In the ADF QM/MM input, each atom in the full system must be designated as a QM, MM or LI atom, where LI refers to link. Figure 1-1c shows these designations for the example system. Although two atoms are involved in a LINK bond, we only designate the atom in the MM region as the LI atom. We do so because this atom corresponds to a capping atom in the QM model system. In systems where there are no covalent bonds that cross the QM/MM boundary, there will be no LI atoms.
