# CHI298.OAI:  GDOC input file for performing the chi-squares 
# fit of a nonlinear system of differential equations to data.
# Requires the data file CHI298.INP
#
# Written by Adam Singer.
# Modified 2005-05-15 by James W. Taylor.

DECLARATION
# x(1) = C_{c-C6H7}, x(2) = C_{(CH3)3CO}, x(3) = C_{1,4-C6H8}, 
# x(4) = C_{p-C6H7OO}, x(5) = C_{o-C6H7OO}
  state: x(1:5)
# p(1) = k2, p(2) = k3, p(3) = k4
  parameter: p(1:3)
  time: [0, 4.46]
# q(1) = k1, q(2) = k5, q(3) = C_{O_2}, q(4) = K1, q(5) = K2  
  constant: q(1:5)
  data: xdata(1:2)
END
# this is scaled
PARAMETER VALUES
  p(1)= 340.548 : [10.0, 1200.0]
  p(2)= 1118.710 : [10.0, 1200.0]
  p(3)= 1.403 : [0.001, 40.0]
END

# this is not scaled
EQUATION
  $x(1) = q(1)*x(2)*x(3) - q(3)*(p(1)+p(2))*x(1) + p(1)/q(4)*x(4)
        + p(2)/q(5)*x(5) - q(2)*x(1)^2; 
  $x(2) = -q(1)*x(2)*x(3);
  $x(3) = -q(1)*x(2)*x(3);
  $x(4) = p(1)*x(1)*q(3) - p(1)/q(4)*x(4);
  $x(5) = p(2)*q(3)*x(1) - (p(3)+p(2)/q(5))*x(5);
END  

REFERENCE
  xRef(1) = xL(1);
  xRef(2) = xL(2);
  xRef(3) = xL(3);
  xRef(4) = xL(4);
  xRef(5) = xL(5);
  pRef(1) = pL(1);
  pRef(2) = pL(2);
  pRef(3) = pL(3);
END

INITIAL
  x(1)=0;
  x(2)=1.4E-4;
  x(3)=4.0E-1; 
  x(4)=0 ; 
  x(5)=0 ;
END

OBJECTIVE
  ((2100.0*x(1)+200.0*(x(4)+x(5))-xdata(1))/xdata(2))^2;
END

NATURAL BOUNDS
  x(1):[0,1.4E-4]
  x(2):[0,1.4E-4]
  x(3):[0,4.0E-1]
  x(4):[0,1.4E-4]
  x(5):[0,1.4E-4]
END

CONSTANT VALUES
  q(1) = 73;
  q(2) = 1750;
  q(3) = 0.0014;  
  # 46*exp(6500/T-18)    
  q(4) = 385; 
  # 2*q(4) 
  q(5) = 770;
END

PLOT
  2100.0*x(1)+200.0*(x(4)+x(5));
END