From LIN@ubaclu.unibas.ch  Thu Jan 23 06:18:11 1997
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Date: Thu, 23 Jan 1997 11:54:15 +0100
From: Shu-Kun Lin <LIN@ubaclu.unibas.ch>
Subject: CCL:What is EXACTLY a "resonance"?
To: chemistry@www.ccl.net
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Dear CCLers,

"What is EXACTLY a "resonance"?"is a very good question. Let's
go on a little bit. The whole book of Pauling's The Nature of the Chemical
Bond is about this concept. Pauling's definition is based on
Heisenburg's definition.

To my understanding, also as implied in
von Newmann's "Mathematical Foundation of Quantum Mechanics", respnance is
a dynamic process of mixing quantum states which can happen
in an equilibrium state (time-independent) of a molecular or
atomic system. Normally resonance happends among energetically
identical and in many cases configurationally identical
quantum states. If you think this problem deeply, there is a
big problem never solved so far: why a quantum system
spontaneously resonances among several states? What is the
driving force? Energy minimization (based on what kind of
electromagnetic interaction?), or entropy maximization
(based on what kind of formula of entropy of mixing of quantum states?)?

I tried to understand why resonance. The explanation of resonance
phenomena can be done if some more foundamental problem is
solved. I tried a lot lonely so far and almost lost my job because
I spent too much time on it. Interested colleagues may obtain
a couple of papers published last year by me and they are
downloadable from www.mdpi.org/lin.htm

Shu-Kun
---------------------------------------------------------
Dr. Shu-Kun Lin
Molecular Diversity Preservation International (MDPI)
Saengergasse 25, CH-4054 Basel, Switzerland
MDPI: www.mdpi.org/
Molecules: www.mdpi.org/molecules/
ECSOC-1: www.mdpi.org/ecsoc-1.htm
e-mails: Lin@ubaclu.unibas.ch
         Lin@mdpi.org
Tel. +41 79 322 3379, Fax  +41 61 302 8918
--------------------------------------------------------

From alain.kessi@psi.ch  Thu Jan 23 09:18:19 1997
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From: Alain Kessi <alain.kessi@psi.ch>
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Subject: Re: CCL:What is EXACTLY a "resonance"?
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Shu-Kun Lin wrote:
>If you think this problem deeply, there is a
> big problem never solved so far: why a quantum system
> spontaneously resonances among several states? What is the
> driving force? Energy minimization (based on what kind of
> electromagnetic interaction?), or entropy maximization
> (based on what kind of formula of entropy of mixing of quantum
> states?)?

I rather thought there was no secret to that, the matter being simply
that the states you're looking at are not eigenstates of your
hamiltonian and therefore the hamiltonian has non-diagonal elements.
Hence the states couple, and there is a way to lower the energy by
taking linear combinations of those states. Of course, in most cases,
you will still not get the energy minimum (you can only scan the
subspace spanned by the states you put in), but still, you can get a
better approximation than the states you are currently looking at.

A classic example is the ammonia (NH3) maser, which can be described by
a potential with respect to the N position which has two equal energy
minima, separated by a wall of some given height. The minima correspond
to some pyramid and its mirror image. These two states, however, are not
eigenstates of the hamiltonian. If you write down the energy matrix (2
by 2 in this case) in the subspace they span, it's not diagonal, which
means that by diagonalizing the hamiltonian you'll find a state with
lower energy (and one with higher energy, accordingly).

Alain

-- Alain Kessi (alain.kessi@psi.ch), at Paul Scherrer Institut, Zurich
     ++++ stop the execution of Mumia Abu-Jamal ++++
 ++++ if you agree copy these 3 sentences in your own sig ++++
++++ see: http://www.xs4all.nl/~tank/spg-l/sigaction.htm ++++

From F.Schouren@Uni-Koeln.DE  Thu Jan 23 10:18:16 1997
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From: Frank Schouren <F.Schouren@Uni-Koeln.DE>
To: "Comp. Chem. Mailing List" <CHEMISTRY@www.ccl.net>
Subject: Probl. with CASSCF: Where are the CSF's?
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Dear CCLers,

the output file of my GAUSSIAN94 CASSCF(10,9)-calculation on diatomics
tells me, that there are 5290 configuration state functions, but it does
not show them in detail. Instead it says:

"NOTE: configs are not shown in a direct CI Matel calc, unless iop(43) 
eq 2"

I think, that i've got to change the route section of the job, but i 
don't know how to do it. Thanks in advance for your help.

e-mail: F.Schouren@Uni-Koeln.de



From LIN@ubaclu.unibas.ch  Thu Jan 23 12:18:17 1997
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Date: Thu, 23 Jan 1997 17:29:18 +0100
From: Shu-Kun Lin <LIN@ubaclu.unibas.ch>
Subject: What is EXACTLY a "resonance"?
To: chemistry@www.ccl.net
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Dear colleagues:

There is no clear division between a resonance
and a chemical reaction e.g., the so-called "degenerate reaction"
(NH3 masser is a perfect example. If it is NR3, where R is big groups,
its a reaction: if it is NR'R"R"' where the three groups
are all different, the process is a typical and well-known
chemical reaction process - racemization!).

All the chemical processes, according to thermodynamics,
are driven by either energy or entropy effect. Then the
problem is still a big one.
Coulombic integral is very clearly understandable. Its sister term,
the resonance term contributed to energy eigenvalues
is by no means clear, even though there is
no special computational problem about it.

(Reply to the comment of Alain Kessi (alain.kessi@psi.ch))

Shu-Kun
LIN@ubaclu.unibas.ch

From berriz@chasma.harvard.edu  Thu Jan 23 12:24:37 1997
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From: berriz@chasma.harvard.edu (Gabriel Berriz)
Message-Id: <9701231657.AA19303@chasma.harvard.edu>
To: chemistry@www.ccl.net
Subject: Quanta on AlphaStation clones?







Dear netters:

Our lab is (still!) in the process of overhauling its computer
equipment.  We are trying to decide between SGI and Alpha workstations
(or, more precisely, AlphaStation clones).  By far, the greatest
fraction of our lab computers' CPU cycles are devoted to running our
(in-house written) number crunching programs; this makes the Alpha
clones more attractive, since they give us more number crunching power
per buck.  However, occasionally some of us need to visualize
molecules with Quanta, and therefore strongly prefer the SGI
alternative, even if Quanta takes up only a minuscule fraction of our
total CPU load.

Therefore, I would appreciate to hear about the experiences of anyone
out there running Quanta on an Alpha 21164 chip (we're considering
either 433 or 500 Mhz).  Do you require and/or recommend any special
graphics hardware (e.g. graphics card or monitor)?  How good are the
Quanta graphics?  In particular, is the mouse-driven rotation of
molecules quick and smooth to the eye, or is it lagging and jerky?  I
would appreciate any comments pertinent to the high-end graphics
possibilities of Alpha clones.

Thank you very much advance.

Gabriel Berriz
berriz@chasma.harvard.edu
Department of Chemistry and Chemical Biology
Harvard University

From rmuller@rcf.usc.edu  Thu Jan 23 13:18:17 1997
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Date: Thu, 23 Jan 1997 09:28:48 -0800
From: "Richard P. Muller" <rmuller@rcf.usc.edu>
Organization: University of Southern California
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I posted a message earlier this week asking for references to Java
utilities on the net, and have received many helpful replies.

I have created a web page, http://www-rcf.usc.edu/~rmuller/java.html, to
help chemists develop and use their own Java applications.

I have included some basic sites, links to a Java tutorial, links to
other chemistry sites, and a few simple scripts that I wrote myself. I
hope that chemists can download theses applets and experiment with them
for their own particular problems. 

The site is currently quite primative. I will expand it in the future.

If you have any applets, links, or any other suggestions for the site,
send them to me at rmuller@rcf.usc.edu. There seems to be a great deal
of interest in Java in the computational chemistry community. Anyone
interested in a mailing list?

Thanks for all of the help. 

Rick
-- 
Richard P. Muller, Ph.D.                  rmuller@invitro.usc.edu        
Department of Chemistry, SGM 418  http://www-rcf.usc.edu/~rmuller
University of Southern California             Office 213-740-7671
Los Angeles, CA  90089-1062                   FAX    213-740-2701

From boyd@chem.iupui.edu  Thu Jan 23 14:18:18 1997
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Date: Thu, 23 Jan 1997 13:34:26 -0500
From: Boyd <boyd@chem.iupui.edu>
Subject: reprints wanted
To: OSC CCL <chemistry@www.ccl.net>
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CCLers,
I'm trying to build a collection of reprints that cite "Reviews in 
Computational Chemistry."  If you are the author of such a paper 
in the last 12-13 months, please help by sending me a copy today.  
Thanks very much.
Don
Dr. D. B. Boyd
"Reviews in Computational Chemistry"
402 North Blackford Street
Indianapolis, IN 46202-3274, U.S.A.
REVIEWS IN COMPUTATIONAL CHEMISTRY Home Page on the 
World Wide Web URL http://chem.iupui.edu/~boyd/rcc.html

From Lchen@mdli.com  Thu Jan 23 14:22:22 1997
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Date: Thu, 23 Jan 1997 10:40:09 -0800
From: Lingran Chen <Lchen@mdli.com>
Subject: Chemical Programs for Linux
To: chemistry@www.ccl.net
Cc: Lchen@mdli.com
Reply-to: Lchen@mdli.com
Message-id: <32E7B089.5872@mdli.com>
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Hi CCL friends:

In the past years I used Pentium PC/Linux as a main platform 
for developing the SYNGEN system
(http://syngen2.chem.brandeis.edu/syngen.html) and for Web Server.
I found this PC workstation is just fine. 

And I would like to know how many chemical programs have been ported
to or developed on Linux and/or how many chemists are using Linux.
Any information on this question will welcome and I will summarize
the responses. Thanks.

-Lingran

*************************************************
Lingran Chen, Ph.D.
Senior Scientific Programmer
MDL Information Systems, Inc.
14600 Catalina Street
San Leandro
CA 94577
USA

Phone: (510) 895-1313
FAX:   (510) 614-3616

Email: LCHEN@MDLI.COM
URL: syngen2.chem.brandeis.edu/~chen/lingran.html
*************************************************

From serg@markov.chem.rochester.edu  Thu Jan 23 14:27:47 1997
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Date: Thu, 23 Jan 1997 13:47:03 -0500 (EST)
From: Sergei Tretiak <serg@markov.chem.rochester.edu>
To: CHEMISTRY@www.ccl.net
Subject: Molecular Geometries: Database 
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Dear CCL's:

We need for our work geometries of various molecules. Instead of diving 
to the long ab initio calculations, probably, it will be wise to check 
whether somebody already did such job. 
Are any Databases that include results of molecular structure calculations
simulations, experimental, etc. available for public?

	Thank you all for your time,
					Sergei
				  

 .-----------------------------------------------------------------------.
|   			Sergei Tretiak                                  | 
|.......................................................................|
| Department of Chemistry     | Voice: (716) 275-8289                   |
| University of Rochester     | Fax:   (716) 475 -1185                  | 
| Rochester, NY 14627         | E-mail: serg@markov.chem.rochester.edu  |
|_______________________________________________________________________|


From tasaki@mcaca.com  Thu Jan 23 15:18:20 1997
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A just simple question: does anyone know what to say "isodesmic reaction" in
Japanese?
Sincerely,


Ken Tasaki, Ph.D.
Chief Scientist
Mitsubishi Chemical America, Inc.
99 W Tasman Dr. Suite 200
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From bear@ellington.pharm.arizona.edu  Thu Jan 23 16:18:20 1997
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Date: Thu, 23 Jan 1997 13:53:52 -0700
From: bear@ellington.pharm.arizona.edu (Soaring Bear)
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To: chemistry@www.ccl.net
Subject: flavone redox potentials


Does anyone know of a collected source of redox potentials
for compounds: perhaps a CRC type of book?   I'm looking
redox potentials of flavones and only found a few
measurements in preliminary lit search.

thankyou,
bear

[7m[5m
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(___        |.)     bear@ellington.pharm.arizona.edu    5'  :      : .*
 ___)OARING |_)EAR,    UA Pharmacy 404, Tucson 85721     |'*.    .*'| |
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From bdavis@yorku.ca  Thu Jan 23 17:18:25 1997
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Hi!

I was wondering if anyone could shed some light on a curious problem I'm
having running g94 under linux on a Pentium Pro 100.  The analytic
frequencies using DFT seem to take twice as long as they should.  The
numerical frequencies work fine and take the same amount of time as the
analytic frequencies.  Running the same job on other machines (sgi indigo
and 8 processor PowerChallenge) indicate link 1002 is the culprit.  It is
using double the CPU time it should on the Pentium.  Anyone else have this
problem or any suggestions on how to resolve it?  Thanks.

g94 revision D.1


Email replies to bdavis@yorku.ca

Dr. Bill Davis


From g-recht@chem.nwu.edu  Thu Jan 23 18:18:18 1997
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From: g-recht@chem.nwu.edu (Gregory Rechtsteiner)
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Subject: fortran ising models
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Hello:

I was wondering if anyone has any fortran
code for simulating one-dimensional
(1x10) Ising and/or two-dimensional Ising
models (via Monte Carlo method).
I have located plenty of books
offering suggestions for computer programs,
but no detailed code.

Thank you for your help,

Greg Rechtsteiner
grechtst@pepvax.pepperdine.edu


From berriz@chasma.harvard.edu  Thu Jan 23 18:26:54 1997
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From: berriz@chasma.harvard.edu (Gabriel Berriz)
Message-Id: <9701232223.AA26909@chasma.harvard.edu>
To: chemistry@www.ccl.net
In-Reply-To: <9701231657.AA19303@chasma.harvard.edu> (berriz@chasma.harvard.edu)
Subject: Running Quanta remotely (Was: Quanta on AlphaStation clones?)





[This is a follow-up to an earlier question of mine (quoted below, for
reference)...]

Another option that has come up is to consolidate all our CPU power on
a single server, and to use NCD X-terminals as consoles on people's
desks.  Does anyone know if it is possible to view and interact with
Quanta (which is running on the server) remotely through an NCD
X-terminal?



Gabriel Berriz
berriz@chasma.harvard.edu
Department of Chemistry and Chemical Biology
Harvard University




==========================================================================
   Date: Thu, 23 Jan 1997 11:57:49 -0500
   From: berriz@chasma.harvard.edu (Gabriel Berriz)

   Dear netters:

   Our lab is (still!) in the process of overhauling its computer
   equipment.  We are trying to decide between SGI and Alpha workstations
   (or, more precisely, AlphaStation clones).  By far, the greatest
   fraction of our lab computers' CPU cycles are devoted to running our
   (in-house written) number crunching programs; this makes the Alpha
   clones more attractive, since they give us more number crunching power
   per buck.  However, occasionally some of us need to visualize
   molecules with Quanta, and therefore strongly prefer the SGI
   alternative, even if Quanta takes up only a minuscule fraction of our
   total CPU load.

   Therefore, I would appreciate to hear about the experiences of anyone
   out there running Quanta on an Alpha 21164 chip (we're considering
   either 433 or 500 Mhz).  Do you require and/or recommend any special
   graphics hardware (e.g. graphics card or monitor)?  How good are the
   Quanta graphics?  In particular, is the mouse-driven rotation of
   molecules quick and smooth to the eye, or is it lagging and jerky?  I
   would appreciate any comments pertinent to the high-end graphics
   possibilities of Alpha clones.

   Thank you very much advance.

   Gabriel Berriz
   berriz@chasma.harvard.edu
   Department of Chemistry and Chemical Biology
   Harvard University

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