Implementation of a two state (activation and fiber-length) Muscle model by Thelen 2003. This a complete rewrite of a previous implementation (present in OpenSim 2.4 and earlier) contained numerous errors. More...

#include <Thelen2003Muscle.h>

Inheritance diagram for OpenSim::Thelen2003Muscle:

Public Types
enum	CurveType { FiberActiveForceLength, FiberPassiveForceLength, FiberForceVelocity, TendonForceLength }

Public Member Functions
	Thelen2003Muscle ()
	Thelen2003Muscle (const std::string &aName, double aMaxIsometricForce, double aOptimalFiberLength, double aTendonSlackLength, double aPennationAngle)
double	getActivationTimeConstant () const
double	getMinimumActivation () const
double	getDeactivationTimeConstant () const
double	getFmaxTendonStrain () const
double	getFmaxMuscleStrain () const
double	getKshapeActive () const
double	getKshapePassive () const
double	getAf () const
double	getFlen () const
double	getForceVelocityExtrapolationThreshold () const
double	getMinimumFiberLength () const
double	getMaximumPennationAngle () const
bool	setActivationTimeConstant (double aActivationTimeConstant)
bool	setDeactivationTimeConstant (double aDeactivationTimeConstant)
bool	setMinimumActivation (double aActivationMinValue)
bool	setFmaxTendonStrain (double aFmaxTendonStrain)
bool	setFmaxFiberStrain (double aFmaxMuscleStrain)
bool	setKshapeActive (double aKShapeActive)
bool	setKshapePassive (double aKshapePassive)
bool	setAf (double aAf)
bool	setFlen (double aFlen)
bool	setForceVelocityExtrapolationThreshold (double aFvThresh)
const MuscleFirstOrderActivationDynamicModel &	getActivationModel () const
const MuscleFixedWidthPennationModel &	getPennationModel () const
void	printCurveToCSVFile (const CurveType ctype, const std::string &path)
virtual double	computeActuation (const SimTK::State &s) const override
	Actuator interface for a muscle computes the tension in the muscle and applied by the tendon to bones (i.e.
void	computeInitialFiberEquilibrium (SimTK::State &s) const override
	Compute initial fiber length (velocity) such that muscle fiber and tendon are in static equilibrium and update the state.
Property declarations
These are the serializable properties associated with this class.
	OpenSim_DECLARE_PROPERTY (activation_time_constant, double,"time constant for ramping up muscle activation")
	OpenSim_DECLARE_PROPERTY (deactivation_time_constant, double,"time constant for ramping down of muscle activation")
	OpenSim_DECLARE_PROPERTY (FmaxTendonStrain, double,"tendon strain at maximum isometric muscle force")
	OpenSim_DECLARE_PROPERTY (FmaxMuscleStrain, double,"passive muscle strain at maximum isometric muscle force")
	OpenSim_DECLARE_PROPERTY (KshapeActive, double,"shape factor for Gaussian active muscle force-length relationship")
	OpenSim_DECLARE_PROPERTY (KshapePassive, double,"exponential shape factor for passive force-length relationship")
	OpenSim_DECLARE_PROPERTY (Af, double,"force-velocity shape factor")
	OpenSim_DECLARE_PROPERTY (Flen, double,"maximum normalized lengthening force")
	OpenSim_DECLARE_PROPERTY (fv_linear_extrap_threshold, double,"fv threshold where linear extrapolation is used")
Public Member Functions inherited from OpenSim::ActivationFiberLengthMuscle
	ActivationFiberLengthMuscle ()
double	getDefaultActivation () const
void	setDefaultActivation (double activation)
double	getDefaultFiberLength () const
void	setDefaultFiberLength (double length)
void	setActivation (SimTK::State &s, double activation) const
	DEPRECATED: only for backward compatibility.
void	setFiberLength (SimTK::State &s, double fiberLength) const
virtual Array< std::string >	getStateVariableNames () const override
	Get the names of "continuous" state variables maintained by the ModelComponent and its subcomponents.
virtual SimTK::SystemYIndex	getStateVariableSystemIndex (const std::string &stateVariableName) const override
	Get the System Index of a state variable allocated by this ModelComponent.
double	getActivationRate (const SimTK::State &s) const
	OpenSim_DECLARE_PROPERTY (default_activation, double,"Assumed activation level if none is assigned.")
	OpenSim_DECLARE_PROPERTY (default_fiber_length, double,"Assumed fiber length, unless otherwise assigned.")
Public Member Functions inherited from OpenSim::Muscle
	OpenSim_DECLARE_PROPERTY (max_isometric_force, double,"Maximum isometric force that the fibers can generate")
	OpenSim_DECLARE_PROPERTY (optimal_fiber_length, double,"Optimal length of the muscle fibers")
	OpenSim_DECLARE_PROPERTY (tendon_slack_length, double,"Resting length of the tendon")
	OpenSim_DECLARE_PROPERTY (pennation_angle_at_optimal, double,"Angle between tendon and fibers at optimal fiber length expressed in radians")
	OpenSim_DECLARE_PROPERTY (max_contraction_velocity, double,"Maximum contraction velocity of the fibers, in optimal fiberlengths/second")
	OpenSim_DECLARE_PROPERTY (ignore_tendon_compliance, bool,"Compute muscle dynamics ignoring tendon compliance. Tendon is assumed to be rigid.")
	OpenSim_DECLARE_PROPERTY (ignore_activation_dynamics, bool,"Compute muscle dynamics ignoring activation dynamics. Activation is equivalent to excitation.")
	Muscle ()
	Default constructor.
double	getMaxIsometricForce () const
	get/set the maximum isometric force (in N) that the fibers can generate
void	setMaxIsometricForce (double maxIsometricForce)
double	getOptimalFiberLength () const
	get/set the optimal length (in m) of the muscle fibers (lumped as a single fiber)
void	setOptimalFiberLength (double optimalFiberLength)
double	getTendonSlackLength () const
	get/set the resting (slack) length (in m) of the tendon that is in series with the muscle fiber
void	setTendonSlackLength (double tendonSlackLength)
double	getPennationAngleAtOptimalFiberLength () const
	get/set the angle (in radians) between fibers at their optimal fiber length and the tendon
void	setPennationAngleAtOptimalFiberLength (double pennationAngle)
double	getMaxContractionVelocity () const
	get/set the maximum contraction velocity of the fibers, in optimal fiber-lengths per second
void	setMaxContractionVelocity (double maxContractionVelocity)
bool	getIgnoreTendonCompliance (const SimTK::State &s) const
	Get/set Modeling (runtime) option to ignore tendon compliance when computing muscle dynamics.
