Hi all,
I’ve just been giving a comp chem lecture series here at UCC, and have
been demoing the Avogadro/GAMESS/MacMolPlt approach as shown by Jan
Jensen on his blog.
I’ve got a lot of possible feedback regarding Avogadro, but also some
suggestions…
It doesn’t seem to be possible to view the orbitals from a GAMESS
calculation within GAMESS. Is this correct? If so, is this a planned
feature, because it would make things a lot easier.
It would also be nice to have a simple viewer of the energy levels,
and some way to access the calculated energy of the molecule.
It doesn’t seem to be possible to view the orbitals from a GAMESS
calculation within GAMESS. Is this correct?
No, this is not yet possible. It is planned.
It would also be nice to have a simple viewer of the energy levels,
and some way to access the calculated energy of the molecule.
If you have a good suggestion for the calculated energy, please let me know – perhaps under Molecular Properties?
Energy levels is planned, but needs some work through Open Babel, which does not yet read or store the orbital energies.
Hope that helps,
-Geoff
On 27 April 2010 19:24, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:
It doesn’t seem to be possible to view the orbitals from a GAMESS
calculation within GAMESS. Is this correct?
No, this is not yet possible. It is planned.
It would also be nice to have a simple viewer of the energy levels,
and some way to access the calculated energy of the molecule.
If you have a good suggestion for the calculated energy, please let me know – perhaps under Molecular Properties?
It would be nice to have a generic “Molecular Properties” panel on the
side which could contain a variety of random things (in the manner of
OBPairData) such as SD file tags, molecule title, SMILES, InChI, IUPAC
name and so forth. This could be particularly useful when moving
through a large SD file or through geometry optimisation steps (could
show convergence criteria for example).
Energy levels is planned, but needs some work through Open Babel, which does not yet read or store the orbital energies.
Don’t worry about this - just stick the code into Avogadro, and I’ll
populate it from cclib 
Hope that helps,
-Geoff
On Thu, May 6, 2010 at 10:48 AM, Noel O’Boyle baoilleach@gmail.com wrote:
On 27 April 2010 19:24, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:
It doesn’t seem to be possible to view the orbitals from a GAMESS
calculation within GAMESS. Is this correct?
No, this is not yet possible. It is planned.
It would also be nice to have a simple viewer of the energy levels,
and some way to access the calculated energy of the molecule.
If you have a good suggestion for the calculated energy, please let me know – perhaps under Molecular Properties?
It would be nice to have a generic “Molecular Properties” panel on the
side which could contain a variety of random things (in the manner of
OBPairData) such as SD file tags, molecule title, SMILES, InChI, IUPAC
name and so forth. This could be particularly useful when moving
through a large SD file or through geometry optimisation steps (could
show convergence criteria for example).
The project tree could be used for this, it is a powerful but little
known feature. New properties can be added by adding delegates. See
avogadro/src/projectdelegates for examples. Adding a delegate to show
all OBPairData (or Qt properties) should be trivial. These delegates
can also have settings, set in the project tree editor (Settings >
Configure Avogadro… > Project Tree). This would allow for only
certain types of properties to be shown for example.
For performance reasons, the model starts with only labels and is
populated when the user expands a label (item). The examples show how
to do this.
It is also possible to create simple items and combine them. For
example, the Molecule delegate combines the Atom, Bond and Residue
delegates.
I hope this mail will make the project tree a more popular feature. I
think most people see it as a Molecule/Atom/Bond/Residue model only…
Cheers,
Tim
Energy levels is planned, but needs some work through Open Babel, which does not yet read or store the orbital energies.
Don’t worry about this - just stick the code into Avogadro, and I’ll
populate it from cclib
Hope that helps,
-Geoff
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