#include <ReferenceValuePack.h>

Public Member Functions
	ReferenceValuePack (const unsigned &nargs, const unsigned &natoms, MultiValue &vals)

void	resize (const unsigned &nargs, const unsigned &natoms)

void	clear ()

unsigned	getNumberOfDerivatives () const

unsigned	getNumberOfArguments () const

unsigned	getNumberOfAtoms () const

void	setAtomIndex (const unsigned &iatom, const unsigned &jindex)

unsigned	getAtomIndex (const unsigned &iatom) const

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

void	addArgumentDerivatives (const unsigned &iarg, const double &der)

void	setArgumentDerivatives (const unsigned &iarg, const double &der)

void	setAtomDerivatives (const unsigned &jder, const Vector &der)

void	addAtomDerivatives (const unsigned &iatom, const Vector &der)

void	addBoxDerivatives (const Tensor &vir)

bool	updateComplete () const

void	updateDynamicLists ()

void	scaleAllDerivatives (const double &scalef)

void	setValIndex (const unsigned &ind)

void	moveDerivatives (const unsigned &from, const unsigned &to)

bool	virialWasSet () const

Vector	getAtomDerivative (const unsigned &iatom) const

double	getArgumentDerivative (const unsigned &ival) const

Tensor	getBoxDerivatives () const

bool	calcUsingPCAOption () const

void	switchOnPCAOption ()

std::vector< Vector > &	getAtomVector ()

std::vector< Vector > &	getAtomsDisplacementVector ()

Private Attributes
bool	boxWasSet
	Was the virial set. More...

unsigned	numberOfArgs

bool	oind_set

unsigned	oind

MultiValue &	myvals
	Copy of the values that we are adding to. More...

std::vector< unsigned > &	atom_indices
	Ths list of atom indices. More...

bool	pca
	Are we using pca. More...

std::vector< Vector >	centeredpos
	A vector of vectors to save us some overhead for vector resizes. More...

std::vector< Vector >	displacement

std::vector< Tensor >	rot

Matrix< std::vector< Vector > >	DRotDPos

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 Function 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

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

reference/ReferenceValuePack.h
reference/ReferenceValuePack.cpp

Public Member Functions

Private Attributes

Friends

Constructor & Destructor Documentation

◆ ReferenceValuePack()

Member Function Documentation

◆ addArgumentDerivatives()

◆ addAtomDerivatives()

◆ addBoxDerivatives()

◆ calcUsingPCAOption()

◆ clear()

◆ copyScaledDerivatives()

◆ getArgumentDerivative()

◆ getAtomDerivative()

◆ getAtomIndex()

◆ getAtomsDisplacementVector()

◆ getAtomVector()

◆ getBoxDerivatives()

◆ getNumberOfArguments()

◆ getNumberOfAtoms()

◆ getNumberOfDerivatives()

◆ moveDerivatives()

◆ resize()

◆ scaleAllDerivatives()

◆ setArgumentDerivatives()

◆ setAtomDerivatives()

◆ setAtomIndex()

◆ setValIndex()

◆ switchOnPCAOption()

◆ updateComplete()

◆ updateDynamicLists()

◆ virialWasSet()

Friends And Related Function Documentation

◆ MultiDomainRMSD

◆ OptimalRMSD

Member Data Documentation

◆ atom_indices

◆ boxWasSet

◆ centeredpos

◆ displacement

◆ DRotDPos

◆ myvals

◆ numberOfArgs

◆ oind

◆ oind_set

◆ pca

◆ rot