[cclib-devel] yet another adf bug

[Adam T. <a-t...@st...>]

So I think there's another ADF bug. In the dvb_sp.adfout file, the  
atom number in fonames doesn't agree with the atom number in  
atomcoords. As near as I can tell, this is because ADF reorders the  
atoms. This is seen near the GEOMETRY section. The next section is  
FRAGMENTS, and there's not an obvious 1 to 1 mapping between the  
fragment names (also element names) and atoms in the fragment.

As I recall, ADF is the only program that does fragment orbitals  
involving combinations of atomic orbitals. If this is the case, I  
propose we create a dictionary (say 'fragments') to store information  
about which fragment contains which atoms. The value of the  
dictionary is simply a tuple of atomic numbers and atomic coords. I  
propose a dictionary simply because it would make accessing the info  
for a specific fragment easier.

What do you think?

Adam