Integrated data manager

Development
1

OK, this is my puny opinion. OpenBabel, if it won’t get functionalized, will be the bottleneck for Avogadro. I can illustrate. Take a look at the image attached. It’s from PHASE GUI. What one can do with it, he/she can select a file in a folder and then see all the possible info of this file in numbers: convergence, calculated DOS, band structure, IR, NMR etc. Then selected data can be seamlessly plotted from the same window. Now that’s functionality

http://www.mediafire.com/?amzzdm2mqzw

I am not promoting PHASE or demoting Avogadro, I am being honest. As far as I understand to display any numbers in Avogadro is impossible since it’s not implemented in OB. My opinion is that displaying molecule should be only a very small part of any GUI.

I propose creating integrated data manager as the one in the image, from which one could manipulate (add, subtract spectra) and plot in various ways the meaningful information obtained during calcs. Face it, structure itself is almost trivial in QM.

That would start uniting features that now sit without a right place, such as IR spectra.

Of course, it means dramatically expanding what OB reads. That goes back for example to multistep jobs as well

I am only a potential user and Geoff encouraged me to come up with ideas…

Jonas

2

OK, first off, I can’t see that image – there are just too many ads
on that site, it’s not clear where to click. I suggest uploading to
the wiki.

I’ve created an “Inspiration” category on the wiki. For those who
don’t know how to add pages, here’s a quick run-down.
Search for a page. If it doesn’t exist, there’s a link to create it
(if you’re logged into an account on the Avo wiki). Write up a quick
draft.
Key points:

  • To include a graphic, use [[Image:File.png]] where File.png is the
    name of the graphic you want. You can upload it later.
  • To mark the page as part of a particular category, make sure the
    page has [[Category:Inspiration]] at the end.
  • Once you’ve saved a page, you can upload images by clicking on the
    red image links, and uploading the files.
  • We use MediaWiki, so the syntax is exactly like editing on Wikipedia.

So Jonas, please feel free to go ahead and create some inspiration
pages with images.

What one can do with it, he/she can select a file in a folder and
then see all the possible info of this file in numbers: convergence,
calculated DOS, band structure, IR, NMR etc. Then selected data can
be seamlessly plotted from the same window. Now that’s functionality
…
I propose creating integrated data manager as the one in the image,
from which one could manipulate (add, subtract spectra) and plot in
various ways the meaningful information obtained during calcs. Face
it, structure itself is almost trivial in QM.

While file format readers in Open Babel are getting more and more
feature-full (and I encourage that trend to continue), there’s nothing
limiting Avogadro to reading files again. For example, while OB reads
fchk files, Avogadro reads them for orbital eigenvectors and
eigenvalues. We’ve got the filenames, so extensions can do whatever
they want.

Anyway, my last “editorial” comment is that there are probably 100s of
features we might want to implement. But the goal was to start simple,
get things right, and grow from there. Without attracting new users
and new developers, it’s highly unlikely much of a TODO list can be
implemented in a reasonable period of time. That’s why it’s important
to get a nice, stable, solid 1.0 release finished.

I think a “data manager” or “spectra manager” would be nice. Since I
can’t see the image, I hope you’ll write it up on the wiki. :slight_smile:

Please continue! I don’t have a monopoly on good ideas.
-Geoff

3

On Fri, May 08, 2009 at 07:19:15PM -0700, Jonas Baltrusaitis wrote:

OK, this is my puny opinion. OpenBabel, if it won’t get
functionalized, will be the bottleneck for Avogadro. I can illustrate.

Certainly; OpenBabel should get extended and Avogadro should take
advantage of its new possibilities.

Take a look at the image attached. It’s from PHASE GUI. What one can
do with it, he/she can select a file in a folder and then see all the
possible info of this file in numbers: convergence, calculated DOS,
band structure, IR, NMR etc. Then selected data can be seamlessly
plotted from the same window. Now that’s functionality

http://www.mediafire.com/?amzzdm2mqzw

I am not promoting PHASE or demoting Avogadro, I am being honest. As
far as I understand to display any numbers in Avogadro is impossible
since it’s not implemented in OB.

What do you mean with “any numbers”?

Right now, you can at least display the geometry, the dipole vector, the
vibrations and the molecular orbitals in Avogadro. Not all of those are
supported by all file formats in OpenBabel yet probably, and work is
needed.

My opinion is that displaying molecule should be only a very small
part of any GUI.

I am not sure I agree with you here. If I look at the text-file output
of a QM calculation, I think the most difficult things to drag out of it
are the 3D geometry, the molecular orbitals and maybe the normal modes.

It is really hard to visualize those by just looking at the numbers.

Things like the energy convergence or the frequency/intensity of
vibrations are somewhat easier to understand by looking at the numbers,
but of course having them plotted helps.

I agree that having the DOS for periodical calculations plotted is
probably also required or at least very important to get an
understanding, but I am not sure whether somebody with the required
experience and expertise is working on this for OpenBabel/Avogadro right
now.

I only do MO-based calculation, so I cannot comment on what would be
needed for periodic systems.

Of course, it means dramatically expanding what OB reads. That goes
back for example to multistep jobs as well

Yes, certainly. In the end, OpenBabel should be able to extract all or
at least most of the information possible from a QM calculation output
file. However, not so many people are working on this and they have
their own priorities. That said, multi-step jobs are certainly very
important and should be high up on the list.

Michael

4

On May 10, 2009, at 10:33 AM, Michael Banck wrote:

Right now, you can at least display the geometry, the dipole vector,
the
vibrations and the molecular orbitals in Avogadro.

Partial charges are almost always supported by OB as well, plus a
variety of “cube” and a few “trajectory” formats.

My opinion is that displaying molecule should be only a very small
part of any GUI.

Remember that the main goal of Avogadro is an editor/builder. So this
is a huge part of Avogadro. My view is if you can’t build the
molecule or crystal, you can’t do the calculation in the first place.

I am not sure I agree with you here. If I look at the text-file
output
of a QM calculation, I think the most difficult things to drag out
of it
are the 3D geometry, the molecular orbitals and maybe the normal
modes.

Agreed.

I only do MO-based calculation, so I cannot comment on what would be
needed for periodic systems.

Many of the pieces are probably already in Avogadro and Open Babel
(e.g., OB supports unit cells, translation vectors, and space groups
just fine). I don’t have the least idea how solid state codes actually
store QM data, although if they already generate some type of
volumetric data (e.g., cube or OpenDX), then Avogadro can already
handle it.

That said, multi-step jobs are certainly very important and should
be high up on the list.

The core OB library supports multi-step jobs. I even experimented with
multi-step support for GAMESS. I’d be glad to give pointers, but it
hasn’t been at the top of my TODO list.

-Geoff