Re: [cclib-devel] nmo proposal

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

On 31/10/06, Adam Tenderholt <a-t...@st...> wrote:
> >> Some quantum chemistry programs (eg. Jaguar) don't always have the
> >> same number of alpha orbitals as beta orbitals. Therefore, I propose
> >> that we change nmo from an integer to a list of integers like
> >> mocoeffs currently is. This would also mean in these cases, mocoeffs
> >> should have dimension (1 or 2, nbasis, nbasis) as nmo should always
> >> be less than or equal to nbasis. Comments?
> >
> > Sounds good, except that mocoeffs is *not* currently a list of
> > integers. It's a rank 3 array.
>
> Right. Which is why the size of the mocoeffs array should have
> dimension (1 or 2, nbasis, nbasis). Anything not assigned would be
> zero, and it's up to the user of cclib to decide what elements are
> valid based on nmo and nbasis (and spin). I think it's a safe
> assumption that the orbitals we know about run from zero to nmo (even
> in the one ADF case, I think mocoeffs was correct).
>
> > So, how many attributes will we need to change?:
> > (1) nmo
>
> Change this to a list. In most cases we've seen, nmo[0] == nmo[1] but
> we're making this change to address the case when nmo[0] != nmo[1].

> > (2) mocoeffs
>
> See above.
>
> > (3) moenergies
>
> This should probably be a rank two array with size (1 or 2, nbasis)
> with unassigned elements 99999 like we did with the one ADF file.
>
> > (4) mosyms (maybe, it's fine as it is though)
>
> My guess is for most cases this is fine, although we may want to
> consider size (1 or 2, nbasis) and unassigned elements get A symmetry.
>
> > So we need to...
> > (1) update the wiki
> > (2) update the unit tests/regression tests
> > (3) add any extra tests we need to make sure we're obeying the wiki
> > (4) change the code (let's just work off the HEAD revision).
>
> Sounds good.
>
> > And the best part is that I'll even do some of this myself, as I'll
> > start to have a bit more free time after next Monday (yippee!).

OK - thanks for explaining this in depth - I actually had the wrong
idea. I thought we were going to split everything into two separate
arrays for alpha and beta, e.g. moenergies[0] and moenergies[1] which
would be of lengths nmo[0] and nmo[1] respectively (and similarly for
mocoeffs, mosyms and so on).

I'm happy to make the changes you suggest; I'll start by making some
changes to the wiki which you might doublecheck. I'll put the new
information on the attribute pages under a subheading like
"Development version" or "cclib 0.7" or something, to avoid confusing
users.

BTW, I've merged the zip branch to the HEAD and compressed the
regression files on the web server. See r402.

Regards,
   Noel