Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | List of all members
SurgSim::Physics::DeformableRepresentation Class Referenceabstract

Base class for all deformable representations MassSprings, Finite Element Models,... More...

#include <SurgSim/Physics/DeformableRepresentation.h>

Inheritance diagram for SurgSim::Physics::DeformableRepresentation:
SurgSim::Physics::Representation SurgSim::Math::OdeEquation SurgSim::Framework::Representation SurgSim::Framework::Component SurgSim::Framework::Accessible SurgSim::Physics::FemRepresentation SurgSim::Physics::MassSpringRepresentation SurgSim::Physics::Fem1DRepresentation SurgSim::Physics::Fem2DRepresentation SurgSim::Physics::Fem3DRepresentation SurgSim::Blocks::MassSpring1DRepresentation SurgSim::Blocks::MassSpring2DRepresentation SurgSim::Blocks::MassSpring3DRepresentation SurgSim::Physics::DivisbleCubeRepresentation SurgSim::Physics::TruthCubeRepresentation

Public Member Functions

 DeformableRepresentation (const std::string &name)
 Constructor. More...
 
virtual ~DeformableRepresentation ()
 Destructor. More...
 
virtual void resetState () override
 Reset the representation to its initial/default state. More...
 
virtual void setInitialState (std::shared_ptr< SurgSim::Math::OdeState > initialState)
 
virtual const std::shared_ptr< SurgSim::Math::OdeStategetCurrentState () const
 
virtual const std::shared_ptr< SurgSim::Math::OdeStategetPreviousState () const
 
virtual const std::shared_ptr< SurgSim::Math::OdeStategetFinalState () const
 
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...
 
virtual void addExternalGeneralizedForce (std::shared_ptr< Localization > localization, 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::VectorgetExternalGeneralizedForce () const
 
const SurgSim::Math::MatrixgetExternalGeneralizedStiffness () const
 
const SurgSim::Math::MatrixgetExternalGeneralizedDamping () const
 
const SurgSim::Math::MatrixgetComplianceMatrix () const
 Gets the compliance matrix associated with motion. More...
 
virtual void update (double dt) override
 Update the representation state to the current time step. More...
 
virtual void afterUpdate (double dt) override
 Postprocessing done after the update call This needs to be called from the outside usually from a Computation. More...
 
virtual 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 (void)
 Deactivate and call resetState. More...
 
virtual 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...
 
- Public Member Functions inherited from SurgSim::Physics::Representation
 Representation (const std::string &name)
 Constructor. More...
 
virtual ~Representation ()
 Destructor. More...
 
virtual RepresentationType getType () const =0
 Query the representation type. More...
 
virtual void resetParameters ()
 Reset the representation parameters to their initial/default values. More...
 
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 void beforeUpdate (double dt)
 Preprocessing done before the update call This needs to be called from the outside usually from a Computation. More...
 
virtual std::shared_ptr< LocalizationcreateLocalization (const SurgSim::DataStructures::Location &location)
 Computes a localized coordinate w.r.t this representation, given a Location object. More...
 
std::shared_ptr< SurgSim::Collision::RepresentationgetCollisionRepresentation () const
 
- Public Member Functions inherited from SurgSim::Framework::Representation
 Representation (const std::string &name)
 Constructor. More...
 
virtual void setLocalPose (const SurgSim::Math::RigidTransform3d &pose)
 Set the pose of the representation with respect to the Scene Element. 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. More...
 
std::string getName () const
 Gets component name. More...
 
void setName (const std::string &name)
 Sets the name of component. More...
 
boost::uuids::uuid getUuid () const
 Gets the id of the component. More...
 
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 setScene (std::weak_ptr< Scene > scene)
 Sets the scene. More...
 
std::shared_ptr< ScenegetScene ()
 Gets the scene. More...
 
void setSceneElement (std::weak_ptr< SceneElement > sceneElement)
 Sets the scene element. More...
 
std::shared_ptr< SceneElementgetSceneElement ()
 Gets the scene element. More...
 
std::shared_ptr< const SceneElementgetSceneElement () const
 Gets the scene element, constant version. More...
 
std::shared_ptr< RuntimegetRuntime () 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< ComponentgetSharedPtr ()
 Gets a shared pointer to this component. More...
 
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. More...
 
 ~Accessible ()
 Destructor. More...
 
template<class 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...
 
