From chemistry-request@ccl.net Mon May 9 11:34:23 2005 Received: from linus.imcm.cas.cz (Linus.imcm.cas.cz [147.231.77.250]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j49FYMNq014530 for ; Mon, 9 May 2005 11:34:22 -0400 Received: from linus.imcm.cas.cz (localhost [127.0.0.1]) by linus.imcm.cas.cz (8.12.11/8.12.11) with ESMTP id j49DwUDl023863 for ; Mon, 9 May 2005 15:58:30 +0200 Received: from localhost (ccl@localhost) by linus.imcm.cas.cz (8.12.11/8.12.11/Submit) with ESMTP id j49DwOMO023860 for ; Mon, 9 May 2005 15:58:30 +0200 Date: Mon, 9 May 2005 15:58:23 +0200 (CEST) From: Petr Toman To: CHEMISTRY!at!ccl.net Subject: CCL: Correction of Koopmans ionization potentials Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear colleagues, I heard that the Koopmans ionization potentials (HF method) can be corrected by a multiplication factor of about 0.92, but I am not sure it is true. Could anybody provide me some references to the corrections of Koopmans ionization potentials? Best regards, Petr Toman From chemistry-request@ccl.net Mon May 9 05:37:49 2005 Received: from fwncism1.leidenuniv.nl (chem.leidenuniv.nl [132.229.170.40]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j499bltf025674 for ; Mon, 9 May 2005 05:37:48 -0400 Received: from localhost (localhost [127.0.0.1]) by fwncism1.leidenuniv.nl (Postfix) with ESMTP id C626234023; Mon, 9 May 2005 09:38:30 +0200 (CEST) Received: from fwncism1.leidenuniv.nl ([127.0.0.1]) by localhost (fwncism1.leidenuniv.nl [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 22159-08; Mon, 9 May 2005 09:38:27 +0200 (CEST) Received: from fwnc7003.leidenuniv.nl (fwnc7003.leidenuniv.nl [132.229.116.26]) by fwncism1.leidenuniv.nl (Postfix) with ESMTP id 228523401D; Mon, 9 May 2005 09:38:27 +0200 (CEST) From: mark somers Reply-To: m.somers*&*chem.leidenuniv.nl To: Luigi Cavallo Subject: Re: CCL:Opteron or Nocona ? Date: Mon, 9 May 2005 09:38:06 +0200 User-Agent: KMail/1.6.2 References: In-Reply-To: Cc: chemistry*&*ccl.net MIME-Version: 1.0 Content-Disposition: inline Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Message-Id: <200505090938.06554.m.somers*&*chem.leidenuniv.nl> X-Virus-Scanned: by amavisd-new at chem.leidenuniv.nl X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear Luigi Cavallo, we have recently purchased and setup a new Beowulf cluster here in Leiden, dedicated to run ADF and other DFT codes (Dacapo and Vasp) on it. We have found the Nocona's, in combination with the Intel compilers, to be the best combination especially for ADF and ADF-BAND. Before we decided to go for the Nocona's, we did try with two test machines, one being a dual-cpu AMD Opteron 246 (2.0 GHz) and the other being a dual-cpu Nocona (3.0 GHz). Tests showed that the AMD has, in general, a slightly better cache hierarchy and a better memory scalability, but also that the lack of compilers able to tune for the Opterons is severe. Of course we took the differences in cpu clocks into account. As it turns out, after having contacted the SCM people in Amsterdam, ADF can effectively use the SSE3 registers and cpu intruction set and that makes it run fast on the Nocona's. This, together with the prices being roughly the same, made us decide to go for the Nocona's. BTW, maybe this is known to you already, but Intel offers you their OpenMP capable compilers for free for academic use. The machine is up and running now in 64 bit mode and doing fine ;-). Maybe the information can help you in your decision. Best regards, Mark Somers. > Hi, > > we are going to invest some money for a few computers, and we have to > make a decision between the AMD-Opterons and the Intel-Nocona. What's > better ? We are experienced with the Opterons, but we have no idea about > the Noconas... > > Major codes to run on them will be classical QM packages as ADF, G03, TM, > some AIMD as CPMD, and possibly some classical MD as gromacs. > > Thanks, > Luigi -- Dr. M. F. Somers Theoretical Chemistry - Leiden Institute of Chemistry - Leiden University Einsteinweg 55, P.B. 9502, 2300 RA Leiden, The Netherlands tel: +31715274437 mail: m.somers*&*chem.leidenuniv.nl web: http://rulgla.leidenuniv.nl/Researchers/Somers.htm room: HB322 From chemistry-request@ccl.net Mon May 9 03:58:19 2005 Received: from ozone.few.vu.nl (ozone.few.vu.nl [130.37.20.6]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j497wFmi018867 for ; Mon, 9 May 2005 03:58:16 -0400 Received: from [130.37.144.98] (europium.chem.vu.nl [130.37.144.98]) by ozone.few.vu.nl with esmtp (Smail #108) id m1DV38c-00005lC; Mon, 9 May 2005 09:57 +0200 In-Reply-To: <20050508101637.97482.qmail [] web26805.mail.ukl.yahoo.com> References: <20050508101637.97482.qmail [] web26805.mail.ukl.yahoo.com> Mime-Version: 1.0 (Apple Message framework v622) Content-Type: multipart/alternative; boundary=Apple-Mail-3--120720120 Message-Id: Cc: ccl From: Marcel Swart Subject: Re: CCL:Quantum Biochemistry activities and meetings Date: Mon, 9 May 2005 09:57:13 +0200 To: may abdelghani X-Mailer: Apple Mail (2.622) X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net --Apple-Mail-3--120720120 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed On May 8, 2005, at 12:16 PM, may abdelghani wrote: > dear CCL's > if we change the frozen core electron for a given > atom in the input files to optimize a given geometry > ander DFT calculation, will this affect the resultat. > best regards If using ADF, then not that much, see: M. Swart, J.G. Snijders "Accuracy of geometries: Influence of basis set, exchange-correlation=20= potential, inclusion of core electrons, and relativistic corrections" Theor. Chem. Acc., 110 (2003), p. 34-41 =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Theoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart [] few.vu.nl Web http://www.few.vu.nl/~swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-3--120720120 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 On May 8, 2005, at 12:16 PM, may abdelghani wrote: dear CCL's if we change the frozen core electron for a given atom in the input files to optimize a given geometry ander DFT calculation, will this affect the resultat. best regards If using ADF, then not that much, see: M. Swart, J.G. Snijders "Accuracy of geometries: Influence of basis set, exchange-correlation potential, inclusion of core electrons, and relativistic corrections" Theor. Chem. Acc., 110 (2003), p. 34-41 = Helvetica=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96 = Papyrusdr. Marcel Swart = Papyrus = OsakaTheoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart [] few.vu.nl Web http://www.few.vu.nl/~swart = Helvetica=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-3--120720120-- From chemistry-request@ccl.net Mon May 9 15:07:46 2005 Received: from pilsener.srv.ualberta.ca (pilsener.srv.ualberta.ca [129.128.5.19]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j49J7jx0028792 for ; Mon, 9 May 2005 15:07:46 -0400 Received: from [129.128.168.123] (brownpowerbookG4.chem.ualberta.ca [129.128.168.123]) by pilsener.srv.ualberta.ca (8.13.3/8.13.3) with ESMTP id j49I1KUg002105; Mon, 9 May 2005 12:01:24 -0600 (MDT) In-Reply-To: <200505090938.06554.m.somers ~~ chem.leidenuniv.nl> References: <200505090938.06554.m.somers ~~ chem.leidenuniv.nl> Mime-Version: 1.0 (Apple Message framework v622) Content-Type: multipart/alternative; boundary=Apple-Mail-1--84476647 Message-Id: Cc: chemistry ~~ ccl.net, Luigi Cavallo From: Alex Brown Subject: Re: Intel compilers: was Opteron or Nocona ? Date: Mon, 9 May 2005 12:01:16 -0600 To: mark somers X-Mailer: Apple Mail (2.622) X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net --Apple-Mail-1--84476647 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Dear Mark, Luigi, and others, > BTW, maybe this is known to you already, but Intel offers you their > OpenMP > capable compilers for free for academic use. I have seen this stated several times on the list. While I believe that this used to be the case, Intel has clarified their position on academic use of their non-commercial compilers. As taken from their FAQ page (http://www.intel.com/software/products/noncom/faq.htm) Q. I am engaged in academic research. Can I use the non-commercial 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 use license. However, you may qualify for the academic license (Click to academic page) Note that I do not have any affiliation with Intel nor does it bother me what individuals choose to do with their copies of the non-commercial compilers. However, I wanted to clear up what I think is a common misconception about their compilers. Cheers, Alex Alex Brown Assistant Professor Department of Chemistry University of Alberta Edmonton, AB T6G 2G2 http://www.chem.ualberta.ca/~abrown/ --Apple-Mail-1--84476647 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Dear Mark, Luigi, and others, BTW, maybe this is known to you already, but Intel offers you their OpenMP capable compilers for free for academic use. I have seen this stated several times on the list. While I believe that this used to be the case, Intel has clarified their position on academic use of their non-commercial compilers. As taken from their FAQ page (http://www.intel.com/software/products/noncom/faq.htm) ArialQ. I am engaged in academic research. Can I use the non-commercial product? Arial 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 use license. However, you may qualify for the academic license (0000,0000,FFFFClick to academic page) Note that I do not have any affiliation with Intel nor does it bother me what individuals choose to do with their copies of the non-commercial compilers. However, I wanted to clear up what I think is a common misconception about their compilers. Cheers, Alex Alex Brown Assistant Professor Department of Chemistry University of Alberta Edmonton, AB T6G 2G2 http://www.chem.ualberta.ca/~abrown/ --Apple-Mail-1--84476647-- From chemistry-request@ccl.net Mon May 9 15:14:10 2005 Received: from smtp.nist.gov (rimp1.nist.gov [129.6.16.226]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j49JE9ln029027 for ; Mon, 9 May 2005 15:14:09 -0400 Received: from postmark.nist.gov (pushme.nist.gov [129.6.16.92]) by smtp.nist.gov (8.12.10/8.12.10) with ESMTP id j49I7FDP032564; Mon, 9 May 2005 14:07:17 -0400 Received: from cccbdb1.nist.gov (cccbdb1.nist.gov [129.6.178.184]) by postmark.nist.gov (8.12.5/8.12.5) with ESMTP id j49I719r015534; Mon, 9 May 2005 14:07:01 -0400 (EDT) Message-Id: <6.0.0.22.2.20050509135543.01c231b0 ~~ mailserver.nist.gov> X-Sender: rdj3 ~~ mailserver.nist.gov X-Mailer: QUALCOMM Windows Eudora Version 6.0.0.22 Date: Mon, 09 May 2005 14:07:00 -0400 To: Petr Toman , CHEMISTRY ~~ ccl.net From: Russell D Johnson III Subject: Re: CCL:Correction of Koopmans ionization potentials In-Reply-To: References: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-NIST-MailScanner: Found to be clean X-MailScanner-From: russell.johnson ~~ nist.gov X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hello, The NIST CCCBDB (Computational Chemistry Comparison and Benchmark Database) has some experiment vs theory comparisons of Koopman's ionization potentials. It provides differences rather than ratios, but a cursory glance makes it look like a general multiplication factor will not do very well. The CCCBDB is online at: http://srdata.nist.gov/cccbdb See section IV.E.3 and try entering C?H? to get a list of hydrocarbons. After selecting some or all the molecules from the list choose the table cell for HF/6-31G*. The differences range from -0.5 to 1.7, which doesn't look easy to correct using a scale factor. Even if you choose a subset, such as molecules with a carbon-carbon triple bond, there is still a spread. At 09:58 AM 2005-05-09, you wrote: >Dear colleagues, > >I heard that the Koopmans ionization potentials (HF method) can be >corrected by a multiplication factor of about 0.92, but I am not sure it >is true. >Could anybody provide me some references to the corrections of Koopmans >ionization potentials? Dr. Russell D. Johnson III Research Chemist National Institute of Standards and Technology Computational Chemistry Group 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301+975-2513 fax:301+869-4020 email: russell.johnson ~~ nist.gov From chemistry-request@ccl.net Mon May 9 14:00:52 2005 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j49I0ooS023777 for ; Mon, 9 May 2005 14:00:51 -0400 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 j49I0OZ3069369 for ; Mon, 9 May 2005 20:00:24 +0200 (CEST) X-Ids: 168 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id j49I0h0g159957; Mon, 9 May 2005 20:00:43 +0200 (MEST) Date: Mon, 9 May 2005 20:00:43 +0200 (MEST) From: Michel Petitjean Message-Id: <200505091800.j49I0h0g159957 %a% ds10.itodys.jussieu.fr> To: chemistry %a% ccl.net Subject: CCL: ACPS Conference announcement X-Greylist: Sender IP whitelisted, not delayed by milter-greylist-1.7.2 (shiva.jussieu.fr [134.157.0.168]); Mon, 09 May 2005 20:00:24 +0200 (CEST) X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Miltered: at shiva.jussieu.fr with ID 427FA538.000 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Subj: ACPS Conference announcement /* We apologize for unwanted or multiple receipts */ On the behalf of the ACPS Organizing Committee, I would like to announce the 2005 African Conference for Physics Students, which will be held at Abuja, Nigeria, from the 15th to the 18th of November 2005. Detailed informations are available on: http://www.ibe.tu-berlin.de/ACPS/ Thanks. Michel Petitjean Email: petitjean %a% itodys.jussieu.fr entropy %a% mdpi.org ptitjean %a% 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