void	setIgnoreTendonCompliance (SimTK::State &s, bool ignore) const
bool	getIgnoreActivationDynamics (const SimTK::State &s) const
	Get/set Modeling (runtime) option to ignore activation dynamics when computing muscle dynamics.
void	setIgnoreActivationDynamics (SimTK::State &s, bool ignore) const
virtual double	getActivation (const SimTK::State &s) const
	get the activation level of the muscle, which modulates the active force of the muscle and has a normalized (0 to 1) value Note: method remains virtual to permit override by deprecated muscles.
double	getFiberLength (const SimTK::State &s) const
	get the current working fiber length (m) for the muscle
double	getPennationAngle (const SimTK::State &s) const
	get the current pennation angle (radians) between the fiber and tendon at the current fiber length
double	getCosPennationAngle (const SimTK::State &s) const
	get the cosine of the current pennation angle (radians) between the fiber and tendon at the current fiber length
double	getTendonLength (const SimTK::State &s) const
	get the current tendon length (m) given the current joint angles and fiber length
double	getNormalizedFiberLength (const SimTK::State &s) const
	get the current normalized fiber length (fiber_length/optimal_fiber_length)
double	getFiberLengthAlongTendon (const SimTK::State &s) const
	get the current fiber length (m) projected (*cos(pennationAngle)) onto the tendon direction
double	getTendonStrain (const SimTK::State &s) const
	get the current tendon strain (delta_l/tendon_slack_length is dimensionless)
double	getFiberPotentialEnergy (const SimTK::State &s) const
	the potential energy (J) stored in the fiber due to its parallel elastic element
double	getTendonPotentialEnergy (const SimTK::State &s) const
	the potential energy (J) stored in the tendon
double	getMusclePotentialEnergy (const SimTK::State &s) const
	the total potential energy (J) stored in the muscle
double	getPassiveForceMultiplier (const SimTK::State &s) const
	get the passive fiber (parallel elastic element) force multiplier
double	getActiveForceLengthMultiplier (const SimTK::State &s) const
	get the active fiber (contractile element) force multiplier due to current fiber length
double	getFiberVelocity (const SimTK::State &s) const
	get current fiber velocity (m/s) positive is lengthening
double	getNormalizedFiberVelocity (const SimTK::State &s) const
	get normalize fiber velocity (fiber_lengths/s / max_contraction_velocity)
double	getFiberVelocityAlongTendon (const SimTK::State &s) const
	get the current afiber velocity (m/s) projected onto the tendon direction
double	getPennationAngularVelocity (const SimTK::State &s) const
	get pennation angular velocity (radians/s)
double	getTendonVelocity (const SimTK::State &s) const
	get the tendon velocity (m/s) positive is lengthening
double	getForceVelocityMultiplier (const SimTK::State &s) const
	get the dimensionless multiplier resulting from the fiber's force-velocity curve
double	getFiberForce (const SimTK::State &s) const
	get the current fiber force (N) applied to the tendon
double	getFiberForceAlongTendon (const SimTK::State &s) const
	get the force of the fiber (N/m) along the direction of the tendon
double	getActiveFiberForce (const SimTK::State &s) const
	get the current active fiber force (N) due to activationforce_lengthforce_velocity relationships
double	getPassiveFiberForce (const SimTK::State &s) const
	get the current passive fiber force (N) passive_force_length relationship
double	getActiveFiberForceAlongTendon (const SimTK::State &s) const
	get the current active fiber force (N) projected onto the tendon direction
double	getPassiveFiberForceAlongTendon (const SimTK::State &s) const
	get the current passive fiber force (N) projected onto the tendon direction
double	getTendonForce (const SimTK::State &s) const
	get the current tendon force (N) applied to bones
double	getFiberStiffness (const SimTK::State &s) const
	get the current fiber stiffness (N/m) defined as the partial derivative of fiber force w.r.t.
double	getFiberStiffnessAlongTendon (const SimTK::State &s) const
	get the stiffness of the fiber (N/m) along the direction of the tendon, that is the partial derivative of the fiber force along the tendon with respect to small changes in fiber length along the tendon
double	getTendonStiffness (const SimTK::State &s) const
	get the current tendon stiffness (N/m) defined as the partial derivative of tendon force w.r.t.
double	getMuscleStiffness (const SimTK::State &s) const
	get the current muscle stiffness (N/m) defined as the partial derivative of muscle force w.r.t.
double	getFiberActivePower (const SimTK::State &s) const
	get the current active fiber power (W)
double	getFiberPassivePower (const SimTK::State &s) const
	get the current passive fiber power (W)
double	getTendonPower (const SimTK::State &s) const
	get the current tendon power (W)
double	getMusclePower (const SimTK::State &s) const
	get the current muscle power (W)
double	getStress (const SimTK::State &s) const
	get the stress in the muscle (part of the Actuator interface as well)
void	setExcitation (SimTK::State &s, double excitation) const
	set the excitation (control) for this muscle.
double	getExcitation (const SimTK::State &s) const
void	equilibrate (SimTK::State &s) const
	Find and set the equilibrium state of the muscle (if any)
Public Member Functions inherited from OpenSim::PathActuator
	PathActuator ()
GeometryPath &	updGeometryPath ()
const GeometryPath &	getGeometryPath () const
virtual bool	hasGeometryPath () const
	Return a flag indicating whether the Force is applied along a Path.
void	setOptimalForce (double aOptimalForce)
double	getOptimalForce () const
virtual double	getLength (const SimTK::State &s) const
virtual double	getLengtheningSpeed (const SimTK::State &s) const
virtual double	getPower (const SimTK::State &s) const
void	addNewPathPoint (const std::string &proposedName, OpenSim::Body &aBody, const SimTK::Vec3 &aPositionOnBody)
	Note that this function does not maintain the State and so should be used only before a valid State is created.
virtual double	computeMomentArm (const SimTK::State &s, Coordinate &aCoord) const
virtual void	updateFromXMLNode (SimTK::Xml::Element &aNode, int versionNumber=-1)
	Use this method to deserialize an object from a SimTK::Xml::Element.
virtual void	preScale (const SimTK::State &s, const ScaleSet &aScaleSet)
virtual void	scale (const SimTK::State &s, const ScaleSet &aScaleSet)
virtual const VisibleObject *	getDisplayer () const
	Methods to support making the object displayable in the GUI or Visualizer Implemented only in few objects.
virtual void	updateDisplayer (const SimTK::State &s) const
	In case the ModelComponent has a visual representation (VisualObject), override this method to update it.
	OpenSim_DECLARE_UNNAMED_PROPERTY (GeometryPath,"The set of points defining the path of the muscle.")
	OpenSim_DECLARE_PROPERTY (optimal_force, double,"The maximum force this actuator can produce.")
Public Member Functions inherited from OpenSim::Actuator
	Actuator ()
virtual double	getControl (const SimTK::State &s) const
	Convenience method to set controls given scalar (double) valued control.
virtual int	numControls () const
virtual void	setForce (const SimTK::State &s, double aForce) const
virtual double	getForce (const SimTK::State &s) const
virtual void	setSpeed (const SimTK::State &s, double aspeed) const
virtual double	getSpeed (const SimTK::State &s) const
void	setMinControl (const double &aMinControl)
double	getMinControl () const
void	setMaxControl (const double &aMaxControl)
double	getMaxControl () const
void	overrideForce (SimTK::State &s, bool flag) const
	-------------------------------------------------------------------------- Overriding forces -------------------------------------------------------------------------- The force normally produced by an Actuator can be overriden and When the Actuator's force is overriden, the Actuator will by defualt produce a constant force which can be set with setOverrideForce().
bool	isForceOverriden (const SimTK::State &s) const
	return Actuator's override status
void	setOverrideForce (SimTK::State &s, double value) const
	set the force value used when the override is true
double	getOverrideForce (const SimTK::State &s) const
	return override force
	OpenSim_DECLARE_PROPERTY (min_control, double,"Minimum allowed value for control signal. Used primarily when solving ""for control values.")
	Default is -Infinity (no limit).
	OpenSim_DECLARE_PROPERTY (max_control, double,"Maximum allowed value for control signal. Used primarily when solving ""for control values.")
	Default is Infinity (no limit).
Public Member Functions inherited from OpenSim::Actuator_
	Actuator_ ()
virtual const SimTK::Vector	getDefaultControls ()
	Actuator default controls are zero.
virtual const SimTK::VectorView_< double >	getControls (const SimTK::State &s) const
virtual void	getControls (const SimTK::Vector &modelControls, SimTK::Vector &actuatorControls) const
	Convenience methods for getting, setting and adding to actuator controls from/into the model controls.
virtual void	setControls (const SimTK::Vector &actuatorControls, SimTK::Vector &modelControls) const
	set actuator controls subvector into the right slot in the system-wide model controls
virtual void	addInControls (const SimTK::Vector &actuatorControls, SimTK::Vector &modelControls) const
	add actuator controls to the values already occupying the slot in the system-wide model controls
virtual void	computeEquilibrium (SimTK::State &s) const
Public Member Functions inherited from OpenSim::Force
	Force (const Force &aForce)
	Implements a copy constructor just so it can invalidate the SimTK::Force index after copying.
Force &	operator= (const Force &aForce)
	Implements a copy assignment operator just so it can invalidate the SimTK::Force index after the assignment.
bool	isDisabled (const SimTK::State &s) const
	Return if the Force is disabled or not.
void	setDisabled (SimTK::State &s, bool disabled)
	Set the Force as disabled (true) or not (false).
	OpenSim_DECLARE_PROPERTY (isDisabled, bool,"Flag indicating whether the force is disabled or not. Disabled means"" that the force is not active in subsequent dynamics realizations.")
	A Force element is active (enabled) by default.
Public Member Functions inherited from OpenSim::ModelComponent
	ModelComponent ()
	Default constructor.
	ModelComponent (const std::string &aFileName, bool aUpdateFromXMLNode=true) SWIG_DECLARE_EXCEPTION
	Construct ModelComponent from an XML file.
	ModelComponent (SimTK::Xml::Element &aNode)
	Construct ModelComponent from a specific node in an XML document.
	ModelComponent (const ModelComponent &source)
	Construct ModelComponent with its contents copied from another ModelComponent; this is a deep copy so nothing is shared with the source after the copy.
virtual	~ModelComponent ()
	Destructor is virtual to allow concrete model component cleanup.
ModelComponent &	operator= (const ModelComponent &aModelComponent)
	Assignment operator to copy contents of an existing component.
const Model &	getModel () const
	Get a const reference to the Model this component is part of.
Model &	updModel ()
	Get a modifiable reference to the Model this component is part of.
virtual int	getNumStateVariables () const
	Get the number of "Continuous" state variables maintained by the ModelComponent and its specified subcomponents.
int	getModelingOption (const SimTK::State &state, const std::string &name) const
	Get a ModelingOption flag for this ModelComponent by name.
void	setModelingOption (SimTK::State &state, const std::string &name, int flag) const
	Set the value of a ModelingOption flag for this ModelComponent.
double	getStateVariable (const SimTK::State &state, const std::string &name) const
	Get the value of a state variable allocated by this ModelComponent.
void	setStateVariable (SimTK::State &state, const std::string &name, double value) const
	Set the value of a state variable allocated by this ModelComponent by name.
double	getDiscreteVariable (const SimTK::State &state, const std::string &name) const
	Get the value of a discrete variable allocated by this ModelComponent by name.
void	setDiscreteVariable (SimTK::State &state, const std::string &name, double value) const
	Set the value of a discrete variable allocated by this ModelComponent by name.
template<typename T >
const T &	getCacheVariable (const SimTK::State &state, const std::string &name) const
	Get the value of a cache variable allocated by this ModelComponent by name.
template<typename T >
T &	updCacheVariable (const SimTK::State &state, const std::string &name) const
	Obtain a writable cache variable value allocated by this ModelComponent by name.
void	markCacheVariableValid (const SimTK::State &state, const std::string &name) const
	After updating a cache variable value allocated by this ModelComponent, you can mark its value as valid, which will not change until the realization stage falls below the minimum set at the time the cache variable was created.
void	markCacheVariableInvalid (const SimTK::State &state, const std::string &name) const
	Mark a cache variable value allocated by this ModelComponent as invalid.
bool	isCacheVariableValid (const SimTK::State &state, const std::string &name) const
	Enables the to monitor the validity of the cache variable value using the returned flag.
template<typename T >
void	setCacheVariable (const SimTK::State &state, const std::string &name, const T &value) const
	Set cache variable value allocated by this ModelComponent by name.
Public Member Functions inherited from OpenSim::Object
virtual	~Object ()
	Virtual destructor for cleanup.
virtual Object *	clone () const =0
	Create a new heap-allocated copy of the concrete object to which this Object refers.
virtual const std::string &	getConcreteClassName () const =0
	Returns the class name of the concrete Object-derived class of the actual object referenced by this Object, as a string.
virtual VisibleObject *	updDisplayer ()
	get Non const pointer to VisibleObject
bool	isEqualTo (const Object &aObject) const
	Equality operator wrapper for use from languages not supporting operator overloading.
Object &	operator= (const Object &aObject)
	Copy assignment copies he base class fields, including the properties.
virtual bool	operator== (const Object &aObject) const
	Determine if two objects are equal.
virtual bool	operator< (const Object &aObject) const
	Provide an ordering for objects so they can be put in sorted containers.
void	setName (const std::string &name)
	Set the name of the Object.
const std::string &	getName () const
	Get the name of this Object.
void	setDescription (const std::string &description)
	Set description, a one-liner summary.
const std::string &	getDescription () const
	Get description, a one-liner summary.
const std::string &	getAuthors () const
	Get Authors of this Object.
void	setAuthors (const std::string &authors)
	Set Authors of this object, call this method in your constructor if needed.
const std::string &	getReferences () const
	Get references or publications to cite if using this object.
void	setReferences (const std::string &references)
	Set references or publications to cite if using this object.
int	getNumProperties () const
	Determine how many properties are stored with this Object.
const AbstractProperty &	getPropertyByIndex (int propertyIndex) const
	Get a const reference to a property by its index number, returned as an AbstractProperty.
AbstractProperty &	updPropertyByIndex (int propertyIndex)
	Get a writable reference to a property by its index number, returned as an AbstractProperty.
bool	hasProperty (const std::string &name) const
	Return true if this Object has a property of any type with the given name, which must not be empty.
const AbstractProperty &	getPropertyByName (const std::string &name) const
	Get a const reference to a property by its name, returned as an AbstractProperty.
AbstractProperty &	updPropertyByName (const std::string &name)
	Get a writable reference to a property by its name, returned as an AbstractProperty.
template<class T >
bool	hasProperty () const
	Return true if this Object contains an unnamed, one-object property that contains objects of the given template type T.
template<class T >
const Property< T > &	getProperty (const PropertyIndex &index) const
	Get property of known type Property<T> as a const reference; the property must be present and have the right type.
template<class T >
Property< T > &	updProperty (const PropertyIndex &index)
	Get property of known type Property<T> as a writable reference; the property must be present and have the right type.
void	setObjectIsUpToDateWithProperties ()
	When an object is initialized using the current values of its properties, it can set a flag indicating that it is up to date.
bool	isObjectUpToDateWithProperties () const
	Returns `true` if no property's value has changed since the last time setObjectIsUpToDateWithProperties() was called.
void	readObjectFromXMLNodeOrFile (SimTK::Xml::Element &objectElement, int versionNumber)
	We're given an XML element from which we are to populate this Object.
virtual void	updateXMLNode (SimTK::Xml::Element &parent)
	Serialize this object into the XML node that represents it.
bool	getInlined () const
	Inlined means an in-memory Object that is not associated with an XMLDocument.
void	setInlined (bool aInlined, const std::string &aFileName="")
	Mark this as inlined or not and optionally provide a file name to associate with the new XMLDocument for the non-inline case.
std::string	getDocumentFileName () const
	If there is a document associated with this object then return the file name maintained by the document.
void	setAllPropertiesUseDefault (bool aUseDefault)
bool	print (const std::string &fileName)
	Write this Object into an XML file of the given name; conventionally the suffix to use is ".osim".
std::string	dump (bool dumpName=false)
	dump the XML representation of this Object into an std::string and return it.
void	clearObjectIsUpToDateWithProperties ()
	For testing or debugging purposes, manually clear the "object is up to date with respect to properties" flag.
virtual bool	isA (const char *type) const
	The default implementation returns true only if the supplied string is "Object"; each Object-derived class overrides this to match its own class name.
const std::string &	toString () const
	Wrapper to be used on Java side to display objects in tree; this returns just the object's name.
PropertySet &	getPropertySet ()
	OBSOLETE: Get a reference to the PropertySet maintained by the Object.
const PropertySet &	getPropertySet () const

Protected Member Functions
void	calcMuscleLengthInfo (const SimTK::State &s, MuscleLengthInfo &mli) const override
	calculate muscle's position related values such fiber and tendon lengths, normalized lengths, pennation angle, etc...
void	calcFiberVelocityInfo (const SimTK::State &s, FiberVelocityInfo &fvi) const override
	calculate muscle's velocity related values such fiber and tendon velocities,normalized velocities, pennation angular velocity, etc...
void	calcMuscleDynamicsInfo (const SimTK::State &s, MuscleDynamicsInfo &mdi) const override
	calculate muscle's active and passive force-length, force-velocity, tendon force, relationships and their related values
void	calcMusclePotentialEnergyInfo (const SimTK::State &s, MusclePotentialEnergyInfo &mpei) const
	calculate muscle's fiber and tendon potential energy
double	calcActivationRate (const SimTK::State &s) const override
	Calculate activation rate.
virtual void	addToSystem (SimTK::MultibodySystem &system) const
	Model Component Interface.
virtual void	initStateFromProperties (SimTK::State &s) const
	Subclass should override; be sure to invoke Force::initStateFromProperties() at the beginning of the overriding method.
virtual void	setPropertiesFromState (const SimTK::State &state)
	Subclass should override; be sure to invoke Force::setPropertiesFromState() at the beginning of the overriding method.
virtual void	connectToModel (Model &aModel)
	Model Component creation interface.
Protected Member Functions inherited from OpenSim::ActivationFiberLengthMuscle
virtual void	postScale (const SimTK::State &s, const ScaleSet &aScaleSet)
virtual void	computeForce (const SimTK::State &state, SimTK::Vector_< SimTK::SpatialVec > &bodyForces, SimTK::Vector &generalizedForce) const
	Force interface applies tension to bodies, and Muscle also checks that applied muscle tension is not negative.
virtual SimTK::Vector	computeStateVariableDerivatives (const SimTK::State &s) const
	If a model component has allocated any continuous state variables using the addStateVariable() method, then computeStateVariableDerivatives() must be implemented to provide time derivatives for those states.
void	setStateVariableDeriv (const SimTK::State &s, const std::string &aStateName, double aValue) const
	State derivative access helper methods.
double	getStateVariableDeriv (const SimTK::State &s, const std::string &aStateName) const
Protected Member Functions inherited from OpenSim::Muscle
const MuscleLengthInfo &	getMuscleLengthInfo (const SimTK::State &s) const
	Developer Access to intermediate values calculate by the muscle model.
MuscleLengthInfo &	updMuscleLengthInfo (const SimTK::State &s) const
const FiberVelocityInfo &	getFiberVelocityInfo (const SimTK::State &s) const
FiberVelocityInfo &	updFiberVelocityInfo (const SimTK::State &s) const
const MuscleDynamicsInfo &	getMuscleDynamicsInfo (const SimTK::State &s) const
MuscleDynamicsInfo &	updMuscleDynamicsInfo (const SimTK::State &s) const
const MusclePotentialEnergyInfo &	getMusclePotentialEnergyInfo (const SimTK::State &s) const
MusclePotentialEnergyInfo &	updMusclePotentialEnergyInfo (const SimTK::State &s) const
virtual void	computeFiberEquilibriumAtZeroVelocity (SimTK::State &s) const
	Provide a quick estimate of the fiber length assuming the musculotendon unit velocity is zero.
double	computePotentialEnergy (const SimTK::State &state) const override
	Potential energy stored by the muscle.
SimTK::Vec3	computePathColor (const SimTK::State &state) const override
	Override PathActuator virtual to calculate a preferred color for the muscle path based on activation.
virtual void	updateGeometry (const SimTK::State &s)
Protected Member Functions inherited from OpenSim::PathActuator
void	realizeDynamics (const SimTK::State &state) const override
	Extension of parent class method; derived classes may extend further.
Protected Member Functions inherited from OpenSim::Actuator
double	computeOverrideForce (const SimTK::State &s) const
OpenSim::Array< std::string >	getRecordLabels () const
	Methods to query a Force for the value actually applied during simulation The names of the quantities (column labels) is returned by this first function getRecordLabels()
OpenSim::Array< double >	getRecordValues (const SimTK::State &state) const
	Given SimTK::State object extract all the values necessary to report forces, application location frame, etc.
Protected Member Functions inherited from OpenSim::Actuator_
virtual void	updateGeometry ()
Protected Member Functions inherited from OpenSim::Force
	Force ()
	Default constructor sets up Force-level properties; can only be called from a derived class constructor.
	Force (SimTK::Xml::Element &node)
	Deserialization from XML, necessary so that derived classes can (de)serialize.
void	applyForceToPoint (const SimTK::State &state, const OpenSim::Body &body, const SimTK::Vec3 &point, const SimTK::Vec3 &force, SimTK::Vector_< SimTK::SpatialVec > &bodyForces) const
	Apply a force at a particular point (a "station") on a given body.
void	applyTorque (const SimTK::State &state, const OpenSim::Body &body, const SimTK::Vec3 &torque, SimTK::Vector_< SimTK::SpatialVec > &bodyForces) const
	Apply a torque to a particular body.
void	applyGeneralizedForce (const SimTK::State &state, const Coordinate &coord, double force, SimTK::Vector &generalizedForces) const
	Apply a generalized force.
Protected Member Functions inherited from OpenSim::ModelComponent
virtual void	generateDecorations (bool fixed, const ModelDisplayHints &hints, const SimTK::State &state, SimTK::Array_< SimTK::DecorativeGeometry > &appendToThis) const
	Optional method for generating arbitrary display geometry that reflects this ModelComponent at the specified state.
virtual void	realizeTopology (SimTK::State &state) const
	Obtain state resources that are needed unconditionally, and perform computations that depend only on the system topology.
virtual void	realizeModel (SimTK::State &state) const
	Obtain state resources that may be needed, depending on modeling options, and perform computations that depend only on topology and selected modeling options.
virtual void	realizeInstance (const SimTK::State &state) const
	Perform computations that depend only on instance variables, like lengths and masses.
virtual void	realizeTime (const SimTK::State &state) const
	Perform computations that depend only on time and earlier stages.
virtual void	realizePosition (const SimTK::State &state) const
	Perform computations that depend only on position-level state variables and computations performed in earlier stages (including time).
virtual void	realizeVelocity (const SimTK::State &state) const
	Perform computations that depend only on velocity-level state variables and computations performed in earlier stages (including position, and time).
virtual void	realizeAcceleration (const SimTK::State &state) const
	Perform computations that may depend on applied forces.
virtual void	realizeReport (const SimTK::State &state) const
	Perform computations that may depend on anything but are only used for reporting and cannot affect subsequent simulation behavior.
void	includeAsSubComponent (ModelComponent *aComponent)
	Include another ModelComponent as a Subcomponent of this ModelComponent.
void	addModelingOption (const std::string &optionName, int maxFlagValue) const
	Add a modeling option (integer flag stored in the State) for use by this ModelComponent.
void	addStateVariable (const std::string &stateVariableName, SimTK::Stage invalidatesStage=SimTK::Stage::Dynamics) const
	Add a continuous system state variable belonging to this ModelComponent, and assign a name by which to refer to it.
void	addDiscreteVariable (const std::string &discreteVariableName, SimTK::Stage invalidatesStage) const
	Add a system discrete variable belonging to this ModelComponent, give it a name by which it can be referenced, and declare the lowest Stage that should be invalidated if this variable's value is changed.
template<class T >
void	addCacheVariable (const std::string &cacheVariableName, const T &variablePrototype, SimTK::Stage dependsOnStage) const
	Add a state cache entry belonging to this ModelComponent to hold calculated values that must be automatically invalidated when certain state values change.
const int	getStateIndex (const std::string &name) const
	Get the index of a ModelComponent's continuous state variable in the Subsystem for allocations.
const SimTK::DiscreteVariableIndex	getDiscreteVariableIndex (const std::string &name) const
	Get the index of a ModelComponent's discrete variable in the Subsystem for allocations.
const SimTK::CacheEntryIndex	getCacheVariableIndex (const std::string &name) const
	Get the index of a ModelComponent's cache variable in the Subsystem for allocations.
Protected Member Functions inherited from OpenSim::Object
	Object ()
	The default constructor is only for use by constructors of derived types.
	Object (const std::string &fileName, bool aUpdateFromXMLNode=true) SWIG_DECLARE_EXCEPTION
	Constructor from a file, to be called from other constructors that take a file as input.
	Object (const Object &source)
	Copy constructor is invoked automatically by derived classes with default copy constructors; otherwise it must be invoked explicitly.
	Object (SimTK::Xml::Element &aElement)
	Construct the base class portion of an Object from a given Xml element that describes this Object.
template<class T >
PropertyIndex	addProperty (const std::string &name, const std::string &comment, const T &value)
	Define a new single-value property of known type T, with the given name, associated comment, and initial value.
template<class T >
PropertyIndex	addOptionalProperty (const std::string &name, const std::string &comment)
	Add an optional property, meaning it can contain either no value or a single value.
template<class T >
PropertyIndex	addOptionalProperty (const std::string &name, const std::string &comment, const T &value)
	Add an optional property, meaning it can contain either no value or a single value.
template<class T >
PropertyIndex	addListProperty (const std::string &name, const std::string &comment, int minSize, int maxSize)
	Define a new list-valued property of known type T, with the given name, associated comment, minimum (==0) and maximum (>0) allowable list lengths, and a zero-length initial value.
template<class T , template< class > class Container>
PropertyIndex	addListProperty (const std::string &name, const std::string &comment, int minSize, int maxSize, const Container< T > &valueList)
	Define a new list-valued property as above, but assigning an initial value via some templatized container class that supports size() and indexing.
PropertyIndex	getPropertyIndex (const std::string &name) const
	Look up a property by name and return its PropertyIndex if it is found.
template<class T >
PropertyIndex	getPropertyIndex () const
	Look up an unnamed property by the type of object it contains, and return its PropertyIndex if it is found.
void	updateFromXMLDocument ()
	Use this method only if you're deserializing from a file and the object is at the top level; that is, primarily in constructors that take a file name as input.
void	setDocument (XMLDocument *doc)
	Unconditionally set the XMLDocument associated with this object.
const XMLDocument *	getDocument () const
	Get a const pointer to the document (if any) associated with this object.
XMLDocument *	updDocument ()
	Get a writable pointer to the document (if any) associated with this object.

Additional Inherited Members
Static Public Member Functions inherited from OpenSim::Object
static void	registerType (const Object &defaultObject)
	Register an instance of a class; if the class is already registered it will be replaced.
static void	renameType (const std::string &oldTypeName, const std::string &newTypeName)
	Support versioning by associating the current Object type with an old name.
static const Object *	getDefaultInstanceOfType (const std::string &concreteClassName)
	Return a pointer to the default instance of the registered (concrete) Object whose class name is given, or NULL if the type is not registered.
template<class T >
static bool	isObjectTypeDerivedFrom (const std::string &concreteClassName)
	Return true if the given concrete object type represents a subclass of the template object type T, and thus could be referenced with a T*.
static Object *	newInstanceOfType (const std::string &concreteClassName)
	Create a new instance of the concrete Object type whose class name is given as concreteClassName.
static void	getRegisteredTypenames (Array< std::string > &typeNames)
	Retrieve all the typenames registered so far.
template<class T >
static void	getRegisteredObjectsOfGivenType (ArrayPtrs< T > &rArray)
	Return an array of pointers to the default instances of all registered (concrete) Object types that derive from a given Object-derived type that does not have to be concrete.
static void	PrintPropertyInfo (std::ostream &os, const std::string &classNameDotPropertyName)
	Dump formatted property information to a given output stream, useful for creating a "help" facility for registered objects.
static void	PrintPropertyInfo (std::ostream &os, const std::string &className, const std::string &propertyName)
	Same as the other signature but the class name and property name are provided as two separate strings.
static Object *	makeObjectFromFile (const std::string &fileName)
	Create an OpenSim object whose type is based on the tag at the root node of the XML file passed in.
static const std::string &	getClassName ()
	Return the name of this class as a string; i.e., "Object".
static void	setSerializeAllDefaults (bool shouldSerializeDefaults)
	Static function to control whether all registered objects and their properties are written to the defaults section of output files rather than only those values for which the default was explicitly overwritten when read in from an input file or set programmatically.
static bool	getSerializeAllDefaults ()
	Report the value of the "serialize all defaults" flag.
static bool	isKindOf (const char *type)
	Returns true if the passed-in string is "Object"; each Object-derived class defines a method of this name for its own class name.
static void	setDebugLevel (int newLevel)
	Set the debug level to get verbose output.
static int	getDebugLevel ()
	Get current setting of debug level.
static Object *	SafeCopy (const Object *aObject)
	Use the clone() method to duplicate the given object unless the pointer is null in which case null is returned.
static void	RegisterType (const Object &defaultObject)
	OBSOLETE alternate name for registerType().
static void	RenameType (const std::string &oldName, const std::string &newName)
	OBSOLETE alternate name for renameType().
Static Public Attributes inherited from OpenSim::Object
static const std::string	DEFAULT_NAME
	Name used for default objects when they are serialized.
Protected Attributes inherited from OpenSim::Muscle
double	_muscleWidth
	The assumed fixed muscle-width from which the fiber pennation angle can be calculated.
double	_maxIsometricForce
	to support deprecated muscles
double	_optimalFiberLength
double	_pennationAngleAtOptimal
double	_tendonSlackLength
Static Protected Attributes inherited from OpenSim::ActivationFiberLengthMuscle
static const std::string	STATE_ACTIVATION_NAME
static const std::string	STATE_FIBER_LENGTH_NAME
Related Functions inherited from OpenSim::Object
#define	OpenSim_DECLARE_CONCRETE_OBJECT(ConcreteClass, SuperClass)
	Macro to be included as the first line of the class declaration for any non-templatized, concrete class that derives from OpenSim::Object.
#define	OpenSim_DECLARE_ABSTRACT_OBJECT(ConcreteClass, SuperClass)
	Macro to be included as the first line of the class declaration for any still-abstract class that derives from OpenSim::Object.
#define	OpenSim_DECLARE_CONCRETE_OBJECT_T(ConcreteClass, TArg, SuperClass)
	Macro to be included as the first line of the class declaration for any templatized, concrete class that derives from OpenSim::Object, like Set<T>.
#define	OpenSim_DECLARE_ABSTRACT_OBJECT_T(ConcreteClass, TArg, SuperClass)
	Macro to be included as the first line of the class declaration for any templatized, still-abstract class that derives from OpenSim::Object.

Detailed Description

Implementation of a two state (activation and fiber-length) Muscle model by Thelen 2003. This a complete rewrite of a previous implementation (present in OpenSim 2.4 and earlier) contained numerous errors.

The Thelen2003Muscle model uses a standard equilibrium muscle equation

$(a(t) f_{AL}(l_{CE}) f_{V}(\dot{l}_{CE}) - f_{PE}(l_{CE}))\cos \phi - f_{SE}(l_{T}) = 0$

Rearranging the above equation and solving for $f_{V}(\dot{l}_{CE})$ yields

$f_{V}(\dot{l}_{CE}) = \frac{ \frac{f_{SE}(l_{T})}{\cos\phi} - f_{PE}(l_{CE}) }{ a(t) f_{AL}(l_{CE}) }$

The force velocity curve is usually inverted to compute the fiber velocity,

$\dot{l}_{CE} = f_{V}^{-1}( \frac{ \frac{f_{SE}(l_{T})}{\cos\phi} - f_{PE}(l_{CE}) }{ a(t) f_{AL}(l_{CE}) } )$

which is then integrated to simualate the musculotendon dynamics. In general, the previous equation has 4 singularity conditions:

$a(t) \rightarrow 0$
$f_{AL}(l_{CE}) \rightarrow 0$
$\phi \rightarrow \frac{\pi}{2}$
$f_{V}(\dot{l}_{CE}) \le 0$ or $f_{V}(\dot{l}_{CE}) \ge F^M_{len}$

This implementation has been slightly modified from the model presented in the journal paper (marked with a *) to prevent some of these singularities:

* $a(t) \rightarrow a_{min} > 0$ : A modified activation dynamic equation is used - MuscleFirstOrderActivationDynamicModel - which smoothly approaches some minimum value that is greater than zero.
$f_{AL}(l_{CE}) > 0$ . The active force length curve of the Thelen muscle is a Gaussian, which is always greater than 0.
$\phi \rightarrow \frac{\pi}{2}$ . This singularity cannot be removed without changing the first equation, and still exists in the present Thelen2003Muscle formulation.
* $f_{V}(\dot{l}_{CE}) \le 0$ or $f_{V}(\dot{l}_{CE}) \ge F^M_{len}$ : Equation 6 in Thelen 2003 has been modified so that is linearly extrapolated when (during a concentric contraction), and when $F^M > 0.95 F^M_{len}$ (during an eccentric contraction). These two modifications make the force velocity curve invertible. The original force velocity curve as published by Thelen was not invertible.
A unilateral constraint has been implemented to prevent the fiber from approaching a fiber length that is smaller than 0.01*optimal fiber length, or a fiber length that creates a pennation angle greater than the maximum pennation angle specified by the pennation model. Note that this unilateral constraint does not prevent the muscle fiber from becoming shorter than is physiologically possible (that is shorter than approximately half a normalized fiber length).

Usage This object should be updated through the set methods provided. These set methods will take care of rebuilding the object correctly. If you modify the properties directly, the object will not be rebuilt, and upon calling any functions an exception will be thrown because the object is out of date with its properties.

References

DG Thelen, Adjustment of muscle mechanics model parameters to simulate dynamic contractions in older adults. Journal of biomechanical engineering, 2003.

Author: Matt Millard; Ajay Seth; Peter Loan

Member Enumeration Documentation

enum OpenSim::Thelen2003Muscle::CurveType

Enumerator:

FiberActiveForceLength
FiberPassiveForceLength
FiberForceVelocity
TendonForceLength

Constructor & Destructor Documentation

OpenSim::Thelen2003Muscle::Thelen2003Muscle ( )

OpenSim::Thelen2003Muscle::Thelen2003Muscle	(	const std::string &	aName,
		double	aMaxIsometricForce,
		double	aOptimalFiberLength,
		double	aTendonSlackLength,
		double	aPennationAngle
	)

Member Function Documentation

virtual void OpenSim::Thelen2003Muscle::addToSystem ( SimTK::MultibodySystem & system ) const

protectedvirtual

Model Component Interface.

Reimplemented from OpenSim::ActivationFiberLengthMuscle.

double OpenSim::Thelen2003Muscle::calcActivationRate ( const SimTK::State & s ) const

overrideprotectedvirtual

Calculate activation rate.

Implements OpenSim::ActivationFiberLengthMuscle.

void OpenSim::Thelen2003Muscle::calcFiberVelocityInfo	(	const SimTK::State &	s,
		FiberVelocityInfo &	fvi
	)		const

overrideprotectedvirtual

calculate muscle's velocity related values such fiber and tendon velocities,normalized velocities, pennation angular velocity, etc...

Reimplemented from OpenSim::Muscle.

void OpenSim::Thelen2003Muscle::calcMuscleDynamicsInfo	(	const SimTK::State &	s,
		MuscleDynamicsInfo &	mdi
	)		const

overrideprotectedvirtual

calculate muscle's active and passive force-length, force-velocity, tendon force, relationships and their related values

Reimplemented from OpenSim::Muscle.

void OpenSim::Thelen2003Muscle::calcMuscleLengthInfo	(	const SimTK::State &	s,
		MuscleLengthInfo &	mli
	)		const

overrideprotectedvirtual

calculate muscle's position related values such fiber and tendon lengths, normalized lengths, pennation angle, etc...

