Switch default solver form ode45 to ode15s

Author: Steven-Roberts

src/+otp/+allencahn/AllenCahnProblem.m

@@ -40,9 +40,5 @@ function validateNewState(obj, newTimeSpan, newY0, newParameters)
                 .checkField('beta', 'scalar', 'real', 'finite', 'positive') ...
                 .checkField('forcing', @(f) isempty(f) || isa(f, 'function_handle'));
         end
-        
-        function sol = internalSolve(obj, varargin)
-            sol = internalSolve@otp.Problem(obj, 'Method', @ode15s, varargin{:});
-        end
     end
 end

src/+otp/+ascherlineardae/AscherLinearDAEProblem.m

@@ -27,10 +27,6 @@ function validateNewState(obj, newTimeSpan, newY0, newParameters)
             otp.utils.StructParser(newParameters) ...
                 .checkField('beta', 'scalar', 'real', 'finite');
         end
-        
-        function sol = internalSolve(obj, varargin)
-            sol = internalSolve@otp.Problem(obj, 'Method', @ode15s, varargin{:});
-        end
     end
 end
 

src/+otp/+bouncingball/BouncingBallProblem.m

@@ -5,7 +5,7 @@
         end
     end
 
-    methods (Access = protected)        
+    methods (Access = protected)
         function onSettingsChanged(obj)
             g   = obj.Parameters.g;
             gF  = obj.Parameters.groundFunction;
@@ -43,6 +43,10 @@ function validateNewState(obj, newTimeSpan, newY0, newParameters)
             mov = otp.bouncingball.BouncingBallMovie(obj.Name, obj.Parameters.groundFunction, varargin{:});
             mov.record(t, y);
         end
+        
+        function sol = internalSolve(obj, varargin)
+            sol = internalSolve@otp.Problem(obj, 'Method', @ode45, varargin{:});
+        end
     end
 end
 

src/+otp/+brusselator/BrusselatorProblem.m

@@ -31,7 +31,7 @@
         RhsNonlinear
     end
 
-    methods (Access = protected)        
+    methods (Access = protected)
         function onSettingsChanged(obj)
             a = obj.Parameters.a;
             b = obj.Parameters.b;
@@ -63,5 +63,9 @@ function validateNewState(obj, newTimeSpan, newY0, newParameters)
                 label = 'Reactant Y';
             end
         end
+        
+        function sol = internalSolve(obj, varargin)
+            sol = internalSolve@otp.Problem(obj, 'Method', @ode45, varargin{:});
+        end
     end
 end

src/+otp/+cusp/CUSPProblem.m

@@ -48,9 +48,5 @@ function validateNewState(obj, newTimeSpan, newY0, newParameters)
                 .checkField('epsilon', 'finite', 'positive') ...
                 .checkField('sigma', 'finite', 'positive');
         end
-        
-        function sol = internalSolve(obj, varargin)
-            sol = internalSolve@otp.Problem(obj, 'Method', @ode15s, varargin{:});
-        end
     end
 end

src/+otp/+e5/E5Problem.m

@@ -23,7 +23,8 @@ function onSettingsChanged(obj)
             M = obj.Parameters.M;
 
             obj.Rhs = otp.Rhs(@(t, y) otp.e5.f(t, y, A, B, C, M), ...
-                otp.Rhs.FieldNames.Jacobian, @(t, y) otp.e5.jac(t, y, A, B, C, M));
+                otp.Rhs.FieldNames.Jacobian, @(t, y) otp.e5.jac(t, y, A, B, C, M), ...
+                otp.Rhs.FieldNames.NonNegative, 1:obj.NumVars);
         end
 
         function fig = internalPlot(obj, t, y, varargin)
@@ -32,7 +33,8 @@ function onSettingsChanged(obj)
         end
 
         function sol = internalSolve(obj, varargin)
-            sol = internalSolve@otp.Problem(obj, 'Method', @ode15s, varargin{:});
+            % Set tolerances due to the very small scales
+            sol = internalSolve@otp.Problem(obj, 'AbsTol', 1e-50, 'RelTol', 1e-10, varargin{:});
         end
     end
 end

src/+otp/+hires/HiresProblem.m

@@ -17,9 +17,5 @@ function onSettingsChanged(obj)
                 otp.Rhs.FieldNames.JacobianVectorProduct, @otp.hires.jvp, ...
                 otp.Rhs.FieldNames.JacobianAdjointVectorProduct, @otp.hires.javp);
         end
-        
-        function sol = internalSolve(obj, varargin)
-            sol = internalSolve@otp.Problem(obj, 'Method', @ode15s, varargin{:});
-        end
     end
 end

src/+otp/+inverterchain/InverterChainProblem.m

@@ -1,12 +1,12 @@
-classdef InverterChainProblem < otp.Problem    
+classdef InverterChainProblem < otp.Problem
     methods
         function obj = InverterChainProblem(timeSpan, y0, parameters)
             obj@otp.Problem('Inverter Chain', [], timeSpan, y0, parameters);
         end
     end
 
     methods (Access = protected)
-        function fig = internalPlot(obj, t, y, varargin)            
+        function fig = internalPlot(obj, t, y, varargin)
             fig = internalPlot@otp.Problem(obj, t, y, ...
                 'ylabel', 'Voltage', varargin{:});
         end
@@ -34,4 +34,4 @@ function validateNewState(obj, newTimeSpan, newY0, newParameters)
                 .checkField('gamma', 'scalar', 'real', 'finite', 'positive');
         end
     end
-end
+end

src/+otp/+kpr/KPRProblem.m

@@ -24,9 +24,5 @@ function onSettingsChanged(obj)
             obj.RhsSlow = otp.Rhs(@(t,y) otp.kpr.fslow(t, y, Omega, omega), ...
                 otp.Rhs.FieldNames.Jacobian, @(t, y) otp.kpr.jacslow(t, y, Omega, omega));
         end
-        
-        function sol = internalSolve(obj, varargin)
-            sol = internalSolve@otp.Problem(obj, 'Method', @ode15s, varargin{:});
-        end
     end
-end
+end

src/+otp/+lienard/LienardProblem.m

@@ -29,10 +29,6 @@ function validateNewState(obj, newTimeSpan, newY0, newParameters)
                 .checkField('p', 'function') ...
                 .checkField('dp', 'function');
         end
-        
-        function sol = internalSolve(obj, varargin)
-            sol = internalSolve@otp.Problem(obj, 'Method', @ode15s, varargin{:});
-        end
     end
 end