Model: Model for a FEM-discretized muscle model. More...

Detailed Description

Model: Model for a FEM-discretized muscle model.

The global time unit for this model is milliseconds [ms] and the spatial quantities are in [mm]. Weight is in [g]. This results in pressure values of [MPa] and the forces K(u,v,w) are measured in [N] (Newton).

Author: Daniel Wirtz

Date: 2012-11-22

Definition at line 19 of file Model.m.

Public Member Functions
	Model (conf, basedir)

function [ double t , matrix< double > y ] =	simulateAndPlot (withResForce, varargin)

function [ double t , colvec< double > x , time , cache ] =	computeTrajectory (colvec< double > mu,integer inputidx)
	Allows to also call prepareSimulation for any quantities set by the AMuscleConfig class. More...

function double t =	getConfigTable (colvec< double > mu)

function	plotForceLengthCurve (colvec< double > mu, pm)

function	plotAnisotropicPressure (colvec< double > mu)

function	plotActivation ()

function varargout =	plotGeometrySetup (varargin)

function	plotGeometryInfo (varargin)

function [ residuals_dirichlet , residuals_neumann ] =	getResidualForces (double t, uvw)

function colvec < integer > idx =	getFaceDofsGlobal (integer elem,rowvec< integer > faces,rowvec< integer > dim)
	Returns the indices in the global uvw vector (including dirichlet values) of the given faces in the given element. More...

function idx =	getPositionDirichletBCFaceIdx (integer elem,integer face,rowvec< integer > dim)
	Returns the positions of dofs of a specified face within the boundary conditions residual vector. Applies to dirichlet boundary conditions of POSITION (u) More...

function idx =	getVelocityDirichletBCFaceIdx (integer elem,integer face,rowvec< integer > dim)
	Returns the positions of dofs of a specified face within the boundary conditions residual vector. Applies to dirichlet boundary conditions of VELOCITY (v) More...

function	setConfig (value)

function	setGaussIntegrationRule (value)
	Sets the gauss integration rule for the model. More...

function varargout =	plot (varargin)

Public Member Functions inherited from models.BaseFullModel
	BaseFullModel (char name)
	Creates a new instance of a full model. More...

function	delete ()

function	off1_createParamSamples ()
	Offline phase 1: Sample generation. More...

function	off2_genTrainingData ()
	Offline phase 2: Snapshot generation for subspace computation. More...

function	off3_computeReducedSpace ()
	Offline phase 3: Generate state space reduction. More...

function	off4_genApproximationTrainData ()
	Generates the training data \(x_i\) for the \(\hat{f}\)-approximation and precomputes \(f(x_i)\) values. More...

function	off5_computeApproximation ()
	Offline phase 5: Core function approximation. More...

function	off6_prepareErrorEstimator ()
	Prepares offline data for a possible error estimator. More...

function	offlineGenerations ()
	Performs all large offline computations for model reduction. More...

function [ models.ReducedModel reduced , double time ] =	buildReducedModel (varargin)
	Builds a reduced model from a full model. More...

function [ t , x , time , cache ] =	computeTrajectory (colvec< double > mu, inputidx)
	Computes a solution/trajectory for the given mu and inputidx in the SCALED state space. More...

function [ double t , matrix< double > y , colvec < double > mu , in , ct ] =	getSimCacheTrajectory (nr)

function	plotTrajectoryNr (nr)

function [ V , W ] =	assembleProjectionMatrices (target_dim)

function file =	save (char directory,char filename)
	Saves this instance inside the data.ModelData.DataDirectory folder using the model's SaveTag if set or "model.mat". More...

Public Member Functions inherited from models.BaseModel
	BaseModel ()

function	delete ()

function	initDefaultParameter ()
	Reads the default values of the System's ModelParam list and initializes the BaseModel.DefaultMu with it. More...

function [ rowvec< double > t , matrix < double > y , double sec , x ] =	simulate (colvec< double > mu,integer inputidx)
	Simulates the system and produces the system's output. More...

function [ handle f , handle ax ] =	plot (rowvec< double > t,matrix< double > y, varargin)
	Plots the results of the simulation. Override in subclasses for a more specific plot if desired. More...

function [ handle f , handle ax ] =	plotState (rowvec t,matrix< double > x, varargin)
	Plots the results of the simulation. Override in subclasses for a more specific plot if desired. More...

function [ f , ax ] =	plotSingle (double t,colvec< double > y, varargin)
	Plots a single solution. Override in subclasses for specific plot behaviour. More...

function	plotInputs (pm)

function [ double t , colvec< double > x , double ctime ] =	solveStatic (colvec< double > mu,integer inputidx)
	Solves the linear system \(A(t,\mu)x + f(t,\mu) + B(t,\mu)u(t) = 0\). Spatial dependence of f is neglected in the current implementation (since this would require solving a nonlinear system). More...

function [ rowvec< double > t , matrix < double > x , double ctime ] =	computeTrajectory (colvec< double > mu,integer inputidx)
	Computes a solution/trajectory for the given mu and inputidx in the SCALED state space. More...

function matrix < double > mu =	getRandomParam (integer num,integer seed)
	Gets a random parameter sample from the system's parameter domain P. 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 ()

Static Public Member Functions
static function res =	test_ModelVersions ()

static function res =	test_JacobianApproxGaussRules ()
	Tests the precision of the analytical jacobian computation using different gauss integration rules. More...

Static Public Member Functions inherited from models.BaseFullModel
static function	test_BaseModels ()

static function res =	test_BareModel ()

static function	test_LinearModel ()

static function	test_LinearModelNoProj ()

static function	test_LinearModelNoApprox ()

static function	test_LinearModelParams ()

static function	test_LinearModelInputs ()

static function	test_LinearModelParamsInput ()

static function	test_NonlinearModel ()

static function	test_NonlinearModelParams ()

static function	test_NonlinearModelInputs ()

static function	test_NonlinearModelParamsInput ()

static function	test_TimeDependentOutput ()

static function res =	test_FileSystemTidyness ()
	Plain small model. More...

Public Attributes
	MuscleDensity = 1.1e-3
	g/mm³ More...

	Plotter
	The plotter class for visualization. More...

int	RandSeed = 1
	Seed that can be used by random number generator instances in order to enable result reproduction. More...

	Config

	Gravity = 9.80665e-3
	[mm/ms²] More...

	Geo

Public Attributes inherited from models.BaseFullModel
data.ModelData	Data
	The full model's data container. Defaults to an empty container. More...

export.JKerMorExport	JKerMorExport
	Export instance for possible export of this model to JKerMor. More...

sampling.BaseSampler	Sampler
	The sampling strategy the Model uses. More...

spacereduction.BaseSpaceReducer	SpaceReducer
	The reduction algorithm for subspaces. More...

approx.BaseApprox	Approx = "[]"
	The approximation method for the CoreFunction. More...

function_handle	preApproximationTrainingCallback
	Advanced property. Must be a function handle taking the current model instance. More...

function_handle	postApproximationTrainingCallback
	Advanced property. Must be a function handle taking the current model instance. More...

logical	EnableTrajectoryCaching = false
	Flag that enables caching of computed trajectories in a simulation cache stored in KerMor's TempDirectory folder. More...

error.BaseEstimator	ErrorEstimator = "[]"
	The associated error estimator for this model. More...

logical	ComputeTrajectoryFxiData = false
	Flag that determines whether fxi data should be computed along with the trajectories or not. More...

logical	ProjectApproxTrainingData = false
	Flag to determine if the data collected by the approx.Approx.TrainDataSelector should be projected into the previously computed projection space V (see offline phase 3). If so, the \(f(x_i)\) values are also re-computed for the updated \(x_i\) samples. More...

logical	AutoSave = false
	Flag to enable automatic saving of the model after each individual offline phase step and at other locations prone to data loss due to lengthy computations. More...

char	SaveTag = ""
	A custom tag that can be used as a prefix to files for corresponding model identification. More...

integer	TrainingInputs
	The indices of inputs to use for training data generation. Uses the DefaultInput if not set (and DefaultInput is not empty) More...

rowvec< integer >	TrainingParams
	The indices of the model parameters to use for training data generation. More...

integer	TrainingInputCount
	Gets the number of inputs used for training. More...

rowvec< double >	OfflinePhaseTimes = "[]"
	The computation times for all phases of the last offline generation. More...

	TrajectoriesCompleted = "[]"
	Contains a flag for each input/parameter combination which has been successfully computed completely during the offline phase. More...

Public Attributes inherited from models.BaseModel
models.BaseFirstOrderSystem	System = "[]"
	The actual dynamical system used in the model. More...

char	Name = ""
	The name of the Model. More...

matrix< double >	G = 1
	The custom scalar product matrix \(\vG\). More...

double	RealTimePlottingMinPause = .1
	Minimum pause between successive steps when RealTimePlotting is enabled. More...

logical	isStatic = false
	Determines if the model is time dependent or static. More...

integer	DefaultInput = "[]"
	The default input to use if none is given. More...

