From chemistry-request@server.ccl.net Fri Aug 13 06:29:12 1999 Received: from originqf.uib.es (originqf.uib.es [130.206.133.180]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA04082 for ; Fri, 13 Aug 1999 06:26:47 -0400 Received: from originqf.uib.es (localhost [127.0.0.1]) by originqf.uib.es (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id DAA01515 for ; Fri, 13 Aug 1999 03:30:08 -0700 (PDT) Sender: juan@originqf.uib.es Message-ID: <37B3F3AF.41C6@originqf.uib.es> Date: Fri, 13 Aug 1999 03:30:07 -0700 From: Juan Frau Munar X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP27) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Getting freq in g98 solvated structures Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everybody I am trying to get with g98 a vibrational analysis of some solvated structures, but I have a lot of problems. Following I will show the methodology I have been using. 1) Optimization using the continuum model dpcm -- %Chk=pmp1-631s98 #P SCRF=(DPCM,solvent=1) Opt HF/6-31+G* SCF=(direct,tight) .... OK, I got the minimised structures 2) Vibrational analysis %Chk=pmp3b-631s98 #P freq Geom=Allcheckpoint Guess=read HF/6-31+G* In this analysis I got always one or two negative frequencies, and finally the system starts an optimization and it ends with a non converged structure message: Item Value Threshold Converged? Maximum Force 0.036807 0.000450 NO RMS Force 0.010077 0.000300 NO Maximum Displacement 0.159966 0.001800 NO RMS Displacement 0.051859 0.001200 NO Predicted change in Energy=-7.193508D-03 Does anybody know what is the problem? Thanks in advance ____________________________________ Juan Frau Munar Universitat Illes Balears Departament de Quimica Palma de Mallorca - 07071 Baleares. Spain email: juan@originqf.uib.es fax: 971 - 173426 telf: 971 - 173254 From chemistry-request@server.ccl.net Thu Aug 12 22:40:06 1999 Received: from relay1.smtp.psi.net (relay1.smtp.psi.net [38.8.14.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA02071 for ; Thu, 12 Aug 1999 22:40:06 -0400 Received: from [206.232.104.11] (helo=gcd.ara.com) by relay1.smtp.psi.net with smtp (Exim 1.90 #1) id 11F7Cq-0006me-00; Thu, 12 Aug 1999 22:36:33 -0400 Received: from POP3 Client by gcd.ara.com (ccMail Link to SMTP R8.20.00.25) id AA934511411; Thu, 12 Aug 1999 21:30:17 -0600 Message-Id: <9908129345.AA934511411@gcd.ara.com> X-Mailer: ccMail Link to SMTP R8.20.00.25 Date: Thu, 12 Aug 1999 03:48:27 -0600 From: "Michael D. Bartberger" To: Cc: , , , , , , , Subject: CCL:Xeon processors MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="simple boundary" --simple boundary Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: "cc:Mail Note Part" Dear Dino and Gary: Thanks for posting this; these are very valuable numbers to know, especially with the high price of the Xeon processors. Now, this only leaves me to wonder if anyone has been able to get hold of one of an AMD Athlon-based system for some testing.... it would appear that AMD has at last surpassed Intel, at least for now, in raw FPU performance. Some computing magazines and web sites have recieved test boxes and the results are surprising, to say the least! With best regards, -Michael Bartberger UCLA On Thu, 12 Aug 1999, Szieberth Denes wrote: > > > > Has anyone seen a comparison of the performance of a Xeon processor > > with a straight Pentium II or III at the same (or nearly the same) > > clock speed? I'm interested in performance comparisons using > > the usual chemistry applications, good cache-optimized code-- > > not implying there is no good cache-optimized chemistry code--or > > any other benchmark. > > > Hi, > I was testing a normal pII450 against a pII450 xeon with 1024 kb cache. > The application was Gaussian94 compiled with the f2c-gcc combination, the > tests jobs were geom. optimizations and freq. calculations on 10-atom > molecules with 70-250 basis functions and the results were disappointing: > the xeon was only about 5 % faster, despite the bigger and faster cache. > > dino > dino@iris.inc.bme.hu > > > > > > > > > --simple boundary-- From chemistry-request@server.ccl.net Fri Aug 13 13:13:57 1999 Received: from mercury.chem.nwu.edu (root@mercury.chem.nwu.edu [129.105.116.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA06569 for ; Fri, 13 Aug 1999 13:13:57 -0400 Received: from chem.nwu.edu (kedziora@mordecai.chem.nwu.edu [129.105.14.32]) by mercury.chem.nwu.edu (8.9.1/8.9.1) with SMTP id MAA03832 for ; Fri, 13 Aug 1999 12:13:28 -0500 (CDT) Date: Fri, 13 Aug 1999 12:13:28 -0500 (CDT) From: Gary Kedziora Message-Id: <199908131713.MAA03832@mercury.chem.nwu.edu> To: chemistry@ccl.net Subject: Xeon Summary X-Status: N X-Mailer: Applixware 4.41 (1021.211.13) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii; name="Body" Content-Transfer-Encoding: 7bit I must leave on vacation this weekend, so I will summarize now what little information I have Xeon processors compared directly with Pentium II/III. I recieved only two substantive replies. ORIGINAL QUESTION: Has anyone seen a comparison of the performance of a Xeon processor with a straight Pentium II or III at the same (or nearly the same) clock speed? I'm interested in performance comparisons using the usual chemistry applications, good cache-optimized code-- not implying there is no good cache-optimized chemistry code--or any other benchmark. ----------------------------------------------------------------------------- REPLY 1 (from dino@iris.inc.bme.hu): Hi, I was testing a normal pII450 against a pII450 xeon with 1024 kb cache. The application was Gaussian94 compiled with the f2c-gcc combination, the tests jobs were geom. optimizations and freq. calculations on 10-atom molecules with 70-250 basis functions and the results were disappointing: the xeon was only about 5 % faster, despite the bigger and faster cache. dino dino@iris.inc.bme.hu ------------------------------------------------------------------------------- REPLY 2 (from jochen@uni-duesseldorf.de): The German magazine c't has published SPEC values from a comprehensive comparison of P-III/600, Athlon-600 and some Xeon-450 (?) based machines. Basically the result is, AMD wins every category (x86-only, of course :-), I can look up the numbers or fax you a copy of the article if you want. (Its German, numbers are understandable, though, I guess) -- Jochen -------------------------------------------------------------------------------- MY FINDINGS/THOUGHTS: I found a review on the web with direct comparisons between regular PIIs and PIIIs and corresponding Xeon processors. This used benchmarks I'm not familiar with and may not be very relavent to scientific programs. The results are that Xeon helps by a few percent. The URL for the review is http://www.review-zone.com/hardware/processors/intel_pentium-iii_xeon_500/Page1. html One must have to work hard to squeeze out significant (or more likely marginal) improvement over the PIII. Is it worth the money to get a Xeon? Probably not. I spent some time hunting around Intel's web pages looking for a direct comparison and found nothing obvious. I think that tells you something. AMD's website says "a 550MHz AMD Athlon processor has more than 35 percent higher performance than either a 550MHz Pentium III or a Pentium III Xeon on the SPECfp_base95 benchmark" (http://www.amd.com/news/prodpr/9988.html). AMD now has a 650 MHz version with a 200 MHz bus. That sounds good. __ Gary Kedziora // Department of Chemistry // Northwestern University email: kedziora@chem.nwu.edu//ph: (847)467-4857//fax: (847)491-7713 From chemistry-request@server.ccl.net Fri Aug 13 03:08:43 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA03288 for ; Fri, 13 Aug 1999 03:08:42 -0400 Received: from localhost (jochen@localhost) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with ESMTP id JAA16732; Fri, 13 Aug 1999 09:04:50 +0200 Date: Fri, 13 Aug 1999 09:04:50 +0200 (CEST) From: Jochen Kuepper To: "Michael D. Bartberger" cc: Szieberth Denes , Gary Kedziora , chemistry@ccl.net Subject: Re: CCL:Xeon processors In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id DAA03289 On Thu, 12 Aug 1999, Michael D. Bartberger wrote: > Now, this only leaves me to wonder if anyone has been able to get > hold of one of an AMD Athlon-based system for some testing.... > it would appear that AMD has at last surpassed Intel, at least for > now, in raw FPU performance. Some computing magazines and web sites > have recieved test boxes and the results are surprising, to say > the least! The German magazine c't has published SPEC values from a comprehensive comparison of P-III/600, Athlon-600 and some Xeon-450 (?) based machines. Basically the result is, AMD wins every category (x86-only, of course :-), I can look up the numbers or fax you a copy of the article if you want. (Its German, numbers are understandable, though, I guess) -- Jochen Heinrich-Heine-Universität Düsseldorf jochen@uni-duesseldorf.de Institut für Physikalische Chemie I phone ++49-211-8113681 Universitätsstr. 26.43.02.29 fax ++49-211-8115195 40225 Düsseldorf, Germany www-public.rz.uni-duesseldorf.de/~jochen From chemistry-request@server.ccl.net Fri Aug 13 05:14:26 1999 Received: from nic.savba.sk (nic.savba.sk [147.213.1.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA03786 for ; Fri, 13 Aug 1999 05:14:13 -0400 Received: (from comczitn@localhost) by nic.savba.sk (8.8.5/8.8.8) id LAA21715 for chemistry@ccl.net; Fri, 13 Aug 1999 11:06:45 +0200 (MET DST) Date: Fri, 13 Aug 1999 11:06:45 +0200 (MET DST) From: Peter Zitnan Message-Id: <199908130906.LAA21715@nic.savba.sk> Subject: Interative method for large dense (sparse) linerar equat & eigen probs To: chemistry@ccl.net Dear colleagues, Recently I have developed a new iterative method for solving large dense (sparse) systems of linear equations and matrix eigenvalue problems resulting from the spectral solution of differential equations. The corresponding algorithm solves a dense system of linear equations of order m*n as a few partial systems of order n+m-1 and, con- sequently, for n >> m this algorithm needs m*m times less main computer memory than using a classical direct solver storing whole matrix of order m*n. The computational behaviour of this algorithm is examined by solving dense systems of linear equations up to the order 40000. If this method is of interest for you, let me know. I will send you the PostScript files of the corresponding articles by return of E-mail. With best regards, Dr. Peter Zitnan Computing Centre Slovak Academy of Sciences Dubravska cesta 9 842 35 Bratislava SLOVAKIA ////////////////////////// zitnan@savba.sk From chemistry-request@server.ccl.net Fri Aug 13 18:42:12 1999 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA09206 for ; Fri, 13 Aug 1999 18:42:12 -0400 Received: from ccshst01 (ccshst01.cs.uoguelph.ca [131.104.96.14]) by ccshst09.cs.uoguelph.ca (8.8.6 (PHNE_17135)/8.8.6) with SMTP id SAA17560 for ; Fri, 13 Aug 1999 18:38:28 -0400 (EDT) Date: Fri, 13 Aug 1999 18:38:27 -0400 (EDT) From: Ruth Tanner X-Sender: rtanner@ccshst01 To: chemistry@ccl.net Subject: Frequency Scaling Factors Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Earlier someone was asking about scaling factors for B3LYP cc-pVTZ frequency calculations. Could anyone give me a good reference for scaling factors for B3LYP cc-pVDZ, MP2 cc-pVDZ and cc-pVTZ? thank you, Ruth ----------------------------------------------------------------------------- Ruth Tanner rtanner@uoguelph.ca M.Sc. Candidate in Physical Chemistry University of Guelph ----------------------------------------------------------------------------- "Women and cats will do as they please, and men and dogs should relax and get used to the idea." --Robert A. Heinlein ============================================================================= From chemistry-request@server.ccl.net Fri Aug 13 11:27:48 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA06228 for ; Fri, 13 Aug 1999 11:27:47 -0400 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id LAA16538 for ; Fri, 13 Aug 1999 11:24:05 -0400 (EDT) Received: from feldmann.nist.gov (feldmann.nist.gov [129.6.178.78]) by email.nist.gov (8.9.3/8.9.3) with ESMTP id LAA27710; Fri, 13 Aug 1999 11:23:41 -0400 (EDT) Received: from localhost (chem@localhost) by feldmann.nist.gov (8.8.8+Sun/8.8.8) with SMTP id LAA20756; Fri, 13 Aug 1999 11:10:36 -0400 (EDT) Date: Fri, 13 Aug 1999 11:10:36 -0400 (EDT) From: Steve Heller To: ACSMEDI@LISTS.WAYNE.EDU, amber@cgl.ucsf.edu, APPLSPEC@listserv.uga.edu, cache@pacificu.edu, CHEMCHAT@UAFSYSB.UARK.EDU, CHEME-L@ULKYVM.LOUISVILLE.EDU, CHEMED-L@atlantis.uwf.edu, CHEMIG@LIST.NIH.GOV, CHEMISTRY@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, ICS-L@UMDD.UMD.EDU, isisforum-l@mdli.com, ISOGEOCHEM@LIST.UVM.EDU, listproc@msi.com Subject: ChemInt'99 - Upcoming Deadlines/Workshops Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII This note is a reminder that the deadline for poster abstracts for Chemistry & the Internet - ChemInt'99 is September 1, 1999. September is the deadline for the special hotel rates for the conference. In addition to the previously announced program, two vendor workshops - from ACD Labs and Synopsys - have been added to the meeting. The Chemistry and the Internet (ChemInt'99) meeting being held in at Georgetown University in Washington DC on September 25-27, 1999. The program of invited speakers and panel members of the 3 panel sessions is available on the meeting web site - www.chemint.org You are urged to look at the program and to consider submitting a poster paper to the meeting. The main lecturers for the meeting will be: Alan Arnold, University College (UNSW) Steven Bachrach, Northern Illinois University Robert Bovenschulte, ACS Stephen Boyer, IBM Donald DeCoste, University of Illinois at Urbana-Champaign Karl Harrison, Oxford University Clemens Jochum, Deutsche Bank Gary Mallard, NIST Tom Pierce, Rohm & Haas Jerome Reichman, Vanderbilt Achim Zielesny, Bayer AG The (current) corporate sponsors for the meeting are: ChemWeb and the Internet Journal of Chemistry Technical Sponsors are: ACS CINF Division ACS COMP Division The Chemical Structure Association (CSA) Georgetown University - Department of Chemistry International Union of Pure and Applied Chemistry (IUPAC) (pending) Japan Association for International Chemical Information (JAICI) Special Libraries Association (SLA) Chemistry Division Royal Society of Chemistry (RSC)/ChemSoc Steve Heller Steve Heller, Guest Researcher NIST/SRD, Mail Stop: 820/113 820 Diamond Avenue, Room 101 Gaithersburg, MD 20899-2310 USA E-mail: chem@feldmann.nist.gov *** Details on how to be removed from this list as well as an *** *** archive of recent postings are available at *** *** http://www.rcsb.org/pdb/forum.html *** From chemistry-request@server.ccl.net Sat Aug 14 14:27:58 1999 Received: from hartree.chem.kuleuven.ac.be (hartree.quantchem.kuleuven.ac.be [134.58.49.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA15202 for ; Sat, 14 Aug 1999 14:27:58 -0400 Received: from localhost (alk@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id UAA32724; Sat, 14 Aug 1999 20:25:32 +0100 Date: Sat, 14 Aug 1999 20:25:32 +0100 (NFT) From: Alk Dransfeld To: CHEMISTRY@ccl.net cc: Alk Dransfeld Subject: XML: nmr-sharc2cml conversion Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer Enhance the use of your ab initio NMR data ! Until now the platform independent NMR-SHARC system allowed you to archive your ab initio NMR results efficiently (programm independent format). NEW 1999-08-14: NMR-SHARC format data can now be transformed into experimental CML (chemical markup language) in the context of XML. See: demo http://www.quantchem.kuleuven.ac.be/sharc/demo/jumbo_xcm1.html download sharc2xml 0.2 skript http://www.quantchem.kuleuven.ac.be/sharc/utils/index.html#sharc2some With best regards A. Dransfeld BTW: - all parts of the NMR-SHARC system are freeware + Thanx to CCC Erlangen and Quantumchemie KULeuven TMHO: The XML file is best viewed with JUMBO http://www.vsms.nottingham.ac.uk/vsms/java/jumbo/ # # # |\ # NMR-#___________________________| \ _________#-SHARC