This is the main class of this project. More...

#include <PhysicalModel.h>

Collaboration diagram for PhysicalModel:

Public Member Functions
properties general manipulation
const std::string	getName () const
	Return the name of the physical model. More...

void	setName (const std::string)
	set the name of the physical model More...

Properties *	getProperties ()
	get all properties (beware of what you do with them!): please consider calling setModified(). More...

bool	isModified ()
	check if something have changed More...

void	setModified ()
	tell the physical model something has changed (for example: a property was modified/added). More...

export to files
void	xmlPrint (std::ostream &o, bool opt=false)
	print the physical model to an output stream in a XML format (see physicalmodel.xsd for detail about the XML format). More...

void	exportPatran (std::string filename)
	Save the geometry (atoms/cells) of this PhysicalModel in the Patran format. More...

void	exportAnsysMesh (std::string filename)
	Save the mesh (atoms/cells) of this PhysicalModel in the Ansys format. More...

constructors and destructors.
static const char *	VERSION
	Current PML library version. More...

	PhysicalModel () noexcept
	Default constructor : this one just initialize everything. More...

	PhysicalModel (const char *fileName, PtrToSetProgressFunction pspf=nullptr)
	instantiate a physical model object using a XML native format file This method may throw a PMLAbortException if a problem occurs. More...

virtual	~PhysicalModel ()
	destructor More...

component manipulations
unsigned int	getNumberOfExclusiveComponents () const
	get the total number of exclusive components More...

unsigned int	getNumberOfInformativeComponents () const
	get the total number of informative components More...

unsigned int	getNumberOfAtoms () const
	get the number of atoms More...

unsigned int	getNumberOfCells () const
	get the total nr of cell in the physical model (exclusive as well as informative) More...

Component *	getExclusiveComponent (const unsigned int) const
	get an exclusive component by its index in the list More...

void	setExclusiveComponents (MultiComponent *)
	set the exclusive multi component. Becareful: the physical model takes control of this MultiComponent More...

MultiComponent *	getExclusiveComponents () const
	get all the exclusive components More...

MultiComponent *	getInformativeComponents () const
	get all the informative components More...

StructuralComponent *	getAtoms () const
	get all the atoms More...

Component *	getInformativeComponent (const unsigned int) const
	get an informative component by its index in the list More...

void	setInformativeComponents (MultiComponent *)
	set the exclusive multi component. Becareful: the physical model takes control of this MultiComponent More...

void	setAtoms (StructuralComponent *, bool deleteOld=true)
	set the atom structural component. More...

bool	addAtom (Atom *)
	Add a new atom to the atoms' structural component. More...

Atom *	getAtom (const unsigned int id)
	Get the atom that has the global index given in parameters. More...

bool	addGlobalIndexAtomPair (std::GlobalIndexStructurePair)
	add or update a pair to the atom map. More...

bool	addGlobalIndexCellPair (std::GlobalIndexStructurePair)
	add or update a pair to the cell map. More...

Cell *	getCell (const unsigned int id)
	get the cell that has the global index given in parameters. More...

Structure *	getStructureByName (const std::string n)
	get a cell using its name More...

Component *	getComponentByName (const std::string n)
	get a structural or multi component by its name. More...

virtual void	setProgress (const float donePercentage)
	this method is called during a long process everytime a little bit of the process is finished. More...

virtual void	setAtomPosition (Atom *atom, const double pos[3])
	Set the new position of an atom. More...

double *	getPositionPointer () const
	get the pointer to the memory space allocated for the atom's position. More...

double *	getPositionPointer (const unsigned int index) const
	get the pointer to the memory space allocated for atom #index's position (using global index) More...

double *	getPositionPointer (const Atom *a) const
	get the pointer to the memory space allocated for a given atom More...

Detailed Description

This is the main class of this project.

Following a nice concept, a physical model is able to represent any kind of 3D physical model that appeared, appears or will appear on earth. This include FEM meshes, spring-mass networks, phymulob etc...

Constructor & Destructor Documentation

◆ PhysicalModel() [1/2]

PhysicalModel::PhysicalModel ( )

noexcept

Default constructor : this one just initialize everything.

Structures and atoms are empty.

◆ PhysicalModel() [2/2]

PhysicalModel::PhysicalModel	(	const char *	fileName,
		PtrToSetProgressFunction	pspf = `nullptr`
	)

instantiate a physical model object using a XML native format file This method may throw a PMLAbortException if a problem occurs.

Parameters

fileName	the name of the xml file to use
pspf	is a pointer to the method that will be called by the setProgress(...) method (default = NULL)

◆ ~PhysicalModel()

PhysicalModel::~PhysicalModel ( )

virtual

destructor

Member Function Documentation

◆ addAtom()

bool PhysicalModel::addAtom ( Atom * newA )

Add a new atom to the atoms' structural component.

It does add the atom only if it has a unique index, otherwise nothing is done. (if index is correct, then it also call the addGlobalIndexAtomPair method).

Returns: true only if the atom was added

References addGlobalIndexAtomPair(), and Structure::getIndex().

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◆ addGlobalIndexAtomPair()

bool PhysicalModel::addGlobalIndexAtomPair ( std::GlobalIndexStructurePair p )

add or update a pair to the atom map.

It does nothing if the atom already exist in the map

Returns: true only if the atom was added

Referenced by addAtom(), setAtoms(), and Atom::setIndex().

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◆ addGlobalIndexCellPair()

bool PhysicalModel::addGlobalIndexCellPair ( std::GlobalIndexStructurePair p )

add or update a pair to the cell map.

It does nothing if the cell already exist in the map

Returns: true only if the cell was added

Referenced by Cell::setIndex().

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◆ exportAnsysMesh()

void PhysicalModel::exportAnsysMesh ( std::string filename )

Save the mesh (atoms/cells) of this PhysicalModel in the Ansys format.

//@@ This method is useful only for a FEM (?) mesh. Maybe it's better to put it in a femPM class that inherits PhysicalModel???

References Component::getCell(), getComponentByName(), Structure::getIndex(), getNumberOfAtoms(), Component::getNumberOfCells(), StructuralComponent::getNumberOfStructures(), Atom::getPosition(), StructuralComponent::getStructure(), Structure::getType(), StructureProperties::HEXAHEDRON, StructureProperties::QUAD, StructureProperties::TETRAHEDRON, and StructureProperties::WEDGE.

Referenced by PrepWriter::write().

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◆ exportPatran()

void PhysicalModel::exportPatran ( std::string filename )

Save the geometry (atoms/cells) of this PhysicalModel in the Patran format.

%%% This method is useful only for a FEM (?) mesh. Maybe it's better to put it in a femPM class that inherits PhysicalModel???

References getAtom(), Component::getCell(), getExclusiveComponent(), Structure::getIndex(), getName(), getNumberOfAtoms(), Component::getNumberOfCells(), StructuralComponent::getNumberOfStructures(), Atom::getPosition(), StructuralComponent::getStructure(), Structure::getType(), StructureProperties::HEXAHEDRON, and StructureProperties::WEDGE.

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◆ getAtom()

Atom * PhysicalModel::getAtom ( const unsigned int id )

inline

Get the atom that has the global index given in parameters.

The global index of an atom is the index stored as its property. This is different from its rank in the atoms list as Physical Model do not nessecarily have consecutive indexes starting at 0.

Therefore:

getAtom(id) can therefore be different than getAtoms()->getStructure(id)
getAtom(id) is equivalent to getAtoms()->getStructureByIndex(id)

Parameters

id	the atom index in the physical model

Returns: the corresponding atom or NULL if non existant (i.e. no atoms have this index)

References Structure::getIndex(), and StructuralComponent::getStructure().

Referenced by AtomIterator::AtomIterator(), MonitorDisplacement::calculate(), MonitorNormDisplacement::calculate(), MonitorRen::calculate(), Cell::Cell(), SofaSimulator::createPml(), exportPatran(), SurfaceExtractor::generateExternalSurface(), Facet::getCell(), PMLComponentExtension::save(), Arrows::update(), Colors::update(), and Simulator::updatePositions().

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◆ getAtoms()

StructuralComponent * PhysicalModel::getAtoms ( ) const

inline

get all the atoms

Referenced by CreateSC::apply(), getComponentByName(), Position::Position(), SofaSimulator::SofaSimulator(), Simulator::updatePositions(), and Atom::xmlPrint().

