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API
4.2
For C++ developers
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API
4.2
For C++ developers
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This class implements the metabolic energy model of Bhargava et al (2004) and provides an option to use smooth (i.e., twice continuously differentiable) approximations. More...
Inheritance diagram for OpenSim::Bhargava2004SmoothedMuscleMetabolics:OpenSim Properties, Sockets, Outputs, Inputs | |
Properties (single-value) | |
| bool | enforce_minimum_heat_rate_per_muscle |
| "Specify whether the total heat rate for a muscle will be clamped " "to a minimum value of 1.0 W/kg (default is true). When set to " "true, the sum of the reported individual heat rates + work rate " "will not equal the reported total metabolic rate if the total " "heat rate falls below 1.0 W/kg." More... | |
| bool | use_force_dependent_shortening_prop_constant |
| "Specify whether to use a force dependent shortening " "proportionality constant (default is false)." More... | |
| double | basal_coefficient |
| "Basal metabolic " "coefficient (default is 1.2)." More... | |
| double | basal_exponent |
| "Basal metabolic " "exponent (default is 1)." More... | |
| double | muscle_effort_scaling_factor |
| "Scale the excitation and activation values to compensate for " "solutions with excessive coactivation (e.g., when a suboptimal " "tracking strategy is used) (default is 1)." More... | |
| bool | include_negative_mechanical_work |
| "Specify whether negative mechanical work will be included in " "mechanicalWorkRate (default is true)." More... | |
| bool | forbid_negative_total_power |
| "Specify whether the total power for each muscle must remain " "positive (default is true)." More... | |
Properties (optional) | |
| bool | use_smoothing |
| "An optional flag that allows the user to explicitly specify " "whether a smooth approximation of the metabolic energy model " "should be used (default is false)." More... | |
| std::string | smoothing_type |
| "An optional flag that allows the user to explicitly specify " "what type of smoothing to use ('tanh' or 'huber'; default is " "'tanh')." More... | |
| double | velocity_smoothing |
| "The parameter that determines the smoothness of the transition " "of the tanh or Huber loss function used to smooth the conditions " "related to contraction type (concentric or eccentric). Note that " "when computing the shortening heat rate while using the force " "dependent shortening proportionality constant, a tanh " "approximation is used even when using the Huber loss smoothing " "approach. The larger the steeper the transition but the worse " "for optimization (default is 10)." More... | |
| double | power_smoothing |
| "The parameter that determines the smoothness of the transition " "of the tanh or Huber loss function used to smooth the condition " "enforcing non-negative total power. The larger the steeper the " "transition but the worse for optimization (default is 10)." More... | |
| double | heat_rate_smoothing |
| "The parameter that determines the smoothness of the transition " "of the tanh or Huber loss function used to smooth the condition " "enforcing total heat rate larger than 1 (W/kg) for a give muscle " ". The larger the steeper the transition but the worse for " "optimization (default is 10)." More... | |
Properties (list) | |
| Bhargava2004SmoothedMuscleMetabolics_MuscleParameters | muscle_parameters |
| "Metabolic parameters for each muscle." More... | |
Outputs | |
| double | total_metabolic_rate |
| Provides the value of getTotalMetabolicRate() and is available at stage SimTK::Stage::Dynamics . More... | |
| double | total_activation_rate |
| Provides the value of getTotalActivationRate() and is available at stage SimTK::Stage::Dynamics . More... | |
| double | total_maintenance_rate |
| Provides the value of getTotalMaintenanceRate() and is available at stage SimTK::Stage::Dynamics . More... | |
| double | total_shortening_rate |
| Provides the value of getTotalShorteningRate() and is available at stage SimTK::Stage::Dynamics . More... | |
| double | total_mechanical_work_rate |
| Provides the value of getTotalMechanicalWorkRate() and is available at stage SimTK::Stage::Dynamics . More... | |
Outputs (list) | |
| double | muscle_metabolic_rate |
| Provides the value of getMuscleMetabolicRate() and is available at stage SimTK::Stage::Dynamics . More... | |
| OpenSim Properties, Sockets, Outputs, Inputs inherited from OpenSim::Component | |
| Component | components |
| "List of components that this component owns and serializes." More... | |
Public Member Functions | |
| Bhargava2004SmoothedMuscleMetabolics () | |
| int | getNumMetabolicMuscles () const |
Get the number of muscles added to the metabolics model by one of the addMuscle() overloads. More... | |
| void | addMuscle (const std::string &name, const Muscle &muscle, double muscle_mass=SimTK::NaN) |
| Specify a muscle that should be included when computing the total metabolic rate. More... | |
| void | addMuscle (const std::string &name, const Muscle &muscle, double ratio_slow_twitch_fibers, double specific_tension, double muscle_mass=SimTK::NaN) |
| Specify a muscle that should be included when computing the total metabolic rate, as well as its ratio of slow to fast twitch fibers and specific tension. More... | |
| void | addMuscle (const std::string &name, const Muscle &muscle, double ratio_slow_twitch_fibers, double specific_tension, double activation_constant_slow_twitch, double activation_constant_fast_twitch, double maintenance_constant_slow_twitch, double maintenance_constant_fast_twitch, double muscle_mass=SimTK::NaN) |
| Specify a muscle that should be included when computing the total metabolic rate, as well as its ratio of slow to fast twitch fibers and specific tension. More... | |
| double | getTotalMetabolicRate (const SimTK::State &s) const |
| double | getTotalActivationRate (const SimTK::State &s) const |
| double | getTotalMaintenanceRate (const SimTK::State &s) const |
| double | getTotalShorteningRate (const SimTK::State &s) const |
| double | getTotalMechanicalWorkRate (const SimTK::State &s) const |
| double | getMuscleMetabolicRate (const SimTK::State &s, const std::string &channel) const |
Property-related functions | |
| const bool & | get_enforce_minimum_heat_rate_per_muscle () const |
| Get the value of the enforce_minimum_heat_rate_per_muscle property. More... | |
| bool & | upd_enforce_minimum_heat_rate_per_muscle () |
| Get a writable reference to the enforce_minimum_heat_rate_per_muscle property. More... | |
| void | set_enforce_minimum_heat_rate_per_muscle (const bool &value) |
| Set the value of the enforce_minimum_heat_rate_per_muscle property. More... | |
| const bool & | get_use_force_dependent_shortening_prop_constant () const |
| Get the value of the use_force_dependent_shortening_prop_constant property. More... | |
| bool & | upd_use_force_dependent_shortening_prop_constant () |
| Get a writable reference to the use_force_dependent_shortening_prop_constant property. More... | |
| void | set_use_force_dependent_shortening_prop_constant (const bool &value) |
| Set the value of the use_force_dependent_shortening_prop_constant property. More... | |
| const double & | get_basal_coefficient () const |
| Get the value of the basal_coefficient property. More... | |
| double & | upd_basal_coefficient () |
| Get a writable reference to the basal_coefficient property. More... | |
| void | set_basal_coefficient (const double &value) |
| Set the value of the basal_coefficient property. More... | |
| const double & | get_basal_exponent () const |
| Get the value of the basal_exponent property. More... | |
| double & | upd_basal_exponent () |
| Get a writable reference to the basal_exponent property. More... | |
| void | set_basal_exponent (const double &value) |
| Set the value of the basal_exponent property. More... | |
| const double & | get_muscle_effort_scaling_factor () const |
| Get the value of the muscle_effort_scaling_factor property. More... | |
| double & | upd_muscle_effort_scaling_factor () |
| Get a writable reference to the muscle_effort_scaling_factor property. More... | |
| void | set_muscle_effort_scaling_factor (const double &value) |
| Set the value of the muscle_effort_scaling_factor property. More... | |
| const bool & | get_include_negative_mechanical_work () const |
| Get the value of the include_negative_mechanical_work property. More... | |
| bool & | upd_include_negative_mechanical_work () |
| Get a writable reference to the include_negative_mechanical_work property. More... | |
| void | set_include_negative_mechanical_work (const bool &value) |
| Set the value of the include_negative_mechanical_work property. More... | |
| const bool & | get_forbid_negative_total_power () const |
| Get the value of the forbid_negative_total_power property. More... | |
| bool & | upd_forbid_negative_total_power () |
| Get a writable reference to the forbid_negative_total_power property. More... | |
| void | set_forbid_negative_total_power (const bool &value) |
| Set the value of the forbid_negative_total_power property. More... | |
| const bool & | get_use_smoothing () const |
| Get the value of the use_smoothing property. More... | |
| bool & | upd_use_smoothing () |
| Get a writable reference to the use_smoothing property. More... | |
| void | set_use_smoothing (const bool &value) |
| Set the value of the use_smoothing property. More... | |
| const std::string & | get_smoothing_type () const |
| Get the value of the smoothing_type property. More... | |
| std::string & | upd_smoothing_type () |
| Get a writable reference to the smoothing_type property. More... | |
| void | set_smoothing_type (const std::string &value) |
| Set the value of the smoothing_type property. More... | |
| const double & | get_velocity_smoothing () const |
| Get the value of the velocity_smoothing property. More... | |
| double & | upd_velocity_smoothing () |
| Get a writable reference to the velocity_smoothing property. More... | |
| void | set_velocity_smoothing (const double &value) |
| Set the value of the velocity_smoothing property. More... | |
| const double & | get_power_smoothing () const |
| Get the value of the power_smoothing property. More... | |
| double & | upd_power_smoothing () |
| Get a writable reference to the power_smoothing property. More... | |
| void | set_power_smoothing (const double &value) |
| Set the value of the power_smoothing property. More... | |
| const double & | get_heat_rate_smoothing () const |
| Get the value of the heat_rate_smoothing property. More... | |
| double & | upd_heat_rate_smoothing () |
| Get a writable reference to the heat_rate_smoothing property. More... | |
| void | set_heat_rate_smoothing (const double &value) |
| Set the value of the heat_rate_smoothing property. More... | |
| const Bhargava2004SmoothedMuscleMetabolics_MuscleParameters & | get_muscle_parameters (int i) const |
| Get the value of the i-th element of the muscle_parameters property. More... | |
| Bhargava2004SmoothedMuscleMetabolics_MuscleParameters & | upd_muscle_parameters (int i) |
| Get a writable reference to the i-th element of the muscle_parameters property. More... | |
| void | set_muscle_parameters (int i, const Bhargava2004SmoothedMuscleMetabolics_MuscleParameters &value) |
| Set the value of the i-th element of muscle_parameters property. More... | |
| int | append_muscle_parameters (const Bhargava2004SmoothedMuscleMetabolics_MuscleParameters &value) |
| Append an element to the muscle_parameters property. More... | |
| Public Member Functions inherited from OpenSim::ModelComponent | |
| ModelComponent () | |
| Default constructor. More... | |
| ModelComponent (const std::string &aFileName, bool aUpdateFromXMLNode=true) | |
| Construct ModelComponent from an XML file. More... | |
| ModelComponent (SimTK::Xml::Element &aNode) | |
| Construct ModelComponent from a specific node in an XML document. More... | |
| virtual | ~ModelComponent () |
| Destructor is virtual to allow concrete model component cleanup. More... | |
| void | connectToModel (Model &model) |
| Connect this ModelComponent to its aggregate- a Model. 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... | |
| bool | hasModel () const |
| Does this ModelComponent have a Model associated with it? More... | |
| void | preScale (const SimTK::State &s, const ScaleSet &scaleSet) |
| Perform any computations that must occur before ModelComponent::scale() is invoked on all ModelComponents in the Model. More... | |
| void | scale (const SimTK::State &s, const ScaleSet &scaleSet) |
| Scale the ModelComponent. More... | |
| void | postScale (const SimTK::State &s, const ScaleSet &scaleSet) |
| Perform any computations that must occur after ModelComponent::scale() has been invoked on all ModelComponents in the Model. More... | |
| void | assign (Object &aObject) override |
| This allows copy assignment in the Java GUI. More... | |
| Public Member Functions inherited from OpenSim::Component | |
| Component () | |
| Default constructor. More... | |
| Component (const std::string &aFileName, bool aUpdateFromXMLNode=true) | |
| Construct Component from an XML file. More... | |
| Component (SimTK::Xml::Element &aNode) | |
| Construct Component from a specific node in an XML document. More... | |
| Component (const Component &)=default | |
| Use default copy constructor and assignment operator. More... | |
| Component & | operator= (const Component &)=default |
| virtual | ~Component ()=default |
| Destructor is virtual to allow concrete Component to cleanup. 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 Component at the specified state. More... | |
| const SimTK::MultibodySystem & | getSystem () const |
| Get the underlying MultibodySystem that this component is connected to. More... | |
| bool | hasSystem () const |
| Check if this component has an underlying MultibodySystem. More... | |
| bool | isComponentInOwnershipTree (const Component *component) const |
| Does the provided component already exist anywhere in the ownership tree (not just subcomponents of this component)? More... | |
| void | addComponent (Component *subcomponent) |
| Add a Component (as a subcomponent) of this component. More... | |
| template<typename T = Component> | |
| ComponentList< const T > | getComponentList () const |
| Get an iterator through the underlying subcomponents that this component is composed of. More... | |
| template<typename T = Component> | |
| ComponentList< T > | updComponentList () |
| Similar to getComponentList(), except the resulting list allows one to modify the components. More... | |
| template<typename T = Component> | |
| unsigned | countNumComponents () const |
| Uses getComponentList<T>() to count the number of underlying subcomponents of the specified type. More... | |
| std::string | getAbsolutePathString () const |
| Get the complete (absolute) pathname for this Component to its ancestral Component, which is the root of the tree to which this Component belongs. More... | |
| ComponentPath | getAbsolutePath () const |
| Return a ComponentPath of the absolute path of this Component. More... | |
| std::string | getRelativePathString (const Component &wrt) const |
| Get the relative path of this Component with respect to another Component, as a string. More... | |
| ComponentPath | getRelativePath (const Component &wrt) const |
| Get the relative path of this Component with respect to another Component. More... | |
| bool | hasComponent (const std::string &pathname) const |
| Query if there is a component (of any type) at the specified path name. More... | |
| template<class C = Component> | |
| bool | hasComponent (const std::string &pathname) const |
| Query if there is a component of a given type at the specified path name. More... | |
| template<class C = Component> | |
| const C & | getComponent (const std::string &pathname) const |
| Get a unique subcomponent of this Component by its path name and type 'C'. More... | |
| template<class C = Component> | |
| const C & | getComponent (const ComponentPath &pathname) const |
| const Component & | getComponent (const std::string &pathname) const |
| Similar to the templatized getComponent(), except this returns the component as the generic Component type. More... | |
| template<class C = Component> | |
| C & | updComponent (const std::string &name) |
| Get a writable reference to a subcomponent. More... | |
| template<class C = Component> | |
| C & | updComponent (const ComponentPath &name) |
| Component & | updComponent (const std::string &pathname) |
| Similar to the templatized updComponent(), except this returns the component as the generic Component type. More... | |
| unsigned | printComponentsMatching (const std::string &substring) const |
| Print a list to the console of all components whose absolute path name contains the given string. More... | |
| int | getNumStateVariables () const |
| Get the number of "continuous" state variables maintained by the Component and its subcomponents. More... | |
| Array< std::string > | getStateVariableNames () const |
| Get the names of "continuous" state variables maintained by the Component and its subcomponents. More... | |
| template<class C = Component> | |
| const C * | findComponent (const ComponentPath &pathToFind) const |
| Find a Component to which this Component is an ancestor—in other words, a Component that is directly owned by this Component or is owned by one of its sub-components, sub-sub-components, etc. More... | |
| template<class C = Component> | |
| const C * | findComponent (const std::string &pathToFind) const |
| Same as findComponent(const ComponentPath&), but accepting a string (a path or just a name) as input. More... | |
| const StateVariable * | traverseToStateVariable (const std::string &pathName) const |
| Get a StateVariable anywhere in the Component tree, given a StateVariable path. More... | |
| void | finalizeFromProperties () |
| Define a Component's internal data members and structure according to its properties. More... | |
| void | finalizeConnections (Component &root) |
| Satisfy the Component's connections specified by its Sockets and Inputs. More... | |
| void | clearConnections () |
| Disconnect/clear this Component from its aggregate component. More... | |
| void | addToSystem (SimTK::MultibodySystem &system) const |
| Have the Component add itself to the underlying computational System. More... | |
| void | initStateFromProperties (SimTK::State &state) const |
| Initialize Component's state variable values from its properties. More... | |
| void | setPropertiesFromState (const SimTK::State &state) |
| Set Component's properties given a state. More... | |
| int | getNumSockets () const |
| Get the number of Sockets in this Component. More... | |
| std::vector< std::string > | getSocketNames () |
| Collect and return the names of the sockets in this component. More... | |
| template<typename T > | |
| const T & | getConnectee (const std::string &name) const |
| Get the "connectee" object that the Component's Socket is bound to. More... | |
| const Object & | getConnectee (const std::string &name) const |
| Get the connectee as an Object. More... | |
| const AbstractSocket & | getSocket (const std::string &name) const |
| Get an AbstractSocket for the given socket name. More... | |
| AbstractSocket & | updSocket (const std::string &name) |
| Get a writable reference to the AbstractSocket for the given socket name. More... | |
| template<typename T > | |
| const Socket< T > & | getSocket (const std::string &name) const |
| Get a const reference to the concrete Socket provided by this Component by name. More... | |
| template<typename T > | |
| Socket< T > & | updSocket (const std::string &name) |
| Get a writable reference to the concrete Socket provided by this Component by name. More... | |
| void | printSubcomponentInfo () const |
| List all subcomponents by name and recurse into these components to list their subcomponents, and so on. More... | |
| void | printSocketInfo () const |
| List all the Sockets of this component and whether or not they are connected. More... | |
| void | printInputInfo () const |
| List all the inputs of this component and whether or not they are connected. More... | |
| template<typename C > | |
| void | printSubcomponentInfo () const |
| void | printOutputInfo (const bool includeDescendants=true) const |
| Print outputs of this component and optionally, those of all subcomponents. More... | |
| int | getNumInputs () const |
| Access the number of Inputs that this component has. More... | |
| int | getNumOutputs () const |
| Access the number of Outputs that this component has. More... | |
| std::vector< std::string > | getInputNames () const |
| Collect and return the names of Inputs in this component as an std::vector. More... | |
| std::vector< std::string > | getOutputNames () const |
| Collect and return the names of Outputs in this component as an std::vector. More... | |
| const AbstractInput & | getInput (const std::string &name) const |
| Get an Input provided by this Component by name. More... | |
| AbstractInput & | updInput (const std::string &name) |
| Get a writable reference to an Input provided by this Component by name. More... | |
| template<typename T > | |
| const Input< T > & | getInput (const std::string &name) const |
| Get a concrete Input that you can directly ask for its values. More... | |
| const AbstractOutput & | getOutput (const std::string &name) const |
| Get the Output provided by this Component by name. More... | |
| AbstractOutput & | updOutput (const std::string &name) |
| Get a writable reference to an Output provided by this Component by name. More... | |
| SimTK::IteratorRange< OutputConstIterator > | getOutputs () const |
| Iterate through all Outputs of this component. More... | |
| void | assign (Object &aObject) override |
| This allows copy assignment in the Java GUI. More... | |
| int | getModelingOption (const SimTK::State &state, const std::string &name) const |
| Get a ModelingOption flag for this Component by name. More... | |
| void | setModelingOption (SimTK::State &state, const std::string &name, int flag) const |
| Set the value of a ModelingOption flag for this Component. More... | |
| template<typename T > | |
| const T & | getInputValue (const SimTK::State &state, const std::string &name) const |
| Get the Input value that this component is dependent on. More... | |
| template<typename T > | |
| const T & | getOutputValue (const SimTK::State &state, const std::string &name) const |
| Get the Output value provided by this Component by name. More... | |
| double | getStateVariableValue (const SimTK::State &state, const std::string &name) const |
| Get the value of a state variable allocated by this Component. More... | |
| void | setStateVariableValue (SimTK::State &state, const std::string &name, double value) const |
| Set the value of a state variable allocated by this Component by name. More... | |
| SimTK::Vector | getStateVariableValues (const SimTK::State &state) const |
| Get all values of the state variables allocated by this Component. More... | |
| void | setStateVariableValues (SimTK::State &state, const SimTK::Vector &values) const |
| Set all values of the state variables allocated by this Component. More... | |
| double | getStateVariableDerivativeValue (const SimTK::State &state, const std::string &name) const |
| Get the value of a state variable derivative computed by this Component. More... | |
| double | getDiscreteVariableValue (const SimTK::State &state, const std::string &name) const |
| Get the value of a discrete variable allocated by this Component by name. More... | |
| void | setDiscreteVariableValue (SimTK::State &state, const std::string &name, double value) const |
| Set the value of a discrete variable allocated by this Component by name. More... | |
| template<class T > | |
| SimTK::CacheEntryIndex | getCacheVariableIndex (const CacheVariable< T > &cv) const |
| Get the index of a Component's cache variable in the Subsystem for allocations. More... | |
| SimTK::CacheEntryIndex | getCacheVariableIndex (const std::string &name) const |
| Get the index of a Component's cache variable in the Subsystem for allocations. More... | |
| template<class T > | |
| const T & | getCacheVariableValue (const SimTK::State &state, const std::string &name) const |
| Get the value of a cache variable allocated by this Component by name. More... | |
| template<class T > | |
| const T & | getCacheVariableValue (const SimTK::State &state, const CacheVariable< T > &cv) const |
| Get the value of a cache variable allocated by this Component. More... | |
| template<typename T > | |
| void | setCacheVariableValue (const SimTK::State &state, const std::string &k, T value) const |
Set the value of a cache variable, identified by name, to a new value and mark the cache variable as valid. More... | |
| template<typename T > | |
| void | setCacheVariableValue (const SimTK::State &state, const CacheVariable< T > &cv, T value) const |
| Set the value of a cache variable to a new value and mark the cache variable as valid. More... | |
| template<typename T > | |
| T & | updCacheVariableValue (const SimTK::State &state, const std::string &name) const |
Returns a mutable reference to the value of a cache variable identified by name. More... | |
| template<typename T > | |
| T & | updCacheVariableValue (const SimTK::State &state, const CacheVariable< T > &cv) const |
| Returns a mutable reference to the value of a cache variable. More... | |
| bool | isCacheVariableValid (const SimTK::State &state, const std::string &name) const |
Returns true if the cache variable, identified by name, is valid. More... | |
| template<class T > | |
| bool | isCacheVariableValid (const SimTK::State &state, const CacheVariable< T > &cv) const |
| Returns true if the cache variable is valid. More... | |
| void | markCacheVariableValid (const SimTK::State &state, const std::string &name) const |
Marks the value of a cache variable, identified by name, as valid. More... | |
| template<typename T > | |
| void | markCacheVariableValid (const SimTK::State &state, const CacheVariable< T > &cv) const |
| Marks the value of a cache variable as valid. More... | |
| void | markCacheVariableInvalid (const SimTK::State &state, const std::string &name) const |
Marks the value of a cache variable, identified by name, as invalid. More... | |
| template<class T > | |
| void | markCacheVariableInvalid (const SimTK::State &state, const CacheVariable< T > &cv) const |
| Marks the value of a cache variable as invalid. More... | |
| const Component & | getOwner () const |
| Access the owner of this Component. More... | |
| bool | hasOwner () const |
| (For advanced users) Check if this Component has an owner. More... | |
| const Component & | getRoot () const |
| Obtain the root Component, which is this component if it is orphaned. More... | |
| Public Member Functions inherited from OpenSim::Object | |
| virtual | ~Object () |
| Virtual destructor for cleanup. 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. 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... | |
| 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... | |
| void | updateXMLNode (SimTK::Xml::Element &parent, const AbstractProperty *prop=nullptr) const |
| 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... | |
| int | getDocumentFileVersion () const |
| If there is a document associated with this object then return its version number. More... | |
| void | setAllPropertiesUseDefault (bool aUseDefault) |
| bool | print (const std::string &fileName) const |
| Write this Object into an XML file of the given name; conventionally the suffix to use is ".osim". More... | |
| std::string | dump () const |
| dump the XML representation of this Object into an std::string and return it. 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 Bhargava2004SmoothedMuscleMetabolics | Self |
| This typedef might be useful within the member functions of this class. More... | |
| typedef ModelComponent | Super |
| Use this typedef to refer to the superclass of this class. More... | |
| Public Types inherited from OpenSim::ModelComponent | |
| typedef ModelComponent | Self |
| This typedef might be useful within the member functions of this class. More... | |
| typedef Component | Super |
| Use this typedef to refer to the superclass of this class. More... | |
| Public Types inherited from OpenSim::Component | |
| typedef Component | Self |
| This typedef might be useful within the member functions of this class. More... | |
| typedef Object | Super |
| Use this typedef to refer to the superclass of this class. More... | |
| typedef std::map< std::string, SimTK::ClonePtr< AbstractOutput > >::const_iterator | OutputConstIterator |
| Define OutputConstIterator for convenience. More... | |
Auto-generated functions | |
| static Bhargava2004SmoothedMuscleMetabolics * | safeDownCast (OpenSim::Object *obj) |
| For use in MATLAB and Python to access the concrete class. More... | |
| static const std::string & | getClassName () |
| This returns "Bhargava2004SmoothedMuscleMetabolics". More... | |
| void | assign (Object &aObject) override |
| This allows copy assignment in the Java GUI. More... | |
| Bhargava2004SmoothedMuscleMetabolics * | clone () const override |
| Create a new heap-allocated copy of the concrete object to which this Object refers. More... | |
| const std::string & | getConcreteClassName () const override |
| Returns the class name of the concrete Object-derived class of the actual object referenced by this Object, as a string. More... | |
Additional Inherited Members | |
| Static Public Member Functions inherited from OpenSim::ModelComponent | |
| static ModelComponent * | safeDownCast (OpenSim::Object *obj) |
| For use in MATLAB and Python to access the concrete class. More... | |
| static const std::string & | getClassName () |
| This returns "ModelComponent". More... | |
| Static Public Member Functions inherited from OpenSim::Component | |
| static Component * | safeDownCast (OpenSim::Object *obj) |
| For use in MATLAB and Python to access the concrete class. More... | |
| static const std::string & | getClassName () |
| This returns "Component". More... | |
| 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 bool | PrintPropertyInfo (std::ostream &os, const std::string &classNameDotPropertyName, bool printFlagInfo=true) |
| Dump formatted property information to a given output stream, useful for creating a "help" facility for registered objects. More... | |
| static bool | PrintPropertyInfo (std::ostream &os, const std::string &className, const std::string &propertyName, bool printFlagInfo=true) |
| 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 amount of logging output. More... | |
| static int | getDebugLevel () |
| Get the 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::ModelComponent | |
| const SimTK::Vec3 & | getScaleFactors (const ScaleSet &scaleSet, const Frame &frame) const |
| Get the scale factors corresponding to the base OpenSim::Body of the specified Frame. More... | |
| virtual void | extendPreScale (const SimTK::State &s, const ScaleSet &scaleSet) |
| Perform any computations that must occur before ModelComponent::scale() is invoked on all ModelComponents in the Model. More... | |
| virtual void | extendScale (const SimTK::State &s, const ScaleSet &scaleSet) |
| Scale the ModelComponent. More... | |
| virtual void | extendPostScale (const SimTK::State &s, const ScaleSet &scaleSet) |
| Perform any computations that must occur after ModelComponent::scale() has been invoked on all ModelComponents in the Model. More... | |
| void | updateFromXMLNode (SimTK::Xml::Element &aNode, int versionNumber) override |
| Handle a change in XML syntax for Sockets. More... | |
| void | extendFinalizeFromProperties () override |
| Perform any time-invariant calculations, data structure initializations, or other configuration based on the component's properties to form a functioning (but not yet connected) component. More... | |
| virtual void | extendConnectToModel (Model &model) |
| Perform any necessary initializations required to connect the component into the Model, and check for error conditions. More... | |
| Protected Member Functions inherited from OpenSim::Component | |
| SimTK_DEFINE_UNIQUE_INDEX_TYPE (MemberSubcomponentIndex) | |
| template<class C = Component> | |
| MemberSubcomponentIndex | constructSubcomponent (const std::string &name) |
| Construct a subcomponent as a data member of this Component. More... | |
| template<class C = Component> | |
| const C & | getMemberSubcomponent (MemberSubcomponentIndex ix) const |
| template<class C = Component> | |
| C & | updMemberSubcomponent (MemberSubcomponentIndex ix) |
| void | adoptSubcomponent (Component *subcomponent) |
| Adopt a component as a subcomponent of this Component. More... | |
| size_t | getNumImmediateSubcomponents () const |
| Get the number of Subcomponents immediately owned by this Component. More... | |
| size_t | getNumMemberSubcomponents () const |
| Get the number of Subcomponents that are data members of this Component. More... | |
| size_t | getNumPropertySubcomponents () const |
| Get the number of Subcomponents that are properties of this Component. More... | |
| size_t | getNumAdoptedSubcomponents () const |
| Get the number of Subcomponents adopted by this Component. More... | |
| std::vector< SimTK::ReferencePtr< const Component > > | getImmediateSubcomponents () const |
| Access this Component's immediate subcomponents (not those owned by subcomponents) More... | |
| template<class C > | |
| const C * | traversePathToComponent (ComponentPath path) const |
| void | setNextSubcomponentInSystem (const Component &sub) const |
| Helper method to enable Component makers to specify the order of their subcomponents to be added to the System during addToSystem(). More... | |
| void | resetSubcomponentOrder () |
| resetSubcomponentOrder clears this Component's list of ordered subcomponents (but otherwise leaves subcomponents untouched). More... | |
| const Component & | get_components (int i) const |
| Get the value of the i-th element of the components property. More... | |
| Component & | upd_components (int i) |
| Get a writable reference to the i-th element of the components property. More... | |
| void | set_components (int i, const Component &value) |
| Set the value of the i-th element of components property. More... | |
| int | append_components (const Component &value) |
| Append an element to the components property. More... | |
| virtual void | extendAddComponent (Component *subcomponent) |
| Perform any secondary operations, e.g. More... | |
| void | initComponentTreeTraversal (const Component &root) const |
| Build the tree of Components from this component through its descendants. More... | |
| virtual void | extendAddToSystemAfterSubcomponents (SimTK::MultibodySystem &system) const |
| Add appropriate Simbody elements (if needed) to the System after your component's subcomponents have had a chance to add themselves to the system. More... | |
| virtual void | extendInitStateFromProperties (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 | extendSetPropertiesFromState (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 void | 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... | |
| void | setStateVariableDerivativeValue (const SimTK::State &state, const std::string &name, double deriv) const |
| Set the derivative of a state variable by name when computed inside of this Component's computeStateVariableDerivatives() method. More... | |
| virtual void | extendRealizeModel (SimTK::State &state) const |
| Obtain and name state resources (like state variables allocated by an underlying Simbody component) that may be needed, depending on modeling options. More... | |
| virtual void | extendRealizeInstance (const SimTK::State &state) const |
| Perform computations that depend only on instance variables, like lengths and masses. More... | |
| virtual void | extendRealizeTime (const SimTK::State &state) const |
| Perform computations that depend only on time and earlier stages. More... | |
| virtual void | extendRealizePosition (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 | extendRealizeVelocity (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 | extendRealizeDynamics (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 | extendRealizeAcceleration (const SimTK::State &state) const |
| Perform computations that may depend on applied forces. More... | |
| virtual void | extendRealizeReport (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 | addModelingOption (const std::string &optionName, int maxFlagValue) const |
| Add a modeling option (integer flag stored in the State) for use by this Component. More... | |
| void | addStateVariable (const std::string &stateVariableName, const SimTK::Stage &invalidatesStage=SimTK::Stage::Dynamics, bool isHidden=false) const |
| Add a continuous system state variable belonging to this Component, and assign a name by which to refer to it. More... | |
| void | addStateVariable (Component::StateVariable *stateVariable) const |
| The above method provides a convenient interface to this method, which automatically creates an 'AddedStateVariable' and allocates resources in the SimTK::State for this variable. More... | |
| void | addDiscreteVariable (const std::string &discreteVariableName, SimTK::Stage invalidatesStage) const |
| Add a system discrete variable belonging to this Component, 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... | |
| SimTK::MultibodySystem & | updSystem () const |
| Get writable reference to the MultibodySystem that this component is connected to. More... | |
| int | getStateIndex (const std::string &name) const |
| Get the index of a Component's continuous state variable in the Subsystem for allocations. More... | |
| SimTK::SystemYIndex | getStateVariableSystemIndex (const std::string &stateVariableName) const |
| Get the System Index of a state variable allocated by this Component. More... | |
| const SimTK::DiscreteVariableIndex | getDiscreteVariableIndex (const std::string &name) const |
| Get the index of a Component's discrete variable in the Subsystem for allocations. More... | |
| template<typename T > | |
| PropertyIndex | constructSocket (const std::string &name, const std::string &propertyComment) |
| Construct a specialized Socket for this Component's dependence on another Component. More... | |
| template<typename T , typename CompType = Component> | |
| bool | constructOutput (const std::string &name, T(CompType::*const memFunc)(const SimTK::State &) const, const SimTK::Stage &dependsOn=SimTK::Stage::Acceleration) |
| Construct an output for a member function of the same component. More... | |
| template<typename T , typename CompType = Component> | |
| bool | constructOutput (const std::string &name, const T &(CompType::*const memFunc)(const SimTK::State &) const, const SimTK::Stage &dependsOn=SimTK::Stage::Acceleration) |
| This variant handles component member functions that return the output value by const reference (const T&). More... | |
| template<typename T , typename CompType > | |
| bool | constructListOutput (const std::string &name, T(CompType::*const memFunc)(const SimTK::State &, const std::string &channel) const, const SimTK::Stage &dependsOn=SimTK::Stage::Acceleration) |
| Construct an output that can have multiple channels. More... | |
| bool | constructOutputForStateVariable (const std::string &name) |
| Construct an Output for a StateVariable. More... | |
