Bhargava2004MuscleMetabolicsProbe is a Probe ModelComponent for computing the net metabolic energy rate of a set of Muscles in the model during a simulation. More...

Inheritance diagram for OpenSim::Bhargava2004MuscleMetabolicsProbe:

Public Member Functions
	Bhargava2004MuscleMetabolicsProbe ()
	Default constructor. More...

	Bhargava2004MuscleMetabolicsProbe (const bool activation_rate_on, const bool maintenance_rate_on, const bool shortening_rate_on, const bool basal_rate_on, const bool work_rate_on)
	Convenience constructor. More...

virtual SimTK::Vector	computeProbeInputs (const SimTK::State &state) const override
	Compute muscle metabolic power. More...

int	getNumProbeInputs () const override
	Returns the number of probe inputs in the vector returned by computeProbeInputs(). More...

virtual OpenSim::Array < std::string >	getProbeOutputLabels () const override
	Returns the column labels of the probe values for reporting. More...

Property declarations
These are the serializable properties associated with this class.
	OpenSim_DECLARE_PROPERTY (activation_rate_on, bool,"Specify whether activation heat rate is to be calculated (true/false).")
	Enabled by default. More...

	OpenSim_DECLARE_PROPERTY (maintenance_rate_on, bool,"Specify whether maintenance heat rate is to be calculated (true/false).")
	Enabled by default. More...

	OpenSim_DECLARE_PROPERTY (shortening_rate_on, bool,"Specify whether shortening heat rate is to be calculated (true/false).")
	Enabled by default. More...

	OpenSim_DECLARE_PROPERTY (basal_rate_on, bool,"Specify whether basal heat rate is to be calculated (true/false).")
	Enabled by default. More...

	OpenSim_DECLARE_PROPERTY (mechanical_work_rate_on, bool,"Specify whether mechanical work rate is to be calculated (true/false).")
	Enabled by default. More...

	OpenSim_DECLARE_PROPERTY (enforce_minimum_heat_rate_per_muscle, bool,"Specify whether the total heat rate for a muscle will be clamped to a ""minimum value of 1.0 W/kg (true/false).")
	Enabled by default. More...

	OpenSim_DECLARE_PROPERTY (normalized_fiber_length_dependence_on_maintenance_rate, PiecewiseLinearFunction,"Contains a PiecewiseLinearFunction object that describes the ""normalized fiber length dependence on maintenance rate.")
	Default curve shown in doxygen. More...

	OpenSim_DECLARE_PROPERTY (use_force_dependent_shortening_prop_constant, bool,"Specify whether to use a force dependent shortening proportionality ""constant (true/false).")
	Disabled by default. More...

	OpenSim_DECLARE_PROPERTY (basal_coefficient, double,"Basal metabolic coefficient.")
	Default value = 1.2. More...

	OpenSim_DECLARE_PROPERTY (basal_exponent, double,"Basal metabolic exponent.")
	Default value = 1.0. More...

	OpenSim_DECLARE_PROPERTY (muscle_effort_scaling_factor, double,"Scale the excitation and activation values used by the probe to ""compensate for solutions with excessive coactivation (e.g., when a ""suboptimal tracking strategy is used).")
	Default value = 1.0. More...

	OpenSim_DECLARE_PROPERTY (include_negative_mechanical_work, bool,"Specify whether negative mechanical work will be included in Wdot ""(true/false).")
	Enabled by default. More...

	OpenSim_DECLARE_PROPERTY (forbid_negative_total_power, bool,"Specify whether the total power for each muscle must remain positive ""(true/false).")
	Enabled by default. More...

	OpenSim_DECLARE_PROPERTY (report_total_metabolics_only, bool,"If set to false, the individual muscle metabolics, basal rate, and ""total summation will be reported. If set to true, only the total ""summation will be reported.")
	Default value = true. More...

	OpenSim_DECLARE_UNNAMED_PROPERTY (Bhargava2004MuscleMetabolicsProbe_MetabolicMuscleParameterSet,"A set containing, for each muscle, the parameters ""required to calculate muscle metabolic power.")

Public Member Functions inherited from OpenSim::Probe
	Probe ()

void	reset (SimTK::State &s)
	Reset (initialize) the underlying Probe SimTK::Measure. More...

int	getNumInternalMeasureStates () const
	Get the number of states in the underlying SimTK::Measure. More...

bool	isDisabled () const
	Returns true if the Probe is disabled or false if the probe is enabled. More...

void	setDisabled (bool isDisabled)
	Set the Probe as disabled (true) or enabled (false). More...

std::string	getOperation () const
	Return the operation being performed on the probe value. More...

void	setOperation (std::string probe_operation)
	Set the operation being performed on the probe value. More...

SimTK::Vector	getInitialConditions () const
	Return the initial conditions (when the probe_operation is set to 'integrate'). More...

void	setInitialConditions (SimTK::Vector initial_conditions_for_integration)
	Set the initial conditions (when the probe_operation is set to 'integrate'). More...

double	getGain () const
	Return the gain to apply to the probe output. More...

void	setGain (double gain)
	Set the gain to apply to the probe output. More...

SimTK::Vector	getProbeOutputs (const SimTK::State &state) const
	Returns the values of the probe after the operation has been performed. More...

	OpenSim_DECLARE_PROPERTY (isDisabled, bool,"Flag indicating whether the Probe is disabled or not.")
	Enabled by default. More...

	OpenSim_DECLARE_PROPERTY (probe_operation, std::string,"The operation to perform on the probe input value: ""'value'(no operation, just return the probe value), 'integrate', ""'differentiate', 'minimum', 'minabs', 'maximum', 'maxabs'.")

	OpenSim_DECLARE_LIST_PROPERTY (initial_conditions_for_integration, double,"Array of initial conditions to be specified if the 'integrate' operation is ""selected. Note that the size of initial conditions must be the same size as ""the data being integrated, otherwise an exception will be thrown.")

	OpenSim_DECLARE_PROPERTY (gain, double,"Constant gain to scale the probe output by.")

Public Member Functions inherited from OpenSim::ModelComponent
	ModelComponent ()
	Default constructor. More...

	ModelComponent (const std::string &aFileName, bool aUpdateFromXMLNode=true) SWIG_DECLARE_EXCEPTION
	Construct ModelComponent from an XML file. More...

	ModelComponent (SimTK::Xml::Element &aNode)
	Construct ModelComponent from a specific node in an XML document. More...

	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. More...

virtual	~ModelComponent ()
	Destructor is virtual to allow concrete model component cleanup. More...

ModelComponent &	operator= (const ModelComponent &aModelComponent)
	Assignment operator to copy contents of an existing component. More...

const Model &	getModel () const
	Get a const reference to the Model this component is part of. More...

Model &	updModel ()
	Get a modifiable reference to the Model this component is part of. More...

virtual void	updateDisplayer (const SimTK::State &s) const
	In case the ModelComponent has a visual representation (VisualObject), override this method to update it. More...

virtual int	getNumStateVariables () const
	Get the number of "Continuous" state variables maintained by the ModelComponent and its specified subcomponents. More...

virtual Array< std::string >	getStateVariableNames () const
	Get the names of "continuous" state variables maintained by the ModelComponent and its subcomponents. More...

virtual SimTK::SystemYIndex	getStateVariableSystemIndex (const std::string &stateVariableName) const
	Get the System Index of a state variable allocated by this ModelComponent. More...

int	getModelingOption (const SimTK::State &state, const std::string &name) const
	Get a ModelingOption flag for this ModelComponent by name. More...

void	setModelingOption (SimTK::State &state, const std::string &name, int flag) const
	Set the value of a ModelingOption flag for this ModelComponent. More...

double	getStateVariable (const SimTK::State &state, const std::string &name) const
	Get the value of a state variable allocated by this ModelComponent. More...

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. More...

double	getDiscreteVariable (const SimTK::State &state, const std::string &name) const
	Get the value of a discrete variable allocated by this ModelComponent by name. More...

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. More...

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. More...

template<typename T >
const T &	getCacheVariable (const SimTK::State &state, SimTK::CacheEntryIndex ceIndex) const

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. More...

template<typename T >
T &	updCacheVariable (const SimTK::State &state, SimTK::CacheEntryIndex ceIndex) const

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. More...

void	markCacheVariableValid (const SimTK::State &state, SimTK::CacheEntryIndex ceIndex) const

void	markCacheVariableInvalid (const SimTK::State &state, const std::string &name) const
	Mark a cache variable value allocated by this ModelComponent as invalid. More...

void	markCacheVariableInvalid (const SimTK::State &state, SimTK::CacheEntryIndex ceIndex) const

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. More...

bool	isCacheVariableValid (const SimTK::State &state, SimTK::CacheEntryIndex ceIndex) const

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. More...

template<typename T >
void	setCacheVariable (const SimTK::State &state, SimTK::CacheEntryIndex ceIndex, const T &value) const

Public Member Functions inherited from OpenSim::Object
virtual	~Object ()
	Virtual destructor for cleanup. More...

virtual Object *	clone () const =0
	Create a new heap-allocated copy of the concrete object to which this Object refers. More...

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. More...

virtual const VisibleObject *	getDisplayer () const
	Methods to support making the object displayable in the GUI or Visualizer Implemented only in few objects. More...

virtual VisibleObject *	updDisplayer ()
	get Non const pointer to VisibleObject More...

bool	isEqualTo (const Object &aObject) const
	Equality operator wrapper for use from languages not supporting operator overloading. More...

Object &	operator= (const Object &aObject)
	Copy assignment copies he base class fields, including the properties. More...

virtual bool	operator== (const Object &aObject) const
	Determine if two objects are equal. More...

virtual bool	operator< (const Object &aObject) const
	Provide an ordering for objects so they can be put in sorted containers. More...

void	setName (const std::string &name)
	Set the name of the Object. More...

const std::string &	getName () const
	Get the name of this Object. More...

void	setDescription (const std::string &description)
	Set description, a one-liner summary. More...

const std::string &	getDescription () const
	Get description, a one-liner summary. More...

const std::string &	getAuthors () const
	Get Authors of this Object. More...

void	setAuthors (const std::string &authors)
	Set Authors of this object, call this method in your constructor if needed. More...

const std::string &	getReferences () const
	Get references or publications to cite if using this object. More...

void	setReferences (const std::string &references)
	Set references or publications to cite if using this object. More...

int	getNumProperties () const
	Determine how many properties are stored with this Object. More...

const AbstractProperty &	getPropertyByIndex (int propertyIndex) const
	Get a const reference to a property by its index number, returned as an AbstractProperty. More...

AbstractProperty &	updPropertyByIndex (int propertyIndex)
	Get a writable reference to a property by its index number, returned as an AbstractProperty. More...

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. More...

const AbstractProperty &	getPropertyByName (const std::string &name) const
	Get a const reference to a property by its name, returned as an AbstractProperty. More...

AbstractProperty &	updPropertyByName (const std::string &name)
	Get a writable reference to a property by its name, returned as an AbstractProperty. More...

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. More...

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. More...

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. More...

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. More...

bool	isObjectUpToDateWithProperties () const
	Returns `true` if no property's value has changed since the last time setObjectIsUpToDateWithProperties() was called. More...

void	readObjectFromXMLNodeOrFile (SimTK::Xml::Element &objectElement, int versionNumber)
	We're given an XML element from which we are to populate this Object. More...

virtual void	updateFromXMLNode (SimTK::Xml::Element &objectElement, int versionNumber)
	Use this method to deserialize an object from a SimTK::Xml::Element. More...

virtual void	updateXMLNode (SimTK::Xml::Element &parent)
	Serialize this object into the XML node that represents it. More...

bool	getInlined () const
	Inlined means an in-memory Object that is not associated with an XMLDocument. More...

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. More...

std::string	getDocumentFileName () const
	If there is a document associated with this object then return the file name maintained by the document. More...

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". More...

std::string	dump (bool dumpName=false)
	dump the XML representation of this Object into an std::string and return it. More...

void	clearObjectIsUpToDateWithProperties ()
	For testing or debugging purposes, manually clear the "object is up to date with respect to properties" flag. More...

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. More...

const std::string &	toString () const
	Wrapper to be used on Java side to display objects in tree; this returns just the object's name. More...

PropertySet &	getPropertySet ()
	OBSOLETE: Get a reference to the PropertySet maintained by the Object. More...

const PropertySet &	getPropertySet () const

Public Types
typedef std::map< std::string, Bhargava2004MuscleMetabolicsProbe_MetabolicMuscleParameter * >	MuscleMap
	MuscleMap typedef. More...

Bhargava2004MuscleMetabolicsProbe Interface
These accessor methods are to be used when setting up a new muscle metabolic analysis from the API. The basic operation is as follows: Bhargava2004MuscleMetabolicsProbe* myProbe new Bhargava2004MuscleMetabolicsProbe(...); model.addProbe(myProbe); myProbe->addMuscle("muscleName1", ... ); myProbe->addMuscle("muscleName2", ... ); myProbe->addMuscle("muscleName3", ... ); myProbe->useProvidedMass("muscleName1", 1.2); // muscle1 mass = 1.2 kg myProbe->useCalculatedMass("muscleName2"); // muscle2 mass is based on muscle properties (below) myProbe->setDensity("muscleName2", 1100.0); // muscle2 density is 1100 kg/m^3 myProbe->setSpecificTension("muscleName2", 0.26e6); // muscle2 specific tension is 0.26e6 Pa myProbe->removeMuscle("muscleName3"); myProbe->setOperation("integrate") // See OpenSim::Probe for other operations Note It is important to first add the metabolic probe to the model before calling any other methods that may modify its properties. This is because some methods (e.g. addMuscle() or useCalculatedMass) may require information about the muscles to sucsessfully execute, and this information can only be obtained if the metabolic probe is already 'connected' to the model.
const int	getNumMetabolicMuscles () const

void	addMuscle (const std::string &muscleName, double ratio_slow_twitch_fibers, double activation_constant_slow_twitch, double activation_constant_fast_twitch, double maintenance_constant_slow_twitch, double maintenance_constant_fast_twitch)
	Add a muscle and its parameters so that it can be included in the metabolic analysis. More...

void	addMuscle (const std::string &muscleName, double ratio_slow_twitch_fibers, double activation_constant_slow_twitch, double activation_constant_fast_twitch, double maintenance_constant_slow_twitch, double maintenance_constant_fast_twitch, double muscle_mass)
	Add a muscle and its parameters so that it can be included in the metabolic analysis. More...

void	removeMuscle (const std::string &muscleName)
	Remove a muscle from the metabolic analysis. More...

void	useProvidedMass (const std::string &muscleName, double providedMass)

void	useCalculatedMass (const std::string &muscleName)
	Set an existing muscle to calculate its own mass. More...

bool	isUsingProvidedMass (const std::string &muscleName)
	Get whether the muscle mass is being explicitly provided. More...

const double	getMuscleMass (const std::string &muscleName) const
	Get the muscle mass used in the metabolic analysis. More...

const double	getRatioSlowTwitchFibers (const std::string &muscleName) const
	Get the ratio of slow twitch fibers for an existing muscle. More...

void	setRatioSlowTwitchFibers (const std::string &muscleName, const double &ratio)
	Set the ratio of slow twitch fibers for an existing muscle. More...

const double	getDensity (const std::string &muscleName) const
	Get the density for an existing muscle (kg/m^3). More...

void	setDensity (const std::string &muscleName, const double &density)
	Set the density for an existing muscle (kg/m^3). More...

const double	getSpecificTension (const std::string &muscleName) const
	Get the specific tension for an existing muscle (Pascals (N/m^2)). More...

void	setSpecificTension (const std::string &muscleName, const double &specificTension)
	Set the specific tension for an existing muscle (Pascals (N/m^2)). More...

const double	getActivationConstantSlowTwitch (const std::string &muscleName) const
	Get the activation constant for slow twitch fibers for an existing muscle. More...

void	setActivationConstantSlowTwitch (const std::string &muscleName, const double &c)
	Set the activation constant for slow twitch fibers for an existing muscle. More...

const double	getActivationConstantFastTwitch (const std::string &muscleName) const
	Get the activation constant for fast twitch fibers for an existing muscle. More...

void	setActivationConstantFastTwitch (const std::string &muscleName, const double &c)
	Set the activation constant for fast twitch fibers for an existing muscle. More...

const double	getMaintenanceConstantSlowTwitch (const std::string &muscleName) const
	Get the maintenance constant for slow twitch fibers for an existing muscle. More...

void	setMaintenanceConstantSlowTwitch (const std::string &muscleName, const double &c)
	Set the maintenance constant for slow twitch fibers for an existing muscle. More...

const double	getMaintenanceConstantFastTwitch (const std::string &muscleName) const
	Get the maintenance constant for fast twitch fibers for an existing muscle. More...

void	setMaintenanceConstantFastTwitch (const std::string &muscleName, const double &c)
	Set the maintenance constant for fast twitch fibers for an existing muscle. More...

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. More...

static void	renameType (const std::string &oldTypeName, const std::string &newTypeName)
	Support versioning by associating the current Object type with an old name. More...

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. More...

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*. More...

static Object *	newInstanceOfType (const std::string &concreteClassName)
	Create a new instance of the concrete Object type whose class name is given as concreteClassName. More...

static void	getRegisteredTypenames (Array< std::string > &typeNames)
	Retrieve all the typenames registered so far. More...

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. More...

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. More...

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. More...

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. More...

static const std::string &	getClassName ()
	Return the name of this class as a string; i.e., "Object". More...

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. More...

static bool	getSerializeAllDefaults ()
	Report the value of the "serialize all defaults" flag. More...

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. More...

static void	setDebugLevel (int newLevel)
	Set the debug level to get verbose output. More...

static int	getDebugLevel ()
	Get current setting of debug level. More...

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. More...

static void	RegisterType (const Object &defaultObject)
	OBSOLETE alternate name for registerType(). More...

static void	RenameType (const std::string &oldName, const std::string &newName)
	OBSOLETE alternate name for renameType(). More...

Static Public Attributes inherited from OpenSim::Object
static const std::string	DEFAULT_NAME
	Name used for default objects when they are serialized. More...

Protected Member Functions inherited from OpenSim::Probe
void	connectToModel (Model &model) override
	Concrete probes may override; be sure to invoke Super::connectToModel() at the beginning of the overriding method. More...

void	addToSystem (SimTK::MultibodySystem &system) const override
	Concrete probes may override; be sure to invoke Super::addToSystem() at the beginning of the overriding method. More...

Protected Member Functions inherited from OpenSim::ModelComponent
virtual void	initStateFromProperties (SimTK::State &state) const
	Transfer property values or other state-independent initial values into this component's state variables in the passed-in state argument. More...

virtual void	setPropertiesFromState (const SimTK::State &state)
	Update this component's property values to match the specified State, if the component has created any state variable that is intended to correspond to a property. More...

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. More...

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. More...

virtual void	realizeTopology (SimTK::State &state) const
	Obtain state resources that are needed unconditionally, and perform computations that depend only on the system topology. More...

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. More...

virtual void	realizeInstance (const SimTK::State &state) const
	Perform computations that depend only on instance variables, like lengths and masses. More...

virtual void	realizeTime (const SimTK::State &state) const
	Perform computations that depend only on time and earlier stages. More...

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). More...

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). More...

virtual void	realizeDynamics (const SimTK::State &state) const
	Perform computations (typically forces) that may depend on dynamics-stage state variables, and on computations performed in earlier stages (including velocity, position, and time), but not on other forces, accelerations, constraint multipliers, or reaction forces. More...

virtual void	realizeAcceleration (const SimTK::State &state) const
	Perform computations that may depend on applied forces. More...

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. More...

void	includeAsSubComponent (ModelComponent *aComponent)
	Include another ModelComponent as a Subcomponent of this ModelComponent. More...

void	addModelingOption (const std::string &optionName, int maxFlagValue) const
	Add a modeling option (integer flag stored in the State) for use by this ModelComponent. More...

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. More...

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. More...

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. More...

const int	getStateIndex (const std::string &name) const
	Get the index of a ModelComponent's continuous state variable in the Subsystem for allocations. More...

const SimTK::DiscreteVariableIndex	getDiscreteVariableIndex (const std::string &name) const
	Get the index of a ModelComponent's discrete variable in the Subsystem for allocations. More...

const SimTK::CacheEntryIndex	getCacheVariableIndex (const std::string &name) const
	Get the index of a ModelComponent's cache variable in the Subsystem for allocations. More...

Protected Member Functions inherited from OpenSim::Object
	Object ()
	The default constructor is only for use by constructors of derived types. More...

	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. More...

	Object (const Object &source)
	Copy constructor is invoked automatically by derived classes with default copy constructors; otherwise it must be invoked explicitly. More...

	Object (SimTK::Xml::Element &aElement)
	Construct the base class portion of an Object from a given Xml element that describes this Object. More...

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. More...

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. More...

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. More...

template<class T >
PropertyIndex	addListProperty (const std::string &name, const std::string &comment, int minSize, int maxSize)
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Protected Attributes inherited from OpenSim::ModelComponent
Model *	_model
	The model this component belongs to. More...

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Detailed Description

Bhargava2004MuscleMetabolicsProbe is a Probe ModelComponent for computing the net metabolic energy rate of a set of Muscles in the model during a simulation.

Bhargava2004MuscleMetabolicsProbe Theory

The discussion here is based on the following paper:

Bhargava, L. J., Pandy, M. G. and Anderson, F. C. (2004). A phenomenological model for estimating metabolic energy consumption in muscle contraction. J Biomech 37, 81-8.

Note that the equations below that describe the particular implementation of Bhargava2004MuscleMetabolicsProbe may slightly differ from the equations described in the representative publication above. Note also that we define positive muscle velocity to indicate lengthening (eccentric contraction) and negative muscle velocity to indicate shortening (concentric contraction).

Muscle metabolic power (or rate of metabolic energy consumption) is equal to the rate at which heat is liberated plus the rate at which work is done:
Edot = Bdot + sumOfAllMuscles(Adot + Mdot + Sdot + Wdot).

  - Bdot is the basal heat rate (W).
  - Adot is the activation heat rate (W).
  - Mdot is the maintenance heat rate (W).
  - Sdot is the shortening heat rate (W).
  - Wdot is the mechanical work rate (W).

This probe also uses muscle parameters stored in the MetabolicMuscle object for each muscle. The full set of all MetabolicMuscles (MetabolicMuscleSet) is a property of this probe:

m = The mass of the muscle (kg).
r = Ratio of slow twitch fibers in the muscle (between 0 and 1).
Adot_slow = Activation constant for slow twitch fibers (W/kg).
Adot_fast = Activation constant for fast twitch fibers (W/kg).
Mdot_slow = Maintenance constant for slow twitch fibers (W/kg).
Mdot_fast = Maintenance constant for slow twitch fibers (W/kg).

BASAL HEAT RATE (W)

If basal_rate_on is set to true, then Bdot is calculated as follows:
Bdot = basal_coefficient * (m_body^basal_exponent)

m_body = mass of the entire model
basal_coefficient and basal_exponent are defined by their respective properties.
Note that this quantity is muscle independant. Rather it is calculated on a whole body level.

ACTIVATION HEAT RATE (W)

If activation_rate_on is set to true, then Adot is calculated as follows:
Adot = phi * m * [ Adot_slow * r * sin((pi/2)*u) + Adot_fast * (1-r) * (1-cos((pi/2)*u)) ]

u = muscle excitation at the current time.
phi = decay function. Bhargava et al. (2004) use a function to model the observation that the rate of heat generation is greatest immediately after the muscle is excited and then decays. We follow the work of Anderson and Pandy, who set this value to 1.0.

MAINTENANCE HEAT RATE (W)

If maintenance_rate_on is set to true, then Mdot is calculated as follows:
Mdot = m * f * [ Mdot_slow * r * sin((pi/2)*u) + Mdot_fast * (1-r) * (1-cos((pi/2)*u)) ]

u = muscle excitation at the current time.
f is a piecewise linear function that describes the normalized fiber length denendence of the maintenance heat rate (default curve is shown below):

SHORTENING HEAT RATE (W)

If shortening_rate_on is set to true, then Sdot is calculated as follows:
Sdot = -alpha * v_CE

If use_force_dependent_shortening_prop_constant = true,

alpha = (0.16 * F_CE_iso) + (0.18 * F_CE) , v_CE >= 0 (concentric / isometric contraction)
alpha = 0.157 * F_CE , v_CE < 0 (eccentric contraction)
v_CE = muscle fiber velocity at the current time.
F_CE = force developed by the contractile (active) element of muscle at the current time.
F_CE_iso = force that would be developed by the contractile element of muscle under isometric conditions with the current activation and fiber length.

If use_force_dependent_shortening_prop_constant = false,

alpha = 0.25 * (F_CE + F_PASSIVE), , v_CE >= 0 (concentric / isometric contraction)
alpha = 0.00 , v_CE < 0 (eccentric contraction)

where F_PASSIVE = passive force developed by the muscle fiber velocity at the current time.

MECHANICAL WORK RATE (W)

If mechanical_work_rate_on is set to true, then Wdot is calculated as follows:
Wdot = -F_CE * v_CE

v_CE = muscle fiber velocity at the current time.
F_CE = force developed by the contractile element of muscle at the current time.
If we draw a control volume around the fiber, the first law of thermodynamics suggests that negative mechanical work should be included in Wdot. As such, we include negative mechanical work in Wdot by default. To exclude negative mechanical work from Wdot, set the 'include_negative_mechanical_work' property to false.

During eccentric contraction, the magnitude of the (negative) mechanical work rate can exceed that of the total (positive) heat rate, resulting in a flow of energy into the fiber. Experiments indicate that the chemical processes involved in fiber contraction cannot be reversed, and most of the energy that is absorbed during eccentric contraction (in increased cross-bridge potentials, for example) is eventually converted into heat. Thus, we increase Sdot (if necessary) to ensure Edot > 0 for each muscle. See Constable, J.K., Barclay, C.J., Gibbs, C.L. (1997) Energetics of lengthening in mouse and toad skeletal muscles. J Physiol 505:205-215. To allow muscles to have negative total power, set the 'forbid_negative_total_power' property to false.

Note that if enforce_minimum_heat_rate_per_muscle == true AND activation_rate_on == shortening_rate_on == maintenance_rate_on == true, then the total heat rate (AMdot + Mdot + Sdot) will be capped to a minimum value of 1.0 W/kg (Umberger(2003), page 104).

Bhargava2004MuscleMetabolicsProbe_MetabolicMuscleParameter

Bhargava2004MuscleMetabolicsProbe_MetabolicMuscleParameter is an Object class that holds the metabolic parameters required to calculate metabolic power for a single muscle.

Bhargava2004MuscleMetabolicsProbe_MetabolicMuscleParameter Properties

REQUIRED PROPERTIES

specific_tension = The specific tension of the muscle (Pascals (N/m^2)).
density = The density of the muscle (kg/m^3).
ratio_slow_twitch_fibers = Ratio of slow twitch fibers in the muscle (must be between 0 and 1).
activation_constant_slow_twitch = Activation constant for slow twitch fibers (W/kg).
activation_constant_fast_twitch = Activation constant for fast twitch fibers (W/kg).
maintenance_constant_slow_twitch = Maintenance constant for slow twitch fibers (W/kg).
maintenance_constant_fast_twitch = Maintenance constant for slow twitch fibers (W/kg).

OPTIONAL PROPERTIES

use_provided_muscle_mass = An optional flag that allows the user to explicitly specify a muscle mass. If set to true, the "provided_muscle_mass" property must be specified. The default setting is false, in which case, the muscle mass is calculated from the following formula: m = (Fmax/specific_tension)*density*Lm_opt, where specific_tension and density are properties defined above (note that their default values are set based on mammalian muscle, 0.25e6 N/m^2 and 1059.7 kg/m^3, respectively); Fmax and Lm_opt are the maximum isometric force and optimal fiber length, respectively, of the muscle.
provided_muscle_mass = The user specified muscle mass (kg).

Author: Tim Dorn

Member Typedef Documentation

typedef std::map<std::string, Bhargava2004MuscleMetabolicsProbe_MetabolicMuscleParameter*> OpenSim::Bhargava2004MuscleMetabolicsProbe::MuscleMap

MuscleMap typedef.

Constructor & Destructor Documentation

OpenSim::Bhargava2004MuscleMetabolicsProbe::Bhargava2004MuscleMetabolicsProbe ( )

Default constructor.

