%T = ... 
%do the first period
    %for all t in the first period
    %for certain time, solve one system
    %transfer initial condition, solve other system
    %fill these into a larger array of zeros to store everything
    %zero the dummy functions
%for the second the the Nth period
    %do like before...
%if first time step use specific initial condtions
%else use  
clear
clc
tic


Period =      [86400	21600	10000	5000	2500	1000	480	  240	 120     40      10      4       3	   2     1     0.5    0.05];
N =           [4        4       4       8       10      20      40    100    200     1000    400     1000    2000  4000  30000  40000   80000 ];
DIVS_Master = [100      100     10      5       2.5     1       0.1   0.05   0.05    0.02    0.01    0.005   0.005 0.005 0.005 0.0025 0.00025];
Samples =      [3       3      3       3        5       5       5     5      5       10       10     10      10    10    10   10   10];
Y_cell = cell(17,7);
T_cell = cell(17,7);
%DUTY_CYCLE = [0.875 0.75 0.625 0.5 0.375 0.25 0.125];
DUTY_CYCLE = [ 0.25 ];
global k;
global K_CAL1
global K_CAL2
K_CAL1 = 2;
K_CAL2 = 10;
k = 0.04365;

for d=1
    d
for q = 1:16
    q
T = Period(q); %period
Nperiods = N(q); %Number of Periods
dc = DUTY_CYCLE(d); %duty cycle
divs = T/DIVS_Master(q); %number of division in a period
Y = zeros(divs*Nperiods,3); %solution array
time = zeros(divs*Nperiods,1); %time array
Light = zeros(divs*Nperiods,1);
dP_REL = zeros(divs*Nperiods,1);
init = [0.5 K_CAL1/(K_CAL1+1) K_CAL2/(K_CAL2+1)];
%opts = odeset('RelTol',1e-4,'AbsTol',1e-4);
%opts = odeset('RelTol',1e-5);

for j = 1:Nperiods
    if j > 1
        init(:) = Y((j-1)*divs,:);  %set initial value as previous value
    end
    for i = 1:2
        if i == 1;
            [time1,Amp1] = ode113(@CRM_TwoRegs_LIGHT_July24_4_RuBP,[0:T/divs:T*dc],[init(1,1) init(1,2) init(1,3)]);
        elseif i == 2;
            [time2,Amp2] = ode113(@CRM_TwoRegs_DARK_July24_4_RuBP,[T*dc:T/divs:T],[Amp1(dc*divs+1,1) Amp1(dc*divs+1,2)  Amp1(dc*divs+1,3)]);
        end
    end
    time(1+(j-1)*divs:(j-1)*divs+divs*dc+1,1) = time1+(j-1)*T;
    time(divs*dc+1+(j-1)*divs:j*divs+1,1) = time2+(j-1)*T;
    Y(1+(j-1)*divs:(j-1)*divs+divs*dc+1,:) = Amp1;
    Y(divs*dc+1+(j-1)*divs:j*divs+1,:) = Amp2;
    Light(1+(j-1)*divs:(j-1)*divs+divs*dc+1,1) = 1;
    Light(divs*dc+1+(j-1)*divs:j*divs+1,1) = 0;

end
a_star_cell = Y(:,1);
a_0_cell = 1-Y(:,1);
b_on_cell = Y(:,2);
b2_on_cell = Y(:,3);
dP_REL = Y(:,1)./(k + Y(:,1)); %P/Pm
dP_REL_pen = dP_REL.*Y(:,2).*Y(:,3);
dP_REL_cell = dP_REL;
dP_REL_cell_pen = dP_REL_pen;
T_cell = time;
muBAR(q,d) = 1.28*((K_CAL1+1)/K_CAL1)*((K_CAL2+1)/K_CAL2)*1.122*mean(dP_REL((Nperiods-2)*divs:Nperiods*divs,1));
muBAR_pen(q,d) = 1.28*((K_CAL1+1)/K_CAL1)*((K_CAL2+1)/K_CAL2)*1.122*mean(dP_REL_pen((Nperiods-2)*divs:Nperiods*divs,1));
S = Samples(q);

        saveable_dP_REL_cell_pen{q,d} = dP_REL_cell_pen((N(q)-S)*Period(q)/DIVS_Master(q):(N(q))*Period(q)/DIVS_Master(q),1);
        saveable_a_star_cell{q,d} = a_star_cell((N(q)-S)*Period(q)/DIVS_Master(q):(N(q))*Period(q)/DIVS_Master(q),1);
        saveable_a_0_cell{q,d} = a_0_cell((N(q)-S)*Period(q)/DIVS_Master(q):(N(q))*Period(q)/DIVS_Master(q),1);
        saveable_b_on_cell{q,d} = b_on_cell((N(q)-S)*Period(q)/DIVS_Master(q):(N(q))*Period(q)/DIVS_Master(q),1);
        saveable_b2_on_cell{q,d} = b2_on_cell((N(q)-S)*Period(q)/DIVS_Master(q):(N(q))*Period(q)/DIVS_Master(q),1);
        saveable_T_cell{q,d} = T_cell((N(q)-S)*Period(q)/DIVS_Master(q):(N(q))*Period(q)/DIVS_Master(q),1);
        

end
toc
end

%making the saveable stuff
save('CRM_TwoRegs_July24th_4_RuBP', 'muBAR_pen', 'DUTY_CYCLE', 'Period', 'saveable_dP_REL_cell_pen', 'saveable_a_star_cell', 'saveable_a_0_cell', 'saveable_b_on_cell', 'saveable_T_cell', 'saveable_b2_on_cell')