PLMD::vatom::ActionWithVirtualAtom Class Reference

Inherit from here if you are calculating the position of a virtual atom (eg a center of mass) More...

#include <ActionWithVirtualAtom.h>

Inheritance diagram for PLMD::vatom::ActionWithVirtualAtom:

Public Member Functions
	ActionWithVirtualAtom (const ActionOptions &ao)
	~ActionWithVirtualAtom ()
const std::map< AtomNumber, Tensor > &	getGradients () const
AtomNumber	getIndex () const
	Return the atom id of the corresponding virtual atom.
void	setGradients ()
void	setGradientsIfNeeded ()

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

Protected Member Functions
void	requestAtoms (const std::vector< AtomNumber > &a)
	Request atoms on which the calculation depends.
void	setAtomsDerivatives (const std::vector< Tensor > &d)
	Set the derivatives of virtual atom coordinate wrt atoms on which it dependes.
void	setBoxDerivatives (const std::array< Tensor, 3 > &d)
	Set the box derivatives.
void	setBoxDerivativesNoPbc ()
	Set box derivatives automatically.
void	setCharge (double)
	Set its charge.
void	setMass (double)
	Set its mass.
void	setPosition (const Vector &)
	Set position of the virtual atom.

Private Member Functions
void	apply () override
	Apply an Action.

Private Attributes
std::array< Tensor, 3 >	boxDerivatives
std::vector< Tensor >	derivatives
std::map< AtomNumber, Tensor >	gradients
const AtomNumber	index

Detailed Description

Inherit from here if you are calculating the position of a virtual atom (eg a center of mass)

Class to add a single virtual atom to the system. (it might be extended to add multiple virtual atoms).

Constructor & Destructor Documentation

ActionWithVirtualAtom()

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

explicit

~ActionWithVirtualAtom()

PLMD::ActionWithVirtualAtom::~ActionWithVirtualAtom

(

)

Member Function Documentation

apply()

void PLMD::ActionWithVirtualAtom::apply ( )

overrideprivatevirtual

Apply an Action.

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

Implements PLMD::Action.

getGradients()

const std::map< AtomNumber, Tensor > & PLMD::ActionWithVirtualAtom::getGradients ( ) const

inline

getIndex()

AtomNumber PLMD::ActionWithVirtualAtom::getIndex ( ) const

inline

Return the atom id of the corresponding virtual atom.

registerKeywords()

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

static

requestAtoms()

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

protected

Request atoms on which the calculation depends.

setAtomsDerivatives()

void PLMD::ActionWithVirtualAtom::setAtomsDerivatives ( const std::vector< Tensor > & d )

inlineprotected

Set the derivatives of virtual atom coordinate wrt atoms on which it dependes.

setBoxDerivatives()

void PLMD::ActionWithVirtualAtom::setBoxDerivatives ( const std::array< Tensor, 3 > & d )

protected

Set the box derivatives.

This should be an array of size 3. First index corresponds to the components of the virtual atom. Notice that this routine subtract the trivial term coming from cell deformation since this term is already implicitly included. Indeed, if the vatom position is a linear function of atomic coordinates it is not necessary to call this function (implicit term is fine) (e.g. vatom::COM and vatom::Center). On the other hand if the vatom position is a non-linear function of atomic coordinates this should be called (see vatom::Ghost).

setBoxDerivativesNoPbc()

void PLMD::ActionWithVirtualAtom::setBoxDerivativesNoPbc ( )

protected

Set box derivatives automatically.

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

Warning

It only works for virtual atoms NOT using PBCs! This implies that all atoms used + the new virtual atom should be in the same periodic image.

setCharge()

void PLMD::ActionWithVirtualAtom::setCharge ( double c )

inlineprotected

Set its charge.

setGradients()

void PLMD::ActionWithVirtualAtom::setGradients

(

)

setGradientsIfNeeded()

void PLMD::ActionWithVirtualAtom::setGradientsIfNeeded

(

)

setMass()

void PLMD::ActionWithVirtualAtom::setMass ( double m )

inlineprotected

Set its mass.

setPosition()

void PLMD::ActionWithVirtualAtom::setPosition ( const Vector & pos )

inlineprotected

Set position of the virtual atom.

Member Data Documentation

boxDerivatives

std::array<Tensor,3> PLMD::ActionWithVirtualAtom::boxDerivatives

private

derivatives

std::vector<Tensor> PLMD::ActionWithVirtualAtom::derivatives

private

gradients

std::map<AtomNumber,Tensor> PLMD::ActionWithVirtualAtom::gradients

private

index

const AtomNumber PLMD::ActionWithVirtualAtom::index

private

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

• core/ActionWithVirtualAtom.h
• core/ActionWithVirtualAtom.cpp