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◆ getCell()

Cell * PhysicalModel::getCell ( const unsigned int id )

inline

get the cell that has the global index given in parameters.

Parameters

id	the cell index in the physical model

Returns: the corresponding cell or NULL if non existant (i.e. no cels have this index)

◆ getComponentByName()

Component * PhysicalModel::getComponentByName ( const std::string n )

get a structural or multi component by its name.

Becareful: this method never returns a cell (only a structural component or a multiple component. To get a cell, use getStructureByName(..)

References getAtoms(), MultiComponent::getComponentByName(), and getName().

Referenced by AtomIterator::AtomIterator(), MonitorForce::calculate(), MonitorSurface::calculate(), MonitorVolume::calculate(), exportAnsysMesh(), CreateSC::getWidget(), and SofaSimulator::SofaSimulator().

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◆ getExclusiveComponent()

Component * PhysicalModel::getExclusiveComponent ( const unsigned int i ) const

get an exclusive component by its index in the list

References MultiComponent::getSubComponent().

Referenced by exportPatran().

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◆ getExclusiveComponents()

MultiComponent * PhysicalModel::getExclusiveComponents ( ) const

inline

get all the exclusive components

Referenced by ParametersWriter::write().

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◆ getInformativeComponent()

Component * PhysicalModel::getInformativeComponent ( const unsigned int i ) const

get an informative component by its index in the list

References MultiComponent::getSubComponent().

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◆ getInformativeComponents()

MultiComponent * PhysicalModel::getInformativeComponents ( ) const

inline

get all the informative components

Referenced by CreateSC::apply(), and PMLComponentExtension::save().

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◆ getName()

const std::string PhysicalModel::getName ( ) const

inline

Return the name of the physical model.

References Properties::getName().

Referenced by exportPatran(), getComponentByName(), and xmlPrint().

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◆ getNumberOfAtoms()

unsigned int PhysicalModel::getNumberOfAtoms ( ) const

get the number of atoms

Referenced by exportAnsysMesh(), exportPatran(), SofaSimulator::SofaSimulator(), Arrows::update(), and Colors::update().

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◆ getNumberOfCells()

unsigned int PhysicalModel::getNumberOfCells ( ) const

get the total nr of cell in the physical model (exclusive as well as informative)

References MultiComponent::getNumberOfCells().

Referenced by xmlPrint().

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◆ getNumberOfExclusiveComponents()

unsigned int PhysicalModel::getNumberOfExclusiveComponents ( ) const

get the total number of exclusive components

References MultiComponent::getNumberOfSubComponents().

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◆ getNumberOfInformativeComponents()

unsigned int PhysicalModel::getNumberOfInformativeComponents ( ) const

get the total number of informative components

References MultiComponent::getNumberOfSubComponents().

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◆ getPositionPointer() [1/3]

double * PhysicalModel::getPositionPointer ( ) const

get the pointer to the memory space allocated for the atom's position.

The memory is a big block of size getNumberOfAtoms()*3*sizeof(double). The atom positions are stored in the same order as in the atoms structural component

◆ getPositionPointer() [2/3]

double * PhysicalModel::getPositionPointer ( const Atom * a ) const

get the pointer to the memory space allocated for a given atom

References a, and StructuralComponent::getStructure().

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◆ getPositionPointer() [3/3]

double * PhysicalModel::getPositionPointer ( const unsigned int index ) const

get the pointer to the memory space allocated for atom #index's position (using global index)

References a, and StructuralComponent::getStructure().

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◆ getProperties()

Properties * PhysicalModel::getProperties ( )

inline

get all properties (beware of what you do with them!): please consider calling setModified().

When you modify/add a property (or the physical model or any component/structure), you should always call setModified() in order to specify that something has changed.

◆ getStructureByName()

Structure * PhysicalModel::getStructureByName ( const std::string n )

inline

get a cell using its name

◆ isModified()

bool PhysicalModel::isModified ( )

inline

check if something have changed

◆ setAtomPosition()

void PhysicalModel::setAtomPosition	(	Atom *	atom,
		const double	pos[3]
	)

virtual

Set the new position of an atom.

References Atom::setPosition().

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◆ setAtoms()

void PhysicalModel::setAtoms	(	StructuralComponent *	sc,
		bool	deleteOld = `true`
	)

set the atom structural component.

Becareful: the physical model takes control of this structural component

Parameters

sc	the new atom structural component
deleteOld	if true, then the old atoms SC is delete (thus deleting its atoms as well)

References a, addGlobalIndexAtomPair(), StructuralComponent::ATOMS, StructuralComponent::composedBy(), StructuralComponent::getNumberOfStructures(), and StructuralComponent::getStructure().

Referenced by SofaSimulator::createPml(), and PMLComponentExtension::save().

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◆ setExclusiveComponents()

void PhysicalModel::setExclusiveComponents ( MultiComponent * mc )

set the exclusive multi component. Becareful: the physical model takes control of this MultiComponent

References MultiComponent::setPhysicalModel().

Referenced by SofaSimulator::createPml(), and PMLComponentExtension::save().

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◆ setInformativeComponents()

void PhysicalModel::setInformativeComponents ( MultiComponent * mc )

set the exclusive multi component. Becareful: the physical model takes control of this MultiComponent

References MultiComponent::setPhysicalModel().

Referenced by CreateSC::apply(), SofaSimulator::createPml(), and PMLComponentExtension::save().

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◆ setModified()

void PhysicalModel::setModified ( )

inline

tell the physical model something has changed (for example: a property was modified/added).

This can be useful to check if something has changed since the PhysicalModel was created.

◆ setName()

void PhysicalModel::setName ( const std::string n )

inline

set the name of the physical model

References Properties::setName().

Referenced by SofaSimulator::createPml().

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◆ setProgress()

void PhysicalModel::setProgress ( const float donePercentage )

virtual

this method is called during a long process everytime a little bit of the process is finished.

This method should be overloaded by the subclass to give a mean to produce a progress bar or equivalent gui/hmi stuff.

Parameters

donePercentage the percentage (between 0 and 100) of the work already done

◆ xmlPrint()

void PhysicalModel::xmlPrint	(	std::ostream &	o,
		bool	opt = `false`
	)

print the physical model to an output stream in a XML format (see physicalmodel.xsd for detail about the XML format).

By default the output is not optimized (optimized = faster loading). In order to optimize, the cell and atom indexes are renumbered to be consecutive, so access to cell_i or atom_i is done in linear time. There are many reasons why you would not want to optimize the output, e.g. if you have a specific cell numbering that you are using somewhere else, in a different software or so.

Parameters

o	the ostream to write to
opt	a boolean indicating if yes or no you want the pm to optimize the output

References Properties::getField(), getName(), getNumberOfCells(), StructuralComponent::getNumberOfStructures(), MultiComponent::getNumberOfSubComponents(), Properties::getString(), Properties::numberOfFields(), MultiComponent::xmlPrint(), and StructuralComponent::xmlPrint().

Referenced by SofaSimulator::createPml(), and PMLComponentExtension::save().

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Member Data Documentation

◆ VERSION

const char* PhysicalModel::VERSION

static

Current PML library version.

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

Public Member Functions

constructors and destructors.

component manipulations

Detailed Description

Constructor & Destructor Documentation

◆ PhysicalModel() [1/2]

◆ PhysicalModel() [2/2]

◆ ~PhysicalModel()

Member Function Documentation

◆ addAtom()

◆ addGlobalIndexAtomPair()

◆ addGlobalIndexCellPair()

◆ exportAnsysMesh()

◆ exportPatran()

◆ getAtom()

◆ getAtoms()

◆ getCell()

◆ getComponentByName()

◆ getExclusiveComponent()

◆ getExclusiveComponents()

◆ getInformativeComponent()

◆ getInformativeComponents()

◆ getName()

◆ getNumberOfAtoms()

◆ getNumberOfCells()

◆ getNumberOfExclusiveComponents()

◆ getNumberOfInformativeComponents()

◆ getPositionPointer() [1/3]

◆ getPositionPointer() [2/3]

◆ getPositionPointer() [3/3]

◆ getProperties()

◆ getStructureByName()

◆ isModified()

◆ setAtomPosition()

◆ setAtoms()

◆ setExclusiveComponents()

◆ setInformativeComponents()

◆ setModified()

◆ setName()

◆ setProgress()

◆ xmlPrint()

Member Data Documentation

◆ VERSION