Reimplemented from OpenSim::Muscle.

void OpenSim::Thelen2003Muscle::calcMusclePotentialEnergyInfo	(	const SimTK::State &	s,
		MusclePotentialEnergyInfo &	mpei
	)		const

protectedvirtual

calculate muscle's fiber and tendon potential energy

Reimplemented from OpenSim::Muscle.

virtual double OpenSim::Thelen2003Muscle::computeActuation ( const SimTK::State & s ) const

overridevirtual

Actuator interface for a muscle computes the tension in the muscle and applied by the tendon to bones (i.e.

not the fiber force)

Implements OpenSim::Muscle.

void OpenSim::Thelen2003Muscle::computeInitialFiberEquilibrium ( SimTK::State & s ) const

overridevirtual

Compute initial fiber length (velocity) such that muscle fiber and tendon are in static equilibrium and update the state.

Part of the Muscle.h interface

Implements OpenSim::Muscle.

virtual void OpenSim::Thelen2003Muscle::connectToModel ( Model & aModel )

protectedvirtual

Model Component creation interface.

Reimplemented from OpenSim::ActivationFiberLengthMuscle.

const MuscleFirstOrderActivationDynamicModel& OpenSim::Thelen2003Muscle::getActivationModel ( ) const

Returns: the MuscleFirstOrderActivationDynamicModel that this muscle model uses

double OpenSim::Thelen2003Muscle::getActivationTimeConstant ( ) const

double OpenSim::Thelen2003Muscle::getAf ( ) const

double OpenSim::Thelen2003Muscle::getDeactivationTimeConstant ( ) const

double OpenSim::Thelen2003Muscle::getFlen ( ) const

double OpenSim::Thelen2003Muscle::getFmaxMuscleStrain ( ) const

double OpenSim::Thelen2003Muscle::getFmaxTendonStrain ( ) const

double OpenSim::Thelen2003Muscle::getForceVelocityExtrapolationThreshold ( ) const

double OpenSim::Thelen2003Muscle::getKshapeActive ( ) const

double OpenSim::Thelen2003Muscle::getKshapePassive ( ) const

double OpenSim::Thelen2003Muscle::getMaximumPennationAngle ( ) const

Returns: the maximum pennation angle allowed by this muscle model (radians)

double OpenSim::Thelen2003Muscle::getMinimumActivation ( ) const

double OpenSim::Thelen2003Muscle::getMinimumFiberLength ( ) const

Returns: the minimum fiber length, which is the maximum of two values: the smallest fiber length allowed by the pennation model, and the minimum fiber length in the active force length curve. When the fiber length reaches this value, it is constrained to this value until the fiber velocity goes positive.

const MuscleFixedWidthPennationModel& OpenSim::Thelen2003Muscle::getPennationModel ( ) const

Returns: the MuscleFixedWidthPennationModel that this muscle model uses

virtual void OpenSim::Thelen2003Muscle::initStateFromProperties ( SimTK::State & state ) const

protectedvirtual

Subclass should override; be sure to invoke Force::initStateFromProperties() at the beginning of the overriding method.

Reimplemented from OpenSim::ActivationFiberLengthMuscle.

OpenSim::Thelen2003Muscle::OpenSim_DECLARE_PROPERTY	(	activation_time_constant	,
		double	,
		"time constant for ramping up muscle activation"
	)

OpenSim::Thelen2003Muscle::OpenSim_DECLARE_PROPERTY	(	deactivation_time_constant	,
		double	,
		"time constant for ramping down of muscle activation"
	)

OpenSim::Thelen2003Muscle::OpenSim_DECLARE_PROPERTY	(	FmaxTendonStrain	,
		double	,
		"tendon strain at maximum isometric muscle force"
	)

OpenSim::Thelen2003Muscle::OpenSim_DECLARE_PROPERTY	(	FmaxMuscleStrain	,
		double	,
		"passive muscle strain at maximum isometric muscle force"
	)

OpenSim::Thelen2003Muscle::OpenSim_DECLARE_PROPERTY	(	KshapeActive	,
		double	,
		"shape factor for Gaussian active muscle force-length relationship"
	)

OpenSim::Thelen2003Muscle::OpenSim_DECLARE_PROPERTY	(	KshapePassive	,
		double	,
		"exponential shape factor for passive force-length relationship"
	)

OpenSim::Thelen2003Muscle::OpenSim_DECLARE_PROPERTY	(	Af	,
		double	,
		"force-velocity shape factor"
	)

OpenSim::Thelen2003Muscle::OpenSim_DECLARE_PROPERTY	(	Flen	,
		double	,
		"maximum normalized lengthening force"
	)

OpenSim::Thelen2003Muscle::OpenSim_DECLARE_PROPERTY	(	fv_linear_extrap_threshold	,
		double	,
		"fv threshold where linear extrapolation is used"
	)

void OpenSim::Thelen2003Muscle::printCurveToCSVFile	(	const CurveType	ctype,
		const std::string &	path
	)

bool OpenSim::Thelen2003Muscle::setActivationTimeConstant ( double aActivationTimeConstant )

bool OpenSim::Thelen2003Muscle::setAf ( double aAf )

bool OpenSim::Thelen2003Muscle::setDeactivationTimeConstant ( double aDeactivationTimeConstant )

bool OpenSim::Thelen2003Muscle::setFlen ( double aFlen )

bool OpenSim::Thelen2003Muscle::setFmaxFiberStrain ( double aFmaxMuscleStrain )

bool OpenSim::Thelen2003Muscle::setFmaxTendonStrain ( double aFmaxTendonStrain )

bool OpenSim::Thelen2003Muscle::setForceVelocityExtrapolationThreshold ( double aFvThresh )

bool OpenSim::Thelen2003Muscle::setKshapeActive ( double aKShapeActive )

bool OpenSim::Thelen2003Muscle::setKshapePassive ( double aKshapePassive )

bool OpenSim::Thelen2003Muscle::setMinimumActivation ( double aActivationMinValue )

virtual void OpenSim::Thelen2003Muscle::setPropertiesFromState ( const SimTK::State & state )

protectedvirtual

Subclass should override; be sure to invoke Force::setPropertiesFromState() at the beginning of the overriding method.

Reimplemented from OpenSim::ActivationFiberLengthMuscle.

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

E:/Projects/OpenSimTrunk/OpenSim/Actuators/Thelen2003Muscle.h

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation