#include <AtomValuePack.h>

Public Member Functions
	AtomValuePack (MultiValue &vals, MultiColvarBase const *mcolv)

void	addBoxDerivatives (const unsigned &, const Tensor &)

void	addComDerivatives (const int &, const Vector &, const CatomPack &)

void	addDerivative (const unsigned &, const unsigned &, const double &)

void	addTemporyBoxDerivatives (const Tensor &vir)

void	addValue (const unsigned &ival, const double &vv)

AtomNumber	getAbsoluteIndex (const unsigned &j) const
	Get the absolute index of the ith atom in the list. More...

unsigned	getIndex (const unsigned &j) const

unsigned	getNumberOfAtoms () const

unsigned	getNumberOfDerivatives () const

Vector &	getPosition (const unsigned &)
	Get the position of the ith atom. More...

MultiValue &	getUnderlyingMultiValue ()

double	getValue (const unsigned &) const

void	setAtom (const unsigned &j, const unsigned &ind)

void	setAtomIndex (const unsigned &j, const unsigned &ind)

void	setIndex (const unsigned &, const unsigned &)
	Set the index for one of the atoms. More...

void	setNumberOfAtoms (const unsigned &)
	Set the number of atoms. More...

unsigned	setupAtomsFromLinkCells (const std::vector< unsigned > &cind, const Vector &cpos, const LinkCells &linkcells)

void	setValue (const unsigned &, const double &)

void	updateDynamicList ()

void	updateUsingIndices ()

Private Member Functions
void	addAtomsDerivatives (const unsigned &, const unsigned &, const Vector &)

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

Private Attributes
std::vector< unsigned >	cells_required
	This is stuff for link cells. More...

std::vector< unsigned > &	indices
	Atom indices. More...

std::vector< Vector > &	myatoms
	This holds atom positions. More...

const MultiColvarBase *	mycolv
	Copy of the underlying multicolvar. More...

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

unsigned	natoms
	Number of atoms at the moment. More...

std::vector< unsigned > &	sort_vector
	This is used to sort the atom indices. More...

Friends
class	LocalAverage

class	MultiColvarBase

Constructor & Destructor Documentation

◆ AtomValuePack()

PLMD::multicolvar::AtomValuePack::AtomValuePack	(	MultiValue &	vals,
		MultiColvarBase const *	mcolv
	)

Member Function Documentation

◆ addAtomsDerivatives()

void PLMD::multicolvar::AtomValuePack::addAtomsDerivatives	(	const unsigned &	ival,
		const unsigned &	jder,
		const Vector &	der
	)

inlineprivate

◆ addBoxDerivatives()

void PLMD::multicolvar::AtomValuePack::addBoxDerivatives	(	const unsigned &	ival,
		const Tensor &	vir
	)

inline

◆ addComDerivatives()

void PLMD::multicolvar::AtomValuePack::addComDerivatives	(	const int &	ind,
		const Vector &	der,
		const CatomPack &	catom_der
	)

◆ addDerivative()

void PLMD::multicolvar::AtomValuePack::addDerivative	(	const unsigned &	ival,
		const unsigned &	jder,
		const double &	der
	)

inline

◆ addTemporyAtomsDerivatives()

void PLMD::multicolvar::AtomValuePack::addTemporyAtomsDerivatives	(	const unsigned &	jder,
		const Vector &	der
	)

inlineprivate

◆ addTemporyBoxDerivatives()

void PLMD::multicolvar::AtomValuePack::addTemporyBoxDerivatives ( const Tensor & vir )

inline

◆ addValue()

void PLMD::multicolvar::AtomValuePack::addValue	(	const unsigned &	ival,
		const double &	vv
	)

inline

◆ getAbsoluteIndex()

AtomNumber PLMD::multicolvar::AtomValuePack::getAbsoluteIndex ( const unsigned & j ) const

inline

Get the absolute index of the ith atom in the list.

◆ getIndex()

unsigned PLMD::multicolvar::AtomValuePack::getIndex ( const unsigned & j ) const

inline

◆ getNumberOfAtoms()

unsigned PLMD::multicolvar::AtomValuePack::getNumberOfAtoms ( ) const

inline

◆ getNumberOfDerivatives()

unsigned PLMD::multicolvar::AtomValuePack::getNumberOfDerivatives ( ) const

inline

◆ getPosition()

Vector & PLMD::multicolvar::AtomValuePack::getPosition ( const unsigned & iatom )

inline

Get the position of the ith atom.

◆ getUnderlyingMultiValue()

MultiValue & PLMD::multicolvar::AtomValuePack::getUnderlyingMultiValue ( )

inline

◆ getValue()

double PLMD::multicolvar::AtomValuePack::getValue ( const unsigned & ival ) const

inline

◆ setAtom()

void PLMD::multicolvar::AtomValuePack::setAtom	(	const unsigned &	j,
		const unsigned &	ind
	)

inline

◆ setAtomIndex()

void PLMD::multicolvar::AtomValuePack::setAtomIndex	(	const unsigned &	j,
		const unsigned &	ind
	)

inline

◆ setIndex()

void PLMD::multicolvar::AtomValuePack::setIndex	(	const unsigned &	j,
		const unsigned &	ind
	)

inline

Set the index for one of the atoms.

◆ setNumberOfAtoms()

void PLMD::multicolvar::AtomValuePack::setNumberOfAtoms ( const unsigned & nat )

inline

Set the number of atoms.

◆ setupAtomsFromLinkCells()

unsigned PLMD::multicolvar::AtomValuePack::setupAtomsFromLinkCells	(	const std::vector< unsigned > &	cind,
		const Vector &	cpos,
		const LinkCells &	linkcells
	)

◆ setValue()

void PLMD::multicolvar::AtomValuePack::setValue	(	const unsigned &	ival,
		const double &	vv
	)

inline

◆ updateDynamicList()

void PLMD::multicolvar::AtomValuePack::updateDynamicList ( )

inline

◆ updateUsingIndices()

void PLMD::multicolvar::AtomValuePack::updateUsingIndices ( )

Friends And Related Function Documentation

◆ LocalAverage

friend class LocalAverage

friend

◆ MultiColvarBase

friend class MultiColvarBase

friend

Member Data Documentation

◆ cells_required

std::vector<unsigned> PLMD::multicolvar::AtomValuePack::cells_required

private

This is stuff for link cells.

◆ indices

std::vector<unsigned>& PLMD::multicolvar::AtomValuePack::indices

private

Atom indices.

◆ myatoms

std::vector<Vector>& PLMD::multicolvar::AtomValuePack::myatoms

private

This holds atom positions.

◆ mycolv

const MultiColvarBase* PLMD::multicolvar::AtomValuePack::mycolv

private

Copy of the underlying multicolvar.

◆ myvals

MultiValue& PLMD::multicolvar::AtomValuePack::myvals

private

Copy of the values that we are adding to.

◆ natoms

unsigned PLMD::multicolvar::AtomValuePack::natoms

private

Number of atoms at the moment.

◆ sort_vector

std::vector<unsigned>& PLMD::multicolvar::AtomValuePack::sort_vector

private

This is used to sort the atom indices.

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

multicolvar/AtomValuePack.h
multicolvar/AtomValuePack.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Constructor & Destructor Documentation

◆ AtomValuePack()

Member Function Documentation

◆ addAtomsDerivatives()

◆ addBoxDerivatives()

◆ addComDerivatives()

◆ addDerivative()

◆ addTemporyAtomsDerivatives()

◆ addTemporyBoxDerivatives()

◆ addValue()

◆ getAbsoluteIndex()

◆ getIndex()

◆ getNumberOfAtoms()

◆ getNumberOfDerivatives()

◆ getPosition()

◆ getUnderlyingMultiValue()

◆ getValue()

◆ setAtom()

◆ setAtomIndex()

◆ setIndex()

◆ setNumberOfAtoms()

◆ setupAtomsFromLinkCells()

◆ setValue()

◆ updateDynamicList()

◆ updateUsingIndices()

Friends And Related Function Documentation

◆ LocalAverage

◆ MultiColvarBase

Member Data Documentation

◆ cells_required

◆ indices

◆ myatoms

◆ mycolv

◆ myvals

◆ natoms

◆ sort_vector