PLMD::sasa::Colvar Class Reference

#include <Colvar.h>

Inherits PLMD::ActionAtomistic, and PLMD::ActionWithValue.

Inherited by PLMD::colvar::Angle< double >, PLMD::colvar::DihedralCorrelation< double >, PLMD::colvar::Dipole< double >, PLMD::colvar::Distance< double >, PLMD::colvar::Gyration< double >, PLMD::colvar::Plane< double >, PLMD::colvar::Position< double >, PLMD::colvar::Torsion< double >, PLMD::colvar::Angle< T >, PLMD::colvar::Cell, PLMD::colvar::ColvarFake, PLMD::colvar::ContactMap, PLMD::colvar::CoordinationBase, PLMD::colvar::DihedralCorrelation< T >, PLMD::colvar::Dimer, PLMD::colvar::Dipole< T >, PLMD::colvar::Distance< T >, PLMD::colvar::EEFSolv, PLMD::colvar::ERMSD, PLMD::colvar::Gyration< T >, PLMD::colvar::PCARMSD, PLMD::colvar::PathMSDBase, PLMD::colvar::Plane< T >, PLMD::colvar::Position< T >, PLMD::colvar::ProjectionOnAxis, PLMD::colvar::Puckering, PLMD::colvar::RMSD, PLMD::colvar::SoftVoronoiBase, PLMD::colvar::Template, PLMD::colvar::Torsion< T >, PLMD::colvar::Volume, PLMD::crystdistrib::Quaternion, PLMD::funnel::FUNNEL_PS, PLMD::isdb::BAIES, PLMD::isdb::FretEfficiency, PLMD::isdb::Shadow, PLMD::maze::Loss, PLMD::maze::Optimizer, PLMD::membranefusion::fusionPoreExpansionP, PLMD::membranefusion::fusionPoreNucleationP, PLMD::membranefusion::memFusionP, PLMD::pines::PINES, PLMD::piv::PIV, PLMD::s2cm::S2ContactModel, PLMD::sasa::SASA_HASEL, PLMD::sasa::SASA_LCPO, PLMD::sizeshape::position_linear_proj, and PLMD::sizeshape::position_maha_dist.

Public Member Functions
	Colvar (const ActionOptions &)
	~Colvar ()
unsigned	getNumberOfDerivatives () override

Static Public Member Functions
static void	registerKeywords (Keywords &keys)

Protected Member Functions
void	apply () override
	Apply an Action.
const Tensor &	getBoxDerivatives () const
const double &	getForce () const
void	requestAtoms (const std::vector< AtomNumber > &a)
void	setAtomsDerivatives (int, const Vector &)
void	setAtomsDerivatives (Value *, int, const Vector &)
void	setBoxDerivatives (const Tensor &)
void	setBoxDerivatives (Value *, const Tensor &)
void	setBoxDerivativesNoPbc ()
	Set box derivatives automatically.
void	setBoxDerivativesNoPbc (Value *)

Friends
class	NeighborList

Constructor & Destructor Documentation

Colvar()

PLMD::Colvar::Colvar ( const ActionOptions & ao )

explicit

~Colvar()

PLMD::Colvar::~Colvar ( )

inline

Member Function Documentation

apply()

void PLMD::Colvar::apply ( )

overrideprotectedvirtual

Apply an Action.

This method is called one time per step. The set of all Actions is applied in backward order.

Implements PLMD::Action.

getBoxDerivatives()

const Tensor & PLMD::Colvar::getBoxDerivatives ( ) const

protected

getForce()

const double & PLMD::Colvar::getForce ( ) const

protected

getNumberOfDerivatives()

unsigned PLMD::Colvar::getNumberOfDerivatives ( )

inlineoverridevirtual

Implements PLMD::ActionWithValue.

registerKeywords()

void PLMD::Colvar::registerKeywords ( Keywords & keys )

static

requestAtoms()

void PLMD::Colvar::requestAtoms ( const std::vector< AtomNumber > & a )

protected

setAtomsDerivatives() [1/2]

void PLMD::Colvar::setAtomsDerivatives ( int i, const Vector & d )

inlineprotected

setAtomsDerivatives() [2/2]

void PLMD::Colvar::setAtomsDerivatives ( Value * v, int i, const Vector & d )

inlineprotected

setBoxDerivatives() [1/2]

void PLMD::Colvar::setBoxDerivatives ( const Tensor & d )

inlineprotected

setBoxDerivatives() [2/2]

void PLMD::Colvar::setBoxDerivatives ( Value * v, const Tensor & d )

inlineprotected

setBoxDerivativesNoPbc() [1/2]

void PLMD::Colvar::setBoxDerivativesNoPbc ( )

inlineprotected

Set box derivatives automatically.

It should be called after the setAtomsDerivatives has been used for all single atoms.

Warning

It only works for collective variable NOT using PBCs!

setBoxDerivativesNoPbc() [2/2]

void PLMD::Colvar::setBoxDerivativesNoPbc ( Value * v )

protected

Friends And Related Symbol Documentation

NeighborList

friend class NeighborList

friend

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

• core/Colvar.h
• core/Colvar.cpp