Making initial condition a parameter.

@Ternary_model/Ternary_model.m

@@ -7,6 +7,7 @@ classdef Ternary_model < handle
     properties
         pa = '/Users/hubatsch/ownCloud/Dropbox_Lars_Christoph/DropletFRAP/FRAP_paper/';
         g0
+        ic = 'FRAP'
         sol
         t
         x
@@ -20,8 +21,9 @@ classdef Ternary_model < handle
         o_g0 = 0.2;
     end
     methods
-        function T = Ternary_model(t, params)
+        function T = Ternary_model(ic, params, t)
             T.t = t;
+            T.ic = ic;
             if ~isempty(params)
                 T.a = params(1);
                 T.b = params(2);

@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
-fh_ic = @(x) flory_ic(x, T.a, T.u0);
+fh_ic = @(x) flory_ic(x, T.a, T.u0, T.ic);
 fh_bc = @(xl, ul, xr, ur, t) flory_bc(xl, ul, xr, ur, t, T.u0);
 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.o_g0);
@@ -23,27 +23,28 @@ f = g0*(1-pt)/pt*(pt*dudx-u*gra_a);
 s = 0;
 end
 
-function u = flory_ic(x, a, u0)
+function u = flory_ic(x, a, u0, ic)
+if strcmp(ic, 'FRAP')
     % FRAP initial condition
     if x < -a; u = 0.0; else; u = u0; end
-    % Peak outside initial condition
-%     if (x < -a+0.2) && (x > -a+0.1); u = 10; else; u = 0; end
-%     u = 0.3;
-%     u = phi_tot(x, -50, 1);
-%%
-%% Frank/Jonathan/Stefano solution to the transfer/rate problem via Laplace transform
-% x0 = 3;
-% D_m = 0.11;%g0(1)*(1-u0-e)/(u0+e); % to make equal to ternary FRAP
-% D_p = 0.342;%g0(end)*(1-u0)/u0;
-% ga = 1/9;
-% p_out = @(D_p, D_m, ga, x0, x, t) 1./(2*sqrt(D_p*pi*t))*...
-%             (exp(-(x+x0).^2./(4*D_p*t))*(ga*sqrt(D_p)-sqrt(D_m))./...
-%             (ga*sqrt(D_p)+sqrt(D_m))+exp(-(x-x0).^2./(4*D_p*t)));
-% if x > -a
-%     u = p_out(D_p, D_m, ga, x0, x, 3/100);
-% else
-%     u = 0;
-% end
+elseif strcmp(ic, 'Gauss')
+    % Frank/Jonathan/Stefano solution to the transfer/rate problem via 
+    % Laplace transform
+    x0 = 3;
+    D_m = 0.11;%g0(1)*(1-u0-e)/(u0+e); % to make equal to ternary FRAP
+    D_p = 0.342;%g0(end)*(1-u0)/u0;
+    ga = 1/9;
+    p_out = @(D_p, D_m, ga, x0, x, t) 1./(2*sqrt(D_p*pi*t))*...
+                (exp(-(x+x0).^2./(4*D_p*t))*(ga*sqrt(D_p)-sqrt(D_m))./...
+                (ga*sqrt(D_p)+sqrt(D_m))+exp(-(x-x0).^2./(4*D_p*t)));
+    if x > -a
+        u = p_out(D_p, D_m, ga, x0, x, 3/100);
+    else
+        u = 0;
+    end
+else
+    disp('Initial condition not supported');
+end
 end
 
 function [pl,ql,pr,qr] = flory_bc(xl, ul, xr, ur, t, u0)