From jtgolab@amoco.com Mon Mar 31 10:33:00 1997 Received: from interlock.amoco.com for jtgolab@amoco.com by www.ccl.net (8.8.3/950822.1) id JAA28568; Mon, 31 Mar 1997 09:36:42 -0500 (EST) Received: by interlock.amoco.com id AA13771 (InterLock SMTP Gateway 3.0 for CHEMISTRY@www.ccl.net); Mon, 31 Mar 1997 08:36:36 -0600 Message-Id: <199703311436.AA13771@interlock.amoco.com> Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-3); Mon, 31 Mar 1997 08:36:36 -0600 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Mon, 31 Mar 1997 08:36:36 -0600 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Mon, 31 Mar 1997 08:36:36 -0600 From: jtgolab@amoco.com (Joe Golab) Date: Mon, 31 Mar 1997 08:35:45 -0600 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Summary of responses to "CCL: IRIX 6.2+ and MSC's XMOL" Cc: jtgolab@amoco.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Sorry for the bandwidth if this made it out there ... I have not seen it yet. >--- Included text 3/27/97 RE: Summary of responses to "CCL: IRIX 6.2+ and MSC's XMOL" >-- Original Question >! Dear CCL: >! >! Recently, we upgraded our Silicon Graphics equipment to IRIX 6.2. After >! that, Xmol stopped working (% xmol - Exec format error) because Xmol uses >! the COFF binary format. According to Xmol's creators (Minnesota's SC), >! "There are not plans to produce a new XMol distribution". >! >! We have been looking for an alternative to Xmol. So far, we haven't had >! much luck to duplicate Xmol's "Extras/Animate" feature. We have found that >! feature very useful when looking at optimization runs, IRC runs, etc. The >! animation button basically reads and displays a series of geometries from an >! Xmol input file. >! >! Can anyone suggest an alternative software product for UNIX machines? >! We have tried Rasmol and have not had any luck getting it to do animation >! using a series of separate geometries. (Which should not be taken as a slam >! to Rasmol which we have found useful for Web presentations.) >! >! If any replies are received, I'll post the summary. Thank you. >! >! -- >! >! :Joe >! jtgolab@amoco.com >! (630) 961-7878 >-- Executive Summary 1) Source Code to Xmol is not available (to the best of my knowledge). It was only distributed via executable code. I (for one) wish one of the commerical software vendors would investigate the possibility of distributing a working copy of Xmol. As far as I know, MSC has no plans for it beyond what is on their web site now. (Hint, Hint, Knudge, Knudge, Wink, Wink - Know what I mean?) 2) Suggested Replacements a) VMD - http://www.ks.uiuc.edu/Research/vmd/ b) MOLDEN - http://www.caos.kun.nl/~schaft/molden/molden.html c) Chime - http://www.mdli.com/chemscape d) gOpenMol - http://laaksonen.csc.fi/gopenmol/gopenmol.htmls >-- Response *> Hi again Joe. I don't use Xmol, but would the MOLDEN program do what *> you need? I use it to visualize geometry optimizations, vibrational *> frequencies, and orbitals from Gaussian and sometimes GAMESS. It's *> free and has a web page: *> http://www.caos.kun.nl/~schaft/molden/molden.html *> *> Good luck! *> *> ---------------------------------------------- *> Dr. Karl K. Irikura *> Physical and Chemical Properties Division *> National Institute of Standards and Technology *> Gaithersburg, MD 20899 *> voice: 301-975-2510 fax: 301-975-3670 *> e-mail: karl.irikura@nist.gov *> ---------------------------------------------- >-- Response *> try using Chime as a plugin of a web page. It allows animations. *> You only will have to set up a web page to do the embedding. *> *> Chemscape Chime is free downloadable from http://www.mdli.com/chemscape *> *> Rene P.F. Kanters *> Chemistry Project Specialist *> Chemistry Department *> University of Richmond VA 23173 *> *> phone: (804) 287-6873 *> email: rkanters@richmond.edu *> www: http://www.richmond.edu/~rkanters *> http://www.science.richmond.edu/~kanters >-- Response *> You might want to try VMD, just released to the public on Mar 25. It's *> homepage is http://www.ks.uiuc.edu/Research/vmd/ *> *> David E. Reichert, Ph.D. *> Mallinckrodt Inst. of Radiology *> Div. Radiation Sciences *> phone: (314)362-8461 *> fax: (314)362-9940 *> e-mail: reichertd@mirlink.wustl.edu >-- Response *> I use vmd to display dynamics (results from MD and normal modes). *> I think vmd can use Xmol's xyz files, however I never tried that. *> Instead, I wrote a little program that generates dcd files that *> vmd can read. You are welcome to have it, if you want. *> I found that vmd makes very fast and very pretty animation. *> I you don't know where to find vmd on the net, I cal dig it up for you. *> *> Hope that helps, Gert *> *> Gert von Helden *> Dept. of molecular and Laser Physics, University of Nijmegen, Netherlands *> e-mail: gertvh@sci.kun.nl, phone: (+31) 24 3652179, fax: (+31) 24 3653311 >-- Response *> Did you tried the molden software ? *> I use it on IRIX6.2 but you should have gaussian output. *> Is it your case *> *> Dorothee Berthomieu *> ************************************************** *> Laboratoire des Materiaux et Procedes Membranaires *> UMR CNRS 5635 *> Ecole Nationale Superieure de Chimie de Montpellier *> 8, rue de l'Ecole Normale *> 34296 MONTPELLIER cedex 5 *> Tel : (33) 467 14 43 40 *> Telecopie : (33) 467 14 43 47 *> email : bertho@crit1.univ-montp2.fr *> http://www.dr13.cnrs.fr/lmpm/fequ.html#DEPOCVD >-- Response *> Have you tried MolDen? It can read various file types (e.g. Gaussian *> output) and animate things like structures and vibrational modes. *> *> Nick *> *> ============================================================================ *> Nicholas A. Nystrom, Ph.D. Pittsburgh Supercomputing Center *> Scientific Specialist Mellon Institute Building *> email: nystrom@psc.edu 4400 Fifth Avenue *> voice: +1 412-268-1592 fax: -5832 Pittsburgh, PA 15213 USA *> ============================================================================ >-- Response *> Can't you get the xmol source code? All you should *> need to do is to rebuild the executable. If the program *> is being distributed form an academic center, I would *> be surprised if they would not hand out the source. *> *> Good luck, *> *> Randy *> *> All opinions expressed here are mine, not my employer's *> *> ///////////////////////////////////////////////////////////////////////// *> \\ Randy J. Zauhar, PhD | E-mail: zauhar@tripos.com // *> \\ Tripos, Inc. | : zauhar@fastrans.net // *> \\ 1699 S. Hanley Rd., Suite 303 | Phone: (314) 647-1099 Ext. 3382 // *> \\ St. Louis, MO 63144 | // *> ///////////////////////////////////////////////////////////////////////// *> ** ** *> ** "If you have conceptions of things that you can have no conception ** *> ** of, then the conception and the thing appear to co-incide." ** *> ** --- C.G. Jung ** *> ************************************************************************* >-- Response *> Joe, I assume the source for XMol was never distributed? Does anybody own *> it currently? If they're not going to make a new distribution, what's *> happening to the program? *> *> All that's required is a recompile on an appropriate SGI... *> *> Joe *> *> -- *> *> Joe Leonard Phone: +1 314 647 8837 x3204 *> Tripos, Inc. Fax: +1 314 647 9241 *> 1699 S. Hanley Rd. email: jle@tripos.com *> St. Louis, MO 63144 USA after-hours: jle@world.std.com >-- Response *> We went through exactly the same process. We're presently using the package *> VMD. You can obtain a copy via http://www.ks.uiuc.edu/Research/vmd/ . It can *> read in multi-frame XYZ files. Might be worth a try.... *> *> Regards, *> Mike *> *> ------------------------------------------------------------------- *> | Mike Fearn, Tel : UK (01684) 896536 | *> | Room PA101, Fax : UK (01684) 896150 | *> | D.R.A, Malvern, | *> | Worcs. WR14 3PS Email : hp003@dra.hmg.gb | *> ------------------------------------------------------------------- >-- Response *> There are certainly a lot of options. Let me suggest one further: *> *> The gOpenMol program at: *> *> http://laaksonen.csc.fi/gopenmol/gopenmol.htmls *> *> Regards, *> *> -leif laaksonen *> *> ------------------------------------------------------------------- *> 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 --------- >-- Response *> This seems to be a common question lately as more and more *> people upgrade to 6.x . You might want to look at our visualization *> program, VMD, at http://www.ks.uiuc.edu/Research/vmd/ . It was *> developed for, amoung other things, the visualization of MD *> trajectories. *> *> I doesn't read XYZ files directly, but if you have Babel *> installed (http://mercury.aichem.arizona.edu/babel.html) it VMD *> will call it and to the conversion to a set of PDB files automatically, *> then read them in. To the user, you wouldn't even notice the exchange. *> *> Andrew *> dalke@ks.uiuc.edu -- :Joe jtgolab@amoco.com (630) 961-7878 +----------------------------------------------------------------------+ | Reality is that which doesn't go away when you stop believing in it. | | -Philp K. Dick | +----------------------------------------------------------------------+ From ccl@www.ccl.net Mon Mar 31 11:33:02 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA29430; Mon, 31 Mar 1997 11:28:46 -0500 (EST) Received: from admiral.umsl.edu for wwelsh@jinx.umsl.edu by bedrock.ccl.net (8.8.3/950822.1) id LAA05147; Mon, 31 Mar 1997 11:28:43 -0500 (EST) Received: from chewwels.umsl.edu ([134.124.77.29]) by admiral.umsl.edu (8.8.5/8.7.2) with SMTP id KAA05380 for ; Mon, 31 Mar 1997 10:28:40 -0600 (CST) Date: Mon, 31 Mar 1997 10:28:40 -0600 (CST) Message-Id: <199703311628.KAA05380@admiral.umsl.edu> X-Sender: wwelsh@jinx.umsl.edu X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: William Welsh Subject: band structures in 3D Dear Netters, Can someone point me to programs available for calculating electronic band structures in 1-, 2-, and 3- dimensions? I remember a few years back that a program known as VEH (Valence Effective Hamiltonian) was capable of doing this, but there may be others (or updated versions of VEH). I would be interested in both semi-empirical and ab initio programs. Thanks ... Prof. Bill Welsh Dept. of Chemistry University of Missouri-St. Louis From ccl@www.ccl.net Mon Mar 31 15:53:17 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id OAA00835; Mon, 31 Mar 1997 14:44:06 -0500 (EST) Received: from rmi.net for factnet@rmi.net by bedrock.ccl.net (8.8.3/950822.1) id OAA14627; Mon, 31 Mar 1997 14:44:04 -0500 (EST) Received: from monster ([206.247.162.97]) by rmi.net (8.8.5/8.8.5) with SMTP id MAA08096; Mon, 31 Mar 1997 12:32:00 -0700 (MST) Message-Id: <3.0.32.19970331123148.0099a800@rmii.com> X-Sender: factnet@rmii.com (Unverified) X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Mon, 31 Mar 1997 12:33:38 -0700 To: factnet@rmi.net From: FACTNet International Subject: Net censorship, access cost increase, and Intellectual Property alert! Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit Net censorship, access cost increase, and Intellectual Property alert! Every netizen or organization that wants low cost net access, net free speech, and uncensored e-mail has a high stake in a court case soon to be decided in the litigation war involving Scientology, the Internet, and a nonprofit electronic library and historic archive called FactNet. An emergency Internