Atom Class Reference

An atom has an unique index in the physical model object, a 3D position, and different basic properties. More...

#include <Atom.h>

Inherits Structure.

Public Member Functions
	Atom (PhysicalModel *myPM)
	Default constructor : set the position to the origin, generate a unique index. More...
	Atom (PhysicalModel *myPM, physicalModel::Atom atom, unsigned int id=-1)
	constructor from xml node: try to read and get the parameters from xml and set the index in atom SC (if possible) More...
	Atom (PhysicalModel *myPM, const double pos[3])
	constructor : generate a unique index More...
	Atom (PhysicalModel *myPM, const unsigned int ind)
	set the position to the origin More...
	Atom (PhysicalModel *myPM, const unsigned int ind, const double pos[3])
	constructor : generate a unique index More...
unsigned int	getIndexInAtoms () const
	get the index of this atom in the global atom structural component, i.e. its order number in atoms More...
void	getPosition (double pos[3]) const
	get the position of the atom (array of 3 doubles) More...
AtomProperties *	getProperties () const
	Get a ptr to the AtomProperties. More...
bool	isInstanceOf (const char *) const override
	return true only if the parameter is equal to "Atom" More...
bool	setIndex (const unsigned int) override
	set the index. More...
void	setPosition (const double [3])
	set the position of the atom More...
void	setPosition (const double, const double, const double)
	set the position of the atom More...
void	xmlPrint (std::ostream &, const StructuralComponent *) override
	print to an output stream in "pseudo" XML format. More...
	~Atom () override
	std destructor More...
Public Member Functions inherited from Structure
virtual void	addStructuralComponent (StructuralComponent *)
	add a particular StructuralComponent in the list More...
std::vector< StructuralComponent * >	getAllStructuralComponents ()
	get the list of all the StructuralComponent that are using this structure More...
unsigned int	getIndex () const
	get the structure unique index (stored in its property) More...
std::string	getName () const
	get the name of the structure More...
unsigned int	getNumberOfStructuralComponents () const
	get the number of StructuralComponent that are using this structure More...
StructuralComponent *	getStructuralComponent (unsigned int i)
	get a particular StructuralComponent that is using this structure More...
StructureProperties::GeometricType	getType () const
	get the type of index More...
void	removeStructuralComponent (StructuralComponent *)
	remove a particular StructuralComponent from the list More...
void	setName (std::string)
	set the name of the structure More...
virtual void	setPhysicalModel (PhysicalModel *)
	set the physical model More...
	Structure ()
	Base constructor. More...
virtual	~Structure ()=default
	Virtual destructor needed here as this is an abstract class (pure virtual) More...

Private Attributes
unsigned int	indexInAtoms

Additional Inherited Members
Public Attributes inherited from Structure
bool	hasIndex
	indicate if the Structure has an index (which is not the case all the time) More...
Protected Attributes inherited from Structure
StructureProperties *	properties {nullptr}
	Property of the current structure. More...

Detailed Description

An atom has an unique index in the physical model object, a 3D position, and different basic properties.

It is the most basic structure composing a physical model. It is on an atoms that the forces and loads could be applied in order to generate dynamics.

Constructor & Destructor Documentation

Atom() [1/5]

Atom::Atom

(

PhysicalModel *

myPM

)

Default constructor : set the position to the origin, generate a unique index.

Parameters

myPM	the physical model the atom belongs to

References Structure::properties.

Atom() [2/5]

Atom::Atom	(	PhysicalModel *	myPM,
		physicalModel::Atom	atom,
		unsigned int	id = -1
	)

constructor from xml node: try to read and get the parameters from xml and set the index in atom SC (if possible)

Parameters

myPM	the physical model the atom belongs to
atom	the xsd class representing the atom to read information from.
id	the index in the atoms structural component (useful to directly access the memory block corresponding to the position)

See also

getIndexInAtoms()

References indexInAtoms, and Structure::properties.

Atom() [3/5]

Atom::Atom	(	PhysicalModel *	myPM,
		const double	pos[3]
	)

constructor : generate a unique index

Parameters

myPM	the physical model the atom belongs to
pos	the initial position of the created atom (array of 3 double)

References Structure::properties.

Atom() [4/5]

Atom::Atom	(	PhysicalModel *	myPM,
		const unsigned int	ind
	)

set the position to the origin

Parameters

myPM	the physical model the atom belongs to
ind	give the unique index

References Structure::properties.

Atom() [5/5]

Atom::Atom	(	PhysicalModel *	myPM,
		const unsigned int	ind,
		const double	pos[3]
	)

constructor : generate a unique index

Parameters

myPM	the physical model the atom belongs to
ind	give the unique index
pos	the initial position of the created atom (array of 3 double)

References Structure::properties.

~Atom()

Atom::~Atom ( )

override

std destructor

References Structure::properties.

Member Function Documentation

getIndexInAtoms()

unsigned int Atom::getIndexInAtoms

(

)

const

get the index of this atom in the global atom structural component, i.e. its order number in atoms

References indexInAtoms.

Referenced by PhysicalModel::getPositionPointer().

getPosition()

void Atom::getPosition ( double  pos[3] ) const

inline

get the position of the atom (array of 3 doubles)

Referenced by CreateSC::apply(), MonitorNormDisplacement::calculate(), MonitorDistanceY::calculate(), MonitorPointSetDistance::calculate(), MonitorDisplacement::calculate(), MonitorDistanceZ::calculate(), MonitorPosition::calculate(), MonitorRen::calculate(), MonitorGeometricDeviation::calculate(), MonitorDistanceX::calculate(), MonitorPointToTriangleMeshDistanceFinal::calculate(), MonitorPointFinalSetDistance::calculate(), Position::calculate(), CreateSC::computeBoundsOfPointIds(), PMLExplorerWidget::createAtomPropertyList(), PhysicalModel::exportAnsysMesh(), PhysicalModel::exportPatran(), Reference::getDistanceToTriangularMesh(), Reference::getNearest(), and SofaSimulator::SofaSimulator().

getProperties()

AtomProperties * Atom::getProperties ( ) const

inline

Get a ptr to the AtomProperties.

Referenced by PMLExplorerWidget::createAtomPropertyList(), PhysicalModel::parseTree(), and PhysicalModel::setAtoms().

isInstanceOf()

bool Atom::isInstanceOf ( const char *  className ) const

inlineoverridevirtual

return true only if the parameter is equal to "Atom"

Implements Structure.

setIndex()

bool Atom::setIndex ( const unsigned int  index )

overridevirtual

set the index.

The index have to be unique otherwise this method has no effect. The sub-classes method will check that this index is not in use.

Returns

true only if the index of the structure was changed

Reimplemented from Structure.

References PhysicalModel::addGlobalIndexAtomPair(), Properties::getPhysicalModel(), Structure::properties, and Structure::setIndex().

setPosition() [1/2]

void Atom::setPosition ( const double  pos[3] )

inline

set the position of the atom

Referenced by PhysicalModel::setAtomPosition(), and Simulator::updatePositions().

setPosition() [2/2]

void Atom::setPosition ( const double  x, const double  y, const double  z  )

inline

set the position of the atom

xmlPrint()

void Atom::xmlPrint ( std::ostream &  o, const StructuralComponent *  sc  )

overridevirtual

print to an output stream in "pseudo" XML format.

Implements Structure.

References PhysicalModel::getAtoms(), Structure::getIndex(), Properties::getPhysicalModel(), and Structure::properties.

Member Data Documentation

indexInAtoms

unsigned int Atom::indexInAtoms

private

Referenced by Atom(), and getIndexInAtoms().

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

• Atom.h
• Atom.cpp