| template<typename T > | |
| PropertyIndex | constructInput (const std::string &name, bool isList, const std::string &propertyComment, const SimTK::Stage &requiredAtStage=SimTK::Stage::Instance) |
| Construct an Input (socket) for this Component's dependence on an Output signal. More... | |
| template<class T > | |
| CacheVariable< T > | addCacheVariable (std::string name, T variablePrototype, SimTK::Stage dependsOnStage) const |
| Add a state cache entry belonging to this Component to hold calculated values that must be automatically invalidated when certain state values change. More... | |
| void | setOwner (const Component &owner) |
| Set this Component's reference to its owning Component 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) | |
| 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) |
| 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. More... | |
| 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. More... | |
| PropertyIndex | getPropertyIndex (const std::string &name) const |
| Look up a property by name and return its PropertyIndex if it is found. More... | |
| 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. More... | |
| template<class T > | |
| void | checkPropertyValueIsPositive (const Property< T > &p) const |
| Throw an exception if any of the property's values are not positive. More... | |
| template<class T > | |
| void | checkPropertyValueIsInSet (const Property< T > &p, const std::set< T > &set) const |
| Throw an exception if any of the property's values are not in the provided set. More... | |
| template<class T > | |
| void | checkPropertyValueIsInRangeOrSet (const Property< T > &p, const T &lower, const T &upper, const std::set< T > &set) const |
| Throw an exception if any of the property's values are neither in the provided range nor in the provided set. 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... | |
| void | clearObjectIsUpToDateWithProperties () |
| For testing or debugging purposes, manually clear the "object is up to
date with respect to properties" flag. More... | |
| void | makeObjectNamesConsistentWithProperties () |
| Make sure the name of an object is consistent with its property type. More... | |
| 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. More... | |
| void | setDocument (XMLDocument *doc) |
| Unconditionally set the XMLDocument associated with this object. More... | |
| const XMLDocument * | getDocument () const |
| Get a const pointer to the document (if any) associated with this object. More... | |
| XMLDocument * | updDocument () |
| Get a writable pointer to the document (if any) associated with this object. More... | |
| Static Protected Member Functions inherited from OpenSim::Component | |
| static void | prependComponentPathToConnecteePath (Component &subcomponent) |
| For internal use. More... | |
| Protected Attributes inherited from OpenSim::ModelComponent | |
| SimTK::ReferencePtr< Model > | _model |
| The model this component belongs to. More... | |
| Protected Attributes inherited from OpenSim::Object | |
| PropertySet | _propertySet |
| OBSOLETE: Property_Deprecated set for serializable member variables of this and derived classes. More... | |
| Static Protected Attributes inherited from OpenSim::ModelComponent | |
| static const SimTK::Vec3 | InvalidScaleFactors |
| Returned by getScaleFactors() if the ScaleSet does not contain scale factors for the base Body associated with the specified Frame. More... | |
| 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. More... | |
| #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. More... | |
| #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>. More... | |
| #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. More... | |
This class implements the metabolic energy model of Bhargava et al (2004) and provides an option to use smooth (i.e., twice continuously differentiable) approximations.
These approximations might be better suited for gradient-based optimization algorithms.
We propose two smooth implementations.
In the first implementation, conditional if statements were approximated by using hyperbolic tangent functions (tanh). For example, the following if statement:
y = a, if x <= d
y = b, if x > d
can be approximated by:
f = 0.5 + 0.5 tanh(b(x-d))
y = a + (-a + b) f
where b is a parameter that determines the smoothness of the transition.
In the second implementation, conditional if statements were approximated by using Huber loss functions, which have the following form:
L(f(x)) = 0.5 f(x)^2, if f(x) <= delta
L(f(x)) = delta(f(x) - 0.5 delta), otherwise.
The Huber loss function is quadratic for f(x) <= delta and linear otherwise, with equal value and slopes of the different sections at the points where f(x) = delta (https://en.wikipedia.org/wiki/Huber_loss). In our implementation, we scaled this function with a parameter b that determines the smootheness of the transition between the quadratic and linear parts. Note that this approximation is piecewise but still continuous.
The metabolic energy model includes components for activation heat rate, maintenance heat rate, shortening heat rate, and mechanical work rate.
The shortening heat rate model differs between concentric contractions and eccentric contractions. We smoothed the transition between both contraction types using our smoothing functions. Note that when using the force dependent shortening proportional constant, we only provide the tanh smoothing option for approximating the shortening heat rate. This is motivated by the fact that the shortening heat rate is defined by linear functions but with different non-zero constants of proportionality for concentric and eccentric contractions. It is therefore easier to smooth the transition between both contraction types with a tanh function than with a Huber loss function. The difference between the original (non-smooth) and the smooth implementations is illustrated in the following figure:
The mechanical work rate model includes negative mechanical work rate (i.e., work rate resulting from eccentric contraction) by default. However, if specified by the user, the model only takes positive mechanical work rate (i.e., work rate resulting from concentric contraction) into account. In such case, we smoothed the transition between positive rate and zero using our smoothing functions. The difference between the original (non-smooth) and the smooth implementations is illustrated in the following figure:
The metabolic energy model implementation includes an optional clamping that prevents the total metabolic rate (i.e., total metabolic power) to be negative. This clamping is done by increasing the shortening heat rate. We smoothed the transition between positive and negative total metabolic rate using our smoothing functions. The difference between the original (non-smooth) and the smooth implementations is illustrated in the following figure:
The metabolic energy model implementation includes an optional clamping (see Umberger et al (2003), page 104) that prevents the total heat rate (i.e., activation heat rate + maintenance heat rate + shortening heat rate) for a given muscle to fall below 1.0 W/kg. Note that, if active, this clamping will cause the sum of the reported individual heat rates and work rate to differ from the reported metabolic rate. We smoothed the transition between total heat rate higher and lower than 1.0 W/kg using our smoothing functions. The difference between the original (non-smooth) and the smooth implementations is illustrated in the following figure:
Note that the maintenance heat rate implementation relies on a PiecewiseLinearFunction. The first and second order derivatives of this function can be evaluated but they are discontinuous. This might cause issues with gradient-based optimization algorithms. Problems using this discontinuous function have successfully converged; therefore, we have included it in this implementation of the model.
