/* 
 * This program is free software; you can redistribute it and/or modify 
 * it under the terms of the GNU General Public License as published by 
 * the Free Software Foundation; either version 2 of the License, or 
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY 
 * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License 
 * for more details.
 * 
 * You should have received a copy of the GNU General Public License along 
 * with this program; if not, write to the Free Software Foundation, Inc., 
 * 59
 */

#include <iostream>
#include <fstream>
#include <math.h>
#include "LuxHeader.h"

using namespace std;

int main() {

// Initilaizes dy array which stores values for change in concentration of each chemical, each increment.
double dy[var];                  
for (int i= 0; i < var; i++) {
            dy[i] = 0.0;
            }

// Creates data file to export data results to.
ofstream datfile;
datfile.open ("LuxRData21.dat");

// Initializes initial values for all chemicals.
double y [var + 2] = {0.0, // HSLout
                      0.0, // HSLin
                      0.0, // HSL-LuxR
                      0.0, // LuxI mRNA
                      0.0, // LuxR mRNA
                      0.0, // GFP mRNA
                     10.0, // LuxI
                     10.0, // LuxR
                      0.0, // GFP        
                      0.0, //VolumeInside
                      0.0} // VolumeOutside

            // Main loop for cell growth.
            for (int j = 0; j < N; j++) {
            RungeKutta(y, dy); // Passes chemical current values to ODEsolver to find values for next increment.
            CellGrowth(y) ; // Passes y[] array to add more cells to y[9]
            datfile << "        " << y[1] << "        " << y[2] << "        " << y[3] << "        " << y[4] << "        " << y[5] << "        " << y[6] << "        " << y[7] << "        " << y[8] << "        " << y[9] << endl; //Print values to data file.
            }
            
            // Main loop for cell death.
            for (int j = 0; j < N; j++) {
            RungeKutta(y, dy);
            CellDeath(y) ;
            datfile << "        " << y[1] << "        " << y[2] << "        " << y[3] << "        " << y[4] << "        " << y[5] << "        " << y[6] << "        " << y[7] << "        " << y[8] << "        " << y[9] << endl;
            }

datfile.close();

return 0;

}