Comparison ML Python works. Spherical still off. Slab fine.

@Ternary_model/create_mesh.m

@@ -4,7 +4,7 @@ function create_mesh(T)
 
 if strcmp(T.mode, 'Constituent') | T.v == 0
 % Start with left side of mesh, at r=0/x=0, with a given step size
-    x = linspace(0, 0.75, 40);
+    x = linspace(0, -0.75*T.a, 40);
     x = [x, x(end)+0.001/T.precision];
     while x(end)<-T.a
         x_temp = x(end)-x(end-1);

@Ternary_model/plot_sim.m

@@ -12,26 +12,26 @@ if strcmp(mode, 'mov')
     for i = 1:nth:length(T.t)
         cla;
         axis([0, T.system_size, 0, max(T.sol(:))]);
-        ax = gca;
-        ax.FontSize = 12;
+        ax = gca; ax.FontSize = 12;
         xlabel('position'); ylabel('probability [not normalized]');
         plot(T.x, T.phi_tot(T.x, T.a, T.b, T.e, T.u0, T.t(i)*T.v), 'LineWidth', 2, ...
             'LineStyle', '--');
         plot(T.x, T.sol(i, :), 'LineWidth', 2);
         text(abs(-T.a+2), 0.7, num2str(T.t(i)));
-        shg
-        pause();
+        shg; pause();
 %         print([num2str(i),'.png'],'-dpng')
     end
 elseif strcmp(mode, 'plot')
     figure(20);
-    cla;
+%     cla;
     hold on;
-%     xlim([-inf, 6.0]); ylim([-inf, max(T.sol(:))]);
+    xlim([-inf, -2*T.a]); %ylim([-inf, max(T.sol(:))]);
     ax = gca;
     ax.FontSize = 12;
     xlabel('x [\mum]'); ylabel('volume fraction'); 
-    plot(T.x, T.sol([1, 2:nth:si(1)], :), 'LineWidth', 1, 'Color', color);
+%     N = max(max(T.sol([1, 2:nth:si(1)], :)));
+    N = 1;
+    plot(T.x, T.sol([1, 1:nth:si(1)], :)/N, 'LineWidth', 1, 'Color', color);
 %     plot(T.x, T.sol(nth, :), 'LineWidth', 1, 'Color', color);
     plot(T.x, Ternary_model.phi_tot(T.x, T.a, T.b, T.e, T.u0, 0),...
         'LineWidth', 1, 'LineStyle', '--', 'Color', [0.97, 0.55, 0.03]);

@Ternary_model/solve_tern_frap.m

 function solve_tern_frap(T)
 %SOLVE_TERN_FRAP solves Fokker Planck equation for ternary FRAP
 % Assumes fixed profile of phi_tot
+tic
 fh_ic = @(x) flory_ic(x, T.a, T.b, T.u0, T.e, T.ic, T.x0);
 fh_bc = @(xl, ul, xr, ur, t) flory_bc(xl, ul, xr, ur, t, T.u0, T.e);
 fh_pde = @(x, t, u, dudx) flory_hugg_pde(x, t, u, dudx, T.a, T.b, T.e,...
                                           T.u0, T.e_g0, T.u_g0, T.v,...
                                           T.mode);
 T.sol = pdepe(T.geometry, fh_pde, fh_ic, fh_bc, T.x, T.t);
+toc
 end
 
