From chemistry-request@www.ccl.net Fri Mar 12 00:14:38 1999 Received: from amon.reed.edu (amon.reed.edu [134.10.2.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id AAA16804 Fri, 12 Mar 1999 00:14:37 -0500 (EST) Received: from isis.reed.edu (isis.reed.edu [134.10.2.1]) by amon.reed.edu (8.8.8/8.8.8) with SMTP id RAA16242 for ; Thu, 11 Mar 1999 17:03:29 -0800 (PST) Message-id: <7971409@isis.reed.edu> Date: 11 Mar 99 17:03:29 PST From: Alan.Shusterman@directory.Reed.EDU (Alan Shusterman) Subject: Re: Avogadro's number To: chemistry@www.ccl.net Several worthwhile articles re: Avogadro's number, its history, and how it is measured have appeared in the Journal of Chemical Education over the last few decades. The Journal has a searchable web site, so you should have no trouble finding these references. Those who are interested in the number may also be interested in current efforts to redefine the kilogram. The current definition = a lump of metal in Paris. The desired definition = a certain number of atoms of a certain substance. The trick is how to count these atoms with sufficient accuracy. Articles about the kilogram effort have appeared in either Science or Nature (I forget which, sorry) during the last year or so. Alan ------------- Alan Shusterman Department of Chemistry Reed College Portland, OR www.reed.edu/~alan From chemistry-request@www.ccl.net Fri Mar 12 04:38:00 1999 Received: from dreamon.oxmol.co.uk (dreamon.oxmol.co.uk [193.132.141.15]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA22066 Fri, 12 Mar 1999 04:37:58 -0500 (EST) Received: from oxmol.co.uk (bludgeon.oxmol.co.uk [193.132.141.84]) by dreamon.oxmol.co.uk (8.9.0/8.9.0/7) with ESMTP id JAA11795; Fri, 12 Mar 1999 09:36:44 GMT Message-ID: <36E8E048.34DAC1E5@oxmol.co.uk> Date: Fri, 12 Mar 1999 09:37:12 +0000 From: Rob Williams Organization: Oxford Molecular Group X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Irena Efremenko CC: CCL Computational Chemistry List , cermsge@techunix.technion.ac.il Subject: Re: CCL:ZINDO program References: <36E8C6CD.EE78A475@tx.technion.ac.il> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > I would like to calculate reliable adsorption energies and optimized > geometries for small molecules on/in relatively large transition metal > clusters (50-100 atoms). My main interest is in adsorbent-induced > changes in metal skeleton. To my best knowledge the ZINDO program is the > best choice for such calculations. May somebody here point me out how > can I get it? Any suggestions on other semiempirical programs with > parametrization for transition metals will be appreciated, as well. Dear Irena, ZINDO is available through one of our products, CAChe. You can find more information on our web site at: http://www.oxmol.co.uk/prods/cache/ CAChe can also includes interfaces to MOPAC, DGauss, and VAMP. Best regards, Rob -- --------------------------------------------------------------------- Dr Rob Williams Tel: (+44) 1865 784600 Deputy Engineering Manager Fax: (+44) 1865 784601 Oxford Molecular Limited E-mail: rwilliams@oxmol.co.uk --------------------------------------------------------------------- From chemistry-request@www.ccl.net Fri Mar 12 08:26:12 1999 Received: from eva.eerie.fr ([146.19.248.34]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA26813 Fri, 12 Mar 1999 08:26:09 -0500 (EST) Received: from syntem.eerie.fr (localhost [127.0.0.1]) by eva.eerie.fr (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id OAA90374 for ; Fri, 12 Mar 1999 14:29:08 +0100 (MET) Sender: elie@syntem.eerie.fr Message-ID: <36E916A3.7898ADD@syntem.eerie.fr> Date: Fri, 12 Mar 1999 14:29:08 +0100 From: Elie Giraud Organization: syntem X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX 6.5 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Convergence percentage parameters Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello, I'm new in the use of GAlib. I have a problem stopping a GA by convergence rather than by generation count. I tried the 'convergence_percentage' and the 'generations_to_convergence' parameters. I could see by using the 'flush_frequency' parameter that the generation best scores converged and remained to a constant value. But the GA doesn't stop. Are these parameters enough ? Thank you for your help. **************************************************************** François Grand Synt:em Software engineer Parc Scientifique G.Besse Computational Drug Discovery 30000 Nimes email: fgrand@syntem.eerie.fr France Tel: +33 (0)4 66 04 86 66 Fax: +33 (0)4 66 04 86 67 **************************************************************** Discover New Drugs, Discover Synt:em http://www.syntem.com **************************************************************** **************************************************************** Elie Giraud Synt:em Parc Scientifique G.Besse Computational Drug Discovery 30000 Nimes email: egiraud@syntem.eerie.fr France Tel: +33 (0)4 66 04 86 66 Fax: +33 (0)4 66 04 86 67 **************************************************************** Discover New Drugs, Discover Synt:em http://www.syntem.com **************************************************************** From chemistry-request@www.ccl.net Fri Mar 12 09:03:45 1999 Received: from wishful.weizmann.ac.il (root@wishful.weizmann.ac.il [132.76.63.17]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA27829 Fri, 12 Mar 1999 09:03:43 -0500 (EST) Received: from wicc.weizmann.ac.il (martin2-per6400.weizmann.ac.il [132.76.57.137]) by wishful.weizmann.ac.il (8.6.5/8.6.5) with ESMTP id QAA33332; Fri, 12 Mar 1999 16:00:45 +0200 Message-ID: <36E91E45.CCB1383E@wicc.weizmann.ac.il> Date: Fri, 12 Mar 1999 16:02:42 +0200 From: "Gershom (Jan M.L.) Martin" Organization: Weizmann Institute of Science X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 To: Luis Salvatella =?iso-8859-1?Q?Ib=E1=F1ez?= CC: chemistry@www.ccl.net Subject: Re: CCL:Avogadro's number References: <36E8F62B.E14C433B@posta.unizar.es> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Luis Salvatella Ibáñez wrote: > > Dear CCLers, > > The Avogadro's number was firstly determined by Loschmidt in 1865, 9 > years after the death of > Avogadro. This calculation was based on the application of the kinetic > theory of gases. Incidentally, in German-speaking countries Avogadro's number is known as Loschmidt's Number. JM --------------------------------------------------------------------- dr. Jan M.L. Martin Senior Lecturer, Computational Chemistry Department of Organic Chemistry/Kimmelman Building, Room 262 Weizmann Institute of Science/IL-76100 Rechovot/ISRAEL Email: comartin@wicc.weizmann.ac.il Phone: +972(8)9342533 Web site: http://theochem.weizmann.ac.il/ FAX: +972(8)9344142 *** finger comartin@winston.weizmann.ac.il for PGP public key *** -- kol ha`olam kulo gesher tzar meod v'ha`ikar lo l'hitpached klal -- From chemistry-request@www.ccl.net Fri Mar 12 19:29:30 1999 Received: from sungod.ccs.yorku.ca (7QvhKRo4GbTpzuc4VMd+06DoxX5cCpbr@sungod.ccs.yorku.ca [130.63.236.104]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA25305 Fri, 12 Mar 1999 19:29:29 -0500 (EST) Received: from mountain.chem.yorku.ca (mountain.chem.yorku.ca [130.63.133.28]) by sungod.ccs.yorku.ca (8.8.7/8.6.11) with ESMTP id TAA14703 for ; Fri, 12 Mar 1999 19:29:32 -0500 (EST) Received: from localhost (waito@localhost) by mountain.chem.yorku.ca (8.8.4/8.6.12) with SMTP id TAA05073 for ; Fri, 12 Mar 1999 19:26:38 -0500 (EST) Date: Fri, 12 Mar 1999 19:26:38 -0500 (EST) From: Wai-To Chan To: chemistry@www.ccl.net Subject: Summary: Visualisation program suggestion Message-ID: Dear CCLers, More than a month ago I asked for suggestion of visualization software and got plenty of responses. I've delayed posting this summary partly because I thought I though I could also provide some of my own comments on my final choices. However I still have not decided on what program to use to this day so I better have all the responses posted. Note that I might have skipped a few replies which suggested the same program. But I do appreciate each and every response. Thanks. Wai-To Chan Department of Chemistry York University Toronto, Ontario Canada My original question: ........................................... Dear colleagues, I am writing this note to solicit your comments on any appropriate visualization package for developing molecular graphics applications on a SGI workstation. I am looking for a program that can extract from a cubic grid of various electron density properties (computed from Gaussian using the cube option) these features: 2D and 3D contour plots 3D multi-isovalued surfaces gradient vectors (in 2D and 3D space) Locations of maxima and minima Specifically the program must enable me to produce an isovalued electron-density surface. The program also must put out the cartesian coordinates of this surface which I will need for subsequent evaluation of other quantities on this surface. At present I have in my mind either AVS (advanced visualization system) or Iris explorer. Can someone comment on these two programs particularly? My primiary considerations are prices, user-friendliness, flexiblity and popularity among computational chemists. Any suggestion of freeware would be very useful although I've not been able to find one free program that meets all my needs. Other than modular graphics package an easy-to-program graphics subroutine library (compatible with C if not FORTRAN) would also be helpful. Thanks. ............................................ Summary of answers: ***************************************** > From: "Fred P. Arnold" gOpenMol is a good choice, though due to the Tk/Tcl interface, it's slower than death and tends to crash under Linux. Molden can calculate the properties, but you'll have to reformat them for it to read cubes generated externally. SciAn (www.scri.fsu.edu) can read generic data, and a program by Laurent Joubert (spelling?) converts gaussian cube files to SciAn native files. In a similar vein (now we're talking commercial, expensive, but powerful software) IBM DataExplorer (www.almaden.ibm.com/dx) or NAG Explorer (www.nag.com) are capable of reading and visualizing general cube data, as well as transformations and other features. Personally, I'd probably use SciAn as a first choice, and proceed from there. If you have the budget DataExplorer (IBM) is a wonderful program, though with a steep learning curve) -fred Frederick P. Arnold, Jr. "...But if you give theorists enough Advanced Research Systems time, they can predict anything." 5640 S. Ellis Ave Dr. M. S. Turner, U. Chicago. Chicago, IL 60637 **************************************** > From: Ken Flurchick Wai-To I am Ken Flurchick and I have written modules to process Gaussian Cube files, and extract freq from a chkpnt file plur display structure Look at http://www.ccl.net/~kenf go to Visualization then Software for a discussion of the software. If you go with AVS this may be of help I recommend AVS, greater flexibility kenf > From laaksone@csc.fi Fri Jan 29 00:40 EST 1999 Hi, I can't promise you everything but please have a look at gOpenMol at http://laaksonen.csc.fi/gopenmol/ Regards, -leif laaksonen ------------------------------------------------------------------- Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- > From joubert@lct.jussieu.fr Fri Jan 29 03:03 EST 1999 Hi, I suggest you take a look at my old homepage : http://134.157.11.11/Pages/LECA/GP/Laurent/soft.html During my PhD thesis, I used the freeware SciAn to visualize some molecular properties. SciAn is a really impressive program if you have a good graphic card on your SGI. I wrote small programs as an interface between SciAn and Gaussian. I think you will be able to modify these programs in order to display supplementary data such as gradients. Sincerely, Laurent > From marc.debacker@hei.fupl.asso.fr Fri Jan 29 04:20 EST 1999 You may try a nice program called VU available from ftp://ftp.cerca.umontreal.ca/VU/bin/. Infos from http://www;cerca.umontreal.ca/VU Free software and lots of documentation including a tutorial. If you have enough money, you may also look to IRIS EXPLORER. Good luck Dr Marc G. De Backer Lasir - HEI - CNRS UMR 8516 13, rue de Toul 59046 LILLE (FRANCE) mdebacker@nordnet.fr (home) Tel : (33) 3 28 38 48 58 Fax : (33) 3 28 38 48 04 --=====================_84563564==_.ALT > From mbdtsnm@mchhpf.ch.man.ac.uk Fri Jan 29 05:22 EST 1999 Wai-to, not sure if this is going to be available to you, but it may be worth a try. MAVIS is and AVS based package developed in manchester a few years ago. It will produce some density plots and contours. The current web-page : (http://www.man.ac.uk/MVC/research/MAVIS/) has a link describing the license, it says that it is available for a nominal fee (1 pound) to all UK HEI's. So I'm not sure if they'd let you have it, get in touch with Matt Cooper and I'm sure he'd let you know. noj -- Dr. Noj Malcolm Theory Group, Dept. of Chemistry, University of Manchester, Oxford Road, Manchester. M13 9PL e-mail noj.malcolm@man.ac.uk > From Christopher.Page@uv.es Fri Jan 29 05:22 EST 1999 Whilst I was at Imperial College, London, I wrote, together with Omer Casher, a number of modules for Iris Explorer to work with Gaussian cube files, and found it to be extraordinarily powerful. Using these modules in conjunction with the standard library, it is possible to create 2D and 3D contour plots and 3D multi-isovalued surfaces. Outputting the Cartesian coordinates and interpolating other data to them is also facile: one of our interests was in projecting MEPs onto either isodensity surfaces or Connolly surfaces. I haven't tried to do gradient vectors, but believe that there is a module in the standard library for extracting these. Similarly there is bound to be one for extracting maximum and minimum values and their coordinates (and if there isn't, it would be trivial to write one). The 3D graphical output is Open Inventor. It is fully optimised for SGI/OpenGL, and, to be honest, I have yet to see anything that beats it either for performance or quality. Conversion to VRML can be performed using standard scripts. The main reservation I have with recommending Explorer is that, to use it effectively, there is quite a steep learning curve, and, in particular, if a module doesn't exist to do what you want, you have to be prepared to write it yourself. That said, if you are interested, I can make the cube file reader available to you, and various other utilities I have written, so hopefully this situation won't arise immediately. A demo version of Explorer can be arranged by contacting Jeremy Walton at NAG (jeremyw@nagalp.nag.co.uk). I have no experience of AVS, but Ian Hillier's group in Manchester, UK, has written a number of chemistry-specific extensions, under the name of "Mavis". Perhaps you can contact ian.hillier@man.ac.uk for details. If I can be of any further help, please let me know. regards, Chris Page __________ Departamento de Quimica Fisica Tel: +34 630 604 375 Universidad de Valencia Dr. Moliner 50 Burjassot E-46100 Valencia > From richard@tc.cornell.edu Fri Jan 29 09:42 EST 1999 I have used IBM's Data Explorer for many years now and find it very appealing, although it is not free. It is supported on all major platforms including NT and can take advantage of OpenGl hardware. One can also build applications directly calling the C module library. Although the user interface is not as snappy as I would like, the underlying structure of the system, including it's sophisticated user-definable data model is very nice. As with AVS, this is a general viz package with little built-in chemistry specifics, however, my chemistry module add-ons are freely available source and all, just ask. There is also considerable interest here in VTK: one member of our center is very enthusiastic about a Python scripting interface to VTK. Personally, I see little point in scripting interfaces, especially unusual ones. The small set of users who are likely to take the time to learn a new language, even a simple one, will already know C or C++. Why not just compile and get the better (superior) performance? Richard Gillilan Cornell Theory Center > From fah@igc.phys.chem.ethz.ch Mon Feb 1 08:43 EST 1999 Dear Wai-To, I read your message on CCL. My favourite is "Vis5d", free, available both in source and precompiled. It comes from weather-forecasting and is the fastest I've seen running on my laptop under Linux. Only problem: I haven't found a way yet (and not been trying hard) to get also balls and sticks for the atoms + bonds. Other suggestions: - gopenmol (from Finland) - vu (from Quebec) Good luck Fred A. Hamprecht Institute of Physical Chemistry | Institute of Organic Chemistry ETH Zentrum | University of Zuerich Tel: +41-1-632 6841 | Tel: +41-1-635 6119 CH-8092 Zuerich fah@igc.phys.chem.ethz.ch CH-8057 Zuerich > From tvd@msi.com Wed Feb 3 15:21 EST 1999 Hi there - You can do these things with the Cerius2 developers kit from MSI. It is available for free. Look at http://www.msi.com/support/sdk/ for details on how to get a license. Also have a look at the iso surface application in the examples sections. This is similar to what you want to do. Regards - Ton From chemistry-request@www.ccl.net Fri Mar 12 21:01:14 1999 Received: from oxmail.ox.ac.uk (oxmail4.ox.ac.uk [163.1.2.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA25950 Fri, 12 Mar 1999 21:01:14 -0500 (EST) Received: from bellatrix.pcl.ox.ac.uk ([163.1.35.131] helo=bellatrix.pcl) by oxmail.ox.ac.uk with esmtp (Exim 2.10 #1) id 10Ldjn-0006U6-00 for CHEMISTRY@www.ccl.net; Sat, 13 Mar 1999 02:01:15 +0000 Received: (from varnai@localhost) by bellatrix.pcl (8.9.1/8.8.8) id CAA29424 for CHEMISTRY@www.ccl.net; Sat, 13 Mar 1999 02:01:14 GMT From: Peter Varnai Message-Id: <199903130201.CAA29424@bellatrix.pcl> Subject: PCM with MP2 To: CHEMISTRY@www.ccl.net Date: Sat, 13 Mar 1999 02:01:14 +0000 (GMT) Dear CCLers, Has anyone succeeded in calculating PCM solvation energy with MP2 density? According to the gaussian98 manual it is possible... Thank you for your help. Peter Varnai From chemistry-request@www.ccl.net Sun Mar 14 11:49:46 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA04113 Sun, 14 Mar 1999 11:49:46 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.9.3/8.9.3) id LAA17133 for chemistry@www.ccl.net; Sun, 14 Mar 1999 11:49:46 -0500 (EST) Date: Sun, 14 Mar 1999 11:49:46 -0500 (EST) From: "E. Lewars" Message-Id: <199903141649.LAA17133@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: G2 AND CBS METHODS: CONVERGENCE FAILURES 1999 March 14 Hello, I find that the high-accuracy G2-type (G2, G2MP2 etc) and CBS (CBS-4, CBS-Q) methods, as implemented in Gaussian 94 and Gaussian 98, useful as they are, fairly frequently fail because of convergence problems. G92MP2 fails in step 5, and CBS-Q and CBS-4 in step 4, that is, after wasting hours on several previous steps. If others have had this problem with G2 and CBS methods and found a solution, I would very much appreciate hearing what it is. Thank you. E. Lewars ========================== From chemistry-request@www.ccl.net Sun Mar 14 13:20:23 1999 Received: from granite.sentex.net (granite.sentex.ca [199.212.134.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA04645 Sun, 14 Mar 1999 13:20:22 -0500 (EST) Received: from pppuser.uoguelph.ca (p13a.neon.sentex.ca [207.245.212.206]) by granite.sentex.net (8.8.8/8.6.9) with SMTP id NAA29241 for ; Sun, 14 Mar 1999 13:20:22 -0500 (EST) Message-Id: <4.1.19990314131347.03b6c1c0@mail.sentex.net> X-Sender: mathtrek@mail.sentex.net X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Sun, 14 Mar 1999 13:15:04 -0500 To: chemistry@www.ccl.net From: "W. R. Smith" Subject: Announcement: Textbook Availability In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello, Mathtrek Systems has recently acquired the remaining stock of my book "Chemical Reaction Equilibrium Analysis: Theory and Algorithms", W. R. Smith and R. W. Missen, Krieger, 1991, Malabar FLA. The book outlines the theory underlying chemical reaction equilibrium and its computation, and its application to a broad range of fields. A description of the book is given on the Mathtrek Systems web site (URL below); it can be ordered directly from the web site. -- W. R. Smith, PhD, P. Eng., Senior Scientist, Mathtrek Systems -- 3-304 Stone Road West, Suite 165, Guelph, Ontario CANADA N1G 4W4 EMail: support@mathtrek.com Tel:519-763-1356,FAX:519-763-4525 --------------------- http://www.mathtrek.com --------------------- -Mathtrek Systems - Home of EQS4WIN Chemical Equilibrium Software - From chemistry-request@www.ccl.net Sun Mar 14 13:39:10 1999 Received: from chrs1.chem.lsu.edu (chrs1.chem.lsu.edu [130.39.132.111]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA04792 Sun, 14 Mar 1999 13:39:09 -0500 (EST) Received: from localhost by chrs1.chem.lsu.edu (AIX 4.1/UCB 5.64/4.03) id AA25144; Sun, 14 Mar 1999 12:38:49 -0600 Date: Sun, 14 Mar 1999 12:38:49 -0600 (CST) From: Chris Harwell To: Peter Shenkin Cc: chemistry@www.ccl.net Subject: Re: CCL:Avogadro's number In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > > On Thu, 11 Mar 1999, Anatoli Korkin wrote: > > > Last time I was visiting my dentist, he asked me how Avogadro > > > could come with his number at that time. > On Thu, 11 Mar 1999, Chris Harwell wrote: > > someone else actually came up with the number after boltzmann & maxwell > > came up with the necessary stat. mech. On Fri, 12 Mar 1999, Peter Shenkin wrote: > Sigh. What do they teach in freshman chemistry these days? oh. so sorry -- Dr Shenkin you must be right! Freshman chemistry was sooo much better in the old days.... > Based on the observation that gasses combine chemically in the > ratio of small whole numbers, Avogadro *hypothesized* that equal > volumes of gasses (at the same T & P) have the same number of > molecules. I believe this was around 1811. > > Still, nobody knew what the number was. In the late 19th century, > people referred to Loschmidt's number, which was something like the > number of molecules in a gram of hydrogen gas. actually peter i think it is more like this: in 1865 J. Loschmidt worked out a good value for Avagadro's number. Loschmidt actually got a number bearing his name as well: the number of moles in 1 cubic centimeter of gas at standard temperature and pressure. this is also equal to Avagadro's number divided by 22415. or something like 2.68683 * 10^19. > It could > be approximated from the kinetic theory of gasses by comparing > several measurements; this gave the right order of magnitude. i think that is what Loschmidt did. > This is what Chris is referring to, I think (though I wouldn't > call it stat mech). well yes. Maxwell & Boltzmann in the 1860s independently worked out what became the kinetic theory of gases. this being "a statistical treatment of the microscopic constituents of a system in order to predict macroscopic properties". it would seem appropriate to call it statistical mechanics. what else would one call it? From chemistry-request@www.ccl.net Sun Mar 14 14:52:47 1999 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id OAA05580 Sun, 14 Mar 1999 14:52:46 -0500 (EST) Received: by bioc1.msi.com (940816.SGI.8.6.9/930416.SGI) id LAA18025; Sun, 14 Mar 1999 11:51:19 -0800 Received: from unknown(146.202.0.100) by bioc1.msi.com via smap (V2.0) id xma018021; Sun, 14 Mar 99 11:50:51 -0800 Message-Id: <3.0.3.32.19990314114937.006ef968@146.202.6.218> X-Sender: nxt@146.202.6.218 X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Sun, 14 Mar 1999 11:49:37 -0800 To: Irena Efremenko , CCL Computational Chemistry List , cermsge@techunix.technion.ac.il From: Noppawan Tanpipat Subject: Re: CCL:ZINDO program Cc: abernstein@msi.com In-Reply-To: <36E8C6CD.EE78A475@tx.technion.ac.il> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Irena, The recent version of Prof. Mike Zerner's ZINDO program is now available in the Cerius2 environment from Molecular Simulations Inc. More information can be found at http://www.msi.com/solutions/products/cerius2/modules/zindo.html Regards, Noppawan Tanpipat At 09:48 AM 3/12/99 +0200, Irena Efremenko wrote: >Dear CCLers, > >I would like to calculate reliable adsorption energies and optimized >geometries for small molecules on/in relatively large transition metal >clusters (50-100 atoms). My main interest is in adsorbent-induced >changes in metal skeleton. To my best knowledge the ZINDO program is the >best choice for such calculations. May somebody here point me out how >can I get it? Any suggestions on other semiempirical programs with >parametrization for transition metals will be appreciated, as well. > >Thanks in advance, > >Irena Efremenko > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: chemistry-request@www.ccl.net >-- Original Sender From: Address: chrirena@techunix.technion.ac.il >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > > ************************************* Noppawan Tanpipat, Ph.D. Product Specialist, Quantum Chemistry Molecular Simulations Inc. 9685 Scranton Road San Diego, CA 92121 Tel: (619) 799-5332 Fax: (619) 458-0136 Email: nxt@msi.com From chemistry-request@www.ccl.net Sun Mar 14 17:37:52 1999 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA06268 Sun, 14 Mar 1999 17:37:51 -0500 (EST) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.8/8.8.8) with SMTP id OAA25788 for ; Sun, 14 Mar 1999 14:37:52 -0800 (PST) Date: Sun, 14 Mar 1999 14:37:52 -0800 (PST) From: "Dale A. Braden" To: CHEMISTRY@www.ccl.net Subject: Re: G9x under IRIX 6.5 ? In-Reply-To: <"36E78D12.10DD.628C.000*Creve_Steven_SJR//RESEARCH/NL/400net/DSM"@MHS> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Steven, When we upgraded to IRIX 6.5.1 on our R8000 PowerChallenge, G94 continued to work, having been compiled under IRIX 6.3. But when we upgraded to IRIX 6.5.2, the multiprocessing capability of G94 quit. I then recompiled the program under 6.5.2 on both R8000 and R10000 machines, and it compiled without any problem using the default makefiles, but it still crashed whenever more than one cpu was requested. Then I saw a posting on the CCL that this problem is due to a bug in the MP libraries which is incompatible with IRIX 6.5.2, and that the temporary fix is to set an environment variable as follows: setenv MP_STACK_OVERFLOW OFF This did indeed allow us to use multiple cpus again, but the results of frequency calculations became garbage unless only 1 cpu was used. So if you're only using 1 cpu, then G94 should compile and run fine under IRIX 6.5.x. Otherwise, I don't know what to do. If it really is an incompatibility between IRIX and the MP libraries, then it presumably affects Gaussian98 as well. Can anyone attest to this? Best wishes, Dale Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu On Thu, 11 Mar 1999 Steven.Creve@dsm-group.com wrote: > > > Hi, > > 1) Is Gaussian9x (94 in particular) available under irix 6.5? > 2) If not, has anyone ever tried to compile it under irix 6.5? > > I would just like to know these things before spending days and nights > recompiling the program... > > thanks in advance, > Steven > > ------------------------------------------------------ > Steven Creve > DSM Research > P.O. Box 18 > NL 6160 MD Geleen, The Netherlands > phone: ++31 46 47 61297 > E-mail: steven.creve@dsm-group.com > ---------------------------------------------- > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- >