Re: [cclib-devel] yet another adf bug

[Noel O'B. <bao...@gm...>]

Remember that a dictionary doesn't have an explicit ordering, so if
you need ordering a list of fragments is better than a dictionary of
fragments. Apart from that, it sounds fine. 'frags' sounds good also,
although it does remind me of Quake.

I wonder though whether, in the end, reading the equivalent of a
checkpoint file would be a more sensible solution. There is a limit to
how complicated the output file can be while still being parsable.
Since you are likely to be doing the coding, you may want to think
about this long and hard, but it's up to you.

Noel

On 28/11/06, Adam Tenderholt <a-t...@st...> wrote:
> 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
>
>
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