PCDIModel.m

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namespace models{
namespace pcdi{


/* (Autoinserted by mtoc++)
 * This source code has been filtered by the mtoc++ executable,
 * which generates code that can be processed by the doxygen documentation tool.
 *
 * On the other hand, it can neither be interpreted by MATLAB, nor can it be compiled with a C++ compiler.
 * Except for the comments, the function bodies of your M-file functions are untouched.
 * Consequently, the FILTER_SOURCE_FILES doxygen switch (default in our Doxyfile.template) will produce
 * attached source files that are highly readable by humans.
 *
 * Additionally, links in the doxygen generated documentation to the source code of functions and class members refer to
 * the correct locations in the source code browser.
 * However, the line numbers most likely do not correspond to the line numbers in the original MATLAB source files.
 */

class PCDIModel
  :public models.BaseFullModel {
    public: /* ( Constant ) */

        static const d1 = 1.8e-11;
        static const d2 = 1.86e-11;
        static const d3 = 1.89e-11;
        static const d4 = 2.27e-11;
        static const d5 = 1.8720e-11;
        static const d6 = 1.9548e-11;
        static const d7 = 1.4850e-11;
        static const d8 = 1.4850e-11;
        static const K1 = 0.08;
        static const K2 = 0.08;
        static const K3 = 0.054;
        static const K4 = 0.36;
        static const K5 = .0005;
        static const K6 = .0005;
        static const K7 = 3.6000e-4;
        static const K8 = 1.8000e-04;
        static const K9 = .0005;
        static const K10 = .0005;
        static const K11 = 0.54;
        static const K12 = 1.8000e-05;
        static const K13 = 1.8000e-4;
        static const Km3 = 0.0360;
        static const Km8 = 1e-04;
        static const Km9 = 1e-04;
        static const Km10 = 1e-04;
        static const Km11 = 0.0360;
        static const Km12 = 1.8000e-06;
        static const tc = 1e-7;
            static const L = 1e-5;
    public:

        WithInhibitors;
    public: /* ( Dependent ) */

        Dimension;

        
    public: /* ( Dependent ) */

        PCDIModel(integer dim,logical inhibitors) {

            if nargin < 2
                inhibitors = true;
                if nargin < 1
                    dim = 2;
                end
            end
            this.WithInhibitors= inhibitors;

            this.T= 3600; /* [s] */

            this.dt= 5; /* [s]
             * time scaling */

            this.tau= this.L^2/this.d1;

            s = sampling.GridSampler;
            this.Sampler= s;

            /*              this.ODESolver = solvers.MLWrapper(@ode23);
             *             this.ODESolver = solvers.ExplEuler(this.dt); */
            o = solvers.MLode15i;
            o.AbsTol= 1e-6;
            o.RelTol= 1e-5;
            o.MaxStep= [];
            this.ODESolver= o;
            /*              this.ODESolver = solvers.SemiImplicitEuler(this); */

            switch dim
                case 3
                    s = models.pcdi.PCDISystem3D(this);
                    this.Name= " Programmed Cell Death 3D ";
                    this.Data.useFileTrajectoryData;
                otherwise
                    s = models.pcdi.PCDISystem2D(this);
                    this.Name= " Programmed Cell Death 2D ";
                    this.Data.useFileTrajectoryData;
            end
            if this.WithInhibitors
                this.Name= [this.Name "  (Inhibitor System) "];
            end            

            s.MaxTimestep= this.dt;
            this.System= s;

            /*  Space reduction setup */
            sr = spacereduction.PODGreedy;
            sr.Eps= 1e-5;
            this.SpaceReducer= sr;

            this.Approx= [];
        }
        function  plot(varargin) {
            this.System.plot(this, varargin[:]);
        }
        function  plotState(varargin) {
            this.System.plotState(this, varargin[:]);
        }
#if 0 //mtoc++: 'get.Dimension'
function value = Dimension() {
            value = this.System.Dims;
        }

#endif


        
#if 0 //mtoc++: 'set.WithInhibitors'
function  WithInhibitors(value) {
            if ~islogical(value) || ~isscalar(value)
                error(" WithInhibitors must be a logical scalar ");
            end
            this.WithInhibitors= value;
        }

#endif

    
    protected: /* ( Dependent ) */

        function ss = getSteadyStates(n);
    
    public: /* ( Static ) */ /* ( Dependent ) */

        static function res = test_PCDIModel_Simulation() {
            m = models.pcdi.PCDIModel;
            [t,y] = m.simulate;
            m.plot(t,y);
            res = 1;
        }

};
}
}