From owner-chemistry@ccl.net Thu Nov 10 04:51:00 2005
From: "Ulrike Salzner salzner,fen.bilkent.edu.tr" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL:G: Linda with Fedora
Message-Id: <-29919-051110013826-20052-y0Qx374WvZhqnYuh6PX9Kg*server.ccl.net>
X-Original-From: Ulrike Salzner <salzner ~~ fen.bilkent.edu.tr>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain
Date: Thu, 10 Nov 2005 08:38:18 +0200
Mime-Version: 1.0


Sent to CCL by: Ulrike Salzner [salzner!^!fen.bilkent.edu.tr]
I am about to built a Linux cluster using Linda/G03. I am using Fedora
Core 3 and 4. Since this version of Linux is not supported by Gaussian,
I need to know whether Linda will work. Gaussian runs fine with Fedora
Core 3 but it seems to have problems with FC4 kernel 2.6.11-1.1369.

Has anyone managed to get a cluster working with Fedora Core 3 or 4?
Thanks in advance for any advice.

Ulrike
-- 
Ulrike Salzner
Associate Professor
Department of Chemistry
Bilkent University
06800 Bilkent, Ankara
Turkey


From owner-chemistry@ccl.net Thu Nov 10 05:37:00 2005
From: "Sigismondo Boschi s.boschi~~cineca.it" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL: Ab initio simulations of ice-X
Message-Id: <-29920-051110051559-20968-GK4I6qI88Tzaqh6Caabf/A:+:server.ccl.net>
X-Original-From: Sigismondo Boschi <s.boschi ~ cineca.it>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Thu, 10 Nov 2005 10:06:32 +0100 (MET)
MIME-Version: 1.0


Sent to CCL by: Sigismondo Boschi [s.boschi:_:cineca.it]
A Collegue of mine is co-author of this, but there are many:

C. Cavazzoni, G.L. Chiarotti, S.Scandolo, E.Tosatti, M.Bernasconi, and 
M. Parrinello "Superprotonic and metallic states of water and ammonia at 
giant planet conditions", Science 283, 44-46, (1999).

Inside the pubblication list of this article you can find many others

Regards,
    Sigismondo


Steven Kirk steven.kirk.-#-.htu.se wrote:
> Sent to CCL by: "Steven  Kirk" [steven.kirk#,#htu.se]
> Hello,
> 
> I would like to ask if anyone on this list is aware of any ab initio electron structure calculations of the high-pressure ice phase ice-X. This is interesting as it has a Cu_{2}O -type structure, and the hydrogen bonds are centrosymmetric (i.e. the H atom is equidistant from both what would be conventionally regarded as the 'donor' and 'acceptor' O atoms).
> 
> I have searched the Phys. Rev. and Nature indices, with no success thus far. I would be grateful for any pointers to literature or web pages of active researchers in this area.
> 
> Many thanks in advance,
> Steve Kirk> 
> 
> 
> 


-- 
Sigismondo Boschi, Ph.D.               tel: +39 051 6171559
CINECA (High Performance Systems)      fax: +39 051 6137273 - 6132198
via Magnanelli, 6/3                    http://instm.cineca.it
40033 Casalecchio di Reno (BO)-ITALY   http://www.cineca.it


From owner-chemistry@ccl.net Thu Nov 10 08:03:01 2005
From: "Marc Baaden baaden]![smplinux.de" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: Intel Fortran compiler (was using DELPHI with g77 and gcc !)
Message-Id: <-29921-051110074959-7058-1fzdspd2GDjEu88OUJP/bA]_[server.ccl.net>
X-Original-From: Marc Baaden <baaden.]_[.smplinux.de>
Content-Type: text/plain; charset=us-ascii
Date: Thu, 10 Nov 2005 13:49:43 +0100
Mime-Version: 1.0


Sent to CCL by: Marc Baaden [baaden#%#smplinux.de]

Dear All,

>>> "David F. Green dfgreen[]ams.sunysb.edu" said:
[..]
 >> If you will be unning under Linux on x86 architecture (Intel or AMD), I 
 >> would suggest using Intel's compilers (free for non-commerical use):
[..]

Just a comment on David's qualification as "free for non-commercial use" for
Intel's Fortran compiler.

It should be noted that Intel has quite a specific interpretation of this,
and I would guess that quite a number of labs are violating the license because
they are not aware of this subtle definition. In particular (from Intel's
FAQ [1]):


Q. I am engaged in research projects. Can I qualify to use the noncommercial product?
A. If you, as an individual, are receiving any form of compensation for the research project (i.e., you receive a salary, or funding, etc.) you do not qualify for a non-commercial license. However, if your research is a personal project for which you are not getting compensated in any way, you do qualify for a noncommercial-use license.

Q. I am a professor. Can I use the non-commercial product as part of the coursework I teach?
A. No. Teaching is a profession and you are getting compensated for it. You may, however, qualify for the academic license. (Click to academic page)

etc.

So this might not be utterly appealing to most researchers.

MB


[1] http://www.intel.com/cd/software/products/asmo-na/eng/compilers/flin/219692.htm
-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden++smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217


From owner-chemistry@ccl.net Thu Nov 10 08:38:00 2005
From: "john furr john.furr ~ gmail.com" <owner-chemistry]^[server.ccl.net>
To: CCL
Subject: CCL:G: Linda with Fedora
Message-Id: <-29922-051110055741-11723-blmwIXlZWwMdPzxhHfSJ2w]^[server.ccl.net>
X-Original-From: john furr <john.furr~~gmail.com>
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Thu, 10 Nov 2005 05:57:36 -0500
MIME-Version: 1.0


Sent to CCL by: john furr [john.furr[]gmail.com]
Both OS's will cluster quite easily.  However mixing them may give you
some issues.  In Fedora Core 4 the default version of gcc is 4.0.0. 
However in Fedora Core 3 it is gcc-3.4.2 (I think).  The two are NOT
binary compatible regardless of what some people say.

Personally I like Core 4 much better than Core 3.  However it sounds
like your application (Gaussian) only works right with Core 3.  I
suggest going with Core 3.

With that said.  I have seen a few stability issues with Core 3.    I
have a small cluster running Core 4 machines and they all have an
uptime of about 3 months...would be longer but the power grid here in
Albany NY is quite pathetic.

Well that certainly wasn't a Gaussian specific answer but I hope there
was some useful information any how.

Cheers

John Furr
Dynamol Inc.
http://www.dynamol.com




On 11/10/05, Ulrike Salzner salzner,fen.bilkent.edu.tr
<owner-chemistry^ccl.net> wrote:
> Sent to CCL by: Ulrike Salzner [salzner!^!fen.bilkent.edu.tr]
> I am about to built a Linux cluster using Linda/G03. I am using Fedora
> Core 3 and 4. Since this version of Linux is not supported by Gaussian,
> I need to know whether Linda will work. Gaussian runs fine with Fedora
> Core 3 but it seems to have problems with FC4 kernel 2.6.11-1.1369.
>
> Has anyone managed to get a cluster working with Fedora Core 3 or 4?
> Thanks in advance for any advice.
>
> Ulrike
> --
> Ulrike Salzner
> Associate Professor
> Department of Chemistry
> Bilkent University
> 06800 Bilkent, Ankara
> Turkey>
>
>
>


From owner-chemistry@ccl.net Thu Nov 10 09:26:01 2005
From: "Marcin Dulak Marcin_Dulak~!~poczta.onet.pl" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: A LaTeX and pdf database of XC and kinetic functionals (by Fabien Tran)
Message-Id: <-29923-051110090515-11848-B3Uk0F94odfmehEVJdXY9g!=!server.ccl.net>
X-Original-From: Marcin Dulak <Marcin_Dulak ~~ poczta.onet.pl>
Content-transfer-encoding: 7BIT
Content-type: text/plain; format=flowed; charset=us-ascii
Date: Thu, 10 Nov 2005 13:03:04 +0100
MIME-version: 1.0


Sent to CCL by: Marcin Dulak [Marcin_Dulak.:.poczta.onet.pl]
Dear CCLers,

it is to announce the first version of the LaTeX database with formulas 
of DFT XC and kinetic functionals (by Fabien Tran).
I'm not aware of any other similar existing one - you just copy and 
paste the formula you need.
I hope this is a first step to save our "scientific" time when writing 
papers.
http://scsg20.unige.ch/~dulak/files/functionals.tex

Please send any comments or "bug" reports directly
Marcin_Dulak(-at-)poczta.onet.pl

Faithfully yours,

Marcin Dulak


From owner-chemistry@ccl.net Thu Nov 10 10:36:00 2005
From: "Abrash, Samuel sabrash-#-richmond.edu" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL:G: Calculation of Counterpoise Corrected Binding Energies using G03
Message-Id: <-29924-051110103252-11980-ns+drQBLiycgT6dhYceXxg-x-server.ccl.net>
X-Original-From: "Abrash, Samuel" <sabrash|-|richmond.edu>
content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
	charset="utf-8"
Date: Thu, 10 Nov 2005 10:32:49 -0500
MIME-Version: 1.0


Sent to CCL by: "Abrash, Samuel" [sabrash(0)richmond.edu]
Hi,

I just started using the Counterpoise keyword in Gaussian to get BSSE corrected optimized geometries and binding energies of hydrogen bonded complexes.

The output includes the BSSE corrected energy.

The question I have now is how to calculate the binding energy.  If I hadn't already done the counterpoise correction, what I'd do is to create a job with an acetylene monomer, plus dummy atoms carrying the basis functions for the other acetylene monomer, calculate this energy, and subtract twice this energy from the non-BSSE corrected dimer energy.

Since the energy I have for the dimer is now BSSE corrected, do I get the binding energy simply by calculating the monomer energy (with no dummy atoms and no extra basis functions), and subtracting twice this energy from the BSSE corrected dimer energy?

Thanks for your time!

Best,

Sam Abrash


From owner-chemistry@ccl.net Thu Nov 10 11:10:00 2005
From: "Eugen Leitl eugen,,leitl.org" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL:G: [nixon(a)nsc.liu.se: Re: [Beowulf] [owner-chemistry(a)ccl.net: CCL:G: Linda with Fedora]]
Message-Id: <-29925-051110110004-31177-xMhPHI4tMqof9y6DAwFmHw(a)server.ccl.net>
X-Original-From: Eugen Leitl <eugen!=!leitl.org>
Content-Disposition: inline
Content-Type: text/plain; charset=us-ascii
Date: Thu, 10 Nov 2005 16:59:46 +0100
Mime-Version: 1.0


Sent to CCL by: Eugen Leitl [eugen(-)leitl.org]
----- Forwarded message from Leif Nixon <nixon]![nsc.liu.se> -----

> From: Leif Nixon <nixon]![nsc.liu.se>
Date: Thu, 10 Nov 2005 16:55:27 +0100
To: Eugen Leitl <eugen]![leitl.org>
Cc: Beowulf]![beowulf.org
Subject: Re: [Beowulf] [owner-chemistry]![ccl.net: CCL:G: Linda with Fedora]
User-Agent: Gnus/5.1006 (Gnus v5.10.6) Emacs/21.3 (gnu/linux)

Eugen Leitl <eugen]![leitl.org> writes:

> On 11/10/05, Ulrike Salzner salzner,fen.bilkent.edu.tr
> <owner-chemistry^-^ccl.net> wrote:
>> Sent to CCL by: Ulrike Salzner [salzner!^!fen.bilkent.edu.tr]
>> I am about to built a Linux cluster using Linda/G03. I am using Fedora
>> Core 3 and 4. Since this version of Linux is not supported by Gaussian,
>> I need to know whether Linda will work. Gaussian runs fine with Fedora
>> Core 3 but it seems to have problems with FC4 kernel 2.6.11-1.1369.

I'd say it's the libc version that creates problems for Gaussian, not
the kernel.

I'd recommend using CentOS 3 or 4 rather than Fedora Core. Fedora is
too rapidly moving, and you never know when an update might cause
Gaussian to keel over. CentOS (a free rebuild of Red Hat Enterprise)
is much more conservative than Fedora, but similar enough that you
won't have any trouble dealing with it if you are used to Fedora.

We have managed to get Gaussian 03 work with Linda on CentOS 3, after
much frustration and swearing. The trick is to use Linda binaries
compiled on Red Hat 8. Those binaries end up having just the right
set of libc dependencies to work with the CentOS 3 libc version.

Of course, you end up paying $500 to Gaussian in "media fee" to get
those binaries, even if you have already paid for the full-out compute
center source code license for Gaussian. (You don't get the Linda
source code, though.)

(I'm assuming Eugen will cross-post back to the correct list, or that
Ulrike reads this list.)

-- 
Leif Nixon                       -            Systems expert
------------------------------------------------------------
National Supercomputer Centre    -      Linkoping University
------------------------------------------------------------
_______________________________________________
Beowulf mailing list, Beowulf]![beowulf.org
To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf

----- End forwarded message -----
-- 
Eugen* Leitl <a href="http://leitl.org">leitl</a>
______________________________________________________________
ICBM: 48.07100, 11.36820            http://www.leitl.org
8B29F6BE: 099D 78BA 2FD3 B014 B08A  7779 75B0 2443 8B29 F6BE


From owner-chemistry@ccl.net Thu Nov 10 12:01:01 2005
From: "David F. Green dfgreen,+,ams.sunysb.edu" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: Intel Fortran compiler (was using DELPHI with g77 and gcc !)
Message-Id: <-29926-051110115852-2487-0uPgJ2zYGhtcBNcd5fiWJg(_)server.ccl.net>
X-Original-From: "David F. Green" <dfgreen]-[ams.sunysb.edu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Thu, 10 Nov 2005 12:00:34 -0500
MIME-Version: 1.0


Sent to CCL by: "David F. Green" [dfgreen%ams.sunysb.edu]
Thanks for the tip, Marc;  I (obviously) wasn't aware of that 
restriction.  I would suggest though, that investing in a good compiler 
that can produce well-optimized instructions for your architecture is 
often a good idea.  If you are doing a lot of calculations, the 
performance boost you get (especially factored over a cluster) is easily 
worth it; a 10% performance gain on each of 10 nodes is equivalent to an 
extra machine. Of course, if you will just be doing the occasional 
calculation, this logic may not apply.  I should note, I'm generally a 
big fan of Free Software, and the Gnu compilers are impressive in the 
range of achitectures they support, but they simply do not produce 
particularly fast code, and sometimes that needs to be considered (this 
applies to C/C++ as well as to Fortran).

Cheers,

David.

========================================================================
David F. Green                                  <dfgreen*_*ams.sunysb.edu>
  Assistant Professor                 http://www.ams.sunysb.edu/~dfgreen/
  Applied Mathematics and Statistics
  Stony Brook University                          Office: +1-631-632-9344
  Math Tower, Room 1-117                          Mobile: +1-617-953-3922
  Stony Brook, NY 11794-3600                         Fax: +1-631-632-8490
========================================================================


Marc Baaden baaden]![smplinux.de wrote:
> Sent to CCL by: Marc Baaden [baaden#%#smplinux.de]
> 
> Dear All,
> 
> 
>>>>"David F. Green dfgreen[]ams.sunysb.edu" said:
> 
> [..]
>  >> If you will be unning under Linux on x86 architecture (Intel or AMD), I 
>  >> would suggest using Intel's compilers (free for non-commerical use):
> [..]
> 
> Just a comment on David's qualification as "free for non-commercial use" for
> Intel's Fortran compiler.
> 
> It should be noted that Intel has quite a specific interpretation of this,
> and I would guess that quite a number of labs are violating the license because
> they are not aware of this subtle definition. In particular (from Intel's
> FAQ [1]):
> 
> 
> Q. I am engaged in research projects. Can I qualify to use the noncommercial product?
> A. If you, as an individual, are receiving any form of compensation for the research project (i.e., you receive a salary, or funding, etc.) you do not qualify for a non-commercial license. However, if your research is a personal project for which you are not getting compensated in any way, you do qualify for a noncommercial-use license.
> 
> Q. I am a professor. Can I use the non-commercial product as part of the coursework I teach?
> A. No. Teaching is a profession and you are getting compensated for it. You may, however, qualify for the academic license. (Click to academic page)
> 
> etc.
> 
> So this might not be utterly appealing to most researchers.
> 
> MB
> 
> 
> [1] http://www.intel.com/cd/software/products/asmo-na/eng/compilers/flin/219692.htm


From owner-chemistry@ccl.net Thu Nov 10 12:35:01 2005
From: "Sergio Emanuel Galembeck segalemb .. usp.br" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL:G: Calculation of Counterpoise Corrected Binding Energies using G03
Message-Id: <-29927-051110115920-2765-zd9//CDZHavFyOT2thLfjA(-)server.ccl.net>
X-Original-From: Sergio Emanuel Galembeck <segalemb**usp.br>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Thu, 10 Nov 2005 14:59:12 -0200
MIME-Version: 1.0


Sent to CCL by: Sergio Emanuel Galembeck [segalemb_-_usp.br]
Dear Samuel,

    The counterpoise method as is implemented in G03 
presents the energies in the following order:
E(complex), E(monomer1, dummy monomer2), E(monomer2, dummy monomer1), 
E(monomer1), E(monomer2),
where E(monomer1, dummy monomer2) is the energy of monomer1 with
dummy atoms for monomer2. and E(monomer1) is the energy of monomer1
in the geometry of the complex. 

                  Best regards,

                         Sergio Galembeck


==============================================================
Sergio Emanuel Galembeck
Assistant Professor in Physical Chemistry
Departamento de Quimica
Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto
Universidade de Sao Paulo
Av Bandeirantes, 3900
Ribeirao Preto, SP
Brasil

phone: +55-16-602-37-65
fax: +55-16-633-81-51
e-mail: segalemb]^[usp.br
==============================================================
  
 

Citando "Abrash, Samuel sabrash-#-richmond.edu" <owner-chemistry]^[ccl.net>:

> Sent to CCL by: "Abrash, Samuel" [sabrash(0)richmond.edu]
> Hi,
> 
> I just started using the Counterpoise keyword in Gaussian to get BSSE
> corrected optimized geometries and binding energies of hydrogen bonded
> complexes.
> 
> The output includes the BSSE corrected energy.
> 
> The question I have now is how to calculate the binding energy.  If I hadn't
> already done the counterpoise correction, what I'd do is to create a job with
> an acetylene monomer, plus dummy atoms carrying the basis functions for the
> other acetylene monomer, calculate this energy, and subtract twice this
> energy from the non-BSSE corrected dimer energy.
> 
> Since the energy I have for the dimer is now BSSE corrected, do I get the
> binding energy simply by calculating the monomer energy (with no dummy atoms
> and no extra basis functions), and subtracting twice this energy from the
> BSSE corrected dimer energy?
> 
> Thanks for your time!
> 
> Best,
> 
> Sam Abrash> 
> 
> 
>


From owner-chemistry@ccl.net Thu Nov 10 15:13:00 2005
From: "Yao-Ying Chien chieny _ msu.edu" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: water melting simulation
Message-Id: <-29928-051110145901-22457-YnMH7SrytD1H++CQ9PnXyA---server.ccl.net>
X-Original-From: Yao-Ying Chien <chieny**msu.edu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Thu, 10 Nov 2005 13:47:29 -0800
MIME-Version: 1.0


Sent to CCL by: Yao-Ying Chien [chieny!^!msu.edu]
Hi,

I am interested in water melting simulation (from ice to water;  (would 
be nice if ) then water to ice). It  must have been done extensively. I 
did a quick search in SCI, but got (too) many returns. Read a few of 
them, but could not pin point who are the first ones simulated water 
melting successfully. Could you please point me the right keywords for 
the literature search? Pointers to Review papers or Web sites are great! 
Names of pioneers who failed but laid the foundation for others to 
succeed are welcome too.

A scientist I ran into 2 years ago at ACS meeting told me a Japanese 
scientist has done it on supercomputer. Could you please tell me the 
name of the Japanese scientist, or  the year, to help me narrow down the 
literature search?

A scientist mentioned that MD can do it. Is that so? My intuition is 
that some quantum level simulation may involve.

Basically, I wish to see motion pictures when water melts (and hopefully 
become ice again). How the 1st few ice molecules decide to break their 
H-bonds to form a cluster of water molecules. And  why  do they break-- 
does  it  require some form of "seed" in the neighborhood to initiate 
the process? Does the same "seed" initiate the freezing as well? Any 
evidences to support or against the observations (or the predictions) in 
the simulations?

Thanks,

Yao-Ying Chien


From owner-chemistry@ccl.net Thu Nov 10 15:48:00 2005
From: "Perry E. Metzger perry*piermont.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: Intel Fortran compiler
Message-Id: <-29929-051110135108-23129-nM9HDi7z4eLaYBu6Rd7UMw:server.ccl.net>
X-Original-From: "Perry E. Metzger" <perry-,-piermont.com>
Content-Type: text/plain; charset=us-ascii
Date: Thu, 10 Nov 2005 13:50:59 -0500
MIME-Version: 1.0


Sent to CCL by: "Perry E. Metzger" [perry::piermont.com]

"David F. Green dfgreen,+,ams.sunysb.edu" <owner-chemistry/./ccl.net> writes:
> I should note, I'm generally a big fan of Free Software, and the Gnu
> compilers are impressive in the range of achitectures they support,
> but they simply do not produce particularly fast code, and sometimes
> that needs to be considered (this applies to C/C++ as well as to
> Fortran).

That depends. For some architectures, languages, target programs, and
versions of GCC, GCC works best. For others, it does not. It is very
dependent, as I said, on the architecture you're running on, the
language you're compiling, what code you're compiling, and (very very
important!) which version of gcc and which optimization flags you set.

I recommend benchmarking the code you're actually going to run on the
machines you'll run it on -- nothing beats an actual experiment in
cases like this. Especially if you're going to do a lot of
computation, taking a little bit of time and trying a few things
(including different settings of the optimization flags in your
compilers) pays off handsomely in the end.

Oh, and repeating that last bit one more time -- modern compilers have
LOTS of optimizations you can turn on and off. Reading the
documentation and experimenting with the flags is key. Never assume
that the same optimizations will produce the best results for all
programs you compile.

Perry


From owner-chemistry@ccl.net Thu Nov 10 16:23:00 2005
From: "Julius Su jsu[#]caltech.edu" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL: very accurate wavefunctions for H2?
Message-Id: <-29930-051110142912-18271-jfV6tO3fFToEnzxvQTowRw[-]server.ccl.net>
X-Original-From: "Julius  Su" <jsu%x%caltech.edu>


Sent to CCL by: "Julius  Su" [jsu-x-caltech.edu]
Hello,

  I am trying to calculate very accurate wavefunctions for H2 for use in developing density functionals.

  So far, I have a partial implementation of the James-Coolidge wavefunction (Rev. Mod. Phys. 32(2) 1960, p. 219):

  psi = exp(-a (z1 + z2)) z1^p n1^q z2^r n2^s r12^u (elliptic coords)

 and am interested in getting coefficients for the Kolos-Wolniewicz wavefunction: (J. Chem. Phys. 43(7) 1965, p. 2429)

  psi = exp(-a1 z1 - a2 z2) cosh (b1 n1 + b2 n2) z1^p n1^q z2^r n2^s r12^u

Does anyone have code for computing coefficients for either of these wavefunctions?  

Thanks,

Julius


From owner-chemistry@ccl.net Thu Nov 10 16:57:00 2005
From: "Osman Guner osman ~~ san.rr.com" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: Second Call for Papers - Advances in Pharmacophores and 3D Screening
Message-Id: <-29931-051110123115-213-D7zuo+GS+2jQeIZKLozYSQ[*]server.ccl.net>
X-Original-From: "Osman Guner" <osman.:.san.rr.com>
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_0000_01C5E5E6.ED26A9E0"
Date: Thu, 10 Nov 2005 11:07:21 -0800
MIME-Version: 1.0


Sent to CCL by: "Osman Guner" [osman===san.rr.com]
This is a multi-part message in MIME format.

------=_NextPart_000_0000_01C5E5E6.ED26A9E0
Content-Type: text/plain;
	charset="us-ascii"
Content-Transfer-Encoding: 7bit

Please note the deadline for submission of abstracts through OASYS is
November 23.  We still have a number of openings for oral presentations.

 

Feel free to contact me for any questions.

 

Cheers.Osman

 

  _____  

From: Osman Guner [mailto:osman^^^san.rr.com] 
Sent: Wednesday, October 19, 2005 2:01 PM
To: 'chemistry-request^^^ccl.net'; 'CHMINF-L^^^LISTSERV.INDIANA.EDU'
Subject: Call for Papers - Advances in Pharmacophores and 3D Screening

 

Advances in Pharmacophores and 3D Screening

Organized by Chemical Information Division (CINF)

Co-sponsored by Computers in Chemistry (COMP), and Medicinal Chemistry
(MEDI) Divisions

 

At 231st ACS National Meeting, Atlanta, GA, March 26-30, 2006 

 

Recent developments in three-dimensional screening and data-mining
techniques will be covered with specific focus in pharmacophores and
3D-searching., 

 

If you are interested in being a speaker for this symposium, please submit
an abstract via the ACS OASYS system. A direct link to the CINF sessions is
below:

 

http://oasys.acs.org/acs/231nm/cinf/papers/index.cgi

 

The deadline for abstract submission is November 23.

 

 

 


------=_NextPart_000_0000_01C5E5E6.ED26A9E0
Content-Type: text/html;
	charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

<html xmlns:v=3D"urn:schemas-microsoft-com:vml" =
xmlns:o=3D"urn:schemas-microsoft-com:office:office" =
xmlns:w=3D"urn:schemas-microsoft-com:office:word" =
xmlns:st1=3D"urn:schemas-microsoft-com:office:smarttags" =
xmlns=3D"http://www.w3.org/TR/REC-html40">

<head>
<meta http-equiv=3DContent-Type content=3D"text/html; =
charset=3Dus-ascii">
<meta name=3DGenerator content=3D"Microsoft Word 11 (filtered medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]--><o:SmartTagType
 namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" =
name=3D"place"/>
<o:SmartTagType =
namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags"
 name=3D"State"/>
<o:SmartTagType =
namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags"
 name=3D"City"/>
<o:SmartTagType =
namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags"
 name=3D"PersonName"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
 /* Font Definitions */
 ^^^font-face
	{font-family:Tahoma;
	panose-1:2 11 6 4 3 5 4 4 2 4;}
 /* Style Definitions */
 p.MsoNormal, li.MsoNormal, div.MsoNormal
	{margin:0in;
	margin-bottom:.0001pt;
	font-size:12.0pt;
	font-family:"Times New Roman";}
a:link, span.MsoHyperlink
	{color:blue;
	text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
	{color:purple;
	text-decoration:underline;}
span.EmailStyle17
	{mso-style-type:personal;
	font-family:Arial;
	color:windowtext;}
span.EmailStyle18
	{mso-style-type:personal-reply;
	font-family:Arial;
	color:navy;}
^^^page Section1
	{size:8.5in 11.0in;
	margin:1.0in 1.25in 1.0in 1.25in;}
div.Section1
	{page:Section1;}
-->
</style>

</head>

<body lang=3DEN-US link=3Dblue vlink=3Dpurple>

<div class=3DSection1>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Please note the deadline for =
submission of
abstracts through OASYS is November 23.&nbsp; We still have a number of
openings for oral presentations.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Feel free to contact me for any =
questions.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Cheers&#8230;Osman<o:p></o:p></span>=
</font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<div>

<div class=3DMsoNormal align=3Dcenter style=3D'text-align:center'><font =
size=3D3
face=3D"Times New Roman"><span style=3D'font-size:12.0pt'>

<hr size=3D2 width=3D"100%" align=3Dcenter tabindex=3D-1>

</span></font></div>

<p class=3DMsoNormal><b><font size=3D2 face=3DTahoma><span =
style=3D'font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font =
size=3D2
face=3DTahoma><span style=3D'font-size:10.0pt;font-family:Tahoma'> Osman =
Guner
[mailto:osman^^^san.rr.com] <br>
<b><span style=3D'font-weight:bold'>Sent:</span></b> Wednesday, October =
19, 2005
2:01 PM<br>
<b><span style=3D'font-weight:bold'>To:</span></b> '<st1:PersonName =
w:st=3D"on">chemistry-request^^^ccl.net</st1:PersonName>';
'CHMINF-L^^^LISTSERV.INDIANA.EDU'<br>
<b><span style=3D'font-weight:bold'>Subject:</span></b> Call for Papers =
-
Advances in Pharmacophores and 3D Screening</span></font><o:p></o:p></p>

</div>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><b><font size=3D3 face=3D"Times New Roman"><span
style=3D'font-size:12.0pt;font-weight:bold'>Advances in Pharmacophores =
and 3D
Screening<o:p></o:p></span></font></b></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Organized by Chemical Information Division =
(CINF)<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Co-sponsored by Computers in Chemistry (COMP), and Medicinal =
Chemistry
(MEDI) Divisions<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>At </span></font><font face=3DArial><span =
style=3D'font-family:Arial'>231st
ACS National Meeting, <st1:place w:st=3D"on"><st1:City =
w:st=3D"on">Atlanta</st1:City>,
 <st1:State w:st=3D"on">GA</st1:State></st1:place>, March 26-30, =
2006</span></font>&nbsp;<o:p></o:p></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Recent developments in three-dimensional screening and =
data-mining
techniques will be covered with specific focus in pharmacophores and
3D-searching., <o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>If you are interested in being a speaker for this symposium, =
please
submit an abstract via the ACS OASYS system. A direct link to the CINF =
sessions
is below:<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><a href=3D"http://oasys.acs.org/acs/231nm/cinf/papers/index.cgi"
title=3D"http://oasys.acs.org/acs/231nm/cinf/papers/index.cgi">http://oas=
ys.acs.org/acs/231nm/cinf/papers/index.cgi</a><o:p></o:p></span></font></=
p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>The deadline for abstract submission is November =
23.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

</div>

</body>

</html>

------=_NextPart_000_0000_01C5E5E6.ED26A9E0--


From owner-chemistry@ccl.net Thu Nov 10 18:08:01 2005
From: "Eric Scerri scerri__chem.ucla.edu" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: question on molecular orbitals in CO and NO
Message-Id: <-29933-051110165048-28829-EQkz2wadQgHxO+61RoyFmA(-)server.ccl.net>
X-Original-From: Eric Scerri <scerri~!~chem.ucla.edu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Date: Thu, 10 Nov 2005 13:48:26 -0800
Mime-Version: 1.0 (Apple Message framework v734)


Sent to CCL by: Eric Scerri [scerri!^!chem.ucla.edu]



In teaching qualitative molecular orbital theory one encounters the  
question of the crossing of the sigma 2p and pi 2p bonding orbitals  
in homonuclear diatomics.


This is such that N2 has the pi orbitals of lower energy than sigma  
whereas for O2 the energies are reversed.

But what about heteronuclear diatomics where each of the atoms ?


The ordering given in general chemistry textbooks shows a wide  
variation.  See for example Oxtoby, Zumdahl or Olmsted and Williams,  
all three of which contradict each other.

Herzberg's, Spectra of Diatomic Molecules specifically states the  
configurations of CO and NO.

For CO the ordering is as in the case of N2 whereas for NO the  
ordering is as in O2.

However Herzberg's book is now a little out of date (1950).

Do more recent calculations on these two molecules suggest anything  
different?  Would anyone be prepared to run these calculations and  
tell me the results?

How about experimental evidence such as PES on CO and NO?



regards,
eric scerri


From owner-chemistry@ccl.net Thu Nov 10 17:33:01 2005
From: "Andy Holder holdera**umkc.edu" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: COMP: Division Survey
Message-Id: <-29932-051110161011-341-FkCz/tYjyjhwyw8TFGyrIg-,-server.ccl.net>
X-Original-From: "Andy  Holder" <holdera^umkc.edu>


Sent to CCL by: "Andy  Holder" [holdera*umkc.edu]
Hello!

The COMP Division of the ACS is interested in hearing your opinion about our current and future activities.  The information will be used to improve our current services to our membership and plan new services.  It will just take a moment to complete, and the results will be sanitized of all personal or indentifying information.

You can access the survey from a link on the Division's webpage at:

http://membership.acs.org/c/Comp/

Thanks!
Andy Holder

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
  CCCC    OOOO   MMM   MMM PPPP  |         ANDREW J. HOLDER
 CC  CC  OO  OO   MM   MM  P  PP |            2005 Chair
CCC     OO    OO  MMM MMM  PPPP  |        Dept. of Chemistry
 CC  CC  OO  OO   M MMM M  PP    |  Univ. of Missouri-Kansas City
  CCCC    OOOO   MMM M MMM PP    |      Kansas City, MO  64110
                                 |          holdera.:.umkc.edu
Computers in Chemistry Division  |  (816)235-2293 * (816)235-6543 F
  American Chemical Society      |
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=


From owner-chemistry@ccl.net Thu Nov 10 18:43:00 2005
From: "Andrey G. Kalinichev kalinich()uiuc.edu" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: water melting simulation
Message-Id: <-29934-051110180210-7992-sg7PrZmlGT5EnkRtNzjuCg-#-server.ccl.net>
X-Original-From: "Andrey G. Kalinichev" <kalinich+/-uiuc.edu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=us-ascii
Date: Thu, 10 Nov 2005 16:24:25 -0600
MIME-Version: 1.0


Sent to CCL by: "Andrey G. Kalinichev" [kalinich|a|uiuc.edu]
Masakazu Matsumoto, Shinji Saito and Iwao Ohmine
Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing
Nature 416, 409-413 (28 March 2002) 

http://www.nature.com/nature/journal/v416/n6879/abs/416409a.html

---- Original message ----
>Date: Thu, 10 Nov 2005 15:19:28 -0500
>From: "Yao-Ying Chien chieny _ msu.edu" <owner-chemistry~!~ccl.net>  
>Subject: CCL: water melting simulation  
>To: "Kalinichev, Andrey G " <andreyk~!~hercules.geology.uiuc.edu>
>
>Sent to CCL by: Yao-Ying Chien [chieny!^!msu.edu]
>Hi,
>
>I am interested in water melting simulation (from ice to water;  (would 
>be nice if ) then water to ice). It  must have been done extensively. I 
>did a quick search in SCI, but got (too) many returns. Read a few of 
>them, but could not pin point who are the first ones simulated water 
>melting successfully. Could you please point me the right keywords for 
>the literature search? Pointers to Review papers or Web sites are great! 
>Names of pioneers who failed but laid the foundation for others to 
>succeed are welcome too.
>
>A scientist I ran into 2 years ago at ACS meeting told me a Japanese 
>scientist has done it on supercomputer. Could you please tell me the 
>name of the Japanese scientist, or  the year, to help me narrow down the 
>literature search?
>
>A scientist mentioned that MD can do it. Is that so? My intuition is 
>that some quantum level simulation may involve.
>
>Basically, I wish to see motion pictures when water melts (and hopefully 
>become ice again). How the 1st few ice molecules decide to break their 
>H-bonds to form a cluster of water molecules. And  why  do they break-- 
>does  it  require some form of "seed" in the neighborhood to initiate 
>the process? Does the same "seed" initiate the freezing as well? Any 
>evidences to support or against the observations (or the predictions) in 
>the simulations?
>
>Thanks,
>
>Yao-Ying Chien>
>
>
--
Andrey Kalinichev
e-mail: kalinich{at}uiuc.edu
http://www.geology.uiuc.edu/~kalinich
Phone: (217) 333-4389


From owner-chemistry@ccl.net Thu Nov 10 19:22:00 2005
From: "shoaleh dehghan sd268#%#georgetown.edu" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: Software to predict crystal structure(MOLPAC,DMAREL)
Message-Id: <-29935-051110191410-26060-U+SVJjY7jCqa4B1UKx5tBw^-^server.ccl.net>
X-Original-From: "shoaleh  dehghan" <sd268:-:georgetown.edu>


Sent to CCL by: "shoaleh  dehghan" [sd268*_*georgetown.edu]
Dear CCLers,

How can I download a version of MOLPAC, DMAREL or any other program for
prediction of crystal structure?
thank you very much for your help.

Regards,

Shoaleh Dehghan
--------------------------------------------------------------------------
Shoaleh Dehghan
Postdoctoral fellow
Department of Chemistry
Georgetown University
37th and O Streets, NW
Washington DC 20057


From owner-chemistry@ccl.net Thu Nov 10 19:56:01 2005
From: "Gardner, Elizabeth A. eagardner-,-utep.edu" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL:G: question on molecular orbitals in CO and NO
Message-Id: <-29936-051110193332-19612-Je68ZFlBuSTYPl7uu8GMdQ]_[server.ccl.net>
X-Original-From: "Gardner, Elizabeth A." <eagardner]![utep.edu>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
	charset="us-ascii"
Date: Thu, 10 Nov 2005 16:46:19 -0700
MIME-Version: 1.0


Sent to CCL by: "Gardner, Elizabeth A." [eagardner a utep.edu]
I can try them on Gaussian 03W.  What level of theory?

Beth

Elizabeth Gardner 
Assistant Professor 
Department of Chemistry 
University of Texas at El Paso 
El Paso, TX  79968 
Phone: (915) 747-7551 
Fax: (915) 747-5748 
Office: 121D Physical Sciences Bldg.
-----Original Message-----
> From: owner-chemistry**ccl.net [mailto:owner-chemistry**ccl.net] 
Sent: Thursday, November 10, 2005 4:12 PM
To: Gardner, Elizabeth A.
Subject: CCL: question on molecular orbitals in CO and NO

Sent to CCL by: Eric Scerri [scerri!^!chem.ucla.edu]



In teaching qualitative molecular orbital theory one encounters the  
question of the crossing of the sigma 2p and pi 2p bonding orbitals  
in homonuclear diatomics.


This is such that N2 has the pi orbitals of lower energy than sigma  
whereas for O2 the energies are reversed.

But what about heteronuclear diatomics where each of the atoms ?


The ordering given in general chemistry textbooks shows a wide  
variation.  See for example Oxtoby, Zumdahl or Olmsted and Williams,  
all three of which contradict each other.

Herzberg's, Spectra of Diatomic Molecules specifically states the  
configurations of CO and NO.

For CO the ordering is as in the case of N2 whereas for NO the  
ordering is as in O2.

However Herzberg's book is now a little out of date (1950).

Do more recent calculations on these two molecules suggest anything  
different?  Would anyone be prepared to run these calculations and  
tell me the results?

How about experimental evidence such as PES on CO and NO?



regards,
eric scerrihttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Thu Nov 10 20:45:01 2005
From: "shoaleh dehghan shoalehd\a/yahoo.com" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: Software to predict crystal structure(MOLPAC,DMAREL)
Message-Id: <-29937-051110201121-12627-fCXFnLaGUOcxVY3OwlqzjQ * server.ccl.net>
X-Original-From: shoaleh dehghan <shoalehd*yahoo.com>
Content-Transfer-Encoding: 8bit
Content-Type: multipart/alternative; boundary="0-1654175072-1131667874=:60506"
Date: Thu, 10 Nov 2005 16:11:14 -0800 (PST)
MIME-Version: 1.0


Sent to CCL by: shoaleh dehghan [shoalehd[A]yahoo.com]
--0-1654175072-1131667874=:60506
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

Dear CCLers,

How can I download a version of MOLPAC, DMAREL or any other program for
prediction of crystal structure?
thank you very much for your help.

Regards,

Shoaleh Dehghan


Shoaleh Dehghan
Postdoctoral fellow
Department of Chemistry
Georgetown University
37th and O Streets, NW
Washington DC 20057


		
---------------------------------
 Yahoo! FareChase - Search multiple travel sites in one click.  
--0-1654175072-1131667874=:60506
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

<DIV>Dear CCLers,<BR><BR>How can I download a version of MOLPAC, DMAREL or any other program for<BR>prediction of crystal structure?<BR>thank you very much for your help.<BR><BR>Regards,<BR><BR>Shoaleh Dehghan<BR><BR><BR>Shoaleh Dehghan<BR>Postdoctoral fellow<BR>Department of Chemistry<BR>Georgetown University<BR>37th and O Streets, NW<BR>Washington DC 20057<BR></DIV><p>
		<hr size=1> <a href="http://us.lrd.yahoo.com/_ylc=X3oDMTFqODRtdXQ4BF9TAzMyOTc1MDIEX3MDOTY2ODgxNjkEcG9zAzEEc2VjA21haWwtZm9vdGVyBHNsawNmYw--/SIG=110oav78o/**http%3a//farechase.yahoo.com/">Yahoo! FareChase - Search multiple travel sites in one click.</a>

 

 
--0-1654175072-1131667874=:60506--