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...
 
template<>
boost::any getValue (const std::string &name) const
 
- Public Member Functions inherited from SurgSim::Math::OdeEquation
virtual ~OdeEquation ()
 Virtual destructor. More...
 
const std::shared_ptr< OdeStategetInitialState () const
 Retrieves the ode initial conditions (x0, v0) (i.e. More...
 
virtual VectorcomputeF (const OdeState &state)=0
 Evaluation of the RHS function f(x,v) for a given state. More...
 
virtual const MatrixcomputeM (const OdeState &state)=0
 Evaluation of the LHS matrix M(x,v) for a given state. More...
 
virtual const MatrixcomputeD (const OdeState &state)=0
 Evaluation of D = -df/dv (x,v) for a given state. More...
 
virtual const MatrixcomputeK (const OdeState &state)=0
 Evaluation of K = -df/dx (x,v) for a given state. More...
 
virtual void computeFMDK (const OdeState &state, Vector **f, Matrix **M, Matrix **D, Matrix **K)=0
 Evaluation of f(x,v), M(x,v), D = -df/dv(x,v), K = -df/dx(x,v) When all the terms are needed, this method can perform optimization in evaluating everything together. More...
 

Protected Member Functions

virtual 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::Vector3dgetGravity () 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< PoseComponentgetPoseComponent ()
 Get the PoseComponent for this component. More...
 
virtual std::shared_ptr< const PoseComponentgetPoseComponent () const
 Get the PoseComponent for this component, constant access. More...
 

Protected Attributes

std::shared_ptr< SurgSim::Math::OdeStatem_previousState
 The previous state inside the calculation loop, this has no meaning outside of the loop. More...
 
std::shared_ptr< SurgSim::Math::OdeStatem_currentState
 The currently calculated state inside the physics loop, after the whole calculation is done this will become m_finalState. More...
 
std::shared_ptr< SurgSim::Math::OdeStatem_newState
 New state is a temporary variable to store the newly computed state. More...
 
std::shared_ptr< SurgSim::Math::OdeStatem_finalState
 Last valid state (a.k.a final state) More...
 
SurgSim::Math::Vector m_f
 Force applied on the deformable representation. More...
 
SurgSim::Math::Matrix m_M
 Mass matrix. More...
 
SurgSim::Math::Matrix m_D
 Damping matrix. More...
 
SurgSim::Math::Matrix m_K
 Stiffness matrix. 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) More...
 
bool m_needToReloadOdeSolver
 Specify if the Ode Solver needs to be (re)loaded (do not exist yet, or integration scheme has changed) More...
 
std::shared_ptr< SurgSim::Math::OdeSolverm_odeSolver
 Ode solver (its type depends on the numerical integration scheme) More...
 
SurgSim::Math::Vector m_externalGeneralizedForce
 External generalized force, stiffness and damping applied on the deformable representation. More...
 
SurgSim::Math::Matrix m_externalGeneralizedStiffness
 External generalized force, stiffness and damping applied on the deformable representation. More...
 
SurgSim::Math::Matrix m_externalGeneralizedDamping
 External generalized force, stiffness and damping applied on the deformable representation. More...
 
- Protected Attributes inherited from SurgSim::Physics::Representation
std::shared_ptr< SurgSim::Collision::Representationm_collisionRepresentation
 This entity's collision representation, these are usually very specific to the physics representation. More...
 
- Protected Attributes inherited from SurgSim::Math::OdeEquation
std::shared_ptr< OdeStatem_initialState
 The initial state (which defines the ODE initial conditions (x0, v0)) More...
 

Private Member Functions

 DeformableRepresentation (const DeformableRepresentation &)
 NO copy constructor. More...
 
DeformableRepresentationoperator= (const DeformableRepresentation &)
 NO assignment operator. More...
 

Additional Inherited Members

- Public Types inherited from SurgSim::Framework::Component
typedef SurgSim::Framework::ObjectFactory1< SurgSim::Framework::Component, std::string > FactoryType
 
- 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
 
- Static Public Member Functions inherited from SurgSim::Framework::Component
static FactoryTypegetFactory ()
 

Detailed Description

Base class for all deformable representations MassSprings, Finite Element Models,...

Note
It is both a Physics::Representation and a Math::OdeEquation
It holds the representation states (common to all deformable) except the initial state,
which is being held by the OdeEquation (initial condition of the ode problem).
It holds the initial pose, which should be set before setting the initial state so the states
can be properly transformed.
The current pose is always identity and therefore cannot be set. Calling setPose will raise an exception.
It holds the force vector; the mass, damping and stiffness matrices
Derived classes must implement the Representation API and the OdeEquation API, also set
m_numDofPerNode and call Representation::setNumDof()

Constructor & Destructor Documentation

SurgSim::Physics::DeformableRepresentation::DeformableRepresentation ( const std::string &  name)
explicit

Constructor.

Parameters
nameThe deformable representation's name
SurgSim::Physics::DeformableRepresentation::~DeformableRepresentation ( )
virtual

Destructor.

SurgSim::Physics::DeformableRepresentation::DeformableRepresentation ( const DeformableRepresentation )
private

NO copy constructor.

Member Function Documentation

virtual void SurgSim::Physics::DeformableRepresentation::addExternalGeneralizedForce ( std::shared_ptr< Localization localization,
SurgSim::Math::Vector generalizedForce,
const SurgSim::Math::Matrix K = SurgSim::Math::Matrix(),
const SurgSim::Math::Matrix D = SurgSim::Math::Matrix() 
)
pure virtual

Add an external generalized force applied on a specific localization.

Parameters
localizationwhere the generalized force is applied
generalizedForceThe force to apply (of dimension getNumDofPerNode())
KThe stiffness matrix associated with the generalized force (Jacobian of the force w.r.t dof's position)
DThe damping matrix associated with the generalized force (Jacobian of the force w.r.t dof's velocity)

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

void SurgSim::Physics::DeformableRepresentation::afterUpdate ( double  dt)
overridevirtual

Postprocessing done after the update call This needs to be called from the outside usually from a Computation.

Parameters
dtThe time step (in seconds)

Reimplemented from SurgSim::Physics::Representation.

Reimplemented in SurgSim::Physics::FemRepresentation.

void SurgSim::Physics::DeformableRepresentation::applyCorrection ( double  dt,
const Eigen::VectorBlock< SurgSim::Math::Vector > &  deltaVelocity 
)
overridevirtual

Update the Representation's current position and velocity using a time interval, dt, and change in velocity, deltaVelocity.

This function typically is called in the physics pipeline (PhysicsManager::doUpdate) after solving the equations that enforce constraints when collisions occur. Specifically it is called in the PushResults::doUpdate step.

Parameters
dtThe time step
deltaVelocityThe block of a vector containing the correction to be applied to the velocity

Reimplemented from SurgSim::Physics::Representation.

void SurgSim::Physics::DeformableRepresentation::deactivateAndReset ( void  )

Deactivate and call resetState.

bool SurgSim::Physics::DeformableRepresentation::doWakeUp ( )
overrideprotectedvirtual

Interface to be implemented by derived classes.

Returns
True if component is woken up successfully; otherwise, false.

Reimplemented from SurgSim::Framework::Representation.

Reimplemented in SurgSim::Physics::Fem3DRepresentation, SurgSim::Physics::Fem1DRepresentation, and SurgSim::Blocks::MassSpring1DRepresentation.

const SurgSim::Math::Matrix & SurgSim::Physics::DeformableRepresentation::getComplianceMatrix ( ) const

Gets the compliance matrix associated with motion.

Returns
The compliance matrix
Note
The compliance matrix is computed automatically by the ode solver in the method 'update'
So one iteration needs to happen before retrieving a compliance matrix
const std::shared_ptr< SurgSim::Math::OdeState > SurgSim::Physics::DeformableRepresentation::getCurrentState ( ) const
virtual
const SurgSim::Math::Matrix & SurgSim::Physics::DeformableRepresentation::getExternalGeneralizedDamping ( ) const
Returns
the external generalized damping matrix
const SurgSim::Math::Vector & SurgSim::Physics::DeformableRepresentation::getExternalGeneralizedForce ( ) const
Returns
the external generalized force vector
const SurgSim::Math::Matrix & SurgSim::Physics::DeformableRepresentation::getExternalGeneralizedStiffness ( ) const
Returns
the external generalized stiffness matrix
const std::shared_ptr< SurgSim::Math::OdeState > SurgSim::Physics::DeformableRepresentation::getFinalState ( ) const
virtual
SurgSim::Math::IntegrationScheme SurgSim::Physics::DeformableRepresentation::getIntegrationScheme ( ) const

Gets the numerical integration scheme.

Returns
The integration scheme currently in use
size_t SurgSim::Physics::DeformableRepresentation::getNumDofPerNode ( ) const

Gets the number of degrees of freedom per node.

