As previously discussed the area of a peak in the PDF will be dependent on the number and type of atoms at a given coordination distance. Consider the example show in Fig. 3.4. This is a primitive cubic lattice occupied by two types of atoms, A and B (shown by blue and red circles respectively).
In the random case the atoms are distributed across all sites. Therefore the the A-A, A-B and B-B partials are the same for all coordination shells, Fig. 3.4a. If, however, the system orders to form a rock salt type structure then certain correlations are removed. For example there are now no A-A and B-B nearest neighbours, as all nearest neighbour correlations are of the type A-B.
Therefore the partials pair correlation functions are different. This can be seen in Fig. 3.4b. The result is that the overall PDF, which is a sum of the partials weighted by the concentrations and scattering factors, are different. Whilst the peaks appear in the same place, the areas have changed due to the change in the occupation of the coordinating shells. This results in the plot shown in Fig. 3.4c