From chemistry-request@ccl.net Sun Jan 23 19:29:20 2005 Received: from exmails2.chem.ucla.edu (exmails2.chem.ucla.edu [169.232.134.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0O0TJi3017196 for ; Sun, 23 Jan 2005 19:29:19 -0500 Received: from [169.232.230.120] (ts17-44.dialup.bol.ucla.edu [169.232.230.120]) (authenticated bits=0) by exmails2.chem.ucla.edu (8.12.8/8.12.8) with ESMTP id j0NMlcuh015382 for ; Sun, 23 Jan 2005 14:47:56 -0800 Mime-Version: 1.0 X-Sender: scerri(at)chlorine.chem.ucla.edu (Unverified) Message-Id: Date: Sat, 22 Jan 2005 14:47:15 -0800 To: ccl From: Eric Scerri Subject: orbitals and reality Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net The discussion has been very interesting. I have worried about these issues before and have published two papers specifically addressing the question of observation or otherwise of orbitals. Both can be accessed on my UCLA web page. One is addressed to chemical educators and the other to philosophers of science. http://www.chem.ucla.edu/dept/Faculty/scerri/ See entries 73 and 90 for the educational question and 81 for the article to the Philosophy of Science Association. # 73 is cited in the textbook by Zumdahl in the section on orbital models that was reproduced on this list a few days ago. These articles were prompted by the claims in 1999, including a front page feature in Nature Magazine that orbitals had been directly observed. I have been too busy to follow all the details of the recent claim but I cannot help thinking that just as in 1999 there is a certain amount of hype going on. This was more or less confirmed a few days ago when I learned from the discussion on this list that Villneuve actually admits that they deliberately used provocative language in their claims. I too wrote to Stepelfeld and Villneuve and sent them copies of my articles, asking them to try to explain why this recent observation is any different from that of 1999, in theoretical/philosophical terms. The response I received from Stepelfeld is identical to the one that was posted on this list a few days ago. Villneuve has yet to respond. The claim would only be worthy of drama and front page news if orbitals had indeed been observed, which we all know in advance cannot ever happen. How is it that we have never heard again from the Arizona State team that observed orbitals in copper oxide? Would it be possible for Villneuve et al. to observe orbitals in an atomic system in order to disentangle any complications that might occur because one is dealing with a molecule in N2? Could they or somebody else turn their technique to atomic hydrogen? Could anyone perform some experiments which are specifically aimed at imaging orbitals rather than just mentioning it in the course of an article to Nature in the knowledge that it will make a splash? The question of whether one could speak meaningfully of an empty orbital is interesting. Well of course we can speak of it, just as we can speak of unicorns etc. That does not make them exist. What I mean is that the whole notion of electrons IN orbitals is something of a confusion in conceptual terms. Admittedly the putting of electrons in orbitals is very useful as a book-keeping device just as it is very useful mathematically to consider the occupation of certain orbitals and not others in calculations, sometimes even with fractional occupations. But if one wants to picture the situation conceptually perhaps an orbital just IS one or more electrons in the sense of wave-particle duality. To return to thinking of electrons as particles IN an orbital (probability waves) maybe a failure to bite the bullet of wave-particle duality in conceptual terms. regards, eric scerri -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri(at)chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.kluweronline.com/issn/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html From chemistry-request@ccl.net Mon Jan 24 11:18:44 2005 Received: from impact.dyn.unipg.it (impact.dyn.unipg.it [141.250.17.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0OGIg6f017071 for ; Mon, 24 Jan 2005 11:18:43 -0500 Received: from localhost (max@localhost) by impact.dyn.unipg.it (8.11.7p1+Sun/8.11.7) with ESMTP id j0OFFwF16463 for ; Mon, 24 Jan 2005 16:15:58 +0100 (MET) Date: Mon, 24 Jan 2005 16:15:58 +0100 (MET) From: Porrini Massimiliano To: chemistry*at*ccl.net Subject: Coupling Constants in Barostats and/or Thermostats In-Reply-To: Message-ID: References: <200501220019.27978.bernd-schubert*at*web.de> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi * Does anybody which knows how can I choose the best values for the time coupling constants \tau_P and/or \tau_T in the Berendsen and Hoover barostats and thermostats? I haven't found any method that I have to follow for fixing these constants. Thanks in Advance massimiliano porrini +++++++++++++++++++++++++++++++++++++++++++++++++++++ Dott. Massimiliano Porrini Dipartimento di Chimica Universita` degli Studi di Perugia Via Elce di Sotto, 8 06123 Perugia (PG) Italia Tel. +39 075 585 5527 Fax +39 075 585 5606 e-mail max*at*dyn.unipg.it +++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@ccl.net Mon Jan 24 13:00:31 2005 Received: from mail7.uno.edu (mail7.uno.edu [137.30.97.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0OHxU6f021537 for ; Mon, 24 Jan 2005 12:59:30 -0500 Received: from mail5.uno.edu ([137.30.97.209]) by mail7.uno.edu with Microsoft SMTPSVC(6.0.3790.211); Mon, 24 Jan 2005 10:12:44 -0600 X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Subject: 05.07.20-26, 5th Congress of Int Soc Theor Chem Physics, New Orleans Date: Mon, 24 Jan 2005 10:12:44 -0600 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Index: AcUCL4lvZBxmXOCHTueHY9VqgzJd8Q== From: "Peter A Politzer" To: Cc: X-OriginalArrivalTime: 24 Jan 2005 16:12:44.0741 (UTC) FILETIME=[89BB7750:01C5022F] X-Spam-Status: No, hits=4.6 required=7.5 tests=HTML_FONT_BIG,HTML_MESSAGE, MIME_HTML_ONLY,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net
=0A=

