# Nose

**URL:** <https://discuss.avogadro.cc/t/nose/1495>\
**Category:** Development\
**Created:** [August 3, 2009, 3:08pm UTC](https://discuss.avogadro.cc/t/nose/1495 "2009-08-03T15:08:56Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [August 3, 2009, 3:08pm UTC](https://discuss.avogadro.cc/t/nose/1495/1 "2009-08-03T15:08:56Z")

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Hi Tomas,

One of the things we’d like to do in Avogadro is to make building  
“molecular systems” easy. Obviously the first step is to easily build  
molecules. But we also build unit cells, and there are ways to build  
sets of molecules too.

So, we’d love to talk about how we can easily build aggregates. Right  
now, you can copy/paste molecules and insert molecules as fragments  
and drag them into place. But perhaps we need a way to move/rotate  
molecules by specific amounts?

We’re still a fairly small project too. 🙂

The output from NOSE looks fine – wavenumbers and normalized  
intensity. Do you have any sort of orbital information about the  
excitations too?

Cheers,  
-Geoff

On Jul 30, 2009, at 4:43 PM, Tomas Mancal wrote:

> Hi Geoff,
> 
> thanks for your interest in NOSE. We are certainly interested in  
> help with  
> plotting capabilities. NOSE calculates some one- and two-dimensional  
> spectra, time evolutions of populations of excited states etc. and it  
> would be great if one could view them in some simple integrated way.
> 
> I looked at Avogadro and it reminded me that NOSE might also benefit  
> from  
> parsing or building its input. The spectroscopy in NOSE is based on  
> excitonic theory of molecular aggregates; in short, its basic blocks  
> are  
> not atoms, but whole molecules. It would be great to be able to put  
> together an aggregate in a way one creates molecules in Avogadro.  
> Another  
> thing is that molecular excited states form delocalized states in the  
> aggregates, and people (at least in our community) would benefit from  
> being able to visualize these states, too. I just want to say that  
> there  
> is a lot of things that can be done in NOSE development that might  
> be of  
> interest for you.
> 
> NOSE is a very small project, which is good and bad 🙂 I develop the  
> program mostly alone as a part of my research, and sometimes I get  
> students to work on some subprojects. So with too few hands the  
> development is rather slow. On the other hand, I am very open to  
> suggestions, e.g. concerning the output formats and I welcome any  
> feedback  
> from people with experience with other projects.
> 
> If you are still interested, let us talk about what can be done.
> 
> Cheers,  
> Tomas
> 
> > Message body follows:
> > 
> > Hi there,
> > 
> > I’m _very_ curious about NOSE. I have an RSS feed of new chemistry  
> > projects and saw your listing.
> > 
> > I’m one of the developers of Avogadro, a molecular builder and  
> > interface to other computational chemistry packages. I’m curious if  
> > we  
> > could work together to add a NOSE interface – we already have  
> > plotting capabilities (e.g., for NMR or IR spectra) so we could  
> > directly  
> > parse and plot the NOSE output.
> > 
> > Please let me know what you think!  
> > [http://avogadro.openmolecules.net/](http://avogadro.openmolecules.net/)  
> > [Avogadro download | SourceForge.net](http://sf.net/projects/avogadro/)
> > 
> > Cheers,  
> > -Geoff
> > 
> > –  
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