FRAP plot works.

@Ternary_model/create_mesh.m

@@ -3,33 +3,33 @@ function create_mesh(T)
 %   Mesh density larger for steeper gradients.
 
 % Start with left side of mesh, at r=0/x=0, with a given step size
-% x = [0, 0.01/T.precision/10];%/10
-% % x = linspace(0, 0.75, 40);
-% % x = [x, x(end)+0.01/T.precision/10];%/10
-% % while x(end)<-T.a
-% %     x_temp = x(end)-x(end-1);
-% %     phi_nm1 = T.phi_tot(x(end), T.a, T.b, T.e, T.u0, 0);
-% %     phi_n = T.phi_tot(x(end)+x_temp, T.a, T.b, T.e, T.u0, 0);
-% %     while phi_nm1-phi_n > 0.002/T.precision
-% %         x_temp = x_temp/2;
-% %         phi_n = T.phi_tot(x(end)+x_temp, T.a, T.b, T.e, T.u0, 0);
-% %     end
-% %     x = [x, x(end)+x_temp];
-% % end
-% % x = [x, x(end)+cumsum(fliplr(diff(x)))];
-% % x_middle = linspace(-2*T.a+x(end)-x(end-1), -10*T.a, 100*T.precision);
-% % x_right = linspace(-10*T.a+0.1, T.system_size, 100*T.precision);
-% % T.x = [x, x_middle, x_right];
-% % T.x = T.x(1:find(T.x-T.system_size>=0, 1)-1);
-% % 
-% % % Fine mesh close to x0 if ic = 'Gauss'
-% % [~, ind] = min(abs(T.x-T.x0));
-% % if T.x(ind+20)-T.x(ind) > 0.1
-% %     T.x = [T.x(1:ind-21), linspace(T.x(ind-20), T.x(ind+20),...
-% %                                    ceil((T.x(ind+20)-T.x(ind-20))*200)),...
-% %            T.x(ind+21:end)];
-% % end
+x = [0, 0.01/T.precision/10];%/10
+x = linspace(0, 0.75, 40);
+x = [x, x(end)+0.01/T.precision/10];%/10
+while x(end)<-T.a
+    x_temp = x(end)-x(end-1);
+    phi_nm1 = T.phi_tot(x(end), T.a, T.b, T.e, T.u0, 0);
+    phi_n = T.phi_tot(x(end)+x_temp, T.a, T.b, T.e, T.u0, 0);
+    while phi_nm1-phi_n > 0.002/T.precision
+        x_temp = x_temp/2;
+        phi_n = T.phi_tot(x(end)+x_temp, T.a, T.b, T.e, T.u0, 0);
+    end
+    x = [x, x(end)+x_temp];
+end
+x = [x, x(end)+cumsum(fliplr(diff(x)))];
+x_middle = linspace(-2*T.a+x(end)-x(end-1), -10*T.a, 100*T.precision);
+x_right = linspace(-10*T.a+0.1, T.system_size, 100*T.precision);
+T.x = [x, x_middle, x_right];
+T.x = T.x(1:find(T.x-T.system_size>=0, 1)-1);
+
+% Fine mesh close to x0 if ic = 'Gauss'
+[~, ind] = min(abs(T.x-T.x0));
+if T.x(ind+20)-T.x(ind) > 0.1
+    T.x = [T.x(1:ind-21), linspace(T.x(ind-20), T.x(ind+20),...
+                                   ceil((T.x(ind+20)-T.x(ind-20))*200)),...
+           T.x(ind+21:end)];
+end
 % T.x = [linspace(3, 5., 500), linspace(5.05, 6.05, 3000),...
 %        linspace(6.06, 7.1, 500), linspace(7.15, 20, 3000)];
-T.x = linspace(0, 20, 8000);
+% T.x = linspace(0, 20, 8000);
 end

@Ternary_model/plot_sim.m

@@ -11,8 +11,8 @@ if strcmp(mode, 'mov')
     figure(20); hold on;
     for i = 1:nth:length(T.t)
         cla; xlim([-T.a-1, -T.a+3]); 
-        xlim([0, 20]);
-        ylim([0, 5.2]);
+        xlim([0, 10]);
+        ylim([0, 0.4]);
         ax = gca;
         ax.FontSize = 12;
         xlabel('position'); ylabel('probability [not normalized]');
@@ -21,7 +21,7 @@ if strcmp(mode, 'mov')
         plot(T.x, T.sol(i, :), 'LineWidth', 2);
         text(abs(-T.a+2), 0.7, num2str(T.t(i)));
         shg
-%         pause();
+        pause();
 %         print([num2str(i),'.png'],'-dpng')
     end
 elseif strcmp(mode, 'plot')

@Ternary_model/solve_tern_frap.m

@@ -17,12 +17,12 @@ function [c, f ,s] = flory_hugg_pde(x, t, u, dudx, a, b, e, u0,...
 
 pt = Ternary_model.phi_tot(x, a, b, e, u0, v*t);
 gra_a = Ternary_model.gradient_analytical(x, a, b, e, v*t);
-% g0 = Ternary_model.gamma0(x, a+t*v, b, e_g0, u_g0, v*t);
-g0 = 0.5;
+g0 = Ternary_model.gamma0(x, a+t*v, b, e_g0, u_g0, v*t);
+% g0 = 0.5;
 c = 1;
-% f = g0*(1-pt)/pt*(pt*dudx-u*gra_a);
-chi_phi = -4.530864768482371;
-f = g0*(dudx+chi_phi*u*gra_a);
+f = g0*(1-pt)/pt*(pt*dudx-u*gra_a);
+% chi_phi = -4.530864768482371;
+% f = g0*(dudx+chi_phi*u*gra_a);
 s = 0;
 end
 

prob_laplace.m

@@ -46,17 +46,16 @@ t = linspace(0, 10, 300);
 tic
 T_mov = Ternary_model(0, 'Uniform', [-10, b(7/3, 10^-6), 0.5, e(7/3),...
                    0, 1, 10, 7, 0.5], t, 0.02);
-T_mov.solve_tern_frap()
+T_mov.solve_tern_frap();
 toc
 %%
 csvwrite('MovingBound.csv', [T_mov.x', T_mov.sol(1, :)', T_mov.sol(end, :)'])
-%% FRAP client
-t = linspace(0, 15, 300);
-tic
-T_mov = Ternary_model(0, 'FRAP', [-10, b(7/3, 10^-6), 0.5, e(7/3),...
-                   0, 1, 10, 7, 0.5], t, 0.02);
-T_mov.solve_tern_frap()
-toc
+%% FRAP jump length
+t = linspace(0, 5, 300);
+T_mov = Ternary_model(0, 'FRAP', [-5, b(7/3, 10^-6), 0.5, e(7/3),...
+                   0, 1, 10, 7, 0], t, 0.02);
+T_mov.solve_tern_frap();
+csvwrite('FRAP.csv', [T_mov.x', T_mov.sol(1, :)', T_mov.sol(end, :)'])
 %% Plot with full ternary model
 T_temp = T_mov;
 D_m = 1*(1-T_temp.u0-T_temp.e); % to make equal to ternary FRAP