  = Fifth =0A= Congress

=0A=

of the

=0A=

International Society for Theoretical Chemical =0A= Physics

=0A=

 

=0A=

July 20 = – July 26, =0A= 2005

=0A=

Renaissance = Arts Hotel, =0A= New Orleans, =0A= Louisiana

=0A=

 

=0A=

Purposes:  =0A=

=0A=

(1)    =0A= To promote interaction, exchange of ideas = and =0A= collaboration on an international level.

=0A=

(2)    =0A= To provide an opportunity for students and =0A= postdoctoral research associates to interact with leaders in their = fields and to =0A= present their own work in poster sessions.

=0A=

 

=0A=

Congress = Format:

=0A=

There will be nine sessions of invited speakers, dealing = with:

=0A=

(1)   =0A= Methodology; (2) Statistical Mechanics; (3) =0A= Noncovalent Interactions;

=0A=

(4) Nanomaterials; (5) Surfaces, = Materials; (6) =0A= Molecular Biophysics;

=0A=

(7) Solvation; (8) Ab Initio/Density = Functional =0A= Theory;

=0A=

(9) Open Problems in Theory.

=0A=

There will also be three poster sessions, involving all areas = of chemical =0A= physics, molecular biology and materials science.

=0A=

 

=0A=

Partial List of =0A= Speakers:

=0A=

L. Adamowicz (University of Arizona)        =            &nbs= p;    =0A= M. Levy = (North Carolina A&T University)  =0A=

=0A=

W. D. Allen (University of Georgia)           &nbs= p;            = ;      =0A= D. Millar (Scripps Research =0A= Institute)

=0A=

A. van der Avoird (University of Nijmegen)            &nbs= p; =0A= K. Mhller-Dethlefs (University of York)

=0A=

P. B. Balbuena (Texas A&M University)           &nbs= p;   =0A= R. R. Netz (University of Munich)

=0A=

R. J. Bartlett (University of Florida)           &nbs= p;           =0A= M. Nooijen (University of Waterloo)

=0A=

S. Boniv = (Halifax University)           =0A=            &nbs= p;            =0A= M. Orozco (University of Barcelona)

=0A=

C. Brooks (Scripps Research Institute)                  =0A= R. Osman (Mt. =0A= Sinai Medical School)

=0A=

K. J. Burke (Rutgers University)           &nbs= p;            = ;  =0A= R. G. Parr (University of North = Carolina)

=0A=

A. M. Chaka (Nat. Inst. Stand. Tech.)           &nbs= p;       =0A= J. P. Perdew (Tulane University)

=0A=

D. Clary (University of Oxford)           &nbs= p;            = ;     =0A= N. Richards (University of Florida)

=0A=

C. J. Cramer (University of Minnesota)           &nbs= p;     =0A= A. Rubio (Donostia International Physics =0A= Center, =0A= Spain)

=0A=

M. J. Frisch (Gaussian Inc.)           &nbs= p;            = ;            =         =0A= D. R. Salahub (University of Calgary)

=0A=

J. Gao (University of Minnesota)           &nbs= p;            = ;  =0A= A. Savin (University of Paris)

=0A=

N. Gidopoulos (Rutherford Appleton Laboratory, =0A= UK)    =0A= G. E. Scuseria (Rice University)

=0A=

A. G=F6rling (University of Bonn)           &nbs= p;            = ;            = =0A= T. Seideman (Northwestern University)

=0A=

M. Havenith (Ruhr-University of = Bochum)           &nbs= p;  =0A= J. M. Seminario (Texas A&M University)

=0A=

S. Hirata =0A= (University of Florida)           &nbs= p;            = ;    =0A= J. F. Stanton (University of Texas)

=0A=

P. Hobza (Czech Academy of Sciences)           &nbs= p;     =0A= M. S. de Vries (University of California, Santa = Barbara)

=0A=

B. Jeziorski (University of Warsaw)           &nbs= p;          =0A= H. Weinstein (Cornell Medical School)

=0A=

K. Jordan (University of Pittsburgh)           &nbs= p;          =0A= D. Woolard (U.S. Army Research Office)

=0A=

H. J. Kreuzer (Dalhousie University)           &nbs= p;        =0A= W. Yang (Duke University)          =0A=            &nbs= p;            =0A=

=0A=

J. Ladik (University of Erlangen-Nuernberg)            =0A= T. Zwier (Purdue University)        =

=0A=

R. Lavery (Institute Biol. Phys. Chim., = Paris)

=0A=

 

=0A=

For further information, please go to www.istcp.org or contact Peter Politzer, Department of = Chemistry, =0A= University of New Orleans, New Orleans, LA, 70148; Tel: 504-280-6850; = E-mail: =0A= ppolitze<>uno.edu

From chemistry-request@ccl.net Mon Jan 24 13:18:45 2005 Received: from nic.upatras.gr (nic.upatras.gr [150.140.129.30]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0OIIf6f022283 for ; Mon, 24 Jan 2005 13:18:42 -0500 Received: (qmail 8224 invoked by uid 111); 24 Jan 2005 16:31:59 -0000 Received: from garoufal(at)physics.upatras.gr by nic.upatras.gr by uid 103 with qmail-scanner-1.22 (clamdscan: 0.71. Clear:RC:1(150.140.159.71):. Processed in 0.074246 secs); 24 Jan 2005 16:31:59 -0000 Received: from pythagoras.physics.upatras.gr (150.140.159.71) by nic.upatras.gr with SMTP; 24 Jan 2005 16:31:58 -0000 Received: (qmail 3953 invoked from network); 24 Jan 2005 16:27:55 -0000 Received: from qchem-w02.physics.upatras.gr (HELO qchemw02) (150.140.159.222) by pythagoras.physics.upatras.gr with SMTP; 24 Jan 2005 16:27:55 -0000 Message-ID: <001701c50232$a9045160$de9f8c96@qchemw02> From: "C. Garoufalis" To: Subject: parallel GAMESS problems Date: Mon, 24 Jan 2005 18:34:38 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0012_01C50243.5C39BF80" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1437 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_30_40,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0012_01C50243.5C39BF80 Content-Type: text/plain; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable Dear CCLers I have successfully compiled the latest version of GAMESS on my linux cluster. When running on a single node, everything goes = fine. When I try to run a parallel job there seems to be a problem. The job starts successfully, but the cpu utilization on the nodes is = less than 1% As a result the parallel job is much slower than the one run on a single = node. Obviously, I am missing something Dr. Christos S. Garoufalis Dept. of Physics, Univ. of Patras Greece ------=_NextPart_000_0012_01C50243.5C39BF80 Content-Type: text/html; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable
Dear CCLers
I have successfully compiled the latest = version of=20 GAMESS
on my linux cluster. When running on a = single node,=20 everything goes fine.
When I try to run a parallel job there = seems to be=20 a problem.
The job starts successfully, but the = cpu=20 utilization on the nodes is less than 1%
As a result the parallel job is much = slower than=20 the one run on a single node.
Obviously, I am missing = something
 
Dr. Christos S. Garoufalis
Dept. of = Physics,=20 Univ. of Patras Greece
------=_NextPart_000_0012_01C50243.5C39BF80-- From chemistry-request@ccl.net Mon Jan 24 17:33:32 2005 Received: from relay2.scripps.edu (relay2.scripps.edu [137.131.200.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0OMXR6f031371 for ; Mon, 24 Jan 2005 17:33:31 -0500 Received: from degas.scripps.edu (degas [137.131.252.44]) by relay2.scripps.edu (8.12.11/TSRI-5.0.2rAV) with ESMTP id j0OMXQYd018863 for ; Mon, 24 Jan 2005 14:33:26 -0800 (PST) Received: (from lou@localhost) by degas.scripps.edu (8.11.7+Sun/TSRI-4.1.0) id j0OMXHR21312; Mon, 24 Jan 2005 14:33:17 -0800 (PST) Date: Mon, 24 Jan 2005 14:33:17 -0800 (PST) From: Lou Noodleman Message-Id: <200501242233.j0OMXHR21312_at_degas.scripps.edu> To: chemistry_at_ccl.net Subject: Re: CCL:[Re]: orbitals and reality Cc: lou_at_scripps.edu X-Sun-Charset: US-ASCII X-CanItPRO-Stream: admin redirected to 10_OptOut X-Spam-Score: undef - spam-scanning disabled X-Scanned-By: CanIt (www . roaringpenguin . com) on 137.131.200.30 X-Spam-Status: No, hits=2.4 required=7.5 tests=OPT_HEADER autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net To CCL group: I want to add a short addition to my previous post, in response to some comments within the discussion. (1) In the discussion, someone proposed that orbitals cannot represent reality when the orbital is complex. This notion contradicts the basic principles of quantum mechanics, since both electron densities and currents, representing the flow of electron density, are represented by wavefunctions-for one electron, these are orbitals. It is readily shown from the conservation of probability that the equation for a current takes a particular form. Only complex wavefunctions (that is, those with both a real + an imaginary part) have a nonzero current. Thus, complex wavefunctions are often required, whenever there is a current. (See for example, Merzbacher (1970) pp.35-39 (Chapter 4); an extensive discussion is found in D. Bohm, Chapter 4 (1951)). Eqivalently, one can use two coupled real functions. (2) Someone also proposed that "empty" orbitals were absurd, since properties cannot depend on "empty" orbitals. However, "empty" or "virtual orbitals" are the simplest example of final states, and the transition from an initial ("occupied") state to a "final" ("empty" or unoccupied) state is fundamental within quantum mechanics. The probability for the transition > from i to f is a function of both i and f, P(i->f)= |A (i->f)| squared, where A is a matrix element depending on both i and f. Neither of these ideas are absurd or contradictory, and do not conflict with reality either for "orbitals" or more generally for wavefunctions. Lou Noodleman The Scripps Research Institute . . From chemistry-request@ccl.net Mon Jan 24 16:57:06 2005 Received: from mx1.nyu.edu (MX1.NYU.EDU [128.122.109.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0OLv56f030377 for ; Mon, 24 Jan 2005 16:57:06 -0500 Received: from [128.122.251.90] (JWMIMACG5.CHEM.NYU.EDU [128.122.251.90]) by mx1.nyu.edu (8.12.10/8.12.10) with ESMTP id j0OK83d0023372 for ; Mon, 24 Jan 2005 15:08:04 -0500 (EST) Mime-Version: 1.0 (Apple Message framework v619) Content-Transfer-Encoding: 7bit Message-Id: <55A57862-6E43-11D9-88D4-000A95D6ED72!at!nyu.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed To: chemistry!at!ccl.net From: Jules Moskowitz Subject: Tinker and IBM xlf Date: Mon, 24 Jan 2005 15:05:46 -0500 X-Mailer: Apple Mail (2.619) X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I have compiled tinker from the tinker/apple/ibmxlf compile.make, etc. scripts. They produce the tinker executables without any error messages. When I run any example, I get a bus error. This occurs both on a G4 and a G5 with OS 10.3.7. The compiler is xlf 8.1 plus the 8.1 update. I would appreciate it if any one can point me to a solution to this problem. Thanks, Jules Moskowitz Professor Jules W. Moskowitz Chemistry Department New York University 100 Washington Square East New York, NY 10003-6688 Phone: (212)998-8437 Fax: (212) 260-7905 Email: jules.moskowitz!at!nyu.edu From chemistry-request@ccl.net Mon Jan 24 19:52:07 2005 Received: from relay2.scripps.edu (relay2.scripps.edu [137.131.200.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0P0q66f003887 for ; Mon, 24 Jan 2005 19:52:06 -0500 Received: from gamow.scripps.edu (gamow [137.131.252.67]) by relay2.scripps.edu (8.12.11/TSRI-5.0.2rAV) with ESMTP id j0ONgV1H023900 for ; Mon, 24 Jan 2005 15:42:31 -0800 (PST) Received: from quine.scripps.edu (gamow [137.131.252.67]) by gamow.scripps.edu (SGI-8.12.5/TSRI-5.0.1) with SMTP id j0ONgb2o077676 for ; Mon, 24 Jan 2005 15:42:38 -0800 (PST) Received: by quine.scripps.edu (sSMTP sendmail emulation); Mon, 24 Jan 2005 15:42:30 -0800 Date: Mon, 24 Jan 2005 15:42:30 -0800 From: "David A. Case" To: chemistry!at!ccl.net Subject: Re: CCL:Coupling Constants in Barostats and/or Thermostats Message-ID: <20050124234117.GJ3172!at!scripps.edu> References: <200501220019.27978.bernd-schubert!at!web.de> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.4.1i X-CanItPRO-Stream: admin redirected to 10_OptOut X-Spam-Score: undef - spam-scanning disabled X-Scanned-By: CanIt (www . roaringpenguin . com) on 137.131.200.30 X-Spam-Status: No, hits=2.4 required=7.5 tests=OPT_HEADER autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Mon, Jan 24, 2005, Porrini Massimiliano wrote: > > Does anybody which knows how can I choose the best values > for the time coupling constants \tau_P and/or \tau_T in the > Berendsen and Hoover barostats and thermostats? > Some experience from liquid water (+solute) simulations: if you are just using these to equilibrate the system (that is, to get to a good starting point to start a "real" simulation), you can use fairly short values, on the order of 0.5 to 1 psec. But don't use such short values for "production" work: generally speaking, the longer the better, but values in the 2-10 ps range seem to be a reasonable compromise in sampling correct average temp and pressure without requiring excessively long simulations. Please note: the above is like a "rule of thumb"; I don't know what an objective criterion would be to determine the "best" value. You might want to look at the following papers: %A A. Mudi %A C. Chakravarty %T Effect of the Berendsen thermostat on the dynamical properties of water %J Mol. Phys. %V 102 %P 681-685 %D 2004 %A T. Morishita %T Fluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath %J J. Chem. Phys. %V 113 %P 2976 %D 2000 Of course, if you system is not a liquid like water, then just ignore this advice.... ...dave case