 %% Function definitions for pde solver

FloryHugg_DiffUnbleached.ipynb

@@ -94,8 +94,9 @@
    "outputs": [],
    "source": [
     "bp = 0.1 # Boundary position at IC\n",
-    "sym = 2 # Symmetry of the problem\n",
-    "dt = 0.0001\n",
+    "sym = 0 # Symmetry of the problem\n",
+    "dt = 0.001\n",
+    "nt = 10\n",
     "\n",
     "c_tot_1 = create_func(F, p_tot(0.9, 0.9), 1)\n",
     "c0_1 = create_func(F, 'x[0]<'+str(bp)+'? 0 :' + p_tot(0.9, 0.9), 1)\n",
@@ -121,12 +122,12 @@
     "c0_9 = create_func(F, 'x[0]<'+str(bp)+'? 0 :' +p_tot(0.9, 0.1), 1)\n",
     "Ga0_9 = create_func(F,p_tot(1, 1), 1)\n",
     "\n",
-    "c0_1 = calc_sim(c0_1, c_tot_1, Ga0_1, dt, 10, sym)\n",
-    "c0_2 = calc_sim(c0_2, c_tot_2, Ga0_2, dt, 10, sym)\n",
-    "c0_3 = calc_sim(c0_3, c_tot_3, Ga0_3, dt, 10, sym)\n",
-    "c0_5 = calc_sim(c0_5, c_tot_5, Ga0_5, dt, 10, sym)\n",
-    "c0_8 = calc_sim(c0_8, c_tot_8, Ga0_8, dt, 10, sym)\n",
-    "c0_9 = calc_sim(c0_9, c_tot_9, Ga0_9, dt, 10, sym)"
+    "c0_1 = calc_sim(c0_1, c_tot_1, Ga0_1, dt, nt, sym)\n",
+    "# c0_2 = calc_sim(c0_2, c_tot_2, Ga0_2, dt, nt, sym)\n",
+    "# c0_3 = calc_sim(c0_3, c_tot_3, Ga0_3, dt, nt, sym)\n",
+    "# c0_5 = calc_sim(c0_5, c_tot_5, Ga0_5, dt, nt, sym)\n",
+    "# c0_8 = calc_sim(c0_8, c_tot_8, Ga0_8, dt, nt, sym)\n",
+    "c0_9 = calc_sim(c0_9, c_tot_9, Ga0_9, dt, nt, sym)"
    ]
   },
   {
@@ -270,6 +271,32 @@
     "plt.ylim(0, 1.1)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Comparison with Matlab"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ML_9 = np.genfromtxt('Matlab_workspaces/ML_9_1.csv', delimiter=',')\n",
+    "ML_1 = np.genfromtxt('Matlab_workspaces/ML_1_9.csv', delimiter=',')\n",
+    "plt.plot(ML_9[0, :], ML_9[-1, :])\n",
+    "plt.plot(x, eval_func(c0_9, x))\n",
+    "plt.xlim(0, 0.5)\n",
+    "# plt.show()\n",
+    "\n",
+    "plt.plot(ML_1[0, :], ML_1[-1, :])\n",
+    "plt.plot(x, eval_func(c0_1, x))\n",
+    "plt.xlim(0, 0.5)\n",
+    "plt.show()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

prob_laplace.m

@@ -2,7 +2,24 @@
 % Define parameters for tanh, according to Weber, Zwicker, Julicher, Lee.
 b = @(chi, nu) nu^(1/3)*sqrt(chi/(chi-2));
 e = @(chi) sqrt(3/8*(chi-2));
-t = [0, 0.0001, 0.02, 0.05, 0.1, 1, 50];
+% t = [0, 0.0001, 0.02, 0.05, 0.1, 1, 50];
+t = linspace(0.0, 0.01, 11);
+% t=0.01;
+% t = logspace(-4, -2, 20);
+%% Comparison with Python
+T1 = Ternary_model(0, 'FRAP', {-0.1, b(7/3, 10^-12), 0.5, 0.4,...
+                                     0, 1, 300, 7, 0, 'Constituent'},...
+                                     t, 1);
+T1.solve_tern_frap();
+csvwrite('ML_9_1.csv', [T1.x; T1.sol]);
+
+
+T2 = Ternary_model(0, 'FRAP', {-0.1, b(7/3, 10^-12), 0.9, 0,...
+                                     -0.895, 1, 300, 7, 0, 'Constituent'},...
+                                     t, 1);
+T2.x = T1.x;
+T2.solve_tern_frap();
+csvwrite('ML_1_9.csv', [T2.x; T2.sol]);
 %% Try out different precisions
 % prec = [0.5, 0.5, 1, 2, 3.5, 5];
 fac = [1, 5, 10];%, 10, 100];