anchor.diff:  
   ! ROUGH DRAFT OF USING BONDS!
                   ! HEAD          TAIL1         TAIL2
  -            IF (Type1==2 .AND. Type2==3 .OR. Type2=4) THEN
  +            IF (Type1==2 .AND. Type2==3 .OR. Type2==4) THEN
                !A bond calculation required
  +!QUESTION: should Energy_bond be Global?? Or, We can specify it here
  +! DONG: The Bonds I still don't quite understand but Energy_bond, bond_Rcut 
  +! should be global and defined from the read in of the data file. We 
  +! probably don't need to reassign them to K-bond, etc as I did here. 
  +! This is a rough draft. 
                 K_bond = Energy_bond
                 Rcut_bond = bond_Rcut
                 Rcutsq_bond = Rcut_bond**2.0
                 IF (R_square .Lt. Rcutsq_bond) THEN
                   sqR_square = sqrt(R_square)
  -                Ff = -K_bond*(2.0-(Rcut_bond/sqR_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 
                   Press = Press + Ff
                   Fx(I) = Fx(I) + Ff*Dx
  
positive.code:          DO J = I + 1,Natom
   
  ! Calculate the distance between the two atoms
              Dx = Rxx(I) - Rxx(J)
              Dy = Ryy(I) - Ryy(J)
   
  ! Apply the periodic boundary conditions
              Dx = Dx - Box*nint(Dx/Box)
              Dy = Dy - Box*nint(Dy/Box)
   
              R_square = Dx*Dx + Dy*Dy  
  ! Determine the Lennard-Jones parameters dependent on the two atom types             
               Type1 = atom_type(I)   !Array list of atom type
               Type2 = atom_type(J)  
              
               ! Type 1 and 2 will be 1-4 integer of atom type
               Rcut = R_cut_matrix(Type1,Type2)
  
negative.code:       Subroutine Force(f,Upot) 
        Implicit None
   
  !     Calculate The Forces And Potential Energy
         
        Include 'globals.inc'
        Double Precision:: f(Maxatom), Upot
        Integer:: I,J,Type1, Type2
        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************
   
        DO I = 1,Natom
  