%%%% solve ODE model to get output time profile
% Modified version (by Peter Halling) of Hui's program 
% This version tries to omit calculation of sensitivities, and focus just
% on progress of state variables.
% Also calls ODE_ProchiralDiol.m

%clear all
clear variables %following help guidance
close all
clc 
format long

% Input values here may be changed

showplot = false;

S0 = 0.2; % M units
Keq = 15;  % Also M units
Evalue = 39;
% Next value here is with concn units, then first order const
% with s-1, then rest are dimensionless
KM = 0.01; % M units
k4 = 1000;
SCRrat = 5;
k24rat = 1;
k2rat = 1;
k4rat = 0.2; %km34rat = 1;
k34rat = 1;
k13Rrat = 1;
k13Srat = 1;

if k4 < 0
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);   % For test
S0=0.001
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);   % For test
S0=0.2
KM=10
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);   % For test
end

if k4 < 0

for prod = [0.005] % 0.01 0.02]% 0.05 0.1 0.2 0.5 1 2]
%for KM = [0.001 0.002 0.005 0.01 0.02 0.05 0.1 0.2 0.5 1 2 5 10]
    %k4rat = 10*KM;
    for SCRrat = [0.5] % 5 50]
        KM = prod/SCRrat;
        for k4rat = [5] %[0.05 5]
        dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
            k4rat, k34rat, k13Rrat, k13Srat, false);  
        end
    end
end
KM = 0.01
SCRrat = 5
end
    
if k4 < 0
    
for S0 = [0.02 0.05 0.1 0.2 0.5 1] 
    for KM = [0.001 0.002 0.005 0.01 0.02 0.05 0.1 0.2 0.5 1 2 5 10]
        dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
            k4rat, k34rat, k13Rrat, k13Srat, false);  
    end
end
S0 = 0.2
KM = 0.01
end

    
if k4 < 0 % never

for S0 = [0.05 0.1 0.2 0.4 1] 
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
end
S0 = 0.2
%end

for Keq = [1 2 4 7.5 15 30 100]
    k4rat = 3/Keq;
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
end
Keq = 15
k4rat = 0.2

end

if k4 < 0 % never
for Evalue = [9 19 39 100]
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
end
Evalue = 39
%end

%if k4 < 0
for KM = [0.001 0.005 0.01 0.02 0.1 0.2 0.4 1 10] 
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
end
KM = 0.01
%end

for k4 = [500 1000 2000]
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
end
k4 = 1000

for SCRrat = [1 2.5 5 10]
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
end
SCRrat = 5

for k24rat = [0.5 1 2]
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
end
k24rat = 1
for k2rat = [0.5 1 2]
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
end
k2rat = 1
for k4rat = [0.1 0.2 0.4 1]
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
end
k4rat = 0.2


%if k14rat < 0
for k34rat = [0.5 1 2]
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
end
k34rat = 1
%end
%if k34Srat < 0 % i.e. never
for k13Rrat = [0.5 1 2]
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
end
k13Rrat = 1
for k13Srat = [0.5 1 2]
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
end
k13Srat = 1

end

if k4<0
for Keq = [1 2 5 10 20]
    for S0 = [0.05 0.1 0.2 0.5 1 2]
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
    end
end
KMD = 0.001
KMS = 0.001
%end

k4=100000
SCRrat = 0.1
for KMS = [0.0005 0.001]
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
end

%end

for SCRrat = [0.5 1 2 5 10 20] %[0.1 0.2 0.5 1 2 5 10]
    for k4rat = [0.05 0.1 0.2 0.5 1 2 5] %[0.0005 0.001 0.002 0.005 0.01 0.02 0.05 0.1 0.2 0.5 1 2 5]
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
    end
end
SCRrat = 5
k4rat = 0.2

end

for KM = [0.2 0.1 0.05 0.02 0.01 0.005 0.002 0.001];
    for k4rat = [0.05 0.1 0.2 0.5 1 2 5] %[0.0005 0.001 0.002 0.005 0.01 0.02 0.05 0.1 0.2 0.5 1 2 5]
dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, k2rat, ...
        k4rat, k34rat, k13Rrat, k13Srat, false);  
    end
end
KM = 0.01
k4rat = 0.2


function dummy = DoOneRun (S0, Keq, Evalue, KM, k4, SCRrat, k24rat, ...
    k2rat, k4rat, k34rat, k13Rrat, k13Srat, showplot)

initrate = 0.005; %sets time scale, used to calculate EobySo


% Now calculate rate constants, at first all on dimensioned basis

k2R = k24rat*k4;
k2S = k2R/(k2rat*Evalue);

k3w = k4*k34rat;
km4 = k4rat*k4/Keq;
km3 = SCRrat*k34rat*k4/k4rat;

