PLMD::multicolvar::AtomValuePack Class Reference

#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.
unsigned	getIndex (const unsigned &j) const
unsigned	getNumberOfAtoms () const
unsigned	getNumberOfDerivatives () const
Vector &	getPosition (const unsigned &)
	Get the position of the ith atom.
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.
void	setNumberOfAtoms (const unsigned &)
	Set the number of atoms.
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.
std::vector< unsigned > &	indices
	Atom indices.
std::vector< Vector > &	myatoms
	This holds atom positions.
MultiColvarBase const *	mycolv
	Copy of the underlying multicolvar.
MultiValue &	myvals
	Copy of the values that we are adding to.
unsigned	natoms
	Number of atoms at the moment.
std::vector< unsigned > &	sort_vector
	This is used to sort the atom indices.

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 Symbol 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

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