You can enable smoothing via the use_smoothing property. The smoothing type ('tanh' or 'huber') can be chosen via the smoothing_type property, and the level of smoothing can be controlled by the velocity_smoothing, power_smoothing, and heat_rate_smoothing properties.
Muscles to be included when computing the total metabolic rate should be specified using one of the three addMuscle() function overloads. See the properties of Bhargava2004SmoothedMuscleMetabolics_MuscleParameters() for the default parameter values used when not specified via the second or third addMuscle() overload.
The total metabolic rate output can be obtained using getTotalMetabolicRate(), which takes a SimTK::State as a argument. You can similarly obtain the individual heat rate and mechanical work rate components of the total metabolic cost via getTotalActivationRate(), getTotalMaintenanceRate(), getTotalShorteningRate(), and getTotalMechanicalWorkRate(). All outputs require realizing the passed SimTK::State to SimTK::Stage::Dynamics.
Bhargava et al. 2004: https://doi.org/10.1016/s0021-9290(03)00239-2
This typedef might be useful within the member functions of this class.
This is generated by the OpenSim_DECLARE_*_OBJECT macros.
Use this typedef to refer to the superclass of this class.
Avoid using the explicit type name of the superclass; this would introduce bugs if the superclass is changed.
This is generated by the OpenSim_DECLARE_*_OBJECT macros.
| OpenSim::Bhargava2004SmoothedMuscleMetabolics::Bhargava2004SmoothedMuscleMetabolics | ( | ) |
| void OpenSim::Bhargava2004SmoothedMuscleMetabolics::addMuscle | ( | const std::string & | name, |
| const Muscle & | muscle, | ||
| double | muscle_mass = SimTK::NaN |
||
| ) |
Specify a muscle that should be included when computing the total metabolic rate.
If the muscle_mass argument is not provided, it is estimated based on the max isometric force, specific tension, muscle density, and optimal fiber length.
| void OpenSim::Bhargava2004SmoothedMuscleMetabolics::addMuscle | ( | const std::string & | name, |
| const Muscle & | muscle, | ||
| double | ratio_slow_twitch_fibers, | ||
| double | specific_tension, | ||
| double | muscle_mass = SimTK::NaN |
||
| ) |
Specify a muscle that should be included when computing the total metabolic rate, as well as its ratio of slow to fast twitch fibers and specific tension.
If the muscle_mass argument is not provided, it is estimated based on the max isometric force, specific tension, muscle density, and optimal fiber length.
| void OpenSim::Bhargava2004SmoothedMuscleMetabolics::addMuscle | ( | const std::string & | name, |
| const Muscle & | muscle, | ||
| double | ratio_slow_twitch_fibers, | ||
| double | specific_tension, | ||
| double | activation_constant_slow_twitch, | ||
| double | activation_constant_fast_twitch, | ||
| double | maintenance_constant_slow_twitch, | ||
| double | maintenance_constant_fast_twitch, | ||
| double | muscle_mass = SimTK::NaN |
||
| ) |
Specify a muscle that should be included when computing the total metabolic rate, as well as its ratio of slow to fast twitch fibers and specific tension.
This overload also allows you to specify the slow and fast twitch fiber constants used to compute the activation and maintenance heat rates. If the muscle_mass argument is not provided, it is estimated based on the max isometric force, specific tension, muscle density, and optimal fiber length.
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Append an element to the muscle_parameters property.
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inlineoverride |
This allows copy assignment in the Java GUI.
| Exception | if the argument is not of type Bhargava2004SmoothedMuscleMetabolics. |
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inlineoverridevirtual |
Create a new heap-allocated copy of the concrete object to which this Object refers.
It is up to the caller to delete the returned object when no longer needed. Every concrete object deriving from Object implements this pure virtual method automatically, via the declaration macro it invokes (e.g., OpenSim_DECLARE_CONCRETE_OBJECT()). Note that the concrete class overrides modify the return type to be a pointer to the concrete object; that still overrides the base class method because the return type is covariant with (that is, derives from) Object.
Implements OpenSim::ModelComponent.
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Get the value of the basal_coefficient property.
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Get the value of the basal_exponent property.
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Get the value of the enforce_minimum_heat_rate_per_muscle property.
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Get the value of the forbid_negative_total_power property.
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Get the value of the heat_rate_smoothing property.
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Get the value of the include_negative_mechanical_work property.
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Get the value of the muscle_effort_scaling_factor property.
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Get the value of the i-th element of the muscle_parameters property.
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Get the value of the power_smoothing property.
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Get the value of the smoothing_type property.
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Get the value of the use_force_dependent_shortening_prop_constant property.
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Get the value of the use_smoothing property.
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Get the value of the velocity_smoothing property.
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inlinestatic |
This returns "Bhargava2004SmoothedMuscleMetabolics".
See getConcreteClassName() if you want the class name of the underlying concrete object instead.
This is generated by the OpenSim_DECLARE_*_OBJECT macros.
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inlineoverridevirtual |
Returns the class name of the concrete Object-derived class of the actual object referenced by this Object, as a string.
This is the string that is used as the tag for this concrete object in an XML file. Every concrete class derived from Object automatically overrides this method via the declaration macro it uses. See getClassName() to get the class name of the referencing (possibly abstract) class rather than the concrete object.
Implements OpenSim::ModelComponent.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::getMuscleMetabolicRate | ( | const SimTK::State & | s, |
| const std::string & | channel | ||
| ) | const |
| int OpenSim::Bhargava2004SmoothedMuscleMetabolics::getNumMetabolicMuscles | ( | ) | const |
Get the number of muscles added to the metabolics model by one of the addMuscle() overloads.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::getTotalActivationRate | ( | const SimTK::State & | s | ) | const |
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::getTotalMaintenanceRate | ( | const SimTK::State & | s | ) | const |
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::getTotalMechanicalWorkRate | ( | const SimTK::State & | s | ) | const |
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::getTotalMetabolicRate | ( | const SimTK::State & | s | ) | const |
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::getTotalShorteningRate | ( | const SimTK::State & | s | ) | const |
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inlinestatic |
For use in MATLAB and Python to access the concrete class.
Example: cObj = Bhargava2004SmoothedMuscleMetabolics.safeDownCast(obj). This is equivalent to dynamic_cast<Bhargava2004SmoothedMuscleMetabolics*>(obj) in C++.
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Set the value of the basal_coefficient property.
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Set the value of the basal_exponent property.
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Set the value of the enforce_minimum_heat_rate_per_muscle property.
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Set the value of the forbid_negative_total_power property.
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Set the value of the heat_rate_smoothing property.
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Set the value of the include_negative_mechanical_work property.
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Set the value of the muscle_effort_scaling_factor property.
