Avogadro on Ubuntu 11.1

Hi,
I am using Avogadro 1.0.3 with Ubuntu Linux 11.10. When I build a
molecule and click on the auto-optimization tool, the optimization does
not work and green lines shoot from the molecular structure in all
directions.
When I start Avogadro from Konsole, I get the warning:

QStackedLayout::setCurrentWidget: Widget 0x1984f10 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area

Is thid warning linked to my problem?
Does anyone know how I will sort this out?

Thanks,

Tim

I am using Avogadro 1.0.3 with Ubuntu Linux 11.10. When I build a
molecule and click on the auto-optimization tool, the optimization does
not work and green lines shoot from the molecular structure in all
directions.

Well, the green lines (forces) tell me that something’s working. So what do you mean by “optimization does not work?” Can you be more specific?

When I start Avogadro from Konsole, I get the warning:
QStackedLayout::setCurrentWidget: Widget 0x1984f10 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area

There’s no problem from that. If I could find the source of these messages, we’d kill them.

Cheers,
-Geoff

Sometimes the molecule goes through optimization. Sometimes the force
lines are shooting round the screen, but the molecule does nothing, even
though it is obviously not optimized. Is there any way of turning the
force field lines off? I have been using Avogadro on Windows 7 until now
with no force field lines shown.

Thanks,

Tim

On 19/12/11 19:03, Geoffrey Hutchison wrote:

Well, the green lines (forces) tell me that something’s working. So what do you mean by “optimization does not work?” Can you be more specific?

When I start Avogadro from Konsole, I get the warning:
QStackedLayout::setCurrentWidget: Widget 0x1984f10 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area
There’s no problem from that. If I could find the source of these messages, we’d kill them.

Cheers,
-Geoff

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Should the ‘surfaces’ tick box work automatically for molecules you draw
in the workspace or do you have other tasks to complete before this works?
One other question. I work as a chemistry teacher and saw a wonderful
demo of Avogadro generating molecular orbitals in stunning detail. I
don’t have access to Gaussian. Is there any other way to generate these
orbitals? Perhaps a database of molecules exist that can be imported to
Avogadro. If so, how do I do this. Avogadro seems like a wonderful
molecular viewer.

Thanks,

Tim

I also forgot to mention that instead of AutoOpt values appearing on the
screen, I get a flashing white bar where this should be shown.

Tim

On 19/12/11 19:16, Tim wrote:

Sometimes the molecule goes through optimization. Sometimes the force
lines are shooting round the screen, but the molecule does nothing, even
though it is obviously not optimized. Is there any way of turning the
force field lines off? I have been using Avogadro on Windows 7 until now
with no force field lines shown.

Thanks,

Tim

On 19/12/11 19:03, Geoffrey Hutchison wrote:

Well, the green lines (forces) tell me that something’s working. So what do you mean by “optimization does not work?” Can you be more specific?

When I start Avogadro from Konsole, I get the warning:
QStackedLayout::setCurrentWidget: Widget 0x1984f10 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area
There’s no problem from that. If I could find the source of these messages, we’d kill them.

Cheers,
-Geoff

Learn Windows Azure Live! Tuesday, Dec 13, 2011
Microsoft is holding a special Learn Windows Azure training event for
developers. It will provide a great way to learn Windows Azure and what it
provides. You can attend the event by watching it streamed LIVE online.
Learn more at http://p.sf.net/sfu/ms-windowsazure


Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss


Learn Windows Azure Live! Tuesday, Dec 13, 2011
Microsoft is holding a special Learn Windows Azure training event for
developers. It will provide a great way to learn Windows Azure and what it
provides. You can attend the event by watching it streamed LIVE online.
Learn more at http://p.sf.net/sfu/ms-windowsazure


Avogadro-Discuss mailing list
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On Mon, 19 Dec 2011 19:26:25 -0000, Tim timmcilveen@talktalk.net wrote:

Should the ‘surfaces’ tick box work automatically for molecules you draw
in the workspace or do you have other tasks to complete before this works?
One other question. I work as a chemistry teacher and saw a wonderful
demo of Avogadro generating molecular orbitals in stunning detail. I
don’t have access to Gaussian. Is there any other way to generate these
orbitals? Perhaps a database of molecules exist that can be imported to
Avogadro. If so, how do I do this. Avogadro seems like a wonderful
molecular viewer.

The surfaces box only gains entries when they are generated or imported by other things - for example, orbitals imported from an output file from a QM program, or the vdW surface Avogadro can generate itself.

I’m not 100% sure whether Avogadro can import orbital information from any of the free QM packages. Others may be able to comment on this more than I can, but I think the only other format you can get orbitals from is GAMESS output, which is free as in beer - you apparently have to contact them for a license application but otherwise it’s free. (I’ve not used it, licensed it, or tried it, so that’s pretty much all I know about that.) And you can apparently use Avogadro to generate the input files, too, handily.

If you just have a few relatively small molecules you want a class to look at, though, I wouldn’t mind running them through Gaussian - I don’t know of any public resources with a stash of Gaussian outputs. It might be a neat idea to have some to use on the Teaching section on the Avogadro website.

-Ian

On Mon, 19 Dec 2011 23:33:18 -0000
"Ian Kirker" ian.kirker@gmail.com wrote:

I’m not 100% sure whether Avogadro can import orbital information
from any of the free QM packages. Others may be able to comment on
this more than I can, but I think the only other format you can get
orbitals from is GAMESS output, which is free as in beer - you
apparently have to contact them for a license application but
otherwise it’s free. (I’ve not used it, licensed it, or tried it, so
that’s pretty much all I know about that.) And you can apparently use
Avogadro to generate the input files, too, handily.

IIRC Avogardo can read formatted checkpoint files from Gaussian. My
free HF / DFT code, ERKALE [1], can currently read in Gaussian formatted
checkpoint files, but I’m planning on implementing a tool to do it the
other way around as well, so that Avogadro could be used to visualize
orbitals and densities computed with ERKALE.

To do this I’d need to know which entries are used in the checkpoint
files, i.e., what I have to write out.

Furthermore I’d like to know where the evaluation of the orbitals and
densities is performed; I might contribute the code necessary to go
beyond d-functions in Avogadro.

[1] http://erkale.googlecode.com


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

On Dec 19, 2011, at 6:33 PM, Ian Kirker wrote:

I’m not 100% sure whether Avogadro can import orbital information from any of the free QM packages. Others may be able to comment on this more than I can, but I think the only other format you can get orbitals from is GAMESS output, which is free as in beer - you apparently have to contact them for a license application but otherwise it’s free.

If people have suggestions on packages for “importing,” we’re all ears. Otherwise, you’ll get the QM packages that my group (and a few others) use. Thus, Gaussian, Q-Chem, MOPAC, GAMESS, Molpro, and Molden for right now.

If you just have a few relatively small molecules you want a class to look at, though, I wouldn’t mind running them through Gaussian - I don’t know of any public resources with a stash of Gaussian outputs. It might be a neat idea to have some to use on the Teaching section on the Avogadro website.

Indeed. The main obstacle right now is working out “the best way” to do this. I’d like to have an open equivalent to the Spartan molecular and spectral databases – thousands of computed structures, IR, NMR, etc. The problem is how to handle it without needing curation. A related effort (Quixote) will probably provide the keys in the next year or so.

In the meantime, my group has a few ideas for a smaller curated database of MOs, IR, etc.

-Geoff

On Dec 19, 2011, at 6:54 PM, Jussi Lehtola wrote:

To do this I’d need to know which entries are used in the checkpoint
files, i.e., what I have to write out.

For all intents and purposes, all this code is in the OpenQube side-project:

Granted, we will soon also support reading orbital eigenvalues/energies and symmetry labels, which are nice. Gaussian finally has a complete description of the format:
http://www.gaussian.com/g_tech/g_ur/f_formchk.htm

Furthermore I’d like to know where the evaluation of the orbitals and
densities is performed; I might contribute the code necessary to go
beyond d-functions in Avogadro.

Before you add code for other functions, please let me know and I’ll get you in touch with someone who’s planning on restructuring the code for improved speed and also the higher-order functions.

-Geoff

On Dec 19, 2011, at 2:30 PM, Tim wrote:

I also forgot to mention that instead of AutoOpt values appearing on the
screen, I get a flashing white bar where this should be shown.

Sounds like you have a crummy graphics driver.

-Geoff

On Mon, 19 Dec 2011 19:28:00 -0500
Geoff Hutchison geoff.hutchison@gmail.com wrote:

On Dec 19, 2011, at 6:54 PM, Jussi Lehtola wrote:

Furthermore I’d like to know where the evaluation of the orbitals
and densities is performed; I might contribute the code necessary
to go beyond d-functions in Avogadro.

https://github.com/cryos/openqube/blob/master/src/gaussianset.cpp

Before you add code for other functions, please let me know and I’ll
get you in touch with someone who’s planning on restructuring the
code for improved speed and also the higher-order functions.

Please do. I’d think that the evaluation could be speeded up,
simplified and written more compactly.


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

On Mon, 19 Dec 2011 19:28:00 -0500
Geoff Hutchison geoff.hutchison@gmail.com wrote:

On Dec 19, 2011, at 6:54 PM, Jussi Lehtola wrote:

To do this I’d need to know which entries are used in the checkpoint
files, i.e., what I have to write out.

For all intents and purposes, all this code is in the OpenQube
side-project:
https://github.com/cryos/openqube/blob/master/src/gaussianfchk.cpp

I’m sure you’ll be pleased to hear that I implemented conversion to
formatted checkpoint files today in ERKALE,
http://erkale.googlecode.com . Thus, there is now a free code for
generating HF/DFT electron densities and orbitals and visualizing them
in Avogadro.

I even made an entry about the use in the users’ guide, with some
rather simple example plots.

If you’re running Fedora or RHEL (e.g., CentOS or Scientific Linux) and
you want to try it out, then I suggest using the RPMs in my yum
repository.


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