Finite Element Model (a.k.a FEM) is a deformable model (a set of nodes connected by FemElement). More...

#include <FemRepresentation.h>

Inheritance diagram for SurgSim::Physics::FemRepresentation:

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

virtual	~FemRepresentation ()
	Destructor.

virtual void	loadFem (const std::string &filename)=0
	Loads the FEM file into an Fem class data structure. More...

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...

virtual 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())=0
	Add an external generalized force applied on a specific localization. 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...

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

virtual void	transformState (std::shared_ptr< SurgSim::Math::OdeState > state, const SurgSim::Math::RigidTransform3d &transform)=0
	Transform a state using a given transformation. 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...

Protected Attributes
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 \(K = -\frac{\partial f}{\partial x}(x,v)\).

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 ()

Detailed Description

Finite Element Model (a.k.a FEM) is a deformable model (a set of nodes connected by FemElement).

Note: A fem is a DeformableRepresentation (Physics::Representation and Math::OdeEquation), therefore it defines a dynamic system \(M.a=F(x,v)\); + The model handles damping through the Rayleigh damping (it is a combination of mass and stiffness); + The model handles compliance warping (optional) from the paper:; "Efficient Contact Modeling using Compliance Warping", G Saupin, C Duriez, S Cotin, L Grisoni; Computer Graphics International (CGI), Istanbul, Turkey, june 2008.; To use compliance warping, it needs to be turned on by calling setComplianceWarping(true) and the method calculateComplianceWarpingTransformation() needs to be overloaded properly.

Constructor & Destructor Documentation

§ FemRepresentation()

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

explicit

Constructor.

Parameters

name	The name of the FemRepresentation

Member Function Documentation

§ addFemElement()

void SurgSim::Physics::FemRepresentation::addFemElement ( const std::shared_ptr< FemElement > element )

Adds a FemElement.

Parameters

element The FemElement to add to the representation

§ addFemElementsForce()

void SurgSim::Physics::FemRepresentation::addFemElementsForce	(	SurgSim::Math::Vector *	f,
		const SurgSim::Math::OdeState &	state,
		double	scale = `1.0`
	)

protected

Adds the FemElements forces to f (given a state)

Parameters

[in,out]	f	The force vector to cumulate the FemElements forces into
	state	The state vector containing positions and velocities
	scale	A scaling factor to scale the FemElements forces with

§ addGravityForce()

void SurgSim::Physics::FemRepresentation::addGravityForce	(	SurgSim::Math::Vector *	f,
		const SurgSim::Math::OdeState &	state,
		double	scale = `1.0`
	)

protected

Adds the gravity force to f (given a state)

Parameters

[in,out]	f	The force vector to cumulate the gravity force into
	state	The state vector containing positions and velocities
	scale	A scaling factor to scale the gravity force with

Note: This method does not do anything if gravity is disabled

§ addRayleighDampingForce()

void SurgSim::Physics::FemRepresentation::addRayleighDampingForce	(	SurgSim::Math::Vector *	f,
		const SurgSim::Math::OdeState &	state,
		bool	useGlobalMassMatrix = `false`,
		bool	useGlobalStiffnessMatrix = `false`,
		double	scale = `1.0`
	)

protected

Adds the Rayleigh damping forces.

Parameters

[in,out]	f	The force vector to cumulate the Rayleigh damping force into
	state	The state vector containing positions and velocities
	useGlobalMassMatrix,useGlobalStiffnessMatrix	True indicates that the global mass and stiffness matrices should be used (F = -c.M.v - d.K.v)
	scale	A scaling factor to apply on the damping force

Note: Damping matrix D = c.M + d.K (Rayleigh damping definition); F = - D.v = -c.M.v - d.K.v; If {useGlobalMassMatrix | useGlobalStiffnessMatrix} is True, {M | K} will be used; If {useGlobalMassMatrix | useGlobalStiffnessMatrix} is False; the {mass|stiffness} component will be computed FemElement by FemElement

§ applyCompliance()

Math::Matrix SurgSim::Physics::FemRepresentation::applyCompliance	(	const Math::OdeState &	state,
		const Math::Matrix &	b
	)

overridevirtual

Calculate the product \(C.b\) where \(C\) is the compliance matrix with boundary conditions applied.

Note that this can be rewritten as \((B^T)(M^{-1})(B.b) = (B^T)((M^{-1})(B.b)) = x\), where \((M^{-1})(B.b) = y\) is simply the solution to \(M.y = B.b\) and \(B^T.y = x\).

Parameters

state	\((x, v)\) the current position and velocity to evaluate the various terms with
b	The input matrix

Returns: The matrix \(C.b\)

Reimplemented from SurgSim::Physics::DeformableRepresentation.

§ beforeUpdate()

void SurgSim::Physics::FemRepresentation::beforeUpdate ( double dt )

overridevirtual

Preprocessing done before the update call.

Parameters

dt	The time step (in seconds)

Reimplemented from SurgSim::Physics::Representation.

§ calculateComplianceWarpingTransformation()

void SurgSim::Physics::FemRepresentation::calculateComplianceWarpingTransformation ( const SurgSim::Math::OdeState & state )

protectedvirtual

Calculates and stores the compliance warping transformation matrix.

Parameters

state The state to extract the node transformation from

Reimplemented in SurgSim::Physics::MockFemRepresentationValidComplianceWarping, and SurgSim::Physics::Fem3DCorotationalTetrahedronRepresentation.

§ computeD()

void SurgSim::Physics::FemRepresentation::computeD ( const SurgSim::Math::OdeState & state )

overrideprotectedvirtual

Evaluation of \(D = -\frac{\partial f}{\partial v}(x,v)\) for a given state.

Parameters

state \((x, v)\) the current position and velocity to evaluate the Jacobian matrix with

Implements SurgSim::Math::OdeEquation.

§ computeF()

void SurgSim::Physics::FemRepresentation::computeF ( const SurgSim::Math::OdeState & state )

overrideprotectedvirtual

Evaluation of the RHS function \(f(x, v)\) for a given state.

Parameters

state \((x, v)\) the current position and velocity to evaluate the function \(f(x,v)\) with

Implements SurgSim::Math::OdeEquation.

§ computeFMDK()

void SurgSim::Physics::FemRepresentation::computeFMDK ( const SurgSim::Math::OdeState & state )

overrideprotectedvirtual

Evaluation of \(f(x,v)\), \(M(x,v)\), \(D = -\frac{\partial f}{\partial v}(x,v)\) and \(K = -\frac{\partial f}{\partial x}(x,v)\).

When all the terms are needed, this method can perform optimization in evaluating everything together

Parameters

state \((x, v)\) the current position and velocity to evaluate the various terms with

Note: computeF(), computeM(), computeD(), computeK()

Implements SurgSim::Math::OdeEquation.

§ computeK()

void SurgSim::Physics::FemRepresentation::computeK ( const SurgSim::Math::OdeState & state )

overrideprotectedvirtual

Evaluation of \(K = -\frac{\partial f}{\partial x}(x,v)\) for a given state.

Parameters

state \((x, v)\) the current position and velocity to evaluate the Jacobian matrix with

Implements SurgSim::Math::OdeEquation.

§ computeM()

void SurgSim::Physics::FemRepresentation::computeM ( const SurgSim::Math::OdeState & state )

overrideprotectedvirtual

Evaluation of the LHS matrix \(M(x,v)\) for a given state.

Parameters

state \((x, v)\) the current position and velocity to evaluate the matrix \(M(x,v)\) with

Implements SurgSim::Math::OdeEquation.

§ doInitialize()

bool SurgSim::Physics::FemRepresentation::doInitialize ( )

overrideprotectedvirtual

Interface to be implemented by derived classes.

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

Reimplemented from SurgSim::Physics::DeformableRepresentation.

Reimplemented in SurgSim::Physics::MockFem1DRepresentation.

§ getComplianceWarping()

bool SurgSim::Physics::FemRepresentation::getComplianceWarping ( ) const

Get the compliance warping flag (default = false)

Returns: True if compliance warping is used, False otherwise

§ getFemElement()

std::shared_ptr< FemElement > SurgSim::Physics::FemRepresentation::getFemElement ( size_t femElementId )

Retrieves a given FemElement from its id.

Parameters

femElementId The FemElement id for which the FemElement is requested

Returns: The FemElement for the given femElementId

Note: The FemElement is returned with read/write access; Out of range femElementId will raise an exception

§ getFemElementType()

const std::string & SurgSim::Physics::FemRepresentation::getFemElementType ( ) const

Gets the FemElement type pulled from the object factory.

Returns: A string of the full registered OSS class name in the factory

§ getMassLumping()

bool SurgSim::Physics::FemRepresentation::getMassLumping ( ) const

Returns: True if lumped masses are enabled

§ getNodeTransformation()

SurgSim::Math::Matrix SurgSim::Physics::FemRepresentation::getNodeTransformation	(	const SurgSim::Math::OdeState &	state,
		size_t	nodeId
	)		const

protectedvirtual

Retrieves a specific node transformation (useful for compliance warping)

Parameters

state	The state to extract the node transformation from
nodeId	The node to update the rotation for

Returns: The node transformation. i.e. a numDofPerNode x numDofPerNode matrix

Reimplemented in SurgSim::Physics::Fem3DCorotationalTetrahedronRepresentation.

§ getNumFemElements()

size_t SurgSim::Physics::FemRepresentation::getNumFemElements ( ) const

Gets the number of FemElement.

Returns: the number of FemElement

§ getRayleighDampingMass()

double SurgSim::Physics::FemRepresentation::getRayleighDampingMass ( ) const

Gets the Rayleigh mass parameter.

Returns: The Rayleigh mass parameter

§ getRayleighDampingStiffness()

double SurgSim::Physics::FemRepresentation::getRayleighDampingStiffness ( ) const

Gets the Rayleigh stiffness parameter.

Returns: The Rayleigh stiffness parameter

§ getTotalMass()

double SurgSim::Physics::FemRepresentation::getTotalMass ( ) const

Gets the total mass of the fem.

Returns: The total mass of the fem (in Kg)

§ isComplianceWarpingSynchronous()

bool SurgSim::Physics::FemRepresentation::isComplianceWarpingSynchronous ( ) const

Get whether or not any compliance warping will be done synchronously.

Default is synchronous.

Returns: True if compliance warping is calculated synchronously.

§ isInitialComplianceMatrixComputed()

bool SurgSim::Physics::FemRepresentation::isInitialComplianceMatrixComputed ( ) const

protected

Gets the flag keeping track of the initial compliance matrix calculation (compliance warping case)

Returns: True if the initial compliance matrix has been computed, False otherwise

§ isValidCoordinate()

bool SurgSim::Physics::FemRepresentation::isValidCoordinate ( const SurgSim::DataStructures::IndexedLocalCoordinate & coordinate ) const

virtual

Determines whether the associated coordinate is valid.

Parameters

coordinate Coordinate to check

Returns: True if coordinate is valid

§ loadFem()

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

pure virtual

Loads the FEM file into an Fem class data structure.

Parameters

filename The file to load

Implemented in SurgSim::Physics::MockFemRepresentation, SurgSim::Physics::Fem1DRepresentation, SurgSim::Physics::Fem3DRepresentation, and SurgSim::Physics::Fem2DRepresentation.

§ setComplianceWarping()

void SurgSim::Physics::FemRepresentation::setComplianceWarping ( bool useComplianceWarping )

Set the compliance warping flag.

Parameters

useComplianceWarping True to use compliance warping, False otherwise

Exceptions

SurgSim::Framework::AssertionFailure If the call is done after initialization

Note: Compliance warping is currently disabled in this version.

§ setComplianceWarpingSynchronous()

void SurgSim::Physics::FemRepresentation::setComplianceWarpingSynchronous ( bool complianceWarpingSynchronous )

If using compliance warping, set the calculation to synchronous or asynchronous.

Defaults to synchronous. Synchronous calculation is slower, but after free motion the compliance matrix will be up-to-date, which means the MLCP will be as accurate as possible. Asynchronous calculation is faster, but the compliance matrix will be stale by at least one update.

Parameters

complianceWarpingSynchronous True for synchronous computation of the compliance warping matrix.

Exceptions

SurgSim::Framework::AssertionFailure If the call is done after initialization.

§ setFemElementType()

void SurgSim::Physics::FemRepresentation::setFemElementType ( const std::string & type )

virtual

Sets the FemElement type pulled from the object factory.

Parameters

type	A string of the full registered OSS class name in the factory

Reimplemented in SurgSim::Physics::Fem3DCorotationalTetrahedronRepresentation.

§ setIsInitialComplianceMatrixComputed()

void SurgSim::Physics::FemRepresentation::setIsInitialComplianceMatrixComputed ( bool flag )

protected

Sets the flag keeping track of the initial compliance matrix calculation (compliance warping case)

Parameters

flag	True if the initial compliance matrix is computed, False otherwise

§ setMassLumping()

void SurgSim::Physics::FemRepresentation::setMassLumping ( bool useMassLumping )

Enable mass lumping for the mass matrix, currently we use the row sum i.e.

\(M_{ii}^{(lumped)} = \sum_{j} M_{ji}\)

Parameters

useMassLumping whether to enable or disable lumped masses

§ setRayleighDampingMass()

void SurgSim::Physics::FemRepresentation::setRayleighDampingMass ( double massCoef )

Sets the Rayleigh mass parameter.

Parameters

massCoef The Rayleigh mass parameter

§ setRayleighDampingStiffness()

void SurgSim::Physics::FemRepresentation::setRayleighDampingStiffness ( double stiffnessCoef )

Sets the Rayleigh stiffness parameter.

Parameters

stiffnessCoef The Rayleigh stiffness parameter

§ update()

void SurgSim::Physics::FemRepresentation::update ( double dt )

overridevirtual

Update the representation state to the current time step.

Parameters

dt	The time step (in seconds)

Reimplemented from SurgSim::Physics::DeformableRepresentation.

§ updateComplianceMatrix()

void SurgSim::Physics::FemRepresentation::updateComplianceMatrix ( const SurgSim::Math::OdeState & state )

protected

Updates the compliance matrix using nodes transformation (useful for compliance warping)

Parameters

state The state to compute the nodes transformation from

Note: This computes the diagonal block matrix m_complianceWarpingTransformation and transforms the initial compliance matrix with it.

§ updateFMDK()

void SurgSim::Physics::FemRepresentation::updateFMDK	(	const SurgSim::Math::OdeState &	state,
		int	options
	)

overridevirtual

Update the OdeEquation (and support data) based on the given state.

Parameters

state	\((x, v)\) the current position and velocity to evaluate the various terms with
options	Flag to specify which of F, M, D, K needs to be updated.

Reimplemented from SurgSim::Math::OdeEquation.

Member Data Documentation

§ m_complianceWarpingTransformationForCalculation

Eigen::SparseMatrix<double> SurgSim::Physics::FemRepresentation::m_complianceWarpingTransformationForCalculation

protected

For the asynchronous compliance matrix multiplication.

§ m_femElementType

std::string SurgSim::Physics::FemRepresentation::m_femElementType

protected

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.

Therefore we do not need to define this type in the ply file, but rather is part of the Representation properties (YAML).

§ m_massPerNode

std::vector<double> SurgSim::Physics::FemRepresentation::m_massPerNode

protected

Useful information per node.

Useful in setting up the gravity force F=mg

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

SurgSim/Physics/FemRepresentation.h
SurgSim/Physics/FemRepresentation.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

§ FemRepresentation()

Member Function Documentation

§ addFemElement()

§ addFemElementsForce()

§ addGravityForce()

§ addRayleighDampingForce()

§ applyCompliance()

§ beforeUpdate()

§ calculateComplianceWarpingTransformation()

§ computeD()

§ computeF()

§ computeFMDK()

§ computeK()

§ computeM()

§ doInitialize()

§ getComplianceWarping()

§ getFemElement()

§ getFemElementType()

§ getMassLumping()

§ getNodeTransformation()

§ getNumFemElements()

§ getRayleighDampingMass()

§ getRayleighDampingStiffness()

§ getTotalMass()

§ isComplianceWarpingSynchronous()

§ isInitialComplianceMatrixComputed()

§ isValidCoordinate()

§ loadFem()

§ setComplianceWarping()

§ setComplianceWarpingSynchronous()

§ setFemElementType()

§ setIsInitialComplianceMatrixComputed()

§ setMassLumping()

§ setRayleighDampingMass()

§ setRayleighDampingStiffness()

§ update()

§ updateComplianceMatrix()

§ updateFMDK()

Member Data Documentation

§ m_complianceWarpingTransformationForCalculation

§ m_femElementType

§ m_massPerNode