From chemistry-request@server.ccl.net Sun Dec 19 13:45:18 1999 Received: from admiral.umsl.edu (admiral.umsl.edu [134.124.15.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA05565 for ; Sun, 19 Dec 1999 13:45:18 -0500 Received: from admiral.umsl.edu (admiral.umsl.edu [134.124.15.13]) by admiral.umsl.edu (8.9.1/8.9.1) with ESMTP id LAA13251; Sun, 19 Dec 1999 11:40:50 -0600 (CST) Date: Sun, 19 Dec 1999 11:40:50 -0600 (CST) From: Gary Stiehr To: eugene.leitl@lrz.uni-muenchen.de cc: CHEMISTRY@server.ccl.net Subject: Re: CCL:Gaussian98/Linda on Linux clusters ... In-Reply-To: <1999xxx12141955.NAA12701@us.networkcs.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Here at the University of Missouri-St. Louis, we have had excellent results with gaussian98/linda. Many calculations that we have done have had high levels of parallelism so that even with the small cluster we had at the beginning, we had great results. With a larger cluster now, we can reduce some calculations by upto 14 times (with 14 processors). Other calculations are not so parallel but still we save many hours. Gary Stiehr Campus Computing University of Missouri - St. Louis gary@umsl.edu On Tue, 14 Dec 1999 eugene.leitl@lrz.uni-muenchen.de wrote: > > From: Richard Walsh > > Greetings, > > What has been people's experience running G98 and Linda > in a Linux cluster environment? I am fairly sure that > this is a supported configuration. Ease of install, nature > of configuration, performance, maintenance, etc. are all > of interest. > > A summary of replies will be posted. > > Thanks, and a prosperous, bug-free 2000 to all, > > > Richard Walsh > > #--------------------------------------------------- > # > # Richard Walsh > # Project Manager and Chemistry Applications Support, > # Customer Support Group, > # Network Computing Services, Inc. (NetworkCS) > # 1200 Washington Ave. So. > # Minneapolis, MN 55415 > # VOX: 612-337-3467 > # FAX: 612-337-3400 > # EMAIL: rbw@networkcs.com > # > #--------------------------------------------------- > # "What you can do, or dream you can, begin it; > # Boldness has genius, power, and magic in it." > # -Goethe > #--------------------------------------------------- > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > ------------------------------------------------------------------- > To unsubscribe send a message body containing "unsubscribe" > to beowulf-request@beowulf.org > From chemistry-request@server.ccl.net Mon Dec 20 07:09:25 1999 Received: from router.dongu.donetsk.ua (dipt-gw.dongu.donetsk.ua [195.184.198.253] (may be forged)) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA10544 for ; Mon, 20 Dec 1999 07:08:34 -0500 Received: by router.dongu.donetsk.ua (8.8.7/8.8.7/dongu) with ESMTP id NAA08255; Mon, 20 Dec 1999 13:08:53 +0200 (EET) Message-ID: <385E0DD6.AE7AC898@dongu.donetsk.ua> Date: Mon, 20 Dec 1999 13:07:04 +0200 From: AnChem Organization: Dept. of Chemistry - Donetsk State University X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en,ru MIME-Version: 1.0 To: chemistry@ccl.net Subject: Looking for correspondence Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Greetings! My scientific specialization is Matrix Modifiers in Atomic Absorption Spectrometry. I am looking for everybody working in this field for e-mail correspondence and exchange of information and experience. If you are interested in it please contact me via e-mail at aas@dongu.donetsk.ua with "AAS" in subject line. I hope this will be useful for both you and me. With best regards, Sergey N. Romanov Dept. of Analytical Chemistry Faculty of Chemistry Donetsk State University Ukraine From chemistry-request@server.ccl.net Mon Dec 20 21:52:39 1999 Received: from darkwing.uoregon.edu (darkwing.uoregon.edu [128.223.142.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA14177 for ; Mon, 20 Dec 1999 21:52:38 -0500 Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.9.3/8.9.3) with SMTP id RAA16427 for ; Mon, 20 Dec 1999 17:46:06 -0800 (PST) Date: Mon, 20 Dec 1999 17:46:06 -0800 (PST) From: "Dale A. Braden" Reply-To: "Dale A. Braden" To: cclpost Subject: Summary: NBO vs AIM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, A while ago I asked for people to tell me their opinions and experiences with the NBO and AIM methods of population analysis. There were many responses, and I am grateful to all who responded. Summarizing will be difficult, but here goes: I think we all agree that there is no right answer, in the sense that one method should not be used at all, as was implied by the comments of a reviewer. A number of respondents said that they use both methods: NBO when orbitals must be discussed, and AIM otherwise. The methods are so fundamentally different that, I think, a proper comparison should involve many calculations on many different kinds of molecules before the different tendencies of each method are really clear. I have a feeling that too much use has been made of a paper claiming that AIM exaggerates the charge associated with an electronegative atom [Perrin, JACS 113 (1991) 2865], even though there were two subsequent papers refuting it [Laidig, JACS 114 (1992) 7912; Gatti and Fantucci, J. Phys. Chem. 97 (1993) 11677]. In my opinion, the papers I've seen which compare both methods AND try to conclude that one or the other is faulty aren't really based on enough evidence to be convincing. The fact that one method or the other doesn't agree with intuition doesn't strike me as a sound argument-- maybe "intuition" needs to be updated. Interestingly, some people found that NBO is more basis set dependent than AIM, and others found exactly the reverse-- another reason why many, many molecules need to be examined before the tendencies of each method are clearly revealed! Some emphasized the fact that AIM is based on an observable electron density while NBO is based on unobservable orbitals. Others said, "So what?", and still others suggested that maybe orbitals are in fact observable after all, witness things like certain STM images and the d_z2 orbital of CuO which made C&E News recently. Um, I'm not going to go there....... That AIM or NBO atomic charges don't by themselves give a "full picture" of electronic structure isn't really a problem. In what is called "NBO analysis", one can also look at hybridizations, bond orders, bond polarizabilities, atomic orbital populations, and energy changes as a function of removing one or more NBOs from the basis. In the AIM method, one can look at the Laplacian and the kinetic and potential energy densities to answer questions about bond orders, bond polarizations, ionicity/covalency, and so forth. Both methods are quite complete. One thing that always bothered me was using NBO results for one resonance structure when I knew that the molecule I was dealing with had at least two very good resonance structures. But with NBO version 4.0 there is included Natural Resonance Theory (NRT) which allows, for example, the calculation of bond orders using the full range of resonance structures for a molecule. It also reports the weights of the different resonance structures. What I still don't understand is why atomic charges are not also re-adjusted. Are they? The one demonstrable shortcoming in this whole business is with the AIM method: sometimes the integrations over the atomic basins won't converge, and then you get no atomic properties at all. A comparison of speed between NBO and AIM isn't that much of an issue, as Cioslowski's AIM methods in the Gaussian program are much faster than those in PROAIM, but not as robust as PROMEGA. On the other hand, PROMEGA is so incredibly slow that it's almost not worth it. AIM definitely could do with some improvements in implementation! A few references for those interested (a Science Citation Index search on these will bring out a lot more, but these are a good starting place): Reed, Curtiss, Weinhold, Chem. Rev. 88 (1988) 899. Bader, Chem. Rev. 91 (1991) 893. (Also Bader's book Atoms in Molecules, Oxford, 1990). Bachrach, Reviews in Computational Chemistry, vol. 5, Chapter 3 (Lipkowitz and Boyd, eds.) VCH, New York, 1994. Macchi, Proserpio, Sironi, JACS, 120 (1998) 13429. Arnold, Organometallics, 18 (1999) 4800. van Alem, Sudho:lter, Zuilhof, J. Phys. Chem. A, 102 (1998) 10860. Levy, Struct. Chem. 10 (1999) 121. Slee, MacDougall, Can. J. Chem. 66 (1988) 2961. Merry Christmas to All and Happy Y2K, Dale Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu