From chemistry-request@ccl.net Thu Nov 4 15:16:05 2004 Received: from mailgate1.uni-kl.de (mailgate1.uni-kl.de [131.246.120.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iA4KG3sE018523 for ; Thu, 4 Nov 2004 15:16:04 -0500 Received: from service.chemie.uni-kl.de (service.chemie.uni-kl.de [131.246.58.77]) by mailgate1.uni-kl.de (8.13.1/8.13.1) with ESMTP id iA4KTBBE006394 for ; Thu, 4 Nov 2004 21:29:12 +0100 Received: from localhost (localhost [127.0.0.1]) by service.chemie.uni-kl.de (Postfix) with ESMTP id C344736D10 for ; Thu, 4 Nov 2004 22:29:11 +0100 (CET) Received: from by localhost (amavisd-new, port ) id XXK3cx9h for ; Thu, 4 Nov 2004 22:29:11 +0100 (CET) Received: from pc1.chemie.uni-kl.de (pc1.chemie.uni-kl.de [131.246.58.1]) by service.chemie.uni-kl.de (Postfix) with ESMTP id F0B6B36CF2 for ; Thu, 4 Nov 2004 22:29:10 +0100 (CET) Received: from pc3.chemie.uni-kl.de (pc3.chemie.uni-kl.de [131.246.58.3]) by pc1.chemie.uni-kl.de (Postfix) with ESMTP id E83DE139EB for ; Thu, 4 Nov 2004 21:29:10 +0100 (CET) From: Elmar Gerwalin Reply-To: elg~at~chemie.uni-kl.de To: CHEMISTRY~at~ccl.net Subject: CCL: Does g98 Rev.A.9 run on IBM Power4 / 64bit ? Date: Thu, 4 Nov 2004 21:29:09 +0100 User-Agent: KMail/1.6.2 MIME-Version: 1.0 Content-Disposition: inline Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 7bit Message-Id: <200411042129.09496.elg~at~chemie.uni-kl.de> X-Virus-Scanned: by amavisd-new at chemie.uni-kl.de X-Spam-Status: No, hits=1.9 required=7.5 tests=IMPRONONCABLE_1,MY_BAD_DOT 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, I recently installed G98RevA.9 on an IBM Power4 machine. Installation from sources went fine as well as a simple %nproc=1 job. But %nproc>=2 jobs fail, ending with the following message: ------------ (Enter /gwork1/gerwalin/g98/l302.exe) One-electron integrals computed using PRISM. RR consistency failure in MakTrN. Error termination via Lnk1e in /gwork1/gerwalin/g98/l302.exe. Job cpu time: 0 days 0 hours 0 minutes .1 seconds. File lengths (MBytes): RWF= 21 Int= 0 D2E= 0 Chk= 1 Scr= 1 Process number 1 did not complete successfully. Error termination via Lnk1e in /gwork1/gerwalin/g98/l302.exe. ------------------------------- My question is: Is it possible to run&install g98RevA.9 (!) correctly parallel using 64bit on a Power4 system or do I really need a later revision ? (I know that lots of improvements have been done, esp. in revisions that followed A9) Thanks for any help. Yours, Elmar -- ======================================================== Elmar Gerwalin , University of Kaiserslautern,Germany Dept. of Theoretical Chemistry and IT Service Team elg~at~chemie.uni-kl.de 0631-205-2749 ======================================================== From chemistry-request@ccl.net Thu Nov 4 10:47:58 2004 Received: from hw-exchsrv01.lexpharma.com ([63.164.5.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iA4FlvsE001929 for ; Thu, 4 Nov 2004 10:47:57 -0500 Received: by HW-EXCHSRV01 with Internet Mail Service (5.5.2657.72) id <4H9AY4JS>; Thu, 4 Nov 2004 11:04:31 -0500 Message-ID: <31E0C088BADBD6119D040008028A9F8D01118829@HW-EXCHSRV01> From: "Shen, Min" To: "'chemistry_at_server.ccl.net'" Subject: Magnesium in crystal structure Date: Thu, 4 Nov 2004 11:04:25 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=3.0 required=7.5 tests=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 How will crystallographer resolve Mg2+? Min Shen, PhD Research Scientist I Lexicon Pharmaceuticals 350 Carter Road Princeton, NJ 08540 Tel: 609.466.5594 Email: mshen_at_lexpharma.com *************************************************************************** The contents of this communication are intended only for the addressee and may contain confidential and/or privileged material. If you are not the intended recipient, please do not read, copy, use or disclose this communication and notify the sender. Opinions, conclusions and other information in this communication that do not relate to the official business of my company shall be understood as neither given nor endorsed by it. *************************************************************************** From chemistry-request@ccl.net Thu Nov 4 05:32:09 2004 Received: from hartree4.UGent.be (hartree4.ugent.be [157.193.91.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iA4AW7sE015794 for ; Thu, 4 Nov 2004 05:32:08 -0500 Received: from hartree4.UGent.be (localhost [127.0.0.1]) by hartree4.UGent.be (8.12.8/8.12.8) with ESMTP id iA49vNoo018161 for ; Thu, 4 Nov 2004 10:57:23 +0100 Received: from localhost (tom@localhost) by hartree4.UGent.be (8.12.8/8.12.8/Submit) with ESMTP id iA49vMxL018157 for ; Thu, 4 Nov 2004 10:57:23 +0100 Date: Thu, 4 Nov 2004 10:57:22 +0100 (CET) From: Tom Kuppens To: CHEMISTRY/at/ccl.net Subject: Gaussian/Gamess distributed computing Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT 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 there, I'm curious if there are people working in a distributed computing environment with Gaussian98/03 or Gamess... I've created a system that allows me to automaticaly schedule and distribute gaussian jobs (in the near future also gamess jobs) over a heterogenous group of linux machines. So each job is distributed to a single node. I do a lot of geometry optimizations (eg an average of 250 gaussian jobs per molecule - B3LYP/6-31G*). Parallellisation with Linda gives bad efficiency compared to distribution of the problems to single nodes. Parallel Gaussian however is great when using very large basis sets (cc-pVTZ etc) on relatively large problems. I am really interested if there are others who do the same, or if this can be done by large/small GNU/commercial packages. Also, is there someone who knows if Gaussian is run in a "Grid" infrastructure somewhere? Thanks, Tom Kuppens Research group Quantumchemistry Department of Inorganic and Physical Chemistry WE06V Ghent University Krijgslaan 281 - S3, 9000 Ghent, Belgium Tel +32(0)9 264 4444 Fax +32(0)9 264 4983 -- http://allserv.UGent.be/~tkuppens/ ---- Life would be so much easier if we only had the source code. -- Anonymous From chemistry-request@ccl.net Thu Nov 4 15:15:38 2004 Received: from smtp-b.ua.edu (smtp-b.ua.edu [130.160.4.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iA4KFWsE018438 for ; Thu, 4 Nov 2004 15:15:32 -0500 Received: from [130.160.44.65] ([130.160.44.65]) by smtp-b.ua.edu (8.12.10/8.12.10) with ESMTP id iA4KSf04021582 for ; Thu, 4 Nov 2004 14:28:41 -0600 (CST) Message-ID: <418A9090.9000500^at^bama.ua.edu> Date: Thu, 04 Nov 2004 14:26:56 -0600 From: "Keith E. Gutowski" User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.3) Gecko/20040916 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry^at^ccl.net Subject: Volume keyword in Gaussian: problem Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=4.5 required=7.5 tests=FROM_ENDS_IN_NUMS,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 I am trying to compute ionic volumes using the 'volume=tight' keyword in Gaussian03. In the manual, it states for a volume calc:* 'Tight* Requests an increased density of points for more accurate integration. By default, the volume is computed to an accuracy of about 10%. Use of this option is recommended if the computed molecular volume is needed more quantitatively.' Now, when I caculate the volume of PF6- using B3LYP, DZVP2 basis set (opt + volume=tight), I get a strange result. Here is the volume output for 6 different runs of the same input file (in cubic cm per mol): 69.815 57.036 65.763 60.465 68.880 54.854 Now, I would hope that Gaussian03 could generate better reproducibility that this, but am I wrong? I have been trying to track down the source of this, but I am a bit stumped. The only this I can come up with has to do with the error on the integrated density. For each run (PF6- or whatever molecule I do), the integrated density is about 4.23D+01, while the error on the integrated density is about -2.75D+01. I thought the error on the integrated density should be around XXXD-06. This is printed out in the output along with the volume output results. Anyone have any idea what may be going on? Keith From chemistry-request@ccl.net Thu Nov 4 18:04:42 2004 Received: from web53901.mail.yahoo.com (web53901.mail.yahoo.com [206.190.36.211]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iA4N4fsE028067 for ; Thu, 4 Nov 2004 18:04:41 -0500 Message-ID: <20041104231750.92692.qmail(at)web53901.mail.yahoo.com> Received: from [129.128.136.71] by web53901.mail.yahoo.com via HTTP; Thu, 04 Nov 2004 18:17:50 EST Date: Thu, 4 Nov 2004 18:17:50 -0500 (EST) From: "A. Boufarik" Subject: Perturbation / Variational To: "Comp. Chem. List" MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1809092931-1099610270=:92495" X-Spam-Status: No, hits=2.8 required=7.5 tests=FROM_ENDS_IN_NUMS,HTML_20_30, HTML_MESSAGE,MK_BAD_HTML_04 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-1809092931-1099610270=:92495 Content-Type: text/plain; charset=us-ascii Greetings all, [1] Suppose that a Hartree-Fock wavefunction W_tot is obtained for some Hamiltonian H_tot = H_0 + H_1 where H_1 is a "small" perturbation. [2] Assuming that I can get the wavefunction W_0 from H_0. Can I safely assume that the first order correction can be calculated as W_(1) = W_tot - W_0 ? References, suggestions, comments, ... are welcome Boufarik --------------------------------- Post your free ad now! Yahoo! Canada Personals --0-1809092931-1099610270=:92495 Content-Type: text/html; charset=us-ascii
Greetings all,
 
[1] Suppose that a Hartree-Fock wavefunction W_tot is obtained for some Hamiltonian H_tot = H_0 + H_1 where H_1 is a "small" perturbation.
 
[2] Assuming that I can get the wavefunction W_0 from H_0.
 
Can I safely assume that the first order correction can be calculated as
W_(1) = W_tot - W_0 ?
 
References, suggestions, comments, ... are welcome
 
 
Boufarik 


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