Adding plot for PKS retreat.

ternary_frap.m

@@ -23,7 +23,7 @@ x = [linspace(-a-1, g_inv(2), 30), g_inv(3:end-2), ...
     linspace(g_inv(end-1), -a+1, 30), linspace(-a+1.1, 300, 300)];
 %% Solve pde
 tic
-t = linspace(0.001, 0.5, 250);
+t = linspace(0, 50, 250);
 fh_ic = @(x) flory_ic(x, a, u0);
 fh_bc = @(xl, ul, xr, ur, t) flory_bc(xl, ul, xr, ur, t, u0);
 fh_pde = @(x, t, u, dudx) flory_hugg_pde(x, t, u, dudx, a, b, e, c, u0,...
@@ -38,8 +38,9 @@ for i = 1:length(t)
     ax.FontSize = 16;
     xlabel('position'); ylabel('volume fraction');
     plot(x, phi_tot(x, a, b, e, u0), 'LineWidth', 2, 'LineStyle', '--'); 
-    plot(x, sol(i, :), 'LineWidth', 2); pause();
-% %     print([num2str(i),'.png'],'-dpng')
+    plot(x, sol(i, :), 'LineWidth', 2);
+%     pause();
+    print([num2str(i),'.png'],'-dpng')
 end
 %% Figures
 % Time course
@@ -59,8 +60,24 @@ plot(x, phi_tot(x, a, b, e, u0));
 plot(x, gradient_analytical(x, a, b, e));
 plot(x(1:end-1)+mean(diff(x))/2, ...
      diff(phi_tot(x, a, b, e, u0)/mean(diff(x))));
-plot(x, gamma0(x, a, b, e));
-figure; plot(gamma0(x, a, b, e), spacing(gamma0(x, a, b, e), a, b, e));
+plot(x, gamma0(x, a, b, e_g0, o_g0));
+figure;
+plot(gamma0(x, a, b, e_g0, o_g0),...
+     spacing(gamma0(x, a, b, e_g0, o_g0), a, b, e_g0, o_g0));
+%% Fit with experimental BCs
+s = sol(1:end, 1:30)./max(sol(1:end, 1:30))/1.022;
+ts = t(1:end)';
+f_min = @(x) to_minimize(s, ts, x, 'simple_drop', s(:, end));
+opt = optimset('MaxFunEvals', 2000, 'PlotFcns',@optimplotfval);
+x_seed = fminsearch(f_min, x_seed, opt);
+%%
+[cost, v_fit, r_n, v_fit_end] = to_minimize(s, ts, x_seed, 'simple_drop', s(:, end));
+%% Plot for 
+figure; hold on;
+plot(s(1:2:100, :)', 'Color', [0.12156   0.4666666   0.7058823], 'LineWidth', 1.5);
+% plot(v_fit(1:2:100, :)', '--', 'Color', [1.   0.49803   0.0549], 'LineWidth', 1.5);
+make_graph_pretty('$x [\mu m]$', 'intensity [a.u.]', '');
+print('Timecourse_model_only.png','-dpng')
 %% Function definitions for pde solver
 function [c, f ,s] = flory_hugg_pde(x, t, u, dudx, a, b, e, c_p, u0,...
                                     e_g0, o_g0)