	Times
	Evaluation points \(\{0=t_0,\ldots,t_n=T\}\) of the model. More...

rowvec< double >	scaledTimes
	The time steps Times in scaled time units \(\tilde{t_i} = \frac{t_i}{\tau}\). More...

double	Tscaled
	The scaled end time \(\tilde{T} = \frac{T}{\tau}\). More...

double	tau
	Time scaling factor \(\tau\). More...

double	T
	The final timestep \(T\) up to which to simulate. More...

double	dt
	The desired time-stepsize \(\Delta t\) for simulations. More...

solvers.BaseSolver	ODESolver
	The solver to use for the ODE. Must be an instance of any solvers.BaseSolver subclass. More...

logical	RealTimePlotting
	Determines if the simulation should plot intermediate steps during computation. More...

colvec< double >	DefaultMu = "[]"
	The default parameter value if none is given. More...

	dtscaled = .1
	The scaled timestep \(\tilde{\Delta t} = \frac{\Delta t}{\tau}\). More...

char	gitRefOnSave = ""
	Contains the GIT revision of this model when it was last saved. More...

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 IParallelizable
	ComputeParallel = false
	Flag whether the code should be run in parallel or not. More...

Static Protected Member Functions
static function this =	loadobj ()

Static Protected Member Functions inherited from models.BaseFullModel
static function this =	loadobj (this, sobj)

Static Protected Member Functions inherited from models.BaseModel
static function this =	loadobj (this, s)

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)

Additional Inherited Members
Protected Member Functions inherited from models.BaseModel
function this =	saveobj ()
	Store the current GIT branch in the object. More...

function	plotstep (src, ed)
	Callback for the ODE solvers StepPerformed event that enables during-simulation-plotting. More...

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)

Constructor & Destructor Documentation

models.muscle.Model.Model	(	conf,
		basedir
	)

Definition at line 89 of file Model.m.

References KerMor.App(), models.BaseFullModel.Data, models.BaseModel.DefaultInput, models.BaseModel.DefaultMu, models.BaseModel.dt, models.BaseModel.initDefaultParameter(), models.BaseFirstOrderSystem.MaxTimestep, data.ModelData.ModelData(), models.BaseModel.ODESolver, models.muscle.System.prepareSimulation(), models.BaseFullModel.SaveTag, setConfig(), models.BaseFullModel.SpaceReducer, models.muscle.System.System(), models.BaseModel.T, and models.BaseFullModel.TrainingParams.

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Member Function Documentation

function [ double t , colvec< double > x , time , cache ] = models.muscle.Model.computeTrajectory	(	colvec< double >	mu,
		integer	inputidx
	)

Allows to also call prepareSimulation for any quantities set by the AMuscleConfig class.

Parameters

mu	The currently used parameter \(\vmu\). Set to \([]\) if not used.
inputidx	The index \(i\) of the currently used input function \(u_i(t)\). Set to \([]\) if not used.

Definition at line 173 of file Model.m.

References Config, models.BaseFirstOrderSystem.f, and t.

function double t = models.muscle.Model.getConfigTable ( colvec< double > mu )

Definition at line 190 of file Model.m.

References models.BaseModel.DefaultMu, models.BaseFirstOrderSystem.f, MuscleDensity, models.BaseModel.Name, and t.

function colvec< integer > idx = models.muscle.Model.getFaceDofsGlobal	(	integer	elem,
		rowvec< integer >	faces,
		rowvec< integer >	dim
	)

Returns the indices in the global uvw vector (including dirichlet values) of the given faces in the given element.

Parameters

elem	The element index
faces	The faces whose indices to return. May also only be one face.
dim	The dimensions which to select. Default: [1 2 3]

Return values

idx	The global indices of the face

Definition at line 387 of file Model.m.

References Config, and k.

function idx = models.muscle.Model.getPositionDirichletBCFaceIdx	(	integer	elem,
		integer	face,
		rowvec< integer >	dim
	)

Returns the positions of dofs of a specified face within the boundary conditions residual vector. Applies to dirichlet boundary conditions of POSITION (u)

Parameters

elem	The element the face belongs to
face	The face number of that element
dim	Optionally, specify a requested dimension to get the indices for. Defaults to return all x,y,z components on every node on the face. Default: 1:3

Definition at line 413 of file Model.m.

References models.muscle.System.bool_u_bc_nodes, Config, and models.muscle.System.idx_u_bc_glob.

function [residuals_dirichlet , residuals_neumann ] = models.muscle.Model.getResidualForces	(	double	t,
			uvw
	)

Definition at line 372 of file Model.m.

References k, models.BaseModel.System, and t.

Referenced by plotGeometrySetup(), and simulateAndPlot().

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function idx = models.muscle.Model.getVelocityDirichletBCFaceIdx	(	integer	elem,
		integer	face,
		rowvec< integer >	dim
	)

Returns the positions of dofs of a specified face within the boundary conditions residual vector. Applies to dirichlet boundary conditions of VELOCITY (v)

Parameters

elem	The element the face belongs to
face	The face number of that element
dim	Optionally, specify a requested dimension to get the indices for. Defaults to return all x,y,z components on every node on the face. Default: 1:3

Definition at line 438 of file Model.m.

References models.muscle.System.bool_expl_v_bc_nodes, models.muscle.System.bool_u_bc_nodes, Config, models.muscle.System.idx_v_bc_glob, and models.muscle.System.val_u_bc.

static function this = models.muscle.Model.loadobj ( )

staticprotected

Definition at line 577 of file Model.m.

References Config, and RandSeed.

function varargout = models.muscle.Model.plot ( varargin )

Definition at line 504 of file Model.m.

References Plotter.

Referenced by plotActivation(), plotForceLengthCurve(), plotGeometrySetup(), and simulateAndPlot().

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function models.muscle.Model.plotActivation ( )

Definition at line 334 of file Model.m.

References models.BaseFirstOrderSystem.f, PlotManager.LeaveOpen, models.BaseModel.Name, plot(), and models.BaseModel.Times.

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function models.muscle.Model.plotAnisotropicPressure ( colvec< double > mu )

Definition at line 306 of file Model.m.

References models.BaseModel.DefaultMu, models.BaseFirstOrderSystem.f, fl(), PlotManager.LeaveOpen, and models.BaseModel.Name.

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function models.muscle.Model.plotForceLengthCurve	(	colvec< double >	mu,
			pm
	)

Definition at line 203 of file Model.m.

References Config, models.BaseModel.DefaultInput, models.BaseModel.DefaultMu, models.BaseFirstOrderSystem.f, fl(), plot(), dscomponents.ACoreFun.prepareSimulation(), models.BaseModel.System, and t.

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function models.muscle.Model.plotGeometryInfo ( varargin )

Definition at line 367 of file Model.m.

References Config.

function varargout = models.muscle.Model.plotGeometrySetup ( varargin )

Definition at line 345 of file Model.m.

References models.BaseModel.DefaultInput, models.BaseModel.DefaultMu, getResidualForces(), models.BaseSecondOrderSystem.getX0(), models.BaseFirstOrderSystem.mu, plot(), Plotter, and models.muscle.System.prepareSimulation().

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function models.muscle.Model.setConfig ( value )

Definition at line 468 of file Model.m.

References Config, models.muscle.System.configUpdated(), and Plotter.

Referenced by Model(), and setGaussIntegrationRule().

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function models.muscle.Model.setGaussIntegrationRule ( value )

Sets the gauss integration rule for the model.

See fem.BaseFEM for possible values. Currently 3,4,5 are implemented.

Definition at line 478 of file Model.m.

References Config, models.BaseModel.DefaultInput, models.BaseModel.DefaultMu, models.BaseFirstOrderSystem.mu, setConfig(), and models.BaseModel.System.

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function [double t , matrix<double>y ] = models.muscle.Model.simulateAndPlot	(	withResForce,
		varargin
	)

Definition at line 159 of file Model.m.

References getResidualForces(), plot(), models.BaseModel.simulate(), and t.

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function res = models.muscle.Model.test_JacobianApproxGaussRules ( )

static

Tests the precision of the analytical jacobian computation using different gauss integration rules.

Definition at line 555 of file Model.m.

static function res = models.muscle.Model.test_ModelVersions ( )

static

Definition at line 521 of file Model.m.

References t.

Member Data Documentation

models.muscle.Model.Geo

Note: [readonly]

Definition at line 84 of file Model.m.

models.muscle.Model.Gravity = 9.80665e-3

[mm/ms²]

Note: This property has non-standard access specifiers: SetAccess = Private, GetAccess = Public; Matlab documentation of property attributes.
Default: 9.80665e-3

Definition at line 71 of file Model.m.

models.muscle.Model.MuscleDensity = 1.1e-3

g/mm³

Default: 1.1e-3

Definition at line 36 of file Model.m.

Referenced by models.muscle.System.assembleMassMatrix(), and getConfigTable().

models.muscle.Model.Plotter

The plotter class for visualization.

Definition at line 44 of file Model.m.

Referenced by plot(), plotGeometrySetup(), and setConfig().

models.muscle.Model.RandSeed = 1

Seed that can be used by random number generator instances in order to enable result reproduction.

Default:: 1

Note: This property has non-standard access specifiers: SetAccess = Private, GetAccess = Public; Matlab documentation of property attributes.
Default: 1

Definition at line 54 of file Model.m.

Referenced by loadobj().

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

+models/+muscle/Model.m

Detailed Description

Public Member Functions

Static Public Member Functions

Public Attributes

Static Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation