Orbital and electrostatic potential plots

Hi,

is Avogadro not capable of plotting spin-unrestricted orbitals? At
least I don’t see an option for choosing alpha vs beta spin in the
surfaces window (when using a formatted checkpoint file as reference).

Furthermore, the electrostatic potential plot doesn’t work for me, the
program just crashes.

And when I try running avogadro under valgrind, it crashes even before
the program finishes its startup.

I’m running Avogadro 1.0.3.


Mr. Jussi Lehtola, M. Sc. Doctoral Student
jussi.lehtola@helsinki.fi Department of Physics
http://www.helsinki.fi/~jzlehtol University of Helsinki
Office phone: +358 9 191 50 632 Finland

Jussi Lehtola, FM Tohtorikoulutettava
jussi.lehtola@helsinki.fi Fysiikan laitos
http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto
Työpuhelin: (0)9 191 50 632

is Avogadro not capable of plotting spin-unrestricted orbitals? At
least I don’t see an option for choosing alpha vs beta spin in the
surfaces window (when using a formatted checkpoint file as reference).

No. I’m kicking myself for not pushing Marcus on this when he was still here at Pitt in 2008-2009. But Albert, a new staff member here, has been working on the GAMESS package with Mark Gordon’s group for the past few years and will be reworking the OpenQube components.

One key task is to allow multiple sets of orbitals. Beyond alpha/beta spins, one may wish to consider other orbitals in an output – natural orbitals, coupled-cluster, CASSCF results, etc.

There’s also currently no way to access the orbital eigenvalues or symmetry labels. We have pieces in Avogadro 1.1 (i.e., the development version), but it’s not a very clean design.

Furthermore, the electrostatic potential plot doesn’t work for me, the
program just crashes.

Works for me, but I’d be happy to look at a backtrace. If you run “ccmake .” in your build directory, you can change the CMAKE_BUILD_TYPE to Debug and get full debugging symbols (e.g., through gdb or your favorite debugger).

You should also consider trying the latest development code.

-Geoff

P.S. When will we see an Erkale input generator extension for Avogadro? :slight_smile:

On Thu, 22 Dec 2011 14:59:15 -0500
Geoff Hutchison geoff.hutchison@gmail.com wrote:

is Avogadro not capable of plotting spin-unrestricted orbitals? At
least I don’t see an option for choosing alpha vs beta spin in the
surfaces window (when using a formatted checkpoint file as
reference).

No. I’m kicking myself for not pushing Marcus on this when he was
still here at Pitt in 2008-2009. But Albert, a new staff member here,
has been working on the GAMESS package with Mark Gordon’s group for
the past few years and will be reworking the OpenQube components.

One key task is to allow multiple sets of orbitals. Beyond alpha/beta
spins, one may wish to consider other orbitals in an output –
natural orbitals, coupled-cluster, CASSCF results, etc.

Right. But in CC, CI and MCSCF you do have to run some algorithm to
construct natural orbitals one way or another, right?

There’s also currently no way to access the orbital eigenvalues or
symmetry labels. We have pieces in Avogadro 1.1 (i.e., the
development version), but it’s not a very clean design.

Furthermore, the electrostatic potential plot doesn’t work for me,
the program just crashes.

Works for me, but I’d be happy to look at a backtrace. If you run
"ccmake ." in your build directory, you can change the
CMAKE_BUILD_TYPE to Debug and get full debugging symbols (e.g.,
through gdb or your favorite debugger).

You should also consider trying the latest development code.

Okay, maybe I’ll have to have a look at it.

P.S. When will we see an Erkale input generator extension for
Avogadro? :slight_smile:

Are you hinting towards me? :smiley:

Basically the generator should have to consist of two parts: an xyz
file generator (which should already exist in Avogadro), and an input
file generator.

Making the generator should be pretty simple, since many exist already.
And since there’s no symmetry or forces implemented, it’s even simpler
xD

Anyway, I think I’ll leave this to someone who already knows Avogadro;
I’m pretty busy with ERKALE itself.


Mr. Jussi Lehtola, M. Sc. Doctoral Student
jussi.lehtola@helsinki.fi Department of Physics
http://www.helsinki.fi/~jzlehtol University of Helsinki
Office phone: +358 9 191 50 632 Finland

Jussi Lehtola, FM Tohtorikoulutettava
jussi.lehtola@helsinki.fi Fysiikan laitos
http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto
Työpuhelin: (0)9 191 50 632