OpenSim::Bhargava2004MuscleMetabolicsProbe::Bhargava2004MuscleMetabolicsProbe	(	const bool	activation_rate_on,
		const bool	maintenance_rate_on,
		const bool	shortening_rate_on,
		const bool	basal_rate_on,
		const bool	work_rate_on
	)

Convenience constructor.

Member Function Documentation

void OpenSim::Bhargava2004MuscleMetabolicsProbe::addMuscle	(	const std::string &	muscleName,
		double	ratio_slow_twitch_fibers,
		double	activation_constant_slow_twitch,
		double	activation_constant_fast_twitch,
		double	maintenance_constant_slow_twitch,
		double	maintenance_constant_fast_twitch
	)

Add a muscle and its parameters so that it can be included in the metabolic analysis.

void OpenSim::Bhargava2004MuscleMetabolicsProbe::addMuscle	(	const std::string &	muscleName,
		double	ratio_slow_twitch_fibers,
		double	activation_constant_slow_twitch,
		double	activation_constant_fast_twitch,
		double	maintenance_constant_slow_twitch,
		double	maintenance_constant_fast_twitch,
		double	muscle_mass
	)

Add a muscle and its parameters so that it can be included in the metabolic analysis.

virtual SimTK::Vector OpenSim::Bhargava2004MuscleMetabolicsProbe::computeProbeInputs ( const SimTK::State & state ) const

overridevirtual

Compute muscle metabolic power.

Implements OpenSim::Probe.

const double OpenSim::Bhargava2004MuscleMetabolicsProbe::getActivationConstantFastTwitch ( const std::string & muscleName ) const

Get the activation constant for fast twitch fibers for an existing muscle.

const double OpenSim::Bhargava2004MuscleMetabolicsProbe::getActivationConstantSlowTwitch ( const std::string & muscleName ) const

Get the activation constant for slow twitch fibers for an existing muscle.

const double OpenSim::Bhargava2004MuscleMetabolicsProbe::getDensity ( const std::string & muscleName ) const

Get the density for an existing muscle (kg/m^3).

const double OpenSim::Bhargava2004MuscleMetabolicsProbe::getMaintenanceConstantFastTwitch ( const std::string & muscleName ) const

Get the maintenance constant for fast twitch fibers for an existing muscle.

const double OpenSim::Bhargava2004MuscleMetabolicsProbe::getMaintenanceConstantSlowTwitch ( const std::string & muscleName ) const

Get the maintenance constant for slow twitch fibers for an existing muscle.

const double OpenSim::Bhargava2004MuscleMetabolicsProbe::getMuscleMass ( const std::string & muscleName ) const

Get the muscle mass used in the metabolic analysis.

The value returned will depend on if the muscle mass is explicitly provided (i.e. isUsingProvidedMass = true), or if it is being automatically calculated from muscle data already present in the model (i.e. isUsingProvidedMass = true).

const int OpenSim::Bhargava2004MuscleMetabolicsProbe::getNumMetabolicMuscles ( ) const

int OpenSim::Bhargava2004MuscleMetabolicsProbe::getNumProbeInputs ( ) const

overridevirtual

Returns the number of probe inputs in the vector returned by computeProbeInputs().

Implements OpenSim::Probe.

virtual OpenSim::Array<std::string> OpenSim::Bhargava2004MuscleMetabolicsProbe::getProbeOutputLabels ( ) const

overridevirtual

Returns the column labels of the probe values for reporting.

Currently uses the Probe name as the column label, so be sure to name your probe appropiately!

Implements OpenSim::Probe.

const double OpenSim::Bhargava2004MuscleMetabolicsProbe::getRatioSlowTwitchFibers ( const std::string & muscleName ) const

Get the ratio of slow twitch fibers for an existing muscle.

const double OpenSim::Bhargava2004MuscleMetabolicsProbe::getSpecificTension ( const std::string & muscleName ) const

Get the specific tension for an existing muscle (Pascals (N/m^2)).

bool OpenSim::Bhargava2004MuscleMetabolicsProbe::isUsingProvidedMass ( const std::string & muscleName )

Get whether the muscle mass is being explicitly provided.

