Finite Element Model 2D is a fem built with 2D FemElement. More...

#include <Fem2DRepresentation.h>

Inheritance diagram for SurgSim::Physics::Fem2DRepresentation:

Public Member Functions
	Fem2DRepresentation (const std::string &name)
	Constructor. More...

virtual	~Fem2DRepresentation ()
	Destructor.

	SURGSIM_CLASSNAME (SurgSim::Physics::Fem2DRepresentation)

void	loadFem (const std::string &fileName) override
	Loads the FEM file into an Fem class data structure. More...

void	setFem (std::shared_ptr< SurgSim::Framework::Asset > mesh)
	Sets the fem mesh asset. More...

std::shared_ptr< Fem2D >	getFem () const

void	addExternalGeneralizedForce (std::shared_ptr< Localization > localization, const SurgSim::Math::Vector &generalizedForce, const SurgSim::Math::Matrix &K=SurgSim::Math::Matrix(), const SurgSim::Math::Matrix &D=SurgSim::Math::Matrix()) override
	Add an external generalized force applied on a specific localization. More...

std::shared_ptr< Localization >	createLocalization (const SurgSim::DataStructures::Location &location) override
	Computes a localized coordinate w.r.t this representation, given a Location object. More...

Public Member Functions inherited from SurgSim::Physics::FemRepresentation
	FemRepresentation (const std::string &name)
	Constructor. More...

virtual	~FemRepresentation ()
	Destructor.

virtual void	setFemElementType (const std::string &type)
	Sets the FemElement type pulled from the object factory. More...

const std::string &	getFemElementType () const
	Gets the FemElement type pulled from the object factory. More...

void	addFemElement (const std::shared_ptr< FemElement > element)
	Adds a FemElement. More...

size_t	getNumFemElements () const
	Gets the number of FemElement. More...

std::shared_ptr< FemElement >	getFemElement (size_t femElementId)
	Retrieves a given FemElement from its id. More...

double	getTotalMass () const
	Gets the total mass of the fem. More...

double	getRayleighDampingStiffness () const
	Gets the Rayleigh stiffness parameter. More...

double	getRayleighDampingMass () const
	Gets the Rayleigh mass parameter. More...

void	setRayleighDampingStiffness (double stiffnessCoef)
	Sets the Rayleigh stiffness parameter. More...

void	setRayleighDampingMass (double massCoef)
	Sets the Rayleigh mass parameter. More...

virtual bool	isValidCoordinate (const SurgSim::DataStructures::IndexedLocalCoordinate &coordinate) const
	Determines whether the associated coordinate is valid. More...

void	beforeUpdate (double dt) override
	Preprocessing done before the update call. More...

void	update (double dt) override
	Update the representation state to the current time step. More...

void	setComplianceWarping (bool useComplianceWarping)
	Set the compliance warping flag. More...

bool	getComplianceWarping () const
	Get the compliance warping flag (default = false) More...

void	setComplianceWarpingSynchronous (bool complianceWarpingSynchronous)
	If using compliance warping, set the calculation to synchronous or asynchronous. More...

bool	isComplianceWarpingSynchronous () const
	Get whether or not any compliance warping will be done synchronously. More...

void	setMassLumping (bool useMassLumping)
	Enable mass lumping for the mass matrix, currently we use the row sum i.e. More...

bool	getMassLumping () const

Math::Matrix	applyCompliance (const Math::OdeState &state, const Math::Matrix &b) override
	Calculate the product \(C.b\) where \(C\) is the compliance matrix with boundary conditions applied. More...

const SurgSim::Math::Matrix &	getComplianceMatrix () const override
	Gets the compliance matrix associated with motion.

void	updateFMDK (const SurgSim::Math::OdeState &state, int options) override
	Update the OdeEquation (and support data) based on the given state. More...

Public Member Functions inherited from SurgSim::Physics::DeformableRepresentation
	DeformableRepresentation (const std::string &name)
	Constructor. More...

virtual	~DeformableRepresentation ()
	Destructor.

void	resetState () override
	Reset the representation to its initial/default state.

virtual void	setInitialState (std::shared_ptr< SurgSim::Math::OdeState > initialState)
	Initialize the state variables to initialState. More...

virtual const std::shared_ptr< SurgSim::Math::OdeState >	getCurrentState () const
	Return the current state of the deformable representation. More...

virtual const std::shared_ptr< SurgSim::Math::OdeState >	getPreviousState () const
	Return the previous state of the deformable representation. More...

virtual const std::shared_ptr< SurgSim::Math::OdeState >	getFinalState () const
	Return the final state of the deformable representation. More...

virtual void	interpolatePreviousState (double t)
	Declare a new previous state by interpolating between the old previous state and the current state using parametric time variable t. More...

size_t	getNumDofPerNode () const
	Gets the number of degrees of freedom per node. More...

void	setIntegrationScheme (SurgSim::Math::IntegrationScheme integrationScheme)
	Sets the numerical integration scheme. More...

SurgSim::Math::IntegrationScheme	getIntegrationScheme () const
	Gets the numerical integration scheme. More...

std::shared_ptr< SurgSim::Math::OdeSolver >	getOdeSolver () const

void	setLinearSolver (SurgSim::Math::LinearSolver linearSolver)
	Sets the linear algebraic solver. More...

SurgSim::Math::LinearSolver	getLinearSolver () const
	Gets the linear algebraic solver. More...

const SurgSim::Math::Vector &	getExternalGeneralizedForce () const

const SurgSim::Math::SparseMatrix &	getExternalGeneralizedStiffness () const

const SurgSim::Math::SparseMatrix &	getExternalGeneralizedDamping () const

void	afterUpdate (double dt) override
	Postprocessing done after the update call This needs to be called from the outside usually from a Computation. More...

void	applyCorrection (double dt, const Eigen::VectorBlock< SurgSim::Math::Vector > &deltaVelocity) override
	Update the Representation's current position and velocity using a time interval, dt, and change in velocity, deltaVelocity. More...

void	deactivateAndReset ()
	Deactivate and call resetState.

void	setCollisionRepresentation (std::shared_ptr< SurgSim::Collision::Representation > representation) override
	Set the collision representation for this physics representation, when the collision object is involved in a collision, the collision should be resolved inside the dynamics calculation. More...

void	setLocalPose (const SurgSim::Math::RigidTransform3d &pose) override
	Set the pose of the representation with respect to the Scene Element. More...

Public Member Functions inherited from SurgSim::Physics::Representation
	Representation (const std::string &name)
	Constructor. More...

virtual	~Representation ()
	Destructor.

size_t	getNumDof () const
	Query the object number of degrees of freedom. More...

void	setIsGravityEnabled (bool isGravityEnabled)
	Set the gravity enable flag. More...

bool	isGravityEnabled () const
	Get the gravity enable flag. More...

void	setIsDrivingSceneElementPose (bool isDrivingSceneElementPose)
	Set whether this Representation is controlling the pose of the SceneElement that it is part of. More...

bool	isDrivingSceneElementPose ()
	Query if this Representation is controlling the pose of the SceneElement that it is part of. More...

std::shared_ptr< SurgSim::Collision::Representation >	getCollisionRepresentation () const

std::shared_ptr< ConstraintImplementation >	getConstraintImplementation (SurgSim::Physics::ConstraintType type)
	Get a constraint implementation of the given type for this representation. More...

Public Member Functions inherited from SurgSim::Framework::Representation
	Representation (const std::string &name)
	Constructor. More...

virtual SurgSim::Math::RigidTransform3d	getLocalPose () const
	Get the pose of the representation with respect to the Scene Element. More...

virtual SurgSim::Math::RigidTransform3d	getPose () const
	Get the pose of the representation in world coordinates. More...

Public Member Functions inherited from SurgSim::Framework::Component
	Component (const std::string &name)
	Constructor. More...

virtual	~Component ()
	Destructor.

std::string	getName () const
	Gets component name. More...

std::string	getFullName () const
	Gets a string containing the name of the Component and (if it has one) its SceneElement. More...

void	setName (const std::string &name)
	Sets the name of component. More...

boost::uuids::uuid	getUuid () const
	Gets the id of the component.

bool	isInitialized () const

bool	initialize (const std::weak_ptr< Runtime > &runtime)
	Initialize this component, this needs to be called before wakeUp() can be called. More...

bool	isAwake () const

bool	wakeUp ()
	Wakeup this component, this will be called when the component is inserted into the ComponentManager that is responsible for handling this component. More...

void	retire ()
	Retire this component, this will be called when the component is removed from the ComponentManager that is responsible for handling this component. More...

void	setScene (std::weak_ptr< Scene > scene)
	Sets the scene. More...

std::shared_ptr< Scene >	getScene ()
	Gets the scene. More...

void	setSceneElement (std::weak_ptr< SceneElement > sceneElement)
	Sets the scene element. More...

std::shared_ptr< SceneElement >	getSceneElement ()
	Gets the scene element. More...

std::shared_ptr< const SceneElement >	getSceneElement () const
	Gets the scene element, constant version. More...

std::shared_ptr< Runtime >	getRuntime () const
	Get the runtime which contains this component. More...

virtual std::string	getClassName () const
	The class name for this class, this being the base class it should return SurgSim::Framework::Component but this would make missing implemenentations of this hard to catch, therefore this calls SURGSIM_FAILURE. More...

std::shared_ptr< Component >	getSharedPtr ()
	Gets a shared pointer to this component. More...

virtual void	doRetire ()
	Interface to be implemented by derived classes Has a default implementation, does nothing.

bool	isActive () const

virtual void	setLocalActive (bool val)
	Set the component's active state. More...

bool	isLocalActive () const

Public Member Functions inherited from SurgSim::Framework::Accessible
	Accessible ()
	Default Constructor.

	~Accessible ()
	Destructor.

template<class T >
T	getValue (const std::string &name) const
	Retrieves the value with the name by executing the getter if it is found and tries to convert it to the given type. More...

boost::any	getValue (const std::string &name) const
	Retrieves the value with the name by executing the getter if it is found. More...

template<class T >
bool	getValue (const std::string &name, T *value) const
	Retrieves the value with the name by executing the getter if it is found, and converts it to the type of the output parameter. More...

void	setValue (const std::string &name, const boost::any &value)
	Sets a value of a property that has setter. More...

bool	isReadable (const std::string &name) const
	Check whether a property is readable. More...

bool	isWriteable (const std::string &name) const
	Check whether a property is writable. More...

void	setGetter (const std::string &name, GetterType func)
	Sets a getter for a given property. More...

void	setSetter (const std::string &name, SetterType func)
	Sets a setter for a given property. More...

void	setAccessors (const std::string &name, GetterType getter, SetterType setter)
	Sets the accessors getter and setter in one function. More...

void	removeAccessors (const std::string &name)
	Removes all the accessors (getter and setter) for a given property. More...

void	forwardProperty (const std::string &name, const Accessible &target, const std::string &targetProperty)
	Adds a property with the given name that uses the targets accessors, in effect forwarding the value to the target. More...

void	setSerializable (const std::string &name, EncoderType encoder, DecoderType decoder)
	Sets the functions used to convert data from and to a YAML::Node. More...

void	setDecoder (const std::string &name, DecoderType decoder)
	Sets the functions used to convert data from a YAML::Node. More...

YAML::Node	encode () const
	Encode this Accessible to a YAML::Node. More...

void	decode (const YAML::Node &node, const std::vector< std::string > &ignoredProperties=std::vector< std::string >())
	Decode this Accessible from a YAML::Node, will throw an exception if the data type cannot be converted. More...

std::vector< std::string >	getProperties ()

template<>
boost::any	getValue (const std::string &name) const

Public Member Functions inherited from SurgSim::Math::OdeEquation
virtual	~OdeEquation ()
	Virtual destructor.

const std::shared_ptr< OdeState >	getInitialState () const
	Retrieves the ode initial conditions \((x0, v0)\) (i.e the initial state) More...

const Vector &	getF () const

const SparseMatrix &	getM () const

const SparseMatrix &	getD () const

const SparseMatrix &	getK () const

bool	hasF () const

bool	hasM () const

bool	hasK () const

bool	hasD () const

Protected Member Functions
void	transformState (std::shared_ptr< SurgSim::Math::OdeState > state, const SurgSim::Math::RigidTransform3d &transform) override
	Transform a state using a given transformation. More...

bool	doInitialize () override
	Interface to be implemented by derived classes. More...

Protected Member Functions inherited from SurgSim::Physics::FemRepresentation
void	addRayleighDampingForce (SurgSim::Math::Vector *f, const SurgSim::Math::OdeState &state, bool useGlobalMassMatrix=false, bool useGlobalStiffnessMatrix=false, double scale=1.0)
	Adds the Rayleigh damping forces. More...

void	addFemElementsForce (SurgSim::Math::Vector *f, const SurgSim::Math::OdeState &state, double scale=1.0)
	Adds the FemElements forces to f (given a state) More...

void	addGravityForce (SurgSim::Math::Vector *f, const SurgSim::Math::OdeState &state, double scale=1.0)
	Adds the gravity force to f (given a state) More...

bool	doInitialize () override
	Interface to be implemented by derived classes. More...

void	updateComplianceMatrix (const SurgSim::Math::OdeState &state)
	Updates the compliance matrix using nodes transformation (useful for compliance warping) More...

virtual SurgSim::Math::Matrix	getNodeTransformation (const SurgSim::Math::OdeState &state, size_t nodeId) const
	Retrieves a specific node transformation (useful for compliance warping) More...

virtual void	calculateComplianceWarpingTransformation (const SurgSim::Math::OdeState &state)
	Calculates and stores the compliance warping transformation matrix. More...

bool	isInitialComplianceMatrixComputed () const
	Gets the flag keeping track of the initial compliance matrix calculation (compliance warping case) More...

void	setIsInitialComplianceMatrixComputed (bool flag)
	Sets the flag keeping track of the initial compliance matrix calculation (compliance warping case) More...

void	computeF (const SurgSim::Math::OdeState &state) override
	Evaluation of the RHS function \(f(x, v)\) for a given state. More...

void	computeM (const SurgSim::Math::OdeState &state) override
	Evaluation of the LHS matrix \(M(x,v)\) for a given state. More...

void	computeD (const SurgSim::Math::OdeState &state) override
	Evaluation of \(D = -\frac{\partial f}{\partial v}(x,v)\) for a given state. More...

void	computeK (const SurgSim::Math::OdeState &state) override
	Evaluation of \(K = -\frac{\partial f}{\partial x}(x,v)\) for a given state. More...

void	computeFMDK (const SurgSim::Math::OdeState &state) override
	Evaluation of \(f(x,v)\), \(M(x,v)\), \(D = -\frac{\partial f}{\partial v}(x,v)\) and \(K = -\frac{\partial f}{\partial x}(x,v)\). More...

Protected Member Functions inherited from SurgSim::Physics::DeformableRepresentation
bool	doWakeUp () override
	Interface to be implemented by derived classes. More...

Protected Member Functions inherited from SurgSim::Physics::Representation
void	setNumDof (size_t numDof)
	Set the number of degrees of freedom. More...

const SurgSim::Math::Vector3d &	getGravity () const
	Get the gravity used by this Representation. More...

void	driveSceneElementPose (const SurgSim::Math::RigidTransform3d &pose)
	This conditionally updates that pose for the scenelement to the given pose The update gets exectuded if the representation actually has sceneelement and isDrivingScenElement() is true. More...

Protected Member Functions inherited from SurgSim::Framework::Component
virtual std::shared_ptr< PoseComponent >	getPoseComponent ()
	Get the PoseComponent for this component. More...

virtual std::shared_ptr< const PoseComponent >	getPoseComponent () const
	Get the PoseComponent for this component, constant access. More...

