Hi all.
Still back with the same problem. Sorry!
In Avogadro-1.1 trunk, using OB-2.3.0, I noticed that
"Conformer properties…" has duplicate entries. This
is due to gaussian files containing many kinds of
cartesian coordinates, depending in part on the route
card, but also on the program’s mood in some cases,
where one will find only “Z-Matrix orientation:” in a
file with nothing special in the route card.
Also, selecting the type of coordinates to extract from
a file has impact on orbitals rendering: it must be the
same type has those appearing in the .chk file, or
display will be incorrect: e.g. if both Input and
Standard orientation appear, only the latter will be
included in the .chk file.
So, I have been trying to find a more or less foolproof
way of doing this, since I was not too satisfied with my
previous attempt.
The attached OB-2.3.0 gaussformat.cpp patch seems
to correct a few things, insofar as I can see from my
limited tests. One’s imagination always has limits and
more extensive tests certainly have to be conducted
before this or a better modification can be adopted
in OB.
Hope this can help,
Regards,
Louis
Hi Louis,
same type has those appearing in the .chk file, or
display will be incorrect: e.g. if both Input and
Standard orientation appear, only the latter will be
included in the .chk file.
Your patch is definitely a good idea – as you mention, Gaussian seems to have different “moods” about the coordinates it writes.
Here’s my thought… We actually read in the coordinates of the .chk file, since it’s needed to define the atomic centers for AOs and MOs. Couldn’t we compute the rotation matrix between the existing coordinates and rotate all conformers?
I think Noel has code which does alignment, so we’d re-use this to align the .chk coords.
Sound like a working strategy?
-Geoff
Hi Geoff.
Yes indeed. I had also considered this option.
A third alternative would be to clear the molecule
pane and redisplay using the fchk file coordinates,
like in Molden.
Which ever solution is simplest to implement and
the most reliable.
And nice to learn about growing interest in Avogadro!
Louis
On 21.11.2010 23:01, Geoffrey Hutchison wrote:
Here’s my thought… We actually read in the coordinates of the .chk file, since it’s needed to define the atomic centers for AOs and MOs. Couldn’t we compute the rotation matrix between the existing coordinates and rotate all conformers?
I think Noel has code which does alignment, so we’d re-use this to align the .chk coords.
Sound like a working strategy?
-Geoff