Make superclass for params

docs/structure/index.rst

@@ -8,4 +8,6 @@ TODO
    :maxdepth: 1
    :glob:
 
-   *
+   problem
+   rhs
+   parameters

docs/structure/parameters.rst

@@ -0,0 +1,6 @@
+Parameters
+================================================================================
+
+.. automodule:: +otp
+.. autoclass:: Parameters
+    :members:

toolbox/+otp/+ascherlineardae/+presets/Canonical.m

@@ -13,15 +13,8 @@
             %
             %    - ``Beta`` – Value of $β$.
 
-            p = inputParser;
-            p.addParameter('beta', 1);
-            p.parse(varargin{:});
-            opts = p.Results;
-
-            params      = otp.ascherlineardae.AscherLinearDAEParameters;
-            params.Beta = opts.beta;
-
-            y0    = [1; params.Beta];
+            params = otp.ascherlineardae.AscherLinearDAEParameters('Beta', 1, varargin{:});
+            y0 = [1; params.Beta];
             tspan = [0.0; 1.0];
 
             obj = obj@otp.ascherlineardae.AscherLinearDAEProblem(tspan, y0, params);

toolbox/+otp/+ascherlineardae/+presets/Petzold.m

@@ -6,10 +6,8 @@
         function obj = Petzold
             % Create the Petzold example of the Ascher linear DAE problem object.
 
-            params      = otp.ascherlineardae.AscherLinearDAEParameters;
-            params.Beta = 0;
-
-            y0    = [1; params.Beta];
+            params = otp.ascherlineardae.AscherLinearDAEParameters('Beta', 0);
+            y0 = [1; params.Beta];
             tspan = [0.0; 1.0];
 
             obj = obj@otp.ascherlineardae.AscherLinearDAEProblem(tspan, y0, params);

toolbox/+otp/+ascherlineardae/+presets/Stiff.m

@@ -5,10 +5,9 @@
     methods
         function obj = Stiff
             % Create the stiff example of the Ascher linear DAE problem object.
-            params      = otp.ascherlineardae.AscherLinearDAEParameters;
-            params.Beta = 100;
-
-            y0    = [1; params.Beta];
+
+            params = otp.ascherlineardae.AscherLinearDAEParameters('Beta', 100);
+            y0 = [1; params.Beta];
             tspan = [0.0; 1.0];
 
             obj = obj@otp.ascherlineardae.AscherLinearDAEProblem(tspan, y0, params);

toolbox/+otp/+ascherlineardae/AscherLinearDAEParameters.m

@@ -1,7 +1,21 @@
-classdef AscherLinearDAEParameters
+classdef AscherLinearDAEParameters < otp.Parameters
     % Parameters for Ascher Linear DAE problem 
     properties
         % A scalar parameter $β$ in the linear model. It affects the stifness of the problem.
         Beta %MATLAB ONLY: (1,1) {mustBeNumeric} = 1
     end
+
+    methods
+        function obj = AscherLinearDAEParameters(varargin)
+            % Create a Ascher Linear DAE parameters object.
+            %
+            % Parameters
+            % ----------
+            % varargin
+            %    A variable number of name-value pairs. A name can be any property of this class, and the subsequent
+            %    value initializes that property.
+
+            obj = obj@otp.Parameters(varargin{:});
+        end
+    end
 end

toolbox/+otp/+cusp/+presets/Canonical.m

@@ -8,7 +8,7 @@
     % b_i(0) &= 2 \sin\left( \frac{2 i \pi}{N} \right), \\
     % $$
     %
-    % for $i = 1, \dots, N$. The parameters are $\varepsilon = 10^{-4}$ and $\sigma = \frac{1}{144}$.
+    % for $i = 1, \dots, N$. The parameters are $ε = 10^{-4}$ and $σ = \frac{1}{144}$.
 
     methods
         function obj = Canonical(varargin)
@@ -20,8 +20,8 @@
             %    A variable number of name-value pairs. The accepted names are
             %
             %    - ``N`` – The number of cells in the spatial discretization.
-            %    - ``epsilon`` – Value of $\varepsilon$.
-            %    - ``sigma`` – Value of $\sigma$.
+            %    - ``epsilon`` – Value of $ε$.
+            %    - ``sigma`` – Value of $σ$.
             %
             % Returns
             % -------
@@ -30,22 +30,19 @@
 
             p = inputParser;
             p.addParameter('N', 32);
-            p.addParameter('epsilon', 1e-4);
-            p.addParameter('sigma', 1/144);
             p.parse(varargin{:});
-            opts = p.Results;
+            n = p.Results.N;
 
-            params = otp.cusp.CUSPParameters;
-            params.Epsilon = opts.epsilon;
-            params.Sigma = opts.sigma;
-
-            ang = 2 * pi / opts.N * (1:opts.N).';
-            y0 = zeros(opts.N, 1);
-            a0 = -2*cos(ang);
-            b0 = 2*sin(ang);
+            ang = 2 * pi * (1:n).' / n;
+            y0 = zeros(n, 1);
+            a0 = -2 * cos(ang);
+            b0 = 2 * sin(ang);
 
             u0 = [y0; a0; b0];
             tspan = [0; 1.1];
+
+            unmatched = namedargs2cell(p.Unmatched);
+            params = otp.cusp.CUSPParameters('Epsilon', 1e-4, 'Sigma', 1/144, unmatched{:});
 
             obj = obj@otp.cusp.CUSPProblem(tspan, u0, params);
         end

toolbox/+otp/+cusp/CUSPParameters.m

@@ -1,11 +1,25 @@
-classdef CUSPParameters
+classdef CUSPParameters < otp.Parameters
     % Parameters for the CUSP problem.
     properties
-        % The stiffness parameter $\varepsilon$ for the "cusp catastrophe" model.
+        % The stiffness parameter $ε$ for the "cusp catastrophe" model.
         Epsilon %MATLAB ONLY: (1,1) {mustBeNumeric}
 
-        % The diffusion coefficient $\sigma$ for all three variables.
+        % The diffusion coefficient $σ$ for all three variables.
         Sigma %MATLAB ONLY: (1,1) {mustBeNumeric}
     end
+
+    methods
+        function obj = CUSPParameters(varargin)
+            % Create a CUSP parameters object.
+            %
+            % Parameters
+            % ----------
+            % varargin
+            %    A variable number of name-value pairs. A name can be any property of this class, and the subsequent
+            %    value initializes that property.
+
+            obj = obj@otp.Parameters(varargin{:});
+        end
+    end
 end
 

