend and make the spacing equal to target.

Member Data Documentation

◆ args

const std::vector<Value*>& PLMD::mapping::PathReparameterization::args
private

The underlying value object for the arguments.

◆ len

std::vector<double> PLMD::mapping::PathReparameterization::len
private

These are the current separations and the total length of the path.

◆ MAXCYCLES

unsigned PLMD::mapping::PathReparameterization::MAXCYCLES
private

Maximum number of cycles in path reparameterization.

◆ mydir

Direction PLMD::mapping::PathReparameterization::mydir
private

Direction that is used to reparameterize configurations.

◆ mydpack

MultiValue PLMD::mapping::PathReparameterization::mydpack
private

Packs that we use to store the vectors connecting frames.

◆ mypack

ReferenceValuePack PLMD::mapping::PathReparameterization::mypack
private

◆ mypath

const std::vector<std::unique_ptr<ReferenceConfiguration> >& PLMD::mapping::PathReparameterization::mypath
private

Reference to path that we are reparameterizing.

◆ mypdb

PDB PLMD::mapping::PathReparameterization::mypdb
private

This is used when setting up frames.

◆ pbc

const Pbc& PLMD::mapping::PathReparameterization::pbc
private

The PBC object that you would like to use to calculate distances.

◆ sfrac

std::vector<double> PLMD::mapping::PathReparameterization::sfrac
private

◆ sumlen

std::vector<double> PLMD::mapping::PathReparameterization::sumlen
private

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