True means that it is using the property 'provided_muscle_mass' False means that the muscle mass is being calculated from muscle properties.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	activation_rate_on	,
		bool	,
		"Specify whether activation heat rate is to be calculated (true/false)."
	)

Enabled by default.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	maintenance_rate_on	,
		bool	,
		"Specify whether maintenance heat rate is to be calculated (true/false)."
	)

Enabled by default.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	shortening_rate_on	,
		bool	,
		"Specify whether shortening heat rate is to be calculated (true/false)."
	)

Enabled by default.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	basal_rate_on	,
		bool	,
		"Specify whether basal heat rate is to be calculated (true/false)."
	)

Enabled by default.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	mechanical_work_rate_on	,
		bool	,
		"Specify whether mechanical work rate is to be calculated (true/false)."
	)

Enabled by default.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	enforce_minimum_heat_rate_per_muscle	,
		bool	,
		"Specify whether the total heat rate for a muscle will be clamped to a ""minimum value of 1.0 W/kg (true/false)."
	)

Enabled by default.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	normalized_fiber_length_dependence_on_maintenance_rate	,
		PiecewiseLinearFunction	,
		"Contains a PiecewiseLinearFunction object that describes the ""normalized fiber length dependence on maintenance rate."
	)

Default curve shown in doxygen.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	use_force_dependent_shortening_prop_constant	,
		bool	,
		"Specify whether to use a force dependent shortening proportionality ""constant (true/false)."
	)

Disabled by default.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	basal_coefficient	,
		double	,
		"Basal metabolic coefficient."
	)

Default value = 1.2.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	basal_exponent	,
		double	,
		"Basal metabolic exponent."
	)

Default value = 1.0.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	muscle_effort_scaling_factor	,
		double	,
		"Scale the excitation and activation values used by the probe to ""compensate for solutions with excessive coactivation (e.g., when a ""suboptimal tracking strategy is used)."
	)

Default value = 1.0.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	include_negative_mechanical_work	,
		bool	,
		"Specify whether negative mechanical work will be included in Wdot ""(true/false)."
	)

Enabled by default.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	forbid_negative_total_power	,
		bool	,
		"Specify whether the total power for each muscle must remain positive ""(true/false)."
	)

Enabled by default.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_PROPERTY	(	report_total_metabolics_only	,
		bool	,
		"If set to	false,
		the individual muscle	metabolics,
		basal	rate,
		and""total summation will be reported.If set to	true,
		only the total""summation will be reported."
	)

Default value = true.

OpenSim::Bhargava2004MuscleMetabolicsProbe::OpenSim_DECLARE_UNNAMED_PROPERTY	(	Bhargava2004MuscleMetabolicsProbe_MetabolicMuscleParameterSet	,
		"A set	containing,
		for each	muscle,
		the parameters""required to calculate muscle metabolic power."
	)

void OpenSim::Bhargava2004MuscleMetabolicsProbe::removeMuscle ( const std::string & muscleName )

Remove a muscle from the metabolic analysis.

void OpenSim::Bhargava2004MuscleMetabolicsProbe::setActivationConstantFastTwitch	(	const std::string &	muscleName,
		const double &	c
	)

Set the activation constant for fast twitch fibers for an existing muscle.

void OpenSim::Bhargava2004MuscleMetabolicsProbe::setActivationConstantSlowTwitch	(	const std::string &	muscleName,
		const double &	c
	)

Set the activation constant for slow twitch fibers for an existing muscle.

void OpenSim::Bhargava2004MuscleMetabolicsProbe::setDensity	(	const std::string &	muscleName,
		const double &	density
	)

Set the density for an existing muscle (kg/m^3).

void OpenSim::Bhargava2004MuscleMetabolicsProbe::setMaintenanceConstantFastTwitch	(	const std::string &	muscleName,
		const double &	c
	)

Set the maintenance constant for fast twitch fibers for an existing muscle.

void OpenSim::Bhargava2004MuscleMetabolicsProbe::setMaintenanceConstantSlowTwitch	(	const std::string &	muscleName,
		const double &	c
	)

Set the maintenance constant for slow twitch fibers for an existing muscle.

void OpenSim::Bhargava2004MuscleMetabolicsProbe::setRatioSlowTwitchFibers	(	const std::string &	muscleName,
		const double &	ratio
	)

Set the ratio of slow twitch fibers for an existing muscle.

void OpenSim::Bhargava2004MuscleMetabolicsProbe::setSpecificTension	(	const std::string &	muscleName,
		const double &	specificTension
	)

Set the specific tension for an existing muscle (Pascals (N/m^2)).

void OpenSim::Bhargava2004MuscleMetabolicsProbe::useCalculatedMass ( const std::string & muscleName )

Set an existing muscle to calculate its own mass.

void OpenSim::Bhargava2004MuscleMetabolicsProbe::useProvidedMass	(	const std::string &	muscleName,
		double	providedMass
	)

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

OpenSim/Simulation/Model/Bhargava2004MuscleMetabolicsProbe.h

Public Member Functions

Public Types

Bhargava2004MuscleMetabolicsProbe Interface

Additional Inherited Members

Detailed Description

Bhargava2004MuscleMetabolicsProbe Theory

BASAL HEAT RATE (W)

ACTIVATION HEAT RATE (W)

MAINTENANCE HEAT RATE (W)

SHORTENING HEAT RATE (W)

MECHANICAL WORK RATE (W)

Bhargava2004MuscleMetabolicsProbe_MetabolicMuscleParameter

Bhargava2004MuscleMetabolicsProbe_MetabolicMuscleParameter Properties

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation