KerMor
0.9
Model order reduction for nonlinear dynamical systems and nonlinear approximation
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PCDISystem2D The inhibited version programmed cell death model for 2D geometry. More...
PCDISystem2D The inhibited version programmed cell death model for 2D geometry.
Geometry layout is with zero in the top left corner and x+ being downwards and y+ towards right (according to matlab matrix indexing)
Homepage
http://www.morepas.org/software/index.htmlDocumentation
http://www.morepas.org/software/kermor/index.htmlLicense
KerMor license conditionsDefinition at line 19 of file PCDISystem2D.m.
Public Member Functions | |
PCDISystem2D (models.BaseFullModel model) | |
function | setConfig (colvec< double > mu,integer inputidx) |
function
varargout = | plot (models.BaseFullModel model,double t,matrix< double > y, varargin) |
function
varargout = | plotState (models.BaseFullModel model,double t,matrix< double > y, mode) |
function pm = | plotDiffusionCoeff (colvec< double > mu, pm, allparts) |
Public Member Functions inherited from models.pcdi.BasePCDISystem | |
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 | |
kernels.KernelExpansion | Kexp |
The kernel expansion used to construct the diffusion coefficient distribution. More... | |
Gammas = "[.01 .02 .03 .04 .05]" | |
Gamma values to use as kernel width for diffusivity Gammas = .08;. More... | |
DiscreteCXMU | |
CurCXMU | |
Public Attributes inherited from models.pcdi.BasePCDISystem | |
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 | newSysDimension () |
Custom updates for new system dimension. More... | |
Protected Member Functions inherited from models.pcdi.BasePCDISystem | |
function | updateDimensions () |
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.PCDISystem2D.PCDISystem2D | ( | models.BaseFullModel | model | ) |
Definition at line 71 of file PCDISystem2D.m.
References models.BaseFirstOrderSystem.f, models.pcdi.BasePCDISystem.h, k, Kexp, models.BaseFirstOrderSystem.Model, and models.pcdi.BasePCDISystem.Omega.
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protectedvirtual |
Custom updates for new system dimension.
Implements models.pcdi.BasePCDISystem.
Definition at line 217 of file PCDISystem2D.m.
References models.BaseFirstOrderSystem.A, models.BaseFirstOrderSystem.C, models.pcdi.BasePCDISystem.Dims, DiscreteCXMU, models.pcdi.BasePCDISystem.hs, k, dscomponents.LinearOutputConv.LinearOutputConv(), models.BaseFirstOrderSystem.M, models.BaseFirstOrderSystem.Model, models.BaseFirstOrderSystem.NumStateDofs, models.pcdi.BasePCDISystem.Omega, handle.reshape, and models.BaseFirstOrderSystem.x0.
function varargout = models.pcdi.PCDISystem2D.plot | ( | models.BaseFullModel | model, |
double | t, | ||
matrix< double > | y, | ||
varargin | |||
) |
Definition at line 108 of file PCDISystem2D.m.
References models.pcdi.BasePCDISystem.h, PlotManager.LeaveOpen, models.BaseModel.Name, and models.BaseFullModel.SaveTag.
Definition at line 172 of file PCDISystem2D.m.
References Gammas, models.pcdi.BasePCDISystem.h, models.pcdi.BasePCDISystem.hs, k, PlotManager.LeaveOpen, models.BaseFirstOrderSystem.Model, models.BaseFirstOrderSystem.mu, and models.pcdi.BasePCDISystem.Omega.
function varargout = models.pcdi.PCDISystem2D.plotState | ( | models.BaseFullModel | model, |
double | t, | ||
matrix< double > | y, | ||
mode | |||
) |
Definition at line 129 of file PCDISystem2D.m.
References k.
Definition at line 99 of file PCDISystem2D.m.
References CurCXMU, and DiscreteCXMU.
models.pcdi.PCDISystem2D.CurCXMU |
Definition at line 66 of file PCDISystem2D.m.
Referenced by setConfig().
models.pcdi.PCDISystem2D.DiscreteCXMU |
Definition at line 64 of file PCDISystem2D.m.
Referenced by newSysDimension(), and setConfig().
models.pcdi.PCDISystem2D.Gammas = "[.01 .02 .03 .04 .05]" |
Gamma values to use as kernel width for diffusivity Gammas = .08;.
Default: "[.01 .02 .03 .04 .05]"
Definition at line 54 of file PCDISystem2D.m.
Referenced by plotDiffusionCoeff().
models.pcdi.PCDISystem2D.Kexp |
The kernel expansion used to construct the diffusion coefficient distribution.
Definition at line 42 of file PCDISystem2D.m.
Referenced by PCDISystem2D().