Returns
The number of degrees of freedom per node for this Deformable Representation
const std::shared_ptr< SurgSim::Math::OdeState > SurgSim::Physics::DeformableRepresentation::getPreviousState ( ) const
virtual
DeformableRepresentation& SurgSim::Physics::DeformableRepresentation::operator= ( const DeformableRepresentation )
private

NO assignment operator.

void SurgSim::Physics::DeformableRepresentation::resetState ( )
overridevirtual

Reset the representation to its initial/default state.

Reimplemented from SurgSim::Physics::Representation.

void SurgSim::Physics::DeformableRepresentation::setCollisionRepresentation ( std::shared_ptr< SurgSim::Collision::Representation representation)
overridevirtual

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.

Specializes for discarding anything besides a rigid collision representation.

Parameters
representationThe collision representation to be used.

Reimplemented from SurgSim::Physics::Representation.

void SurgSim::Physics::DeformableRepresentation::setInitialState ( std::shared_ptr< SurgSim::Math::OdeState initialState)
virtual
void SurgSim::Physics::DeformableRepresentation::setIntegrationScheme ( SurgSim::Math::IntegrationScheme  integrationScheme)

Sets the numerical integration scheme.

Parameters
integrationSchemeThe integration scheme to use
Note
Calling setIntegrationScheme after the component has been awoken will raise an assert
virtual void SurgSim::Physics::DeformableRepresentation::transformState ( std::shared_ptr< SurgSim::Math::OdeState state,
const SurgSim::Math::RigidTransform3d transform 
)
protectedpure virtual

Transform a state using a given transformation.

Parameters
[in,out]stateThe state to be transformed
transformThe transformation to apply

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

void SurgSim::Physics::DeformableRepresentation::update ( double  dt)
overridevirtual

Update the representation state to the current time step.

Parameters
dtThe time step (in seconds)

Reimplemented from SurgSim::Physics::Representation.

Member Data Documentation

std::shared_ptr<SurgSim::Math::OdeState> SurgSim::Physics::DeformableRepresentation::m_currentState
protected

The currently calculated state inside the physics loop, after the whole calculation is done this will become m_finalState.

SurgSim::Math::Matrix SurgSim::Physics::DeformableRepresentation::m_D
protected

Damping matrix.

SurgSim::Math::Matrix SurgSim::Physics::DeformableRepresentation::m_externalGeneralizedDamping
protected

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

SurgSim::Math::Vector SurgSim::Physics::DeformableRepresentation::m_externalGeneralizedForce
protected

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

SurgSim::Math::Matrix SurgSim::Physics::DeformableRepresentation::m_externalGeneralizedStiffness
protected

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

SurgSim::Math::Vector SurgSim::Physics::DeformableRepresentation::m_f
protected

Force applied on the deformable representation.

std::shared_ptr<SurgSim::Math::OdeState> SurgSim::Physics::DeformableRepresentation::m_finalState
protected

Last valid state (a.k.a final state)

Note
Backup of the current state for thread-safety access while the current state is being recomputed.
SurgSim::Math::IntegrationScheme SurgSim::Physics::DeformableRepresentation::m_integrationScheme
protected

Numerical Integration scheme (dynamic explicit/implicit solver)

SurgSim::Math::Matrix SurgSim::Physics::DeformableRepresentation::m_K
protected

Stiffness matrix.

SurgSim::Math::Matrix SurgSim::Physics::DeformableRepresentation::m_M
protected

Mass matrix.

bool SurgSim::Physics::DeformableRepresentation::m_needToReloadOdeSolver
protected

Specify if the Ode Solver needs to be (re)loaded (do not exist yet, or integration scheme has changed)

std::shared_ptr<SurgSim::Math::OdeState> SurgSim::Physics::DeformableRepresentation::m_newState
protected

New state is a temporary variable to store the newly computed state.

size_t SurgSim::Physics::DeformableRepresentation::m_numDofPerNode
protected

Number of degrees of freedom per node (varies per deformable model)

Note
MUST be set by the derived classes
std::shared_ptr<SurgSim::Math::OdeSolver> SurgSim::Physics::DeformableRepresentation::m_odeSolver
protected

Ode solver (its type depends on the numerical integration scheme)

std::shared_ptr<SurgSim::Math::OdeState> SurgSim::Physics::DeformableRepresentation::m_previousState
protected

The previous state inside the calculation loop, this has no meaning outside of the loop.


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