From chemistry-request@ccl.net Sat Jan 22 08:44:36 2005 Received: from relay.unizar.es (relay.unizar.es [155.210.11.72]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0MDiXi3031056 for ; Sat, 22 Jan 2005 08:44:34 -0500 Received: from posta.unizar.es (mail.unizar.es [155.210.11.71]) by relay.unizar.es (8.12.6/8.12.3) with ESMTP id j0MCiOXq023069 for ; Sat, 22 Jan 2005 13:44:24 +0100 Received: from localhost (grio.unizar.es [155.210.11.71]) by posta.unizar.es (8.12.10/8.12.5) with ESMTP id j0MCiTYR008179 for ; Sat, 22 Jan 2005 13:44:30 +0100 Received: from 82.198.37.36 ( [82.198.37.36]) as user jig@155.210.11.71 by webmail.unizar.es with HTTP; Sat, 22 Jan 2005 13:44:29 +0100 Message-ID: <1106397869.41f24aadc34ca.-at-.webmail.unizar.es> Date: Sat, 22 Jan 2005 13:44:29 +0100 From: =?ISO-8859-1?B?Sm9z6SBJZ25hY2lvIA==?==?ISO-8859-1?B?R2FyY+1hIExhdXJlaXJv?= To: chemistry.-at-.ccl.net Subject: CCL: Orbitals and philosophy MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.1 X-Originating-IP: 82.198.37.36 X-Mail-Scanned: Criba 2.0 + Clamd en Unizar X-Spam-Status: No, hits=2.7 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS,RM_ft_Iso8859 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Brian Salter-Duke wrote: >Orbitals are mathematical objects that are "not real" in >a quite different way from wave functions being not real. This immediatly remembered me a delicious tale of Stanislaw Lem in Cyberiad, beginning as follows: "Trurl and Klapaucius were students of the great Kerebron Emtadrat, who had been teaching general dragon theory for 47 years at the Neantic University. As everybody knows, there are no dragons. A simple mind might be satisfied with this statement, but not scientific inquiry. [...] And so, by means of very exact methodology, the highly talented Kerebron discovered three types of dragons: null dragons, imaginary dragons, and negative dragons. As already mentioned, none of these types exist, but each of these do not exist in their own very individual and different manner." Maybe should we assist to some courses in the Neantic University? Just for relax a little bit the discussion... Jose I. Garcia ******************************************** Josi I. Garcma Senior Reasearcher Instituto de Ciencia de Materiales de Aragon CSIC-Univ. de Zaragoza ******************************************** From chemistry-request@ccl.net Sat Jan 22 10:20:13 2005 Received: from usstp10.itcs.purdue.edu (usstp10.itcs.purdue.edu [128.210.5.249]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0MFKCi3002603 for ; Sat, 22 Jan 2005 10:20:12 -0500 Received: from bputnam.dsl-verizon.net (wbar2.chi1-4-13-000-174.dsl-verizon.net [4.13.0.174]) (authenticated bits=0) by usstp10.itcs.purdue.edu (8.13.1/8.13.1/scan-smtp) with ESMTP id j0MFK5qw009957 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Sat, 22 Jan 2005 10:20:12 -0500 Date: Sat, 22 Jan 2005 10:20:09 -0500 (US Eastern Standard Time) From: Bryan Putnam To: Bernd Schubert cc: CCL Subject: Re: CCL:Building g03 on Opteron64 system with RedHat Enterprise In-Reply-To: <200501220019.27978.bernd-schubert/at/web.de> Message-ID: References: <200501220019.27978.bernd-schubert/at/web.de> X-X-Sender: bfp/at/mailhub016.itcs.purdue.edu MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-new X-Spam-Status: No, hits=3.5 required=7.5 tests=MY_DSL,RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Thanks Bernd and CCL for the information and warnings about PGI 5.2-4. Fortunately we have a PGI 5.1 sitting around that I may unearth. I made some progress on my problem building g03. It appears that the supplied atlas libraries need to be rebuilt using the -fpic option if they are to be used in building a shared library (util.so) in 64-bit mode on an Opteron64. Another problem I had run into is that the "-tp p7" compiler option in the g03 makefile was resulting in 32-bit builds for all the entries in the utility library, instead of the 64-bit which I wanted. Thanks for your help, Bryan On Sat, 22 Jan 2005, Bernd Schubert wrote: > Hi Bryan, > > > We're using PGI compilers 5.2-4 > > don't use this version! 32bit G03 binaries compiled with this compiler version > immediately crash in link101 on our our systems (debian sarge) and 64bit > binaries will crash in rather many of the G03 test jobs. We told PGI this and > a much worse issue and were told that we either should use version 5.1 or > wait until February for version 6. > With version 5.1 we could successfully compile G03 and the results of the test > jobs are also fine. On the other hand molpro and molcas have issues with 5.1, > but for those 5.2 works fine... > > > > > If I attempt to build using the shared util.so, I get error messages that > > the libatlas-amd64 and libf77blas-amd64 libraries need to be compiled with > > G03 has its own atlas libraries, are you using them? Those worked fine for us, > though its on a debian biarch64 system. > The PGI compiler also asks you during the installation process to install the > blas/lapack libraries developed by AMD (ACML). Its rather easy to change the > Makefiles to use this library. However, there's another issue with the PGI > compiler: You need to specy the full path to the library, the usual options > "-Lpath_to_acml -lacml" don't work. Must be something PGI and linker (ld) > related, I couldn't find out the reason. > > > Hope it helps, > Bernd > From chemistry-request@ccl.net Sat Jan 22 12:44:10 2005 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0MHi8i3008961 for ; Sat, 22 Jan 2005 12:44:09 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.11/jtpda-5.4) with ESMTP id j0MHi6Ik017398 for ; Sat, 22 Jan 2005 18:44:06 +0100 (CET) X-Ids: 168 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id j0MHi512166047; Sat, 22 Jan 2005 18:44:05 +0100 (MET) Date: Sat, 22 Jan 2005 18:44:05 +0100 (MET) From: Michel Petitjean Message-Id: <200501221744.j0MHi512166047$at$ds10.itodys.jussieu.fr> To: chemistry$at$ccl.net Subject: CCL:[Re]: orbitals and reality X-Greylist: Sender IP whitelisted, not delayed by milter-greylist-1.7.2 (shiva.jussieu.fr [134.157.0.168]); Sat, 22 Jan 2005 18:44:08 +0100 (CET) X-Miltered: at shiva.jussieu.fr with ID 41F290E6.001 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Spam-Status: No, hits=-0.5 required=7.5 tests=SMILEY 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: chemistry$at$ccl.net Subject: CCL:[Re]: orbitals and reality Dear CCLers, This debates remembers to me some dicussions I had when I was student. > From: Rene Fournier : > I'd say it is exactly like the reality of a sphere > x^2+y^2+z^2=r^2 There are objects that are > approximately spherical; on the other hand there is an > ideal (mathematical) concept of a sphere. Same with electrons > and orbitals. To me spheres, orbitals, even Lewis structures, > they all exist, they are all real in my mind, if nowhere else; > they are "productive delusions". :) I would say here that a sphere is a word who has two meanings: a mathematical concept and a physical object. The first one modelizes the second one. Our euclidean space is itself a model of the physical space, this model being not suitable in some situations. > From: Guosheng Wu : > No one is saying wave function is a physical quantity, but some component > of it is meaningful. > > I was talking about the probability amplititude, and it has some meaning. > what is ? It is the probability amplititude, and real! But the probability theory is itself a nice mathematical modelizing tool ! Do you know a probabilist saying that a probability physically exists ? > Just like the velocity of electron is some property which can be derived > from the wave function, . If you agree with it, then could you > say velocity has no any physical meaning since wave function does not? > > You may change your question into: when there is nobody in a room, can the > room still be called a room? Physical things can exist before we are able to measure them. The room exists from its walls. The mathematical concept to modelize the room without its walls could be a domain of R3 (well we have to specify: open, or closed, or other topological details). > From: "Steve Bowlus" : > Hmmm ... the tone of this discussion reminds me of my undergraduate > philosophy of science course. If my memory serves, there was a school of > philosophers which held that "reality" and "real objects" were defined by > the operation(s) that measured them. Essentially, an object was "made" real > by the process of measuring it, and defined by the measurement. An extreme > view within the school held that particular reality was true for only so > long as the measuring operation was applied ... Physical things can exist before we are able to measure them. But equations are models in our mind. When some model permits to have a simplified understanding or permits to predict something with an acceptable accurarcy, it is a useful model. It seems harder to do philosophy than to understand QM, and I am not an expert in these two areas. Fortunately, all this is a nice discussion rather than a theory to publish. I conclude by a joke from Switzerland: when you eat a piece of gruyere, do you eat the holes too ? Michel Petitjean Email: petitjean$at$itodys.jussieu.fr entropy$at$mdpi.org ptitjean$at$ccr.jussieu.fr Editor-in-Chief of Entropy http://www.mdpi.org/entropy FIS2005 coordinator http://www.mdpi.org/fis2005 ITODYS (CNRS, UMR 7086) 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From chemistry-request@ccl.net Sat Jan 22 19:04:25 2005 Received: from electra.cc.umanitoba.ca (electra.cc.umanitoba.ca [130.179.16.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0N04Ni3010009 for ; Sat, 22 Jan 2005 19:04:23 -0500 Received: from Fledermaus (wnpgmb01dc2-106-181.dynamic.mts.net [142.161.106.181]) (authenticated bits=0) by electra.cc.umanitoba.ca (8.13.0/8.13.0) with ESMTP id j0N04LoK009219 for ; Sat, 22 Jan 2005 18:04:22 -0600 (CST) Message-Id: <200501230004.j0N04LoK009219_at_electra.cc.umanitoba.ca> Reply-To: From: "Phil Hultin" To: "Computational Chemistry List" Subject: Orbitals and Reality Date: Sat, 22 Jan 2005 18:04:20 -0600 Organization: Dept. of Chemistry, U. of Manitoba MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0004_01C500AC.CCEA4FD0" X-Mailer: Microsoft Office Outlook, Build 11.0.6353 Thread-Index: AcUA3xaQhEtcDqlBS5Kq+mhAjFk/eQ== X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Spam-Status: No, hits=3.6 required=7.5 tests=HTML_50_60,HTML_MESSAGE, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS 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_0004_01C500AC.CCEA4FD0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I am getting the impression that part of the problem in this discussion is that people mean different things when they talk about "visualizing an orbital". There can be no argument that the mathematical formulation of orbital theory is a human construct, and hence that orbitals so formulated must be artificial models. These models purport to describe the spatial probability density (if that isn't a redundancy) for a single electron having a particular energy in the vicinityof a particular nucleus. Atoms apart from hydrogen have more than one electron, and our mathematical model is approximate in such cases. Therefore, it is highly probable that even if a particular application of the orbital model can give a reasonable agreement with experimental energies in the aggregate, the individual one-electron wavefunctions will not have any direct resemblance to the behaviour of any one electron in reality (whatever that may mean). On the other hand, I think it is possible (albeit not probable) that our orbital model captures some aspect of observable electronic behaviour. Thus, until someone can explain to me how Villeneuve et al's tomographic interpretation of their spectroscopic data is fundamentally wrong, I am prepared to accept that they may have visualized something real, to which our orbital model roughly corresponds. Note that I do not say that they have indeed visualized an orbital, because yes, orbitals are hypothetical objects. And, I quite agree that you cannot observe a hypothetical (or perhaps imaginary) object. So, in the strict sense there is no way that Villeneuve's claim to have observed an orbital can be correct. Is it therefore impossible to observe the spatial distribution of an electron, and for this distribution to bear some resemblance to what our theory predicts? I would welcome any reasoned and referenced rebuttal of my interpretation of Villeneuve et al's Nature paper. Dr. Philip G. Hultin Associate Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin_at_cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin ------=_NextPart_000_0004_01C500AC.CCEA4FD0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Normal Document Template

I am getting the impression that part of the problem = in this discussion is that people mean different things when they talk about = “visualizing an orbital”.

 

There can be no argument that the mathematical = formulation of orbital theory is a human construct, and hence that orbitals so = formulated must be artificial models.

 

These models purport to describe the spatial = probability density (if that isn’t a redundancy) for a single electron having = a particular energy in the vicinityof a particular nucleus.  Atoms = apart from hydrogen have more than one electron, and our mathematical model is = approximate in such cases. Therefore, it is highly probable that even if a = particular application of the orbital model can give a reasonable agreement with = experimental energies in the aggregate, the individual one-electron wavefunctions = will not have any direct resemblance to the behaviour of any one electron in = reality (whatever that may mean).

 

 On the other hand, I think it is possible = (albeit not probable) that our orbital model captures some aspect of observable = electronic behaviour.  Thus, until someone can explain to me how Villeneuve et = al’s tomographic interpretation of their spectroscopic data is fundamentally wrong, I am prepared to accept that they may have visualized something real, to = which our orbital model roughly corresponds.

 

Note that I do not say that they have indeed = visualized an orbital, because yes, orbitals are hypothetical objects.  And, I = quite agree that you cannot observe a hypothetical (or perhaps imaginary) = object.  So, in the strict sense there is no way that Villeneuve’s claim to have = observed an orbital can be correct.  Is it therefore impossible to observe = the spatial distribution of an electron, and for this distribution to bear some = resemblance to what our theory predicts?

 

I would welcome any reasoned and referenced rebuttal = of my interpretation of Villeneuve et al’s Nature = paper.

 

Dr. Philip G. Hultin

Associate Professor of = Chemistry,

University of Manitoba

Winnipeg, MB

R3T 2N2

hultin_at_cc.umanitoba.ca

http://umanitoba.ca/= chemistry/people/hultin

 

------=_NextPart_000_0004_01C500AC.CCEA4FD0-- From chemistry-request@ccl.net Sat Jan 22 20:24:49 2005 Received: from smtp105.mail.sc5.yahoo.com (smtp105.mail.sc5.yahoo.com [66.163.169.225]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0N1Ohi3012970 for ; Sat, 22 Jan 2005 20:24:45 -0500 Received: from unknown (HELO yahoo.com.cn) (yanliangren?2002@61.183.207.53 with plain) by smtp105.mail.sc5.yahoo.com with SMTP; 23 Jan 2005 00:24:43 -0000 Message-ID: <41F2ECF1.9030909:at:yahoo.com.cn> Date: Sun, 23 Jan 2005 08:16:49 +0800 From: yanliangren_2002 User-Agent: Mozilla/5.0 (X11; U; Linux i686; zh-CN; rv:1.2.1) Gecko/20030225 X-Accept-Language: zh-cn,zh MIME-Version: 1.0 To: chemistry:at:ccl.net Subject: about Circular Dichroism and one book! Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.1 required=7.5 tests=BAD_YAHOOMSGID, FROM_ENDS_IN_NUMS,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear everybody: who have calculated the Circular Dichroism Spectrum by using the TDDFT, I have calculated it for different basis set, but the difference of result is very large, who can give me some advice or who can give me some ref or book for detail introduction of Circular Dichroism and Linear Dichroism Spectrum. In additional, I find one book which are introducted the CD spectrum, but I couldn`t get it, who can help me to get it? Circular Dichroism: Principles and Applications, 2nd Edition http://as.wiley.com/WileyCDA/WileyTitle/productCd-0471330035.html Thank u very much!