Cube files

As a teacher of high school chemistry, I would like to be able to show
students the molecular orbitals of various molecules using Avogadro
rendered with POV-Ray, which has some stunning effects. I do not have
access to Gaussian sofware and wonder if there are open source cube
files for common molecules? Alternatively, is there any open source
software that I could use as an alternative to Gaussian?

Thanks,

Tim

On 09/29/2013 06:42 PM, Tim wrote:

As a teacher of high school chemistry, I would like to be able to show
students the molecular orbitals of various molecules using Avogadro
rendered with POV-Ray, which has some stunning effects. I do not have
access to Gaussian sofware and wonder if there are open source cube
files for common molecules? Alternatively, is there any open source
software that I could use as an alternative to Gaussian?

Thanks,

Tim


October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk


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

I think Nwchem may work for you application. It does produce Gaussian
cube files. Also check out PSI4 and quantum espresso.

-Richard

if there are open source cube files for common molecules?

I echo the suggestion of NWChem. OpenMOPAC is also available free to academic users, which I believe applies to high school teachers. (http://openmopac.net/)

As for the “common molecules” question. I’ve been thinking hard about this exact problem for some time. Let’s just say the biggest problem is generating a list of common molecules. If people would like to suggest how to come up with say 100 or 1,000 or 10,000 molecules for teaching use … I think the University of Pittsburgh will gladly donate the CPU time using MOPAC and/or NWChem.

So my big question (to the community)… how do we generate such a list and/or take genuine requests?

Cheers,
-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

Might I suggest the CSD teaching set?

This would save a lot of legwork, and I imagine they would be happy to
have the added value.

  • Noel

On 30 September 2013 04:36, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

if there are open source cube files for common molecules?

I echo the suggestion of NWChem. OpenMOPAC is also available free to academic users, which I believe applies to high school teachers. (http://openmopac.net/)

As for the “common molecules” question. I’ve been thinking hard about this exact problem for some time. Let’s just say the biggest problem is generating a list of common molecules. If people would like to suggest how to come up with say 100 or 1,000 or 10,000 molecules for teaching use … I think the University of Pittsburgh will gladly donate the CPU time using MOPAC and/or NWChem.

So my big question (to the community)… how do we generate such a list and/or take genuine requests?

Cheers,
-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/


October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk


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

Do you know if the full data set can be downloaded, and what license
they applied to the data? It looks like it could be a useful data set,
but from the site I didn’t see clear licensing or a data download
link. We are working on a demo with Avogadro, web services, and
chemical data and I am certainly interested in finding useful open
datasets (I realize this might be useful for teaching if their terms
are acceptable to whoever is teaching).

Marcus

On Mon, Sep 30, 2013 at 7:23 AM, Noel O’Boyle baoilleach@gmail.com wrote:

Might I suggest the CSD teaching set?
http://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/CSDTeachingDatabase.aspx

This would save a lot of legwork, and I imagine they would be happy to
have the added value.

  • Noel

On 30 September 2013 04:36, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

if there are open source cube files for common molecules?

I echo the suggestion of NWChem. OpenMOPAC is also available free to academic users, which I believe applies to high school teachers. (http://openmopac.net/)

As for the “common molecules” question. I’ve been thinking hard about this exact problem for some time. Let’s just say the biggest problem is generating a list of common molecules. If people would like to suggest how to come up with say 100 or 1,000 or 10,000 molecules for teaching use … I think the University of Pittsburgh will gladly donate the CPU time using MOPAC and/or NWChem.

So my big question (to the community)… how do we generate such a list and/or take genuine requests?

Cheers,
-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/


October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk


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


October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk


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

Thanks for the feedback everyone. This gives me a lot of information to
get me started. If I could find open source files, with the data already
generated, it would save a lot of donkey work. I can’t actually work out
how to download the CSD teaching set, but it sounds like it might fit
the bill quite well. It would be great if there was some sort of open
molecule database!

Thanks,

Tim

On 30/09/13 14:00, Marcus D. Hanwell wrote:

Do you know if the full data set can be downloaded, and what license
they applied to the data? It looks like it could be a useful data set,
but from the site I didn’t see clear licensing or a data download
link. We are working on a demo with Avogadro, web services, and
chemical data and I am certainly interested in finding useful open
datasets (I realize this might be useful for teaching if their terms
are acceptable to whoever is teaching).

Marcus

On Mon, Sep 30, 2013 at 7:23 AM, Noel O’Boyle baoilleach@gmail.com wrote:

Might I suggest the CSD teaching set?
http://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/CSDTeachingDatabase.aspx

This would save a lot of legwork, and I imagine they would be happy to
have the added value.

  • Noel

On 30 September 2013 04:36, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

if there are open source cube files for common molecules?
I echo the suggestion of NWChem. OpenMOPAC is also available free to academic users, which I believe applies to high school teachers. (http://openmopac.net/)

As for the “common molecules” question. I’ve been thinking hard about this exact problem for some time. Let’s just say the biggest problem is generating a list of common molecules. If people would like to suggest how to come up with say 100 or 1,000 or 10,000 molecules for teaching use … I think the University of Pittsburgh will gladly donate the CPU time using MOPAC and/or NWChem.

So my big question (to the community)… how do we generate such a list and/or take genuine requests?

Cheers,
-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/


October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk


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


October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk


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


October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk


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

On 30/09/13 04:36, Geoffrey Hutchison wrote:

As for the “common molecules” question. I’ve been thinking hard about
this exact problem for some time. Let’s just say the biggest problem
is generating a list of common molecules. If people would like to
suggest how to come up with say 100 or 1,000 or 10,000 molecules for
teaching use … I think the University of Pittsburgh will gladly
donate the CPU time using MOPAC and/or NWChem. So my big question (to
the community)… how do we generate such a list and/or take genuine
requests?

I live in the UK, and there are a number of molecules that crop up again
and again on ‘A’ level teaching specifications. ‘A’ level in the UK, is
as far as I know, quite similar to your ‘AP’ levels. I don’t know how
the UK specifications compare to those in the States, but I can’t see
them being much different. Most are just small alkanes, alkenes, alkynes
and benzene rings.

Tim