I’ve just started using Avogadro to display molecular orbitals for
transition metal-containing radicals. It’s a very powerful and versatile
program.
I’m reading a Gaussian .fchk file and I’m puzzled by the MO display
results. First off, it lists MOs, but doesn’t allow me to select alpha
vs beta (this is an unrestricted calculation, so the alphas and betas
are different). Second, the MOs displayed don’t look right - they don’t
retain the symmetry of the molecule. Is it possible that Avogadro is
adding the alpha and beta orbitals? Let me know if you want .fchk files
or copies of the graphics.
Thanks,
Rick
Hi Ricardo,
Unfortunately, as far as I’m aware, Avogadro currently only has support displaying orbitals from restricted calculations.
At any rate, the code to parse the fchk files only looks for the alpha orbital coefficients.
Best wishes,
Jens
From: Ricardo Metz [rbmetz@chem.umass.edu]
Sent: 11 January 2011 04:33
To: avogadro-discuss@lists.sourceforge.net
Subject: [Avogadro-Discuss] MO’s for open-shell molecules
I’ve just started using Avogadro to display molecular orbitals for
transition metal-containing radicals. It’s a very powerful and versatile
program.
I’m reading a Gaussian .fchk file and I’m puzzled by the MO display
results. First off, it lists MOs, but doesn’t allow me to select alpha
vs beta (this is an unrestricted calculation, so the alphas and betas
are different). Second, the MOs displayed don’t look right - they don’t
retain the symmetry of the molecule. Is it possible that Avogadro is
adding the alpha and beta orbitals? Let me know if you want .fchk files
or copies of the graphics.
Thanks,
Rick
Gaining the trust of online customers is vital for the success of any company
that requires sensitive data to be transmitted over the Web. Learn how to
best implement a security strategy that keeps consumers’ information secure
and instills the confidence they need to proceed with transactions.
http://p.sf.net/sfu/oracle-sfdevnl
Scanned by iCritical.
Unfortunately, as far as I’m aware, Avogadro currently only has support displaying orbitals from restricted calculations.
As Jens mentioned, this is something we’re working to address. One workaround is to create a Gaussian “cube” file for any open-shell MOs, which will be read OK.
Marcus has currently refactored the MO and surface code into a new library and I believe is attempting to address this and a few related issues.
-Geoff
On Jan 13, 2011, at 12:45 PM, Geoffrey Hutchison wrote:
Unfortunately, as far as I’m aware, Avogadro currently only has support displaying orbitals from restricted calculations.
As Jens mentioned, this is something we’re working to address. One workaround is to create a Gaussian “cube” file for any open-shell MOs, which will be read OK.
Marcus has currently refactored the MO and surface code into a new library and I believe is attempting to address this and a few related issues.
Yes, part of the goal of refactoring our quantum calculation code was to allow it to be shared by more projects, improve our feature set and ideally gain some additional contributors. This is certainly one of the things I am hoping to address, along with higher order GTOs and unit testing to assure correctness of calculated values.
As Geoff said, for now you could certainly calculate cube values.
Marcus