anchor.diff:        DO k = 1, MaxBonds
                 atom1 = BondList(1,k)
                 atom2   BondList(2,k)
  + 
  +              ! Calculate the distance between the two atoms
  +               Dx = Xx(atom1) - Xx(atom2)
  +               Dy = Yy(atom1) - Yy(atom2)
  + 
  +              ! Apply the periodic boundary conditions
  +               Dx = Dx - Box*nint(Dx/Box)
  +               Dy = Dy - Box*nint(Dy/Box)
  + 
  +
  +                R_square = Dx*Dx + Dy*Dy  
  +
                   sqR_square = sqrt(R_square)
                   Ff = -K_bond*(2.0-(Rcut_bond/sqR_square))
                   Upot = Upot + K_bond*((sqR_square - Rcut_bond)**2.0)  !The bond potential at Rcut = 0 
  
positive.code:        
        Include 'globals.inc'
        !Double Precision:: f(Maxatom), Upot
        Integer:: I,J,K,Type1, Type2,atom1,atom2
        Double Precision:: Dx, Dy, Ff, R_square, R_square_i, R_six_i, Rcut, Rcutsq,&
  			 sigma_square, K_bond, Rcut_bond,&
  			 Rcutsq_bond, eps, sigma, sqR_square    
  !**********Initialize the Forces, Potential Energy and Pressure to 0************
   
  
negative.code:              Type2 = AT(J)  
              
               ! Type 1 and 2 will be 1-4 integer of atom type
               Rcut = R_cut(Type1,Type2)
               Rcutsq = Rcut**2.0
               sigma = sigma_matrix(Type1,Type2)
               eps = epsilon_matrix(Type1,Type2)
  