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Set the value of the i-th element of muscle_parameters property.
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Set the value of the power_smoothing property.
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Set the value of the smoothing_type property.
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Set the value of the use_force_dependent_shortening_prop_constant property.
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Set the value of the use_smoothing property.
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Set the value of the velocity_smoothing property.
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Get a writable reference to the basal_coefficient property.
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Get a writable reference to the basal_exponent property.
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Get a writable reference to the enforce_minimum_heat_rate_per_muscle property.
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inline |
Get a writable reference to the forbid_negative_total_power property.
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Get a writable reference to the heat_rate_smoothing property.
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Get a writable reference to the include_negative_mechanical_work property.
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Get a writable reference to the muscle_effort_scaling_factor property.
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Get a writable reference to the i-th element of the muscle_parameters property.
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Get a writable reference to the power_smoothing property.
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Get a writable reference to the smoothing_type property.
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Get a writable reference to the use_force_dependent_shortening_prop_constant property.
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Get a writable reference to the use_smoothing property.
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Get a writable reference to the velocity_smoothing property.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::basal_coefficient |
"Basal metabolic " "coefficient (default is 1.2)."
This property appears in XML files under the tag <basal_coefficient>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::basal_exponent |
"Basal metabolic " "exponent (default is 1)."
This property appears in XML files under the tag <basal_exponent>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| bool OpenSim::Bhargava2004SmoothedMuscleMetabolics::enforce_minimum_heat_rate_per_muscle |
"Specify whether the total heat rate for a muscle will be clamped " "to a minimum value of 1.0 W/kg (default is true). When set to " "true, the sum of the reported individual heat rates + work rate " "will not equal the reported total metabolic rate if the total " "heat rate falls below 1.0 W/kg."
This property appears in XML files under the tag <enforce_minimum_heat_rate_per_muscle>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| bool OpenSim::Bhargava2004SmoothedMuscleMetabolics::forbid_negative_total_power |
"Specify whether the total power for each muscle must remain " "positive (default is true)."
This property appears in XML files under the tag <forbid_negative_total_power>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::heat_rate_smoothing |
"The parameter that determines the smoothness of the transition " "of the tanh or Huber loss function used to smooth the condition " "enforcing total heat rate larger than 1 (W/kg) for a give muscle " ". The larger the steeper the transition but the worse for " "optimization (default is 10)."
This property appears in XML files under the tag <heat_rate_smoothing>. This property was generated with the OpenSim_DECLARE_OPTIONAL_PROPERTY macro; see Property to learn about the property system.
| bool OpenSim::Bhargava2004SmoothedMuscleMetabolics::include_negative_mechanical_work |
"Specify whether negative mechanical work will be included in " "mechanicalWorkRate (default is true)."
This property appears in XML files under the tag <include_negative_mechanical_work>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::muscle_effort_scaling_factor |
"Scale the excitation and activation values to compensate for " "solutions with excessive coactivation (e.g., when a suboptimal " "tracking strategy is used) (default is 1)."
This property appears in XML files under the tag <muscle_effort_scaling_factor>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::muscle_metabolic_rate |
Provides the value of getMuscleMetabolicRate() and is available at stage SimTK::Stage::Dynamics .
This output can have multiple channels. TODO This output was generated with the OpenSim_DECLARE_LIST_OUTPUT macro.
| Bhargava2004SmoothedMuscleMetabolics_MuscleParameters OpenSim::Bhargava2004SmoothedMuscleMetabolics::muscle_parameters |
"Metabolic parameters for each muscle."
This property appears in XML files under the tag <muscle_parameters>. This property holds a list of objects, and was generated with the OpenSim_DECLARE_LIST_PROPERTY macro; see Property to learn about the property system.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::power_smoothing |
"The parameter that determines the smoothness of the transition " "of the tanh or Huber loss function used to smooth the condition " "enforcing non-negative total power. The larger the steeper the " "transition but the worse for optimization (default is 10)."
This property appears in XML files under the tag <power_smoothing>. This property was generated with the OpenSim_DECLARE_OPTIONAL_PROPERTY macro; see Property to learn about the property system.
| std::string OpenSim::Bhargava2004SmoothedMuscleMetabolics::smoothing_type |
"An optional flag that allows the user to explicitly specify " "what type of smoothing to use ('tanh' or 'huber'; default is " "'tanh')."
This property appears in XML files under the tag <smoothing_type>. This property was generated with the OpenSim_DECLARE_OPTIONAL_PROPERTY macro; see Property to learn about the property system.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::total_activation_rate |
Provides the value of getTotalActivationRate() and is available at stage SimTK::Stage::Dynamics .
This output was generated with the OpenSim_DECLARE_OUTPUT macro.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::total_maintenance_rate |
Provides the value of getTotalMaintenanceRate() and is available at stage SimTK::Stage::Dynamics .
This output was generated with the OpenSim_DECLARE_OUTPUT macro.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::total_mechanical_work_rate |
Provides the value of getTotalMechanicalWorkRate() and is available at stage SimTK::Stage::Dynamics .
This output was generated with the OpenSim_DECLARE_OUTPUT macro.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::total_metabolic_rate |
Provides the value of getTotalMetabolicRate() and is available at stage SimTK::Stage::Dynamics .
This output was generated with the OpenSim_DECLARE_OUTPUT macro.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::total_shortening_rate |
Provides the value of getTotalShorteningRate() and is available at stage SimTK::Stage::Dynamics .
This output was generated with the OpenSim_DECLARE_OUTPUT macro.
| bool OpenSim::Bhargava2004SmoothedMuscleMetabolics::use_force_dependent_shortening_prop_constant |
"Specify whether to use a force dependent shortening " "proportionality constant (default is false)."
This property appears in XML files under the tag <use_force_dependent_shortening_prop_constant>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| bool OpenSim::Bhargava2004SmoothedMuscleMetabolics::use_smoothing |
"An optional flag that allows the user to explicitly specify " "whether a smooth approximation of the metabolic energy model " "should be used (default is false)."
This property appears in XML files under the tag <use_smoothing>. This property was generated with the OpenSim_DECLARE_OPTIONAL_PROPERTY macro; see Property to learn about the property system.
| double OpenSim::Bhargava2004SmoothedMuscleMetabolics::velocity_smoothing |
"The parameter that determines the smoothness of the transition " "of the tanh or Huber loss function used to smooth the conditions " "related to contraction type (concentric or eccentric). Note that " "when computing the shortening heat rate while using the force " "dependent shortening proportionality constant, a tanh " "approximation is used even when using the Huber loss smoothing " "approach. The larger the steeper the transition but the worse " "for optimization (default is 10)."
This property appears in XML files under the tag <velocity_smoothing>. This property was generated with the OpenSim_DECLARE_OPTIONAL_PROPERTY macro; see Property to learn about the property system.
1.8.13 