From chemistry-request@server.ccl.net Sat Apr 24 13:31:10 1999 Received: from rzusuntk.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA19288 for ; Sat, 24 Apr 1999 13:31:10 -0400 Received: [from rzusgi.unizh.ch (chburger@rzusgif.unizh.ch [130.60.68.19]) by rzusuntk.unizh.ch (8.8.5/SMI-5.25) with SMTP id TAA10908 for ; Sat, 24 Apr 1999 19:27:09 +0200 (MET DST)] Date: Sat, 24 Apr 1999 19:27:09 +0200 (MDT) From: "Dr. Peter Burger" To: CHEMISTRY@ccl.net Subject: CCL: freely available geometry optimizer? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am in search for a freely available (short) geometry optimizer (for equilibrium & TS opt.), which can read in coordinates, gradients and energies externally from a file and generate geometry updates. The idea is to interface the optimizer with a different program that I am using here in that I would require the source code (Fortran would be best). Preferably the optimizer should be capable of handling cartesian coordinates, Z-matrices and acknowledge applied geometrical constraints. Different optimization routines/algorithms were obviously a plus. Many thanks in advance, Peter ----------------------------------- Peter Burger University of Zuerich chburger@aci.unizh.ch From chemistry-request@server.ccl.net Sat Apr 24 14:24:23 1999 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA19729 for ; Sat, 24 Apr 1999 14:24:22 -0400 Received: from sally.schrodinger.com (sally.schrodinger.com [206.231.140.227]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id LAA12673 for ; Sat, 24 Apr 1999 11:22:59 -0700 Received: from localhost (shenkin@localhost) by sally.schrodinger.com (8.8.5/8.8.5) with ESMTP id LAA01962 for ; Sat, 24 Apr 1999 11:21:36 -0700 X-Authentication-Warning: sally.schrodinger.com: shenkin owned process doing -bs Date: Sat, 24 Apr 1999 11:21:36 -0700 (PDT) From: Peter Shenkin To: chemistry@ccl.net Subject: Re: CCL:Benchmarks and Software In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I quite agree with a number of points that have been raised, including Dave's. But I feel that people should be able to publish benchmarks performed with their software so that prospective users can then decide (1) whether those particular benchmarks are relevant to their prospective uses, and (2) whether speed matters at all. What has only been implicit in all this is that some of the providers of softare disallow, in the standard license agreement which every user must sign, any publication of benchmarks. This, I feel, is inimical to the further development of the entire profession -- in fact, both professions (plural): computational chemistry and software development in this area. -P. On Thu, 22 Apr 1999, David Young wrote: > > Hi, > > I would like to point out that this conversation on benchmarks is > a bit one dimensional. There are some very popular (profitable) chemistry > software packages that do poorly on benchmarks but sell because of other > factors such as ease of use or functionality. ... From chemistry-request@server.ccl.net Sat Apr 24 15:32:53 1999 Received: from mserv1.dl.ac.uk (root@mserv1.dl.ac.uk [148.79.160.65]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA20211 for ; Sat, 24 Apr 1999 15:32:52 -0400 Received: from tcsg7 (tcsg7.dl.ac.uk [193.62.112.46]) by mserv1.dl.ac.uk with SMTP id UAA12946 (8.8.8/5.4[ref postmaster@dl.ac.uk] for dl.ac.uk from P.Sherwood@dl.ac.uk); Sat, 24 Apr 1999 20:28:57 +0100 (BST) Precedence: first-class Received: by tcsg7 (950413.SGI.8.6.12/930817.MJE) id UAA08948; Sat, 24 Apr 1999 20:11:50 +0100 Date: Sat, 24 Apr 1999 20:11:50 +0100 From: P.Sherwood@dl.ac.uk (Paul Sherwood) Message-Id: <199904241911.UAA08948@tcsg7> To: chemistry@server.ccl.net, "Dr. Peter Burger" Subject: Re: CCL:optimizer Peter, There is some optimiser development going on in Prof Thiel's group, did you discuss the matter with him yet? Paul Sherwood From chemistry-request@server.ccl.net Sun Apr 25 17:38:48 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA24300 for ; Sun, 25 Apr 1999 17:38:47 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.9.3/8.9.3) id RAA04553 for chemistry@ccl.net; Sun, 25 Apr 1999 17:34:29 -0400 (EDT) Date: Sun, 25 Apr 1999 17:34:29 -0400 (EDT) From: "E. Lewars" Message-Id: <199904252134.RAA04553@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: VISUALIZATION SUMMARY--THANKS VISUALIZATION These are the replies to my visualization question. Thanks very much to all who replied. QUESTION: Date: Thu, 15 Apr 1999 08:25:31 +0200 Subject: Re: CCL:VISUALIZATION To: "E. Lewars" >1999 April 14 > >Hello, > >Visualization--using computer graphics to present information as pictures-- >has become very important in science--in physics, aerodynamics, meteorology, >and of course computational chemistry. >Has anyone a reference to an article dealing with the importance of computer >visualization (in science in general or in chemistry inparticular)? > > Thanks > > E. Lewars ====================== REPLIES: #1 Dear prof. Lewars, There is a paper by C. L. Habraken - Journal of Science Education and Technology (1996), 5, 193 - 201. Title: "Perceptions of Chemistry: Why is the Common Perception of Chemistry, the Most Visual of Sciences, So Distorted?" Though it mainly deals with the importance of visualization in 'teaching' chemistry, the conceptual border to 'doing' chemistry is easily crossed. Best regards, Han ______________________________________________________________________ Han Zuilhof | E-mail: ZUILHOF@SG1.OC.WAU.NL Laboratory of Organic Chemistry | FAX : 31-317-484914 Wageningen University | phone : 31-317-482367 Dreijenplein 8 | 6703 HB Wageningen | The Netherlands | http://www.spb.wau.nl/oc/perspages/han/index.htm ================== #2 You could look at the following: "Visualising the future of molecular graphics" AJ Olson and ME Pique, SAR and QSAR in Environmental Research, 8, 1998, 233- 247. Strangely enough, not a picture in the artice! "Zelite Computer Graphics" CM Freeman, et al., in "Modelling of Structure and Reactivity in Zeolites" ed CRA Catlow, Academic Press, London, 1992. Leslie ============================================================== (Prof.) Leslie Glasser Dept. of Chemistry E-mail: glasser@aurum.chem.wits.ac.za Univ. of Witwatersrand Tel: Intl + 27 11 716-2070 P. O. WITS 2050 Fax: Intl + 27 11 339-7967 South Africa Home Pages: University http://www.wits.ac.za Chemistry http://www.chem.wits.ac.za ====================================================================== #3 April 15 John P. Ranck (74) Re: CCL:VISUALIZATIONCommand: Read MessageMessage 7/7 from John P. Ranck Apr 15 '99 at 9:30 am Addison Wesley has published a book: Bowie, Jack E., ed., "Data Visualization in Molecular Science: Tools for Insight and Innovation," 1995. ISBN 0-201-58157-4. Some persons very active in this field include Richard Gillilan at the Cornell Theory Center http://www.tc.cornell.edu/~richard/ and Art Olson at Scripps Research Institute. I'm sure you will find many useful links from their web sites. Roy Tasker at the Univ. of Western Sydney has been running a chemical visualization project in Australia. He presented some very impressive chemistry visualizations at the Biennial Conference in Chemical Education at Bucknell University a couple of years ago You might also be interested in the MoleCVUE [Molecular Computation and Visualization in Undergraduate Education] Project, centered at Elizabethtown College, which is a collaboration of a dozen and a half undergraduate chemistry faculty from across the Eastern US to develop instructional materials using computation and visualization. -- John P. Ranck E-mail: ranck@etown.edu Department of Chemistry Phone: 717-361-1315 Elizabethtown College FAX: 717-361-1207 Elizabethtown, PA 17022 ========= #4 X-Sender: rwz7001@axe.humboldt.edu Dear Professor Lewars, I'd like to hear of any answers you might get ... I am currently helping a colleague in our Fisheries and Wildlife department to present information of a chemical nature in visual form to his more environmental science-related student courses. Bob Z. Robert W. Zoellner, Ph.D. Associate Professor Department of Chemistry Humboldt State University One Harpst Street Arcata, California 95521-8299 telephone: (707)826-3244 fax: (707)826-3279 ========= #5 Date: Fri, 16 Apr 1999 14:52:05 -0600 To: elewars@alchemy.chem.utoronto.ca Subject: Re: CCL:VISUALIZATION Hello, you asked for articles dealing with the importance of computer visualization. I am doing my Ph.D. work in the ChemVis project on the topic of chemical visualization on the Internet. We have some slides and papers on our ChemVis homepage. http://www2.ccc.uni-erlangen.de/projects/ChemVis/ http://www2.ccc.uni-erlangen.de/projects/ChemVis/lectures.html http://www2.ccc.uni-erlangen.de/projects/ChemVis/publications.html http://www2.ccc.uni-erlangen.de/projects/ChemVis/projects.html With regards Frank Oellien -- Frank Oellien Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 email: franko@ccc.chemie.uni-erlangen.de WWW : http://www2.ccc.uni-erlangen.de/people/Frank_Oellien/ http://www2.ccc.uni-erlangen.de/projects/ChemVis/ =============== From chemistry-request@server.ccl.net Sat Apr 24 12:28:29 1999 Received: from sun.fqspl.com.pl. ([212.244.147.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA18759 for ; Sat, 24 Apr 1999 12:28:28 -0400 Received: from fqs4 by sun.fqspl.com.pl. (SMI-8.6/SMI-SVR4) id SAA16690; Sat, 24 Apr 1999 18:20:11 +0200 Message-Id: <199904241620.SAA16690@sun.fqspl.com.pl.> From: "Victor Anisimov" To: Subject: Re: CCL:Non-adiabatic MD: multiple configurations? Date: Sat, 24 Apr 1999 18:29:17 +0200 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Dear Andrew, Unfortunately I can not read those article you mentioned but it seems to me there are two general points at this moment to start the discussion. First, of course there is much sense to attribute HOMO-LUMO gap in Cl2 molecule to interparticle interactions. When two chlorine atoms in their ground states are separated on infinity all energy level are degenerated, of course, and correspond to pure chlorine atom levels. When these two atoms become nearer they begin to interact and this causes breaking of degeneration in their energy levels. Frankly speaking when such an interaction arises we can not any more attribute any energy levels of the system of two Cl atoms to separate pieces. In other words any small interaction turns two independent Cl atoms into completely new system, a system of two nuclei and 34 electrons. Energy of ground state of the system is below a sum of energy of two Cl atoms. Energy of excited state of the system is higher than dissociation limit. The later is a reason why excitation of Cl2 molecule leads to dissociation onto two separate atoms. Energy of ground state and excited state of Cl2 is a function of inter-nuclei distance. The more distance between Cl nuclei the less a gap between ground state and excited one. They converge to sum of ground state energies of isolated Cl atoms on infinity. This diagram illustrates that two Cl atoms in their ground state will begin to form Cl2 molecule without any external force as only they become to see each other (become to interact). Of course, dynamic consideration adds here some additional details. Second common moment that would be interesting to discuss is a question what is a goal of configuration interaction methods. Of course everyone uses it for more precise description of given state of a system either ground state or excited one. According to general Hartree-Fock equation each electron of a system is attributed by separate wave function (MO). Simple total wave function of the system is a determinant of such self-consistent molecular orbitals. This simplified picture always causes a misunderstanding that to get excited state we have to put one electron from HOMO onto LUMO. Usually such a total wave function of excited state will be wrong. The reasons are usually bad initial guess and lack of electron correlation. Usually excited state is more sensitive to lack of electron correlation therefore even simple description of excited state requires applying to configuration interaction methods. A question here is why or how configuration interaction takes into account electron correlation. According to standard Hartree-Fock equation a problem of electron correlation is a problem of right chosen wave function. Therefore it is wrong to say in general that Hartree-Fock equation does not take into account electron correlation. Because usually we do not know a priori wave function of a system we have to guess it. The simplest guess is a determinant of molecular orbitals that is good for rough description of a system but it does not take into account those fact that electrons tend to be as much as possible far from each other what we call electron correlation. Next better guess (configuration interaction) of a total wave function is a treatment of a system as consisting of different electron configurations where each configuration is constructed >from occupying of virtual molecular orbitals. In common but wrong terms we have to give a system an ability to occupy excited states (virtual MO's). Why it is wrong? Because it is only common slogan of theoreticians embarrassing most of students and significant part of computational practitioners. In one determinant wave function electrons may become very close to each other that is not good. To allow them to be as far as possible from each other we have to give them such a flexibility in wave function. If we look on MO's of hydrogen molecule we see that occupied MO concentrates electron density between atomic nuclei and virtual MO forces electron density to go out of bond region. The later fact give us a hint if we will construct total wave function as a special combination of occupied and virtual MO's we can give electrons a flexibility to be far from each other as it is done in configuration interaction (CI) methods. Therefore CI (and MCSCF too) methods do not perform electron excitations as people used to say to take into account electron correlation but they give electron only comfortable wave function to feel him better in proximity with other electrons. I'm sorry for this long discussion. I guess not every one is happy to read such long messages in this list. Me too :) Therefore I have to say thanks for attention and take my seat :) Victor. ========================================================================= Victor Anisimov, PhD, Software Researcher - Computational Chemistry FQS Poland, Palac Pugetow, ul. Starowislna 13-15, 31-038 Krakow, Poland Email: victor@fqspl.com.pl Tel.(+48 12) 429 4345 Fax(+48 12) 429 6124 ========================================================================= -----Original Message----- From: hfield@kasei.materials.ox.ac.uk To: chemistry@ccl.net Date: 24 апреля 1999 г. 12:26 Subject: CCL:Non-adiabatic MD: multiple configurations? >I am attempting to repeat the calculations of Gersonde and Gabriel (J. >Chem. Phys. vol 98 (3), p 2094 (1993)) in which the photodissociation of >Cl2 in Xe is discussed. > >I am attempting to describe the electronic degrees of freedom using a >simple one particle model (tight binding), but have found a problem which >I fear is fundamental. Since my background is in DFT, I am not well versed >in multiple configuration interactions, hence the following question. > >Excited states within the model are created by promoting an electron from >a low lying level to an empty higher lying level. When the interactions >are weak I believe this is a reasonable description. But when they are >weak, I suspect the model breaks down. > >Consider the Cl2 dimer. It is unstable with respect to dissociation when >placed into an excited state. Thus, on being excited by a photon the atoms >begin to separate. As this happens, the HOMO-LUMO splitting decreases >until they become nearly degenerate. Thus it is no longer possible to >distinguish the excited from the unexcited states. No transition between >states is observed to take place. This is a problem should the two atoms >meet up again some time later as it is not clear what state they should go >into - ground state or excited state. > >I suspect that the root of the problem is that when the HOMO-LUMO >splitting is very small it no longer makes sense to work with a single >particle picture - it takes no energy to move between configurations, thus >they will mix freely. > >At this point I get lost. Does this analysis really solve the problem of >what state the system is in? Or would there still be ambiguity even if >configurations were allowed to mix? > >Cheers, > >Andrew > > +----------------------------------------------------+ > Andrew Horsfield e-mail: horsfield@fecit.co.uk > FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, > Middlesex UB11 1AB, United Kingdom. > phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 > +----------------------------------------------------+ >