Hi,
First of all: I’m not sure if I should post this to the Avogadro or the
OpenBabel mailing lists. Perhaps both. Anyway, if I’m wrong here, just
point me to the right direction.
I’m doing ab initio DFT calculations with the Turbomole quantum
chemistry package [1] and am interested in using Avogadro to visualize
molecular geometry and orbitals - and then export to povray, for
example. The geometry files Turbomole uses are already supported by
Avogadro/OpenBabel and so I’ve no problems importing them and displaying
the geometry itself. [2]
However, Turbomole also possesses the ability to calculate orbitals on a
grid that then allow visualization. Current versions of Turbomole save
that data in the gOpenMol binary PLT file format. The format is very
simple and described in the gOpenMol documentation [3]. Since it is so
simple, I decided I could try to implement that myself. But while trying
to do so, I realized that either my understanding of the basic concepts
behind OpenBabel/Avogadro is severely lacking or both currently don’t
have the necessary infrastructure to use a workflow compatible with the
output of Turbomole.
Let me explain in details: In order to do ab initio calculations, you
provide Turbomole with a geometry file which contains the positions of
the atoms (you can also use Turbomole to relax the geometry but that’s
irrelevant for this discussion). Using DFT Turbomole then calculates
(iteratively) the orbitals which describe the electronic structure of
that molecule. After the DFT cycle you can have Turbomole calculate the
values of those orbitals on a grid. The orbitals are then saved in files
called .plt, i.e. 312.plt for the orbital #312 and so on
and so forth for every orbital you wanted to calculate.
This plt file contains only the orbital data on the grid, it does
not contain any information on atomar geometry. The geometry is only
available in the coordinate file you supplied Turbomole with - not
anywhere else. Programs that can import these orbitals (I know of
gOpenMol and VMD, there are probably others) provide the following
workflow: First one imports the geometry data and then one starts to add
the orbitals to the current state of the molecule by importing the PLT
files one by one.
Now, as far as I’ve understood it, Avogadro and/or OpenBabel can only
deal with files that contain all data at once or at least contain
pointers to other files, so you only select one file to import. Am I
correct in this or did I simply miss something?
If I missed something, please point me in the right direction.
If I’m correct with my assessment, how would you want to implement this?
The simplest thing for now would probably be some kind of "summary file"
which points to the coordinate files and the orbitals one wants to plot
that causes OpenBabel/Avogadro to read those files all-in-one. This is
however not very user-friendly and I’d prefer some solution similar to
the one other software that can import this already has.
Anyway, if it’s not extremely complicated I’d be willing to implement
support for this in Avogadro/OpenBabel once I know which way would be
best to do so.
[1] http://turbomole.de/
[2] Oh, by the way, unrelated to this issue, a minor annoyance: In the
import dialog there’s a checkbox “Coordinates are in Angstrom” or
similar which is checked by defaults. However, Turbomole coord files are
always in Bohr so the checkbox doesn’t make sense and atomic positions
are incorrect if I forget to uncheck it.
[3] http://www.csc.fi/english/pages/g0penMol/tutorials/gopenmol.pdf
(Appendix 2)
Best regards and thanks in advance,
Christian
I’m including both messages below for