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KerMor
0.9
Model order reduction for nonlinear dynamical systems and nonlinear approximation
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KerMor
0.9
Model order reduction for nonlinear dynamical systems and nonlinear approximation
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BasePCDISystem The base dynamical system class for the the Programmed Cell Death Model by Markus Daub. More...
BasePCDISystem The base dynamical system class for the the Programmed Cell Death Model by Markus Daub.
Homepage http://www.morepas.org/software/index.htmlDocumentation http://www.morepas.org/software/kermor/index.htmlLicense KerMor license conditionsDefinition at line 19 of file BasePCDISystem.m.
Public Member Functions | |
| BasePCDISystem (models.BaseFullModel model) | |
| function | setConfig (colvec< double > mu,integer inputidx) |
 Public Member Functions inherited from models.BaseFirstOrderSystem | |
| BaseFirstOrderSystem (models.BaseFullModel model) | |
| Creates a new base dynamical system class instance. More... | |
| function rsys = | getReducedSystemInstance (models.ReducedModel rmodel) |
| Creates a reduced system given the current system and the reduced model. More... | |
| function | setConfig (mu, inputidx) |
| Sets the dynamical system's configuration. More... | |
| function | prepareSimulation (colvec< double > mu,integer inputidx) |
| function dx = | ODEFun (double t,colvec< double > x) |
| Debug variant for single evaluation. Commented in function above. More... | |
| function y = | computeOutput (matrix< double > x,colvec< double > mu) |
| Computes the output \(y(t) = C(t,\mu)Sx(t)\) from a given state result vector \(x(t)\), using the system's time and current mu (if given). More... | |
| function | updateSparsityPattern () |
| function J = | getJacobian (double t, xc) |
| Computes the global jacobian of the current system. More... | |
| function matrix < double > x0 = | getX0 (rowvec< double > mu) |
| Gets the initial state variable at \(t=0\). More... | |
| function M = | getMassMatrix () |
| For first order systems, only algebraic constraints need to be catered for. More... | |
| function ModelParam p = | addParam (char name, default, varargin) |
| Adds a parameter with the given values to the parameter collection of the current dynamical system. More... | |
| function pidx = | getParamIndexFromName (paramname) |
| Gets the index within the parameter vector \(\mu\) for a given parameter name. More... | |
| function pt = | getParamInfo (colvec< double > mu) |
| function | plotInputs (pm) |
| 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 Attributes | |
| h | |
| Spatial stepwidth (in unscaled size units!) is set in subclasses. More... | |
| Omega | |
| The spatial width/area/region (in unscaled size units!) More... | |
| Diff | |
| Relative diffusion coefficients ([d2/d1, d3/d1, d4/d1]) More... | |
| hs | |
| scaled spatial stepwidth More... | |
| Dims | |
| The system's dimensions. More... | |
| ReacCoeff | |
| The reaction coefficients. More... | |
| Labels | |
| The concentration labels. More... | |
| Tags = {"'c8','c3','pc8','pc3','iap','bar','yb','xb'"} | |
| The concentration image tags. More... | |
| Public Attributes inherited from models.BaseFirstOrderSystem | |
| dscomponents.ACoreFun | f |
| The core f function from the dynamical system. More... | |
| dscomponents.LinearCoreFun | A = "[]" |
| Represents a linear or affine-linear component of the dynamical system. More... | |
| dscomponents.AInputConv | B = "[]" |
| The input conversion. More... | |
| dscomponents.LinearOutputConv | C |
| The output conversion Defaults to an LinearOutputConv instance using a 1-matrix, which just forwards the state variables and supports projection. More... | |
| dscomponents.AInitialValue | x0 = "[]" |
| Function handle to initial state evaluation. More... | |
| dscomponents.AMassMatrix | M = "[]" |
| The system's mass matrix. More... | |
| dscomponents.ACoreFun | g = "[]" |
| The system's algebraic constraints function. More... | |
| Inputs = {""} | |
| The system's possible input functions. A cell array of function handles, each taking a time argument t. More... | |
| Params = data.ModelParam.empty | |
| The parameters usable for the dynamical system. More... | |
| integer | DependentParamIndices = -1 |
| Indices of the parameter vector that are effectively used in the system's core function. More... | |
| double | MaxTimestep = "[]" |
| The maximum timestep allowed for any ODE solvers. More... | |
| colvec | StateScaling = 1 |
| The scaling for the state vectors. More... | |
| SparsityPattern | |
| The global sparsity pattern for the entire RHS. More... | |
| mu = "[]" | |
| The current parameter \(\mu\) for simulations, [] is none used. More... | |
| u = "[]" | |
| The current input function \(u(t)\) as function handle, [] if none used. More... | |
| inputidx = "[]" | |
| The current inputindex of the function \(u(t)\). More... | |
| NumStateDofs = "[]" | |
| NumAlgebraicDofs = 0 | |
| NumTotalDofs = "[]" | |
| InputCount | |
| The number of inputs available. More... | |
| ParamCount | |
| The number of the system's parameters. More... | |
| Model | |
| The Model this System is attached to. 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... | |
Protected Member Functions | |
| function | updateDimensions () |
| virtual function | newSysDimension () |
| Custom updates for new system dimension. More... | |
| Protected Member Functions inherited from models.BaseFirstOrderSystem | |
| function | updateDimensions () |
| function ad_ic = | getAlgebraicDofsInitialConditions () |
| The default is to return all zeros. More... | |
| function | validateModel (models.BaseFullModel model) |
| Validates if the model to be set is a valid BaseModel at least. Extracting this function out of the setter enables subclasses to further restrict the objects that may be passed, as is being done in models.ReducedSystem, for example. 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) |
Additional Inherited Members | |
| 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) |
| models.pcdi.BasePCDISystem.BasePCDISystem | ( | models.BaseFullModel | model | ) |
Definition at line 154 of file BasePCDISystem.m.
References models.BaseFirstOrderSystem.addParam(), Diff, models.BaseFirstOrderSystem.Model, ReacCoeff, DPCMObject.registerProps(), models.BaseFirstOrderSystem.StateScaling, and t.
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protectedpure virtual |
Custom updates for new system dimension.
Implemented in models.pcdi.PCDISystem2D.
Referenced by updateDimensions().
Definition at line 195 of file BasePCDISystem.m.
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protected |
Definition at line 268 of file BasePCDISystem.m.
References Dims, models.BaseFirstOrderSystem.f, h, newSysDimension(), and models.BaseFirstOrderSystem.NumStateDofs.
| models.pcdi.BasePCDISystem.Diff |
Relative diffusion coefficients ([d2/d1, d3/d1, d4/d1])
SetAccess = Private, GetAccess = Public Definition at line 82 of file BasePCDISystem.m.
Referenced by BasePCDISystem().
| models.pcdi.BasePCDISystem.Dims |
The system's dimensions.
SetAccess = Private, GetAccess = Public Definition at line 104 of file BasePCDISystem.m.
Referenced by models.pcdi.PCDISystem2D.newSysDimension(), and updateDimensions().
| models.pcdi.BasePCDISystem.h |
Spatial stepwidth (in unscaled size units!) is set in subclasses.
Dependent set to true. SetObservable set to true. Definition at line 41 of file BasePCDISystem.m.
Referenced by models.pcdi.PCDISystem2D.PCDISystem2D(), models.pcdi.PCDISystem2D.plot(), models.pcdi.PCDISystem2D.plotDiffusionCoeff(), and updateDimensions().
| models.pcdi.BasePCDISystem.hs |
scaled spatial stepwidth
SetAccess = Private, GetAccess = Public Definition at line 93 of file BasePCDISystem.m.
Referenced by models.pcdi.PCDISystem2D.newSysDimension(), and models.pcdi.PCDISystem2D.plotDiffusionCoeff().
| models.pcdi.BasePCDISystem.Labels |
The concentration labels.
SetAccess = Private, GetAccess = Public Definition at line 126 of file BasePCDISystem.m.
| models.pcdi.BasePCDISystem.Omega |
The spatial width/area/region (in unscaled size units!)
Dependent set to true. SetObservable set to true. Definition at line 57 of file BasePCDISystem.m.
Referenced by models.pcdi.PCDISystem2D.newSysDimension(), models.pcdi.PCDISystem2D.PCDISystem2D(), and models.pcdi.PCDISystem2D.plotDiffusionCoeff().
| models.pcdi.BasePCDISystem.ReacCoeff |
The reaction coefficients.
SetAccess = Private, GetAccess = Public Definition at line 115 of file BasePCDISystem.m.
Referenced by BasePCDISystem().
| models.pcdi.BasePCDISystem.Tags = {"'c8','c3','pc8','pc3','iap','bar','yb','xb'"} |
The concentration image tags.
SetAccess = Private, GetAccess = Public Definition at line 140 of file BasePCDISystem.m.
1.8.6