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	setAtom (const unsigned &j, const unsigned &ind)
unsigned	setupAtomsFromLinkCells (const 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	addDerivative (const unsigned &, const unsigned &, const double &)
void	addAtomsDerivatives (const unsigned &, const unsigned &, const Vector &)
void	addBoxDerivatives (const unsigned &, const Tensor &)
void	updateUsingIndices ()
void	updateDynamicList ()
void	addComDerivatives (const unsigned &, const Vector &, CatomPack &)
MultiValue &	getUnderlyingMultiValue ()

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...

Constructor & Destructor Documentation

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

Member Function Documentation

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

inline

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

inline

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

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

Get the position of the ith atom.

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

inline

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

inline

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

inline

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

inline

Set the index for one of the atoms.

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

inline

Set the number of atoms.

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

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

inline

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

inline

void PLMD::multicolvar::AtomValuePack::updateUsingIndices

(

)

Member Data Documentation

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

private

Atom indices.

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

private

This holds atom positions.

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

private

Copy of the underlying multicolvar.

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

private

Copy of the values that we are adding to.

unsigned PLMD::multicolvar::AtomValuePack::natoms

private

Number of atoms at the moment.

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