From 0e8e30738de8e4fc09145d41b2c8faf3a2d481a5 Mon Sep 17 00:00:00 2001
From: mlxd <loriordan@gmail.com>
Date: Fri, 16 Dec 2016 16:49:11 +0900
Subject: [PATCH] Analysis files add

---
 matlab/psi6.m          | 14 ++++++++++++--
 matlab/voronoi_cells.m | 36 ------------------------------------
 2 files changed, 12 insertions(+), 38 deletions(-)
 delete mode 100644 matlab/voronoi_cells.m

diff --git a/matlab/psi6.m b/matlab/psi6.m
index 049b8a2e..683001b8 100644
--- a/matlab/psi6.m
+++ b/matlab/psi6.m
@@ -1,10 +1,20 @@
 function [psi6_pos,nn] = psi6(pos,X,Y,radius)
-    [nn,idx] = findNN(pos,X,Y,radius);
+%Calculate the orientational order parameter defined at point pos
+%between the points (X,Y)
+% pos:       Defines the location to calculate the orientational order
+% X,Y:       Vector of entire X,Y range of points
+% radius:    Radius over which to determine neighbouring points
+%Returns
+% psi6_pos:  The value of orientational order psi_6 at position pos
+% nn:        Number of nearest neighbours
+
+    [nn,idx] = findNN(pos,X,Y,radius); %find number of neighbours and indices of
+                                        %neighbours for X,Y
     psi6_pos = 0;
     
     if size(nn,1) > 0
         for ii=1:size(nn,1)
-            psi6_pos = psi6_pos + exp(6*1i*getAngle2(pos, [X(idx(ii)), Y(idx(ii))] ));
+            psi6_pos = psi6_pos + exp(6*1i*getAngle(pos, [X(idx(ii)), Y(idx(ii))] ));
         end
         psi6_pos = psi6_pos./length(nn);
     end
diff --git a/matlab/voronoi_cells.m b/matlab/voronoi_cells.m
deleted file mode 100644
index 495a9a0f..00000000
--- a/matlab/voronoi_cells.m
+++ /dev/null
@@ -1,36 +0,0 @@
-function [area,avg_area,num_edges,var]=voronoi_cells(x,y,q,dx)
-[v,c]=voronoin([x y]);
-area=zeros(length(c),1);
-num_edges=zeros(length(c),1);
-avg_area = 0;
-clf;
-for jj = 1:length(c)
-    if (all(c{jj}~=1) && all(sqrt((x(jj)).^2 + (y(jj)).^2)<230*dx)); % If at least one of the indices is 1,
-        % then it is an open region and we can't
-        % patch that.
-        area(jj)=polyarea(v(c{jj},1),v(c{jj},2));
-        avg_area = avg_area + area(jj);
-        h = patch(v(c{jj},1),v(c{jj},2),area(jj)); % use area as color
-        if q(jj)< 0
-            h.EdgeColor = 'red';
-            h.LineWidth = '2';
-        elseif q(jj) == 0
-            h.EdgeColor = 'black';
-            h.LineStyle = '-'
-        else
-            h.EdgeColor = 'white';
-            h.LineStyle = '-'
-        end
-        num_edges(jj) = length(c{jj});
-        get(h); 
-    end
-end
-%axis square;axis([200 800 200 800]*dx);caxis([740 860]*dx*dx);;colorbar;
-hold on; plot(x,y,'r*');plot(x,y,'bo');
-set(gca,'FontName','Latin Modern Roman','FontSize',22);
-set(gca,'TickLabelInterpreter', 'latex');axis off;
-drawnow;
-
-avg_area=avg_area./nnz(area);
-var = sum((area(area>1) - avg_area).^2);
-var = var./nnz(area);
\ No newline at end of file