Subject: vibration coordinats.

From: [email-masked] (Avital Shurki)
Date: Mon, 25 Nov 1996 16:20:15 +0200

Dear natters,

I need to get the movements of the different vibrations
in the internal coordinates representation.
Gaussian 94 gives me the movements in the cartesian
coordinates.

Does anyone know how can I get the vibrations in internal
coordinates representation from Gaussian 94.

Thanks in advance

Avital

---

From: "Robert Fraczkiewicz" <[email-masked]>
Date: Mon, 25 Nov 1996 11:47:58 -0600

Dear Avital,

On Nov 25,  4:20pm, Avital Shurki wrote:
> Subject: CCL:G:vibration coordinats.
> Dear natters,
>

In Wilson's GF-matrix formalism internal coordinate displacements (R) are
approximated as linear combinations of their Cartesian counterparts (x):

     R=Bx

where is the Wilson's B-matrix. It is just a matrix-vector multiplication,
but you need B-matrix first. If you are a programmer consult "Molecular
Vibrations" by E.B. Wilson, J.C. Decius and P.C. Cross for definitions
and equations. If not, there are normal mode analysis programs that
can compute B-matrices from known structure of molecules (e.g., well known
GMAT by Schachtschneider). A few years ago I wrote such a program called
RAMVIB; I am going to deposit it in CCL software archives pretty soon.
I am no expert in Gaussian 94, maybe there is an option to compute B-matrix.

Wishing you good luck,
Robert Fraczkiewicz
University of Texas Medical Branch
[email-masked]

>From [email-masked] Mon Nov 25 15:02 EST 1996
From: Jan Labanowski <[email-masked]>
Date: Mon, 25 Nov 1996 15:02:29 -0500
To: [email-masked]
Subject: CCL needs your input NOW!!!

Dear Netters,

The good news is that we have full time person to work on the CCL
improvement and Web site. David Tinapple joins the CCL staff
on Monday, Nov. 25. He has substantial Web authoring experience
in commercial, as well as, non-profit sector. He participated in
creating several multimedia CD-ROMs, and we are told that he has
a good sense of knowing where simplicity meats elegance in the
Web site development. We already have great plans, and once he
goes through the megabytes of stuff in CCL archives, and gets
over the new hire red tape, we will see things happening faster.

We know it, and you know it that CCL discussions get sometimes
too broad for some subscribers. And beside, if we asked you what
is computational chemistry, we would get a lot of different
answers. So for those of you who are interested only in the
subset of CCL messages on a given topic, we want to provide
an automatic filter.

How it will work?
=================
The current list stays as it is for those who want it this way.
Everybody sends messages to the normal address:
[email-masked]. The text of incoming message is analyzed
by the software for contents, and tagged according to the
contents. It may happen that the message will belong to several
subjects. For example, the message dealing with: "The basis set
dependence of Force Field parameters for Molecular Mechanics
derived with Density Functional approaches" may belong to many
subjects, e.g., Molecular Mechanics, Density Functional Methods,
Basis Sets, Quantum Chemistry. The example also shows that
subjects chosen need not be "orthogonal", and can overlap
a great deal, or even be embedded within other subject.

Once we are finished, we will provide a new signup form for
the CCL and you will be able to migrate from the "everything"
CCL to a subject oriented delivery (we may also provide other
options like: the maximum file size for the message, the
"This subject but only if together with that subject",
and others). Of course you will be able to choose as many
subjects as you want. And even if message belongs to several
subjects you belong to, you will only get one message.

What we need from you?
======================
Vote!!! That is, tell us which subjects you would choose for
yourself. and which you do not want to see ever {:-)} ("Never
say never again"). Fill in the form at:

      http://www.ccl.net/ccl/ccl-subjects.html

or simply send a message to [email-masked] (Jan Labanowski) with
subjects which you would be personally interested in receiving,
and which subjects you would not like to see. We need your
initial response to decide how many subjects we want to
implement. WE NEED YOUR MASSIVE RESPONSE to really help us in
making rational choices. So please, participate. BUT PLEASE SEND 
COMMUNICATIONS ABOUT IT TO [email-masked] rather than the list.
PLEASE. This survey at
    http://www.ccl.net/ccl/ccl-subjects.html
will only take you a minute or so to answer unless you are my
type, i.e., "paralysis of analysis"). But do not be pedantic,
since we need general guidance at this time. Save your
deliberations for the moment when we will ask you to make the
actual choice.

How we will approach the problem?
=================================
While it looks simple, it is not. So if you know how such
things are done let us know ([email-masked]). We could use the
sophisticated stuff spooks use with FFT and the like. But we
are considering the following general approach. Each subject
will be defined as a series of keywords (or actually flexible
matches, called regular expressions in UNIX). These keywords
will be checked against the text of the message to qualify
message as belonging  to a given subject. There also has to be
some ranking mechanism, and keywords may be assigned different
weight ("importance"). The proximity of other words can also be
taken into account.

Of course, one could use a training set of past messages in CCL
archives, assign subjects to them and run neural net stuff on
them. While we do not rule out this approach, we will probably
do it in a more deterministic way to be able to use new
buzzwords which appear every month to add to the keywords list.

After we decide on subjects, we will create a Web form, and you
will be asked again for help. This time to provide us with
keywords typical for a given subject. We will also go through
archives and assign past messages to subjects, split messages
to words and rank the frequency of words in a given subject.
While we are sure that "and", "molecule", etc. will be the
leaders, we hope to find also some specific words which occur
within subjects.

Then we will do the software. The software has to be smart and
especially distribution has to be well optimized. We also need
to think about messages which are outside the scope of any field
(did not rank high enough) -- we may simply handle them by hand
and improve our keyword lists. We will also provide a way for
the authors to assign their messages to the subjects, but we do
not want to enforce it. And beside, who knows what will show up 
in the process of doing this. But we think that it may be a nice
and needed tool once we can make it work. If it works well
enough, we may want to make it available, so you can use it as
a filter for your other mailing lists and newsgroups. But do
not be impatient as it will take some time to create it.

So please help us (and help yourself too, in the process).

Jan Labanowski
CCL Admin
[email-masked]