The problem is here:
Rcore = rand(size(Xh))*range(bounds)+bounds(1);
R1core = rand(size(Xl))*range(bounds)+bounds(1);
Those are random matrices of size 6-by-the number of (red/blue) hexagons. This gives each hexagon a (potentially) different radius for each vertex. To have a different radius for each hexagon but the same radius for each vertex in a given hexagon, do this:
Rcore = rand(1,size(Xh,2))*range(bounds)+bounds(1);
R1core = rand(1,size(Xl,2))*range(bounds)+bounds(1);
Then each of those variables is a row vector with one value per hexagon. Then when you use them, just refer to the one element at a time, rather than a column.
%Hexagon radii
r_rod = 9*2/3;
%Wavelength
lambda = 1.550;
% grid size
N_grid = 100;
N_rod=fix(N_grid/r_rod);
highratio = 1/2;
bounds = [1, r_rod]; %possible radii size for the red and blue hexagons
m = N_rod+1; % horizontal count
n = fix(N_rod*2/sqrt(3))+2; % vertical count
rng('shuffle')
highs = rand(m, n) > highratio; %random assignment of white and black color
hexcount = sum(highs(:));
whitecount = m * n - hexcount;
% parametric definition of a hexagon
t = (1/12:1/6:1)' * 2 * pi;
x = cos(t);
y = sin(t);
% coordinates of all black hexagons
Xh = zeros(6, hexcount);
Yh = zeros(6, hexcount);
Xhcore = zeros(6, hexcount);
Yhcore = zeros(6, hexcount);
% coordinates of all white hexagons
Xl = zeros(6, whitecount);
Yl = zeros(6, whitecount);
Xlcore = zeros(6, whitecount);
Ylcore = zeros(6, whitecount);
d=sqrt(3)/2;
hcount = 0;
lcount = 0;
% Rcore = rand(size(Xh))*range(bounds)+bounds(1);
% R1core = rand(size(Xl))*range(bounds)+bounds(1);
Rcore = rand(1,size(Xh,2))*range(bounds)+bounds(1);
R1core = rand(1,size(Xl,2))*range(bounds)+bounds(1);
for ii = 1:m
for jj = 1:n
if highs(ii, jj)
hcount = hcount + 1;
Xh(:, hcount) = x + d * (mod(2 * ii + jj, 2 * m));
Yh(:, hcount) = y + 1.5 * jj;
% Xhcore(:, hcount) = Xh(:, hcount)-Rcore(:, hcount).*x/5; %Problem with this line
% Yhcore(:, hcount) = Yh(:, hcount)-Rcore(:, hcount).*y/5; %Problem with this line
Xhcore(:, hcount) = Xh(:, hcount)-Rcore(hcount).*x/5;
Yhcore(:, hcount) = Yh(:, hcount)-Rcore(hcount).*y/5;
else
lcount = lcount + 1;
Xl(:, lcount) = x + d * (mod(2 * ii + jj, 2 * m));
Yl(:, lcount) = y + 1.5 * jj;
% Xlcore(:, lcount) = Xl(:, lcount)-R1core(:, lcount).*x/5; %Problem with this line
% Ylcore(:, lcount) = Yl(:, lcount)-R1core(:, lcount).*y/5; %Problem with this line
Xlcore(:, lcount) = Xl(:, lcount)-R1core(lcount).*x/5;
Ylcore(:, lcount) = Yl(:, lcount)-R1core(lcount).*y/5;
end
end
end
%figure; hold on
fig_i= figure();
fig_i.Visible='on';
fig_i.Position=[1,500,500,500];
fig_i.PaperUnits='inches';
fig_i.PaperPositionMode='manual';
fig_i.PaperPosition=[0,0,N_grid/150,N_grid/150];
axes_i=axes();
axes_i.Position =[0,0,1,1];
axes_i.Units='inches';
patch(Xh, Yh, 'black', 'EdgeColor', 'None');
patch(Xl, Yl, [0.9999,0.9999,0.9999], 'EdgeColor', 'None');
patch(Xhcore, Yhcore, 'red', 'EdgeColor', 'None');
patch(Xlcore, Ylcore, 'blue', 'EdgeColor', 'None');
axis equal;
xlim([0,N_rod*sqrt(3)]);
ylim([1.5,N_rod*sqrt(3)+1.5]);
axis off;