Additional Inherited Members
Public Types inherited from SurgSim::Framework::Accessible
typedef std::function< boost::any(void)>	GetterType

typedef std::function< void(boost::any)>	SetterType

typedef std::function< YAML::Node(void)>	EncoderType

typedef std::function< void(const YAML::Node *)>	DecoderType

Public Types inherited from SurgSim::Framework::FactoryBase1< Component, std::string >
typedef ObjectFactory1< Component, std::string >	FactoryType

Static Public Member Functions inherited from SurgSim::Framework::FactoryBase1< Component, std::string >
static FactoryType &	getFactory ()

Protected Attributes inherited from SurgSim::Physics::FemRepresentation
std::vector< double >	m_massPerNode
	Useful information per node. More...

std::vector< std::shared_ptr< FemElement > >	m_femElements
	FemElements.

std::string	m_femElementType
	The FemElement factory parameter invoked in doInitialize() when using a MeshAsset either with LoadFem(const std::stirng& filename) or setFem(std::shared_ptr<Asset> mesh) This ensures that when using a mesh Asset, a single FemElement type is used. More...

bool	m_useComplianceWarping
	Are we using Compliance Warping or not ?

bool	m_isComplianceWarpingSynchronous
	Is the compliance warping computation be synchronous (slower but up-to-date results)?

bool	m_isInitialComplianceMatrixComputed
	For compliance warping: Is the initial compliance matrix computed ?

SurgSim::Math::Matrix	m_complianceWarpingMatrix
	The compliance warping matrix if compliance warping in use.

Eigen::SparseMatrix< double >	m_complianceWarpingTransformation
	The system-size transformation matrix. It contains nodes transformation on the diagonal blocks.

Eigen::SparseMatrix< double >	m_complianceWarpingTransformationForCalculation

std::future< SurgSim::Math::Matrix >	m_task

Protected Attributes inherited from SurgSim::Physics::DeformableRepresentation
std::shared_ptr< SurgSim::Math::OdeState >	m_previousState
	The previous state inside the calculation loop, this has no meaning outside of the loop.

std::shared_ptr< SurgSim::Math::OdeState >	m_currentState
	The currently calculated state inside the physics loop, after the whole calculation is done this will become m_finalState.

std::shared_ptr< SurgSim::Math::OdeState >	m_newState
	New state is a temporary variable to store the newly computed state.

std::shared_ptr< SurgSim::Math::OdeState >	m_finalState
	Last valid state (a.k.a final state) More...

size_t	m_numDofPerNode
	Number of degrees of freedom per node (varies per deformable model) More...

SurgSim::Math::IntegrationScheme	m_integrationScheme
	Numerical Integration scheme (dynamic explicit/implicit solver)

SurgSim::Math::LinearSolver	m_linearSolver
	Linear algebraic solver used.

std::shared_ptr< SurgSim::Math::OdeSolver >	m_odeSolver
	Ode solver (its type depends on the numerical integration scheme)

bool	m_hasExternalGeneralizedForce
	External generalized force, stiffness and damping applied on the deformable representation.

SurgSim::Math::Vector	m_externalGeneralizedForce

SurgSim::Math::SparseMatrix	m_externalGeneralizedStiffness

SurgSim::Math::SparseMatrix	m_externalGeneralizedDamping

bool	m_previousHasExternalGeneralizedForce

SurgSim::Math::SparseMatrix	m_previousExternalGeneralizedStiffness

SurgSim::Math::SparseMatrix	m_previousExternalGeneralizedDamping

Protected Attributes inherited from SurgSim::Physics::Representation
std::shared_ptr< SurgSim::Collision::Representation >	m_collisionRepresentation
	This entity's collision representation, these are usually very specific to the physics representation.

std::shared_ptr< SurgSim::Framework::Logger >	m_logger
	Logger for this class.

