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. :slight_smile:

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


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
parsing or building its input. The spectroscopy in NOSE is based on
excitonic theory of molecular aggregates; in short, its basic blocks
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.
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
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 :slight_smile: 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
from people with experience with other projects.

If you are still interested, let us talk about what can be done.


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
could work together to add a NOSE interface – we already have
plotting capabilities (e.g., for NMR or IR spectra) so we could
parse and plot the NOSE output.

Please let me know what you think!


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