PLMD::ReferenceValuePack Class Reference

#include <ReferenceValuePack.h>

Public Member Functions
	ReferenceValuePack (const unsigned &nargs, const unsigned &natoms, MultiValue &vals)
void	addArgumentDerivatives (const unsigned &iarg, const double &der)
void	addAtomDerivatives (const unsigned &iatom, const Vector &der)
void	addBoxDerivatives (const Tensor &vir)
bool	calcUsingPCAOption () const
void	clear ()
void	copyScaledDerivatives (const unsigned &from, const double &scalef, const MultiValue &tvals)
double	getArgumentDerivative (const unsigned &ival) const
Vector	getAtomDerivative (const unsigned &iatom) const
unsigned	getAtomIndex (const unsigned &iatom) const
std::vector< Vector > &	getAtomsDisplacementVector ()
std::vector< Vector > &	getAtomVector ()
Tensor	getBoxDerivatives () const
unsigned	getNumberOfArguments () const
unsigned	getNumberOfAtoms () const
unsigned	getNumberOfDerivatives () const
void	moveDerivatives (const unsigned &from, const unsigned &to)
void	resize (const unsigned &nargs, const unsigned &natoms)
void	scaleAllDerivatives (const double &scalef)
void	setArgumentDerivatives (const unsigned &iarg, const double &der)
void	setAtomDerivatives (const unsigned &jder, const Vector &der)
void	setAtomIndex (const unsigned &iatom, const unsigned &jindex)
void	setValIndex (const unsigned &ind)
void	switchOnPCAOption ()
bool	updateComplete () const
void	updateDynamicLists ()
bool	virialWasSet () const

Private Attributes
std::vector< unsigned > &	atom_indices
	Ths list of atom indices.
bool	boxWasSet
	Was the virial set.
std::vector< Vector >	centeredpos
	A vector of vectors to save us some overhead for vector resizes.
std::vector< Vector >	displacement
Matrix< std::vector< Vector > >	DRotDPos
MultiValue &	myvals
	Copy of the values that we are adding to.
unsigned	numberOfArgs
unsigned	oind
bool	oind_set
bool	pca
	Are we using pca.
std::vector< Tensor >	rot

Friends
class	MultiDomainRMSD
class	OptimalRMSD

Constructor & Destructor Documentation

ReferenceValuePack()

PLMD::ReferenceValuePack::ReferenceValuePack	(	const unsigned &	nargs,
		const unsigned &	natoms,
		MultiValue &	vals )

Member Function Documentation

addArgumentDerivatives()

void PLMD::ReferenceValuePack::addArgumentDerivatives ( const unsigned & iarg, const double & der )

inline

addAtomDerivatives()

void PLMD::ReferenceValuePack::addAtomDerivatives ( const unsigned & iatom, const Vector & der )

inline

addBoxDerivatives()

void PLMD::ReferenceValuePack::addBoxDerivatives ( const Tensor & vir )

inline

calcUsingPCAOption()

bool PLMD::ReferenceValuePack::calcUsingPCAOption ( ) const

inline

clear()

void PLMD::ReferenceValuePack::clear

(

)

copyScaledDerivatives()

void PLMD::ReferenceValuePack::copyScaledDerivatives	(	const unsigned &	from,
		const double &	scalef,
		const MultiValue &	tvals )

getArgumentDerivative()

double PLMD::ReferenceValuePack::getArgumentDerivative ( const unsigned & ival ) const

inline

getAtomDerivative()

Vector PLMD::ReferenceValuePack::getAtomDerivative ( const unsigned & iatom ) const

inline

getAtomIndex()

unsigned PLMD::ReferenceValuePack::getAtomIndex ( const unsigned & iatom ) const

inline

getAtomsDisplacementVector()

std::vector< Vector > & PLMD::ReferenceValuePack::getAtomsDisplacementVector ( )

inline

getAtomVector()

std::vector< Vector > & PLMD::ReferenceValuePack::getAtomVector ( )

inline

getBoxDerivatives()

Tensor PLMD::ReferenceValuePack::getBoxDerivatives ( ) const

inline

getNumberOfArguments()

unsigned PLMD::ReferenceValuePack::getNumberOfArguments ( ) const

inline

getNumberOfAtoms()

unsigned PLMD::ReferenceValuePack::getNumberOfAtoms ( ) const

inline

getNumberOfDerivatives()

unsigned PLMD::ReferenceValuePack::getNumberOfDerivatives ( ) const

inline

moveDerivatives()

void PLMD::ReferenceValuePack::moveDerivatives	(	const unsigned &	from,
		const unsigned &	to )

resize()

void PLMD::ReferenceValuePack::resize	(	const unsigned &	nargs,
		const unsigned &	natoms )

scaleAllDerivatives()

void PLMD::ReferenceValuePack::scaleAllDerivatives

(

const double &

scalef

)

setArgumentDerivatives()

void PLMD::ReferenceValuePack::setArgumentDerivatives ( const unsigned & iarg, const double & der )

inline

setAtomDerivatives()

void PLMD::ReferenceValuePack::setAtomDerivatives ( const unsigned & jder, const Vector & der )

inline

setAtomIndex()

void PLMD::ReferenceValuePack::setAtomIndex ( const unsigned & iatom, const unsigned & jindex )

inline

setValIndex()

void PLMD::ReferenceValuePack::setValIndex ( const unsigned & ind )

inline

switchOnPCAOption()

void PLMD::ReferenceValuePack::switchOnPCAOption ( )

inline

updateComplete()

bool PLMD::ReferenceValuePack::updateComplete ( ) const

inline

updateDynamicLists()

void PLMD::ReferenceValuePack::updateDynamicLists

(

)

virialWasSet()

bool PLMD::ReferenceValuePack::virialWasSet ( ) const

inline

Friends And Related Symbol Documentation

MultiDomainRMSD

friend class MultiDomainRMSD

friend

OptimalRMSD

friend class OptimalRMSD

friend

Member Data Documentation

atom_indices

std::vector<unsigned>& PLMD::ReferenceValuePack::atom_indices

private

Ths list of atom indices.

boxWasSet

bool PLMD::ReferenceValuePack::boxWasSet

private

Was the virial set.

centeredpos

std::vector<Vector> PLMD::ReferenceValuePack::centeredpos

private

A vector of vectors to save us some overhead for vector resizes.

displacement

std::vector<Vector> PLMD::ReferenceValuePack::displacement

private

DRotDPos

Matrix< std::vector<Vector> > PLMD::ReferenceValuePack::DRotDPos

private

myvals

MultiValue& PLMD::ReferenceValuePack::myvals

private

Copy of the values that we are adding to.

numberOfArgs

unsigned PLMD::ReferenceValuePack::numberOfArgs

private

oind

unsigned PLMD::ReferenceValuePack::oind

private

oind_set

bool PLMD::ReferenceValuePack::oind_set

private

pca

bool PLMD::ReferenceValuePack::pca

private

Are we using pca.

rot

std::vector<Tensor> PLMD::ReferenceValuePack::rot

private

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

• reference/ReferenceValuePack.h
• reference/ReferenceValuePack.cpp