Protected Attributes inherited from SurgSim::Math::OdeEquation
std::shared_ptr< OdeState >	m_initialState
	The initial state (which defines the ODE initial conditions \((x0, v0)\)) More...

unsigned int	m_initState

Vector	m_f
	The vector containing \(f(x, v)\).

SparseMatrix	m_M
	The matrix \(M(x,v)\).

SparseMatrix	m_D
	The The matrix \(D = -\frac{\partial f}{\partial v}(x,v)\).

SparseMatrix	m_K
	The The matrix \(K = -\frac{\partial f}{\partial x}(x,v)\).

Detailed Description

Finite Element Model 2D is a fem built with 2D FemElement.

Constructor & Destructor Documentation

§ Fem2DRepresentation()

SurgSim::Physics::Fem2DRepresentation::Fem2DRepresentation ( const std::string & name )

explicit

Constructor.

Parameters

name	The name of the Fem2DRepresentation

Member Function Documentation

§ addExternalGeneralizedForce()

void SurgSim::Physics::Fem2DRepresentation::addExternalGeneralizedForce	(	std::shared_ptr< Localization >	localization,
		const SurgSim::Math::Vector &	generalizedForce,
		const SurgSim::Math::Matrix &	K = `SurgSim::Math::Matrix()`,
		const SurgSim::Math::Matrix &	D = `SurgSim::Math::Matrix()`
	)

overridevirtual

Add an external generalized force applied on a specific localization.

Parameters

localization	where the generalized force is applied
generalizedForce	The force to apply (of dimension getNumDofPerNode())
K	The stiffness matrix associated with the generalized force (Jacobian of the force w.r.t dof's position)
D	The damping matrix associated with the generalized force (Jacobian of the force w.r.t dof's velocity)

Implements SurgSim::Physics::DeformableRepresentation.

§ createLocalization()

std::shared_ptr< Localization > SurgSim::Physics::Fem2DRepresentation::createLocalization ( const SurgSim::DataStructures::Location & location )

overridevirtual

Computes a localized coordinate w.r.t this representation, given a Location object.

Parameters

location A location in 3d space.

Returns: A localization object for the given location.

Reimplemented from SurgSim::Physics::Representation.

§ doInitialize()

bool SurgSim::Physics::Fem2DRepresentation::doInitialize ( )

overrideprotectedvirtual

Interface to be implemented by derived classes.

Returns: True if component is initialized successfully; otherwise, false.

Reimplemented from SurgSim::Physics::DeformableRepresentation.

§ getFem()

std::shared_ptr< Fem2D > SurgSim::Physics::Fem2DRepresentation::getFem ( ) const

Returns: The fem mesh asset as a Fem2D

§ loadFem()

void SurgSim::Physics::Fem2DRepresentation::loadFem ( const std::string & filename )

overridevirtual

Loads the FEM file into an Fem class data structure.

Parameters

filename The file to load

Implements SurgSim::Physics::FemRepresentation.

§ setFem()

void SurgSim::Physics::Fem2DRepresentation::setFem ( std::shared_ptr< SurgSim::Framework::Asset > mesh )

Sets the fem mesh asset.

Parameters

mesh	The fem mesh to assign to this representation

Exceptions

SurgSim::Framework::AssertionFailure if mesh is nullptr or it's actual type is not Fem2D

§ transformState()

void SurgSim::Physics::Fem2DRepresentation::transformState	(	std::shared_ptr< SurgSim::Math::OdeState >	state,
		const SurgSim::Math::RigidTransform3d &	transform
	)

overrideprotectedvirtual

Transform a state using a given transformation.

Parameters

[in,out]	state	The state to be transformed
	transform	The transformation to apply

Implements SurgSim::Physics::DeformableRepresentation.

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

SurgSim/Physics/Fem2DRepresentation.h
SurgSim/Physics/Fem2DRepresentation.cpp

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

§ Fem2DRepresentation()

Member Function Documentation

§ addExternalGeneralizedForce()

§ createLocalization()

§ doInitialize()

§ getFem()

§ loadFem()

§ setFem()

§ transformState()