SHDynamics: Class for nonlinear dynamics of shorten motorunit model. More...

Detailed Description

SHDynamics: Class for nonlinear dynamics of shorten motorunit model.

Author: Daniel Wirtz

Date: 2012-11-22

New in 0.7:: (Daniel Wirtz, 2012-11-22) Added this class.

This class is part of the framework

KerMor - Model Order Reduction using Kernels

Homepage http://www.agh.ians.uni-stuttgart.de/research/software/kermor.html
Documentation http://www.agh.ians.uni-stuttgart.de/documentation/kermor/
License KerMor license conditions

Definition at line 19 of file SHDynamics.m.

Public Member Functions
	SHDynamics (sys)

function	prepareSimulation (colvec< double > mu)

function dy =	evaluate (matrix< double >, y,rowvec< double > t)
	Evaluates the nonlinear core function at given time and state. Can evaluate vectorized arguments. Here, each column represents one state. The parts for motoneuron, spindle and sarcomeres are evaluated seperately in respective rate functions and the rates are concatenated in this function. The sarcomere part is reshaped such that a matrix with 58 rows and one column for each single sarcomere is passed to the function for (single) sarcomere dynamics. More...

function dy =	evaluateCoreFun (matrix< double > y,double t,colvec< double > mu)

function J =	getStateJacobian (matrix< double >, y,rowvec< double > t)
	Evaluates the full Jacobian of the nonlinear core function. More...

function copy =	clone ()
	Create new instance. More...

function	initJSparsityPattern ()
	Initializes the Sparsity pattern of the Jacobian. More...

function f =	getLinkFactor (rowvec< double > y)
	scalar link factor motoneuron to middle sarcomere More...

Public Member Functions inherited from dscomponents.ACoreFun
	ACoreFun (sys)

function	setSystem (sys)

function target =	project (V, W, target)
	Sets the protected \(\vV,\vW\) matrices that can be utilized on core function evaluations after projection. More...

function fx =	evaluate (x, t)
	Evaluates the f-approximation. Depending on a possible projection and the CustomProjection-property the function either calls the inner evaluation directly which assumes \(f = f^r(z)\) or projects the reduced state variable z into the original space and evaluates the function there, so via \(f = V'f(Vz)\). More...

function fx =	evaluateMulti (colvec< double > x,double t,colvec< double > mu)
	Evaluates this function on multiple locations and maybe multiple times and parameters. More...

function	prepareSimulation (colvec< double > mu)
	A method that allows parameter-dependent computations to be performed before a simulation using this parameter starts. More...

function J =	getStateJacobian (x, t)
	Default implementation of jacobian matrix evaluation via finite differences. More...

function J =	getStateJacobianImpl (colvec< double > x,double t)
	Default implementation of state jacobians. uses finite differences. More...

function copy =	clone (copy)
	The interface method with returns a copy of the current class instance. More...

function [ matrix< double > J , dx ] =	getStateJacobianFD (x, t,rowvec< integer > partidx)
	Implementation of jacobian matrix evaluation via finite differences. More...

virtual function fx =	evaluateCoreFun (colvec< double > x,double t)
	Actual method used to evaluate the dynamical sytems' core function. More...

function res =	test_MultiArgEval (mudim)
	Convenience function that tests if a custom MultiArgumentEvaluation works as if called with single arguments. More...

function logical res =	test_Jacobian (matrix< double > xa,rowvec< double > ta,matrix< double > mua)
	Tests the custom provided jacobian matrix against the default finite difference computed one. More...

Public Member Functions inherited from KerMorObject
	KerMorObject ()
	Constructs a new KerMor object. More...

function	display ()
	disp(object2str(this)); More...

function bool =	eq (B)
	Checks equality of two KerMor objects. More...

function bool =	ne (B)
	Checks if two KerMorObjects are different. More...

function cn =	getClassName ()
	Returns the simple class name of this object without packages. More...

Public Member Functions inherited from DPCMObject
	DPCMObject ()
	Creates a new DPCM object. More...

	DPCMObject ()

Public Member Functions inherited from general.AProjectable
function handle target =	project (matrix< double > V,matrix< double > W,handle target)
	Returns a NEW INSTANCE of the projected object that does not rely on data of the old one via references (everything must be copied to ensure separability of reduced(=projected) versions and full versions, unless. More...

function copy =	clone (copy)
	The interface method with returns a copy of the current class instance. More...

Public Attributes
double	MSLink_MaxFactorSignal = 40
	The \(V_s\) value of the motoneuron input at which the MSLink_MaxFactor should be attained. More...

double	MSLink_MaxFactor = 7
	The maximal factor with which the \(V_s\) value of the motoneuron should be amplified when added to the sarcomere equations. More...

double	MSLink_MinFactor = .3
	The minimal factor at which the \(V_s\) value of the motoneuron should be amplified when added to the sarcomere equations. More...

	SarcoConst_slow
	constants for sarcomere submodel specific for slow twitch fibre More...

	SarcoConst_fast
	constants for sarcomere submodel specific for fast twitch fibre More...

	SarcoConst_base
	basis constant set for sarcomere submodel More...

dependent	SarcoConst_dynpos
	Positions constants. More...

	hadpeak = false

	motoconst

	sarcoconst

	signalweight

Public Attributes inherited from dscomponents.ACoreFun
logical	TimeDependent = true
	Flag that indicates if the ACoreFun is (truly) time-dependent. More...

	CustomProjection = false
	Set this property if the projection process is customized by overriding the default project method. More...

sparse< logical >	JSparsityPattern = "[]"
	Sparsity pattern for the jacobian matrix. More...

integer	xDim = "[]"
	The current state space dimension of the function's argument \(x\). More...

integer	fDim = "[]"
	The current output dimension of the function. More...

models.BaseFirstOrderSystem	System
	The system associated with the current ACoreFun. More...

colvec< double >	mu = "[]"
	The current model parameter mu for evaluations. Will not be persisted as only valid for runtime during simulations. More...

	Vcache

	Wcache

Public Attributes inherited from DPCMObject
	WorkspaceVariableName = ""
	The workspace variable name of this class. Optional. More...

	ID = "[]"
	An ID that allows to uniquely identify this DPCMObject (at least within the current MatLab session/context). More...

	PropertiesChanged = "[]"
	The Dictionary containing all the property settings as key/value pairs. More...

Public Attributes inherited from handle
	addlistener
	Creates a listener for the specified event and assigns a callback function to execute when the event occurs. More...

	notify
	Broadcast a notice that a specific event is occurring on a specified handle object or array of handle objects. More...

	delete
	Handle object destructor method that is called when the object's lifecycle ends. More...

	disp
	Handle object disp method which is called by the display method. See the MATLAB disp function. More...

	display
	Handle object display method called when MATLAB software interprets an expression returning a handle object that is not terminated by a semicolon. See the MATLAB display function. More...

	findobj
	Finds objects matching the specified conditions from the input array of handle objects. More...

	findprop
	Returns a meta.property objects associated with the specified property name. More...

	fields
	Returns a cell array of string containing the names of public properties. More...

	fieldnames
	Returns a cell array of string containing the names of public properties. See the MATLAB fieldnames function. More...

	isvalid
	Returns a logical array in which elements are true if the corresponding elements in the input array are valid handles. This method is Sealed so you cannot override it in a handle subclass. More...

	eq
	Relational functions example. See details for more information. More...

	transpose
	Transposes the elements of the handle object array. More...

	permute
	Rearranges the dimensions of the handle object array. See the MATLAB permute function. More...

	reshape
	hanges the dimensions of the handle object array to the specified dimensions. See the MATLAB reshape function. More...

	sort
	ort the handle objects in any array in ascending or descending order. More...

Public Attributes inherited from general.AProjectable
	V
	The \(V\) matrix of the biorthogonal pair \(V,W\). More...

	W
	The \(W\) matrix of the biorthogonal pair \(V,W\). More...

Additional Inherited Members
Protected Member Functions inherited from KerMorObject
function	checkType (obj, type)
	Object typechecker. More...

Protected Member Functions inherited from DPCMObject
function	registerProps (varargin)
	Call this method at any class that defines DPCM observed properties. More...

function	registerProps (varargin)

Static Protected Member Functions inherited from dscomponents.ACoreFun
static function obj =	loadobj (obj, from)

Static Protected Member Functions inherited from DPCMObject
static function obj =	loadobj (obj, from)
	Re-register any registered change listeners! More...

static function obj =	loadobj (obj, from)

Static Protected Member Functions inherited from general.AProjectable
static function obj =	loadobj (obj, from)

Constructor & Destructor Documentation

models.motorunit.SHDynamics.SHDynamics ( sys )

Definition at line 149 of file SHDynamics.m.

References dscomponents.ACoreFun.fDim, initJSparsityPattern(), and dscomponents.ACoreFun.xDim.

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Member Function Documentation

function copy = models.motorunit.SHDynamics.clone ( )

Create new instance.

Definition at line 284 of file SHDynamics.m.

References dscomponents.ACoreFun.System.

function dy = models.motorunit.SHDynamics.evaluate	(	matrix< double >	,
		y	,
		rowvec< double >	t
	)

Evaluates the nonlinear core function at given time and state. Can evaluate vectorized arguments. Here, each column represents one state. The parts for motoneuron, spindle and sarcomeres are evaluated seperately in respective rate functions and the rates are concatenated in this function. The sarcomere part is reshaped such that a matrix with 58 rows and one column for each single sarcomere is passed to the function for (single) sarcomere dynamics.

Parameters

y	each column is one state vector
t	current time
mu	fibre type parameter 0 = slow twitch fibre, 1 = fast twitch fibre

Definition at line 171 of file SHDynamics.m.

References getLinkFactor(), hadpeak, motoconst, MSLink_MaxFactor, MSLink_MaxFactorSignal, sarcoconst, and dscomponents.ACoreFun.System.

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function dy = models.motorunit.SHDynamics.evaluateCoreFun	(	matrix< double >	y,
		double	t,
		colvec< double >	mu
	)

Definition at line 229 of file SHDynamics.m.

function f = models.motorunit.SHDynamics.getLinkFactor ( rowvec< double > y )

scalar link factor motoneuron to middle sarcomere

See Also: FibreDynamics.evaluate

Parameters

y	second state from motoneuron submodel

Definition at line 327 of file SHDynamics.m.

References MSLink_MaxFactor, MSLink_MaxFactorSignal, and MSLink_MinFactor.

Referenced by evaluate(), and getStateJacobian().

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function J = models.motorunit.SHDynamics.getStateJacobian	(	matrix< double >	,
		y	,
		rowvec< double >	t
	)

Evaluates the full Jacobian of the nonlinear core function.

Parameters

y	each column is one state vector
t	current time
mu	fibre type parameter, 0 = slow twitch fibre, 1 = fast twitch fibre,

Definition at line 234 of file SHDynamics.m.

References getLinkFactor(), motoconst, MSLink_MaxFactor, MSLink_MaxFactorSignal, sarcoconst, and dscomponents.ACoreFun.System.

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function models.motorunit.SHDynamics.initJSparsityPattern ( )

Initializes the Sparsity pattern of the Jacobian.

Definition at line 301 of file SHDynamics.m.

References dscomponents.ACoreFun.JSparsityPattern, and dscomponents.ACoreFun.System.

Referenced by SHDynamics().

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function models.motorunit.SHDynamics.prepareSimulation ( colvec< double > mu )

Definition at line 160 of file SHDynamics.m.

References hadpeak, motoconst, dscomponents.ACoreFun.mu, and sarcoconst.

Member Data Documentation

models.motorunit.SHDynamics.hadpeak = false

Definition at line 138 of file SHDynamics.m.

Referenced by evaluate(), and prepareSimulation().

models.motorunit.SHDynamics.motoconst

Definition at line 140 of file SHDynamics.m.

Referenced by evaluate(), getStateJacobian(), and prepareSimulation().

models.motorunit.SHDynamics.MSLink_MaxFactor = 7

The maximal factor with which the \(V_s\) value of the motoneuron should be amplified when added to the sarcomere equations.

Default: 7

Definition at line 49 of file SHDynamics.m.

Referenced by evaluate(), getLinkFactor(), and getStateJacobian().

models.motorunit.SHDynamics.MSLink_MaxFactorSignal = 40

The \(V_s\) value of the motoneuron input at which the MSLink_MaxFactor should be attained.

Default: 40

Definition at line 39 of file SHDynamics.m.

Referenced by evaluate(), getLinkFactor(), and getStateJacobian().

models.motorunit.SHDynamics.MSLink_MinFactor = .3

The minimal factor at which the \(V_s\) value of the motoneuron should be amplified when added to the sarcomere equations.

Between both limits, an exponential Gaussian weight is applied with a certain radius, so that the amplification factor has its minimum value at zero and maximum value at MSLink_MaxFactorSignal.

See Also: FibreDynamics.getLinkFactor

Default: .3

Definition at line 60 of file SHDynamics.m.

Referenced by getLinkFactor().

models.motorunit.SHDynamics.sarcoconst

Definition at line 142 of file SHDynamics.m.

Referenced by evaluate(), getStateJacobian(), and prepareSimulation().

models.motorunit.SHDynamics.SarcoConst_base

basis constant set for sarcomere submodel

See Also: Dynamics.initSarcoConst

Note: This property has non-standard access specifiers: SetAccess = Private, GetAccess = Public; Matlab documentation of property attributes.

Definition at line 105 of file SHDynamics.m.

models.motorunit.SHDynamics.SarcoConst_dynpos

Positions constants.

See Also: Dynamics.initSarcoConst

Note: This property has non-standard access specifiers: SetAccess = Private, GetAccess = Public; Matlab documentation of property attributes.

Definition at line 118 of file SHDynamics.m.

models.motorunit.SHDynamics.SarcoConst_fast

constants for sarcomere submodel specific for fast twitch fibre

See Also: Dynamics.initSarcoConst

Note: This property has non-standard access specifiers: SetAccess = Private, GetAccess = Public; Matlab documentation of property attributes.

Definition at line 92 of file SHDynamics.m.

models.motorunit.SHDynamics.SarcoConst_slow

constants for sarcomere submodel specific for slow twitch fibre

See Also: Dynamics.initSarcoConst

Note: This property has non-standard access specifiers: SetAccess = Private, GetAccess = Public; Matlab documentation of property attributes.

Definition at line 79 of file SHDynamics.m.

models.motorunit.SHDynamics.signalweight

Definition at line 144 of file SHDynamics.m.

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

+models/+motorunit/@SHDynamics/SHDynamics.m
+models/+motorunit/@SHDynamics/dydt_sarcomere.m
+models/+motorunit/@SHDynamics/initSarcoConst.m
+models/+motorunit/@SHDynamics/Jac_Sarco.m

Detailed Description

Public Member Functions

Public Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation