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.

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.
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.
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.

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

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

• mapping/PathReparameterization.h
• mapping/PathReparameterization.cpp