PLMD::multicolvar::AtomValuePack Class Reference

#include <AtomValuePack.h>

Public Member Functions
	AtomValuePack (MultiValue &vals, MultiColvarBase const *mcolv)
void	setNumberOfAtoms (const unsigned &)
	Set the number of atoms. More...
void	setIndex (const unsigned &, const unsigned &)
	Set the index for one of the atoms. More...
void	setAtomIndex (const unsigned &j, const unsigned &ind)
void	setAtom (const unsigned &j, const unsigned &ind)
unsigned	setupAtomsFromLinkCells (const std::vector< unsigned > &cind, const Vector &cpos, const LinkCells &linkcells)
unsigned	getIndex (const unsigned &j) const
unsigned	getNumberOfAtoms () const
unsigned	getNumberOfDerivatives () const
Vector &	getPosition (const unsigned &)
	Get the position of the ith atom. More...
void	setValue (const unsigned &, const double &)
void	addValue (const unsigned &ival, const double &vv)
double	getValue (const unsigned &) const
void	addBoxDerivatives (const unsigned &, const Tensor &)
void	addTemporyBoxDerivatives (const Tensor &vir)
void	updateUsingIndices ()
void	updateDynamicList ()
void	addComDerivatives (const int &, const Vector &, CatomPack &)
MultiValue &	getUnderlyingMultiValue ()

Private Member Functions
void	addDerivative (const unsigned &, const unsigned &, const double &)
void	addAtomsDerivatives (const unsigned &, const unsigned &, const Vector &)
void	addTemporyAtomsDerivatives (const unsigned &jder, const Vector &der)

Private Attributes
MultiValue &	myvals
	Copy of the values that we are adding to. More...
MultiColvarBase const *	mycolv
	Copy of the underlying multicolvar. More...
unsigned	natoms
	Number of atoms at the moment. More...
std::vector< unsigned > &	indices
	Atom indices. More...
std::vector< unsigned > &	sort_vector
	This is used to sort the atom indices. More...
std::vector< Vector > &	myatoms
	This holds atom positions. More...

Friends
class	MultiColvarBase
class	LocalAverage

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,
		CatomPack &	catom_der
	)

addDerivative()

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

inlineprivate

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

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

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

MultiColvarBase const* 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.

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

• multicolvar/AtomValuePack.h
• multicolvar/AtomValuePack.cpp