Pyquante idea

Hi!
This is my first time in this list and I don’t know if it’s the correct list
to write for this proposal…

There’s a python module, “pyquante” http://pyquante.sourceforge.net/ that
computes properties like energy with quantum mechanical methods.

What do you think about pyquante integration with Avogadro? I mean like
energy computation, orbitals etc…

I don’t know much about Avogadro structure, I want to ask you if it’s
possible to integrate deeply a python software in Avogadro, in other words
if there are at least “chances” to do that. It’s also nice to know if
something llike this is “useful” for the Avogadro purposes.

I’m not asking to someone to do this, I just want to get opinions about this
idea.

  • Gabriele Lanaro

I think it would be reasonably easy to do, but be warned, pyquante is
quite slow even for very small systems.

  • Noel

On 4 March 2010 17:50, Gabriele Lanaro gabriele.lanaro@gmail.com wrote:

Hi!
This is my first time in this list and I don’t know if it’s the correct list
to write for this proposal…
There’s a python module, “pyquante” http://pyquante.sourceforge.net/ that
computes properties like energy with quantum mechanical methods.
What do you think about pyquante integration with Avogadro? I mean like
energy computation, orbitals etc…
I don’t know much about Avogadro structure, I want to ask you if it’s
possible to integrate deeply a python software in Avogadro, in other words
if there are at least “chances” to do that. It’s also nice to know if
something llike this is “useful” for the Avogadro purposes.
I’m not asking to someone to do this, I just want to get opinions about this
idea.

  • Gabriele Lanaro

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proactively, and fine-tune applications for parallel performance.
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Hi,

On Thu, Mar 4, 2010 at 6:50 PM, Gabriele Lanaro
gabriele.lanaro@gmail.com wrote:

Hi!
This is my first time in this list and I don’t know if it’s the correct list
to write for this proposal…
There’s a python module, “pyquante” http://pyquante.sourceforge.net/ that
computes properties like energy with quantum mechanical methods.
What do you think about pyquante integration with Avogadro? I mean like
energy computation, orbitals etc…
I don’t know much about Avogadro structure, I want to ask you if it’s
possible to integrate deeply a python software in Avogadro, in other words
if there are at least “chances” to do that. It’s also nice to know if
something llike this is “useful” for the Avogadro purposes.
I’m not asking to someone to do this, I just want to get opinions about this
idea.

The short answer is: yes, this is possible. Avogadro supports python
plugins the same way it supports C++ plugins. The best plugin type
would probably be an extension here. Avogadro also uses PyQt4 as gui
library.

You can design your GUI (.ui files) using Qt designer and load them in
your script. The current molecule is accessible from python allowing
you to create the needed input files (It is also possible to write out
files in various formats with MoleculeFile). Next you can run the
calculation and read the results back. This reading can be implemented
in C++ or python.

some useful links to get started:
http://avogadro.openmolecules.net/wiki/Scripting
http://avogadro.openmolecules.net/wiki/Python_Extensions

Feel free to ask more specific questions if needed. Also, user
contributed python scripts are always welcome.

One more thing: what OS are you using? In windows you need to copy the
pyquanta python module to C:\Program
Files\Avogadro\bin\lib\site-packages since Avogadro has it’s own
python environment.

Cheers,
Tim

  • Gabriele Lanaro

Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev


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Thank you very much for the quick response, it’s exactly what I was looking
for…and more!

I’ll start immediatly reading the documentation.

Thank you again,

  • Gabriele Lanaro

2010/3/4 Tim Vandermeersch tim.vandermeersch@gmail.com

Hi,

On Thu, Mar 4, 2010 at 6:50 PM, Gabriele Lanaro
gabriele.lanaro@gmail.com wrote:

Hi!
This is my first time in this list and I don’t know if it’s the correct
list
to write for this proposal…
There’s a python module, “pyquante” http://pyquante.sourceforge.net/
that
computes properties like energy with quantum mechanical methods.
What do you think about pyquante integration with Avogadro? I mean like
energy computation, orbitals etc…
I don’t know much about Avogadro structure, I want to ask you if it’s
possible to integrate deeply a python software in Avogadro, in other
words
if there are at least “chances” to do that. It’s also nice to know if
something llike this is “useful” for the Avogadro purposes.
I’m not asking to someone to do this, I just want to get opinions about
this
idea.

The short answer is: yes, this is possible. Avogadro supports python
plugins the same way it supports C++ plugins. The best plugin type
would probably be an extension here. Avogadro also uses PyQt4 as gui
library.

You can design your GUI (.ui files) using Qt designer and load them in
your script. The current molecule is accessible from python allowing
you to create the needed input files (It is also possible to write out
files in various formats with MoleculeFile). Next you can run the
calculation and read the results back. This reading can be implemented
in C++ or python.

some useful links to get started:
http://avogadro.openmolecules.net/wiki/Scripting
http://avogadro.openmolecules.net/wiki/Python_Extensions

Feel free to ask more specific questions if needed. Also, user
contributed python scripts are always welcome.

One more thing: what OS are you using? In windows you need to copy the
pyquanta python module to C:\Program
Files\Avogadro\bin\lib\site-packages since Avogadro has it’s own
python environment.

Cheers,
Tim

  • Gabriele Lanaro

Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev


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

What do you think about pyquante integration with Avogadro? I mean like energy computation, orbitals etc…

I think it’s a great idea. As others have noted, the whole idea of Avogadro plugins is that they can interface with other programs.

I should note that I’m also working on “freeing” an open source C++ package for INDO semiempirical calculations.

-Geoff