toolbox/+otp/+cusp/CUSPProblem.m

@@ -4,33 +4,32 @@
     % The CUSP problem :cite:p:`HW96` (pp. 147-148) is the PDE
     %
     % $$
-    % \frac{\partial y}{\partial t} &= -\frac{1}{\varepsilon} (y^3 + a y + b)
-    % + \sigma \frac{\partial^2 y}{\partial x^2}, \\
-    % \frac{\partial a}{\partial t} &= b + 0.07 v + \sigma \frac{\partial^2 a}{\partial x^2}, \\
-    % \frac{\partial b}{\partial t} &= (1 - a^2) b - a - 0.4 y + 0.035 v + \sigma \frac{\partial^2 b}{\partial x^2},
+    % \frac{\partial y}{\partial t} &= -\frac{1}{ε} (y^3 + a y + b) + σ \frac{\partial^2 y}{\partial x^2}, \\
+    % \frac{\partial a}{\partial t} &= b + 0.07 v + σ \frac{\partial^2 a}{\partial x^2}, \\
+    % \frac{\partial b}{\partial t} &= (1 - a^2) b - a - 0.4 y + 0.035 v + σ \frac{\partial^2 b}{\partial x^2},
     % $$
     %
     %
     % where $v = u / (u + 0.1)$ and $u = (y - 0.7)(y - 1.3)$. The spatial domain $x \in [0, 1]$ has period boundary
     % conditions. Discretization with second order finite difference on a grid with $N$ cells gives
     %
     % $$
-    % y'_i &= -\frac{1}{\varepsilon} (y_i^3 + a_i y_i + b_i) + \sigma N^2 (y_{i-1} - 2 y_i + y_{i+1}) \\
-    % a'_i &= b_i + 0.07 v_i + \sigma N^2 (a_{i-1} - 2 a_i + a_{i+1}) \\
-    % b'_i &= (1 - a_i^2) b_i - a_i - 0.4 y_i + 0.035 v_i + \sigma N^2  (b_{i-1} - 2 b_i + b_{i+1}),
+    % y'_i &= -\frac{1}{ε} (y_i^3 + a_i y_i + b_i) + σ N^2 (y_{i-1} - 2 y_i + y_{i+1}) \\
+    % a'_i &= b_i + 0.07 v_i + σ N^2 (a_{i-1} - 2 a_i + a_{i+1}) \\
+    % b'_i &= (1 - a_i^2) b_i - a_i - 0.4 y_i + 0.035 v_i + σ N^2  (b_{i-1} - 2 b_i + b_{i+1}),
     % $$
     %
     % where $i = 1, \dots, N$. Values at cell indices $i=0, N+1$ are specificied by the periodic boundary conditions.
     %
     % Notes
     % -----
-    % +---------------------+----------------------------------------------------------------------------+
-    % | Type                | PDE                                                                        |
-    % +---------------------+----------------------------------------------------------------------------+
-    % | Number of Variables | arbitrary multiple of 3                                                    |
-    % +---------------------+----------------------------------------------------------------------------+
-    % | Stiff               | typically, depending on $\varepsilon$, $\sigma$, and number of grid points |
-    % +---------------------+----------------------------------------------------------------------------+
+    % +---------------------+-------------------------------------------------------------+
+    % | Type                | PDE                                                         |
+    % +---------------------+-------------------------------------------------------------+
+    % | Number of Variables | arbitrary multiple of 3                                     |
+    % +---------------------+-------------------------------------------------------------+
+    % | Stiff               | typically, depending on $ε$, $σ$, and number of grid points |
+    % +---------------------+-------------------------------------------------------------+
     %
     % Example
     % -------
@@ -44,7 +43,7 @@
     end
 
     properties (SetAccess = private)
-        % Right-hand side containing the diffusion terms and the reaction terms multiplied by $\varepsilon^{-1}$.
+        % Right-hand side containing the diffusion terms and the reaction terms multiplied by $ε^{-1}$.
         %
         % This partition of the RHS is used in :cite:p:`JM17`.
         %
@@ -53,7 +52,7 @@
         % RHSNonstiff
        RHSStiff
 
-        % Right-hand side containing the reaction terms not scaled by $\varepsilon^{-1}$.
+        % Right-hand side containing the reaction terms not scaled by $ε^{-1}$.
         %
         % This partition of the RHS is used in :cite:p:`JM17`.
         %

toolbox/+otp/+lorenz63/+presets/Canonical.m

@@ -15,23 +15,10 @@
             %    - ``sigma`` – Value of $σ$.
             %    - ``rho`` – Value of $ρ$.
             %    - ``beta`` – Value of $β$.
-            %
-
-            p = inputParser;
-            p.addParameter('sigma', 10);
-            p.addParameter('rho', 28);
-            p.addParameter('beta', 8/3);
-            p.parse(varargin{:});
-            opts = p.Results;
-
-            params = otp.lorenz63.Lorenz63Parameters;
-
-            params.Sigma = opts.sigma;
-            params.Rho   = opts.rho;
-            params.Beta  = opts.beta;
 
             y0    = [0; 1; 0];
             tspan = [0 60];
+            params = otp.lorenz63.Lorenz63Parameters('Sigma', 10, 'Rho', 28, 'Beta', 8/3, varargin{:});
 
             obj = obj@otp.lorenz63.Lorenz63Problem(tspan, y0, params);            
         end

toolbox/+otp/+lorenz63/+presets/LimitCycle.m

@@ -6,22 +6,13 @@
     methods
         function obj = LimitCycle
             % Create the LimitCycle Lorenz '63 problem object.
-            %
-
-            sigma = 10;
-            rho   = 350;
-            beta  = 8/3;
-
-            params = otp.lorenz63.Lorenz63Parameters;
-            params.Sigma = sigma;
-            params.Rho   = rho;
-            params.Beta  = beta;
 
             % We use Lorenz's initial conditions and timespan as Strogatz
             % does not specify those in his book.
 
             y0    = [0; 1; 0];
             tspan = [0 60];
+            params = otp.lorenz63.Lorenz63Parameters('Sigma', 10, 'Rho', 350, 'Beta', 8/3);
 
             obj = obj@otp.lorenz63.Lorenz63Problem(tspan, y0, params);            
         end

toolbox/+otp/+lorenz63/+presets/Surprise.m

@@ -5,21 +5,11 @@
     methods
         function obj = Surprise
             % Create the Surprise Lorenz '63 problem object.
-            %
-
-            sigma = 10;
-            rho   = 100;
-            beta  = 8/3;
-
-            params = otp.lorenz63.Lorenz63Parameters;
-            params.Sigma = sigma;
-            params.Rho   = rho;
-            params.Beta  = beta;
 
             % Hand-picked initial conditions with the canonical timespan
-
             y0    = [2; 1; 1];
             tspan = [0 60];
+            params = otp.lorenz63.Lorenz63Parameters('Sigma', 10, 'Rho', 100, 'Beta', 8/3);
 
             obj = obj@otp.lorenz63.Lorenz63Problem(tspan, y0, params);
         end

toolbox/+otp/+lorenz63/Lorenz63Parameters.m

@@ -1,4 +1,4 @@
-classdef Lorenz63Parameters
+classdef Lorenz63Parameters < otp.Parameters
     % Parameters for the Lorenz '63 problem.
 
     properties
@@ -11,4 +11,18 @@
         % A geometric factor.
         Beta %MATLAB ONLY: (1, 1) {mustBeReal, mustBeFinite}
     end
+
+    methods
+        function obj = Lorenz63Parameters(varargin)
+            % Create a Lorenz '63 parameters object.
+            %
+            % Parameters
+            % ----------
+            % varargin
+            %    A variable number of name-value pairs. A name can be any property of this class, and the subsequent
+            %    value initializes that property.
+
+            obj = obj@otp.Parameters(varargin{:});
+        end
+    end
 end

toolbox/+otp/+lorenz96/+presets/Canonical.m

@@ -12,31 +12,24 @@
             % varargin
             %    A variable number of name-value pairs. The accepted names are
             %
-            %    - ``Size`` – The size of the problem as a positive integer.
+            %    - ``N`` – The size of the problem as a positive integer.
             %    - ``Forcing`` – The forcing as a scalar, vector of N constants, or as a function.
             %
 
             p = inputParser;
-            p.addParameter('Size', 40, @isscalar);
-            p.addParameter('Forcing', 8);
-
+            p.addParameter('N', 40);
             p.parse(varargin{:});
-
-            s = p.Results;
-
-            n = s.Size;
-
-            params = otp.lorenz96.Lorenz96Parameters;
-            params.F = s.Forcing;
+            n = p.Results.N;
 
             % We initialise the Lorenz96 model as in (Lorenz & Emanuel 1998)
-
             y0 = 8*ones(n, 1);
-
             y0(floor(n/2)) = 8.008;
 
             % roughly ten years in system time
             tspan = [0, 720];
+
+            unmatched = namedargs2cell(p.Unmatched);
+            params = otp.lorenz96.Lorenz96Parameters('F', 8, unmatched{:});
 
             obj = obj@otp.lorenz96.Lorenz96Problem(tspan, y0, params);
 

toolbox/+otp/+lorenz96/Lorenz96Parameters.m

@@ -1,8 +1,22 @@
-classdef Lorenz96Parameters
+classdef Lorenz96Parameters < otp.Parameters
     % Parameters for the Lorenz '96 problem.
 
     properties
         % A forcing function, scalar, or vector.
         F %MATLAB ONLY: {mustBeA(F, {'numeric','function_handle'})}
     end
+
+    methods
+        function obj = Lorenz96Parameters(varargin)
+            % Create a Lorenz '96 parameters object.
+            %
+            % Parameters
+            % ----------
+            % varargin
+            %    A variable number of name-value pairs. A name can be any property of this class, and the subsequent
+            %    value initializes that property.
+
+            obj = obj@otp.Parameters(varargin{:});
+        end
+    end
 end