SCRf = 1/(KM*((1 + 1/Evalue)*(1/k3w + km3/(k3w*k4) + 1/k4) + 1/k2R + 1/(Evalue*k2S)));
SCSf = SCRf/Evalue;
SCRb = SCRf/SCRrat; 
SCSb = SCRb/Evalue;

km1R = k13Rrat*km3;
k1R = SCRf*(k2R + km1R)/k2R;
km2R = SCRb*(k2R + km1R)/km1R;

km1S = k13Srat*km3/Evalue;
k1S = SCSf*(k2S + km1S)/k2S;
km2S = SCSb*(k2S + km1S)/km1S;

term1 =(1+1/Evalue)*(k4+km3+k3w)/(k3w*k4);
term2 = 1/k2R + 1/(Evalue*k2S)+1/(SCRf*S0);

EobySo = initrate*(term1 + term2);

if EobySo > 0.01
    toobig = true;
    %error ('EobySo > 0.01')
else
    toobig = false;
end

% Remove dimensions
k1Rn = S0*k1R;
k1Sn = S0*k1S;
km2Rn = S0*km2R;
km2Sn = S0*km2S;
km4n = S0*km4;


Sn0 = 1; % By definition of non-dimensional basis
En0 = 1; % Same

% All other state variables start at 0

% Set up the values of state variables and simulation parameters
% initial condition of state variables
Xinit = [En0 0 0 0 0 Sn0 0 0 0]';
% nominal parameter values
k = [k1Rn k2R k1Sn k2S k3w k4 km1R km2Rn km1S km2Sn km3 km4n]';

% set up the simulation time and sampling interval
%tspan = 0:0.001:0.1; % start with transient
%tspan = 0:0.4:20; % initial rate period
%tspan = 0:20:1000; % further progress
tspan = 0:100:5000; % for slow reactions


if ~toobig

% With normalised non-dimensional values for all variables and parameters,
% probably similar AbsTol for all, so try keeping default 1e-6.
AbsTol_value = 1e-6;
options = odeset('AbsTol',AbsTol_value);
% Run the ODE simulation
%[t, x_s] = feval(@ode15s, @ODE_Prochiral, tspan, xs_init, options, k, EobySo); 
% This doesn't work any more when have extra parameter EobySo, but managed
% to avoid feval call completely after viewing ode15s help
%[t,y] = ode15s(@(t,y) odefcn(t,y,A,B), tspan, y0);  Example from help
[t, xout] = ode15s(@(t,x) ODE_ProchiralDiol(t,x,k,EobySo), tspan, Xinit, options);

% Help gives "[t,y] = ode15s(odefun,tspan,y0). Each row in the solution array
%y corresponds to a value returned in column vector t."
%disp(xout)
%Yes, xout has a column for each state variable, and a row for each time, so
x = transpose(xout);

% x has one row for each state variable, one col for each time
PRn = x(7,:);
PSn = x(8,:);
diff = PRn - PSn;
conversion = PRn + PSn;
ees = diff./conversion;

else % is toobig
    showplot = false;
    t = '*';
    conversion = 'EobySo too big';
    ees = 'EobySo too big';
end

% Prepare for output
names = ["S0", "Keq", "Eval", "KM", "k4", "SCRrat", ...
    "k24rat", "k2rat", "k4rat", "k34rat", "k13Rrat", "k13Srat"];
values = [S0, Keq, Evalue, KM, k4, SCRrat, k24rat, ...
    k2rat,  k4rat, k34rat, k13Rrat, k13Srat];

nonames = length(names);
if length(values) ~= nonames 
    error ('Different length names and values')
end



if showplot
    nolines = fix((nonames-1)/5) + 1;
    for lineno = 1:nolines
      firstctr = 5*(lineno-1) + 1;
      lastctr = 5*(lineno-1)+ 5;
      if lastctr > nonames
        lastctr = nonames;
      end
      lbl(lineno)="";
      for ctr = firstctr:lastctr
        lbl(lineno) = strcat(lbl(lineno), names(ctr), "=", num2str(values(ctr)), " ");
        %thislbl = strcat(lbl(lineno), names(ctr), "=", num2str(values(ctr)), " ")
      end
  end
 
    figure (1)
    %plot(t,x(1,:),'b--',t,x(2,:),'r-',t,x(3,:),'g-.',t,x(4,:),'m-',t,x(5,:),'c-.','LineWidth',2.5);
    %plot(t,x(6,:),'b--',t,x(7,:),'r-',t,x(8,:),'g-.',t,x(9,:),'m-',t,x(10,:),'c-.','LineWidth',2.5);
    plot(t,conversion,'b--',t,ees,'r-',t,x(1,:),'g-.','LineWidth',2.5);
    hold on;
    %plot(t(b),a,'g.','MarkerSize',24);
    %text(t(b),a+0.05,max_text);xlabel('\fontsize{16}time/s');

    % From help
    %dim = [.2 .5 .3 .3];
    %annotation('textbox',dim,'String',str,'FitBoxToText','on');
    % By trial and error, x and y run from origin in bottom left

    for ctr = 1:nolines
        dim = [0.15 0.67-0.07*ctr .3 .3];
        annotation('textbox',dim,'String',lbl(ctr), 'FitBoxToText', 'on');
    end

    ylabel('\fontsize{16}non-dimensional concentrations');
    %title('\fontsize{14}time profile of state variables');
    %legend('En','EDn','EtRn','EtSn','EQn');
    %legend('Dn','Qn','Sn','PRn','PSn');
    legend('Conv','ee_P','En');
end

% Output_progress

filename = 'C:\Users\ph\My Documents\A Edited\ProgressCurves.xlsx';
%rowno = int8(5)
startcol = 5;

firstdatacol = startcol + nonames + 2;
rowno = FindBlankRow(filename, 5, firstdatacol);

for ctr = 1:nonames
    writematrix(names(ctr), filename, 'Sheet', 1, 'Range', MakeCellRef(rowno, startcol+ctr-1));
    writematrix(values(ctr), filename, 'Sheet', 1, 'Range', MakeCellRef(rowno+ 1, startcol+ctr-1));
end

writematrix('time',filename, 'Sheet', 1, 'Range', MakeCellRef(rowno, firstdatacol));
writematrix('conv',filename, 'Sheet', 1, 'Range', MakeCellRef(rowno+1, firstdatacol));
writematrix('ee_P',filename, 'Sheet', 1, 'Range', MakeCellRef(rowno+2, firstdatacol));

%nextref = MakeCellRef(rowno,startcol+15);
nextref = MakeCellRef(rowno,firstdatacol+1);
writematrix(transpose(t),filename,'Sheet',1,'Range',nextref);
nextref = MakeCellRef(rowno+1, firstdatacol+1);
writematrix(conversion,filename,'Sheet',1,'Range',nextref);
nextref = MakeCellRef(rowno+2, firstdatacol+1);
writematrix(ees,filename,'Sheet',1,'Range',nextref);

dummy = 1; %to prevent warning

% Could look for ee's at various conversions here, but not at the moment

end


function rowno = FindBlankRow(filename, startrow, colno)
%rowno = startrow;
%foundit = false;
%while ~foundit
%    cellref = MakeCellRef(int8(rowno), int8(colno))
%    entry = readmatrix(filename, 'Sheet', 1, 'Range', strcat(cellref, ':', cellref))
    % Doesn't work, reads series of rows, then type mismatch on next
    % statement
%    if entry == ''
%        foundit = true
%    end
%    rowno = rowno + 1;
cellref = MakeCellRef(int8(startrow), int8(colno));
entries = readmatrix(filename, 'Sheet', 1, 'Range', strcat(cellref, ':', cellref));
norows = length(entries);
rowno = startrow + norows;
end

function cellref = MakeCellRef(rowno, colno)
firstletno = idivide(colno - 1, int8(26));
secondletno = mod(colno - 1, int8(26)) + 1;
if firstletno > 0 
    cellref = char(firstletno + 64); 
else
    cellref = '';
end
cellref = strcat(cellref,char(secondletno+64));
cellref = strcat(cellref,num2str(rowno));
end