additional clean up in the files

Author: mrodrig6

src/forward_solver/stress_store.mat src/forward_solver/d_stress_store.matsrc/forward_solver/stress_store.mat renamed to src/forward_solver/d_stress_store.mat

@@ -395,10 +395,6 @@
 end
 
 % Keller-Miksis equation
-% if linkv==1 || neoHook==1 || Yeoh==1
-% JdotA = 4/Re8;
-% elseif sls==1 || nhzen==1 || fdkv==1 || zzzen==1 || fdmax==1  % ZZ - Not exactly true for FDKV, but I also don't think this matters ...
-    % JdotA = 0;
 % elseif nhkv_pld==1
 %     %JdotA = 4/Re8*(2^alpha_g+1)/3*(abs(Rdot)/R)^(alpha_g-1);
 %     JdotA = 4/Re8/3*(2^alpha_g+1)*sign(Rdot)*(abs(Rdot)/R)^(alpha_g)*R^2/Rdot^2;

src/forward_solver/f_call_params.m

@@ -474,8 +474,8 @@
     % integral precomputations
     Lstr = ['L' num2str(L,18)];
     Lstr = strrep(Lstr,'.','p');
-    if exist('stress_store.mat','file') ~= 0
-        load('stress_store.mat','store');
+    if exist('d_stress_store.mat','file') ~= 0
+        load('d_stress_store.mat','store');
         if isfield(store,Lstr) == 1
             if size(store.(Lstr),2) >= N, Nstart = 0;
             else

src/forward_solver/m_imr_spectral.m

@@ -7,7 +7,6 @@
 r_coord = ones(lR,lr_N).*logspace(-0.5,lr_length,lr_N);
 % calculating the shear
 varsigmadot_r = f_gammadot_r(r_coord,R,U,lR,lr_N);
-f_r = sf_carreau(v_nc,v_lambda,varsigmadot_r);
 [xcon,ycon] = meshgrid(t,r_coord(1,:));
 ycon = log10(ycon);
 clevels = 50;
@@ -16,7 +15,7 @@
 ntau_r = tau_r/max_tau_r;
 
 % f contour figure
-figure(5)
+figure(1)
 hold on;
 xlabel('$t / t_c$', 'Interpreter', 'Latex', 'FontSize', 20);
 ylabel('log$_{10}(\it{r}/R_o)$','Interpreter','Latex','FontSize',24);
@@ -39,32 +38,37 @@
 xa.LineWidth = 1.5;
 box on;
 plot(t, log10(R),lm,'LineWidth',3);
-contourf(xcon',ycon',f_r,clevels,'edgecolor','none')
+contourf(xcon',ycon',ntau_r,clevels,'edgecolor','none')
 saveas(gcf,'./figs/baseline/fcon_T','png')
 
-% shear stress contour figure
-figure(6)
-hold on;
-xlabel('$t / t_c$', 'Interpreter', 'Latex', 'FontSize', 20);
-ylabel('log$_{10}(\it{r}/R_o)$','Interpreter','Latex','FontSize',24);
-colormap jet;
-cbar = colorbar;
-cbar.Label.String = '$\tau_{rr}/\mathrm{max}(\tau_{rr})$';
-set(cbar,'TickLabelInterpreter','latex');
-pos = get(cbar,'Position');
-cbar.Label.Position = [1.5*pos(1) -1.2];
-cbar.Label.Rotation = 0;
-cbar.Label.Interpreter = 'latex';
-clim([-1 1])
-xlim([0 fig_tend]);
-xticks(tickrange)
-set(gcf,'color','w');
-set(gca,'FontName','Times','FontSize',20);
-set(gca,'TickLabelInterpreter','latex')
-xa = gca;
-xa.TickLength = [.015 .015];
-xa.LineWidth = 1.5;
-box on;
-plot(t, log10(R),lm,'LineWidth',3);
-contourf(xcon',ycon',ntau_r,clevels,'edgecolor','none');
-saveas(gcf,'./figs/baseline/taucon_T','png')
+% shear as a function of r (radial coordinate) calculation
+function sofr = f_gammadot_r(r,R,Rdot,N,M)
+    
+    sofr = zeros(N,M);
+    for i = 1:N
+        for j = 1:M
+            if r(i,j) >=  R(i,1)
+                sofr(i,j) = -2*Rdot(i,1)*(R(i,1)^2)/((r(i,j))^3);
+            else
+                sofr(i,j) = NaN;
+            end
+        end
+    end
+end
+
+function [feps_r] = f_f_filter(f_r,N,M)
+    eps = 0.01;
+    feps_r = zeros(size(f_r));
+    for i = 1:N
+        for j = 1:M
+            if f_r(i,j) > 1-eps
+                feps_r(i,j) = NaN;
+            elseif f_r(i,j) < eps
+                feps_r(i,j) = NaN;
+            else
+                feps_r(i,j) = f_r(i,j);
+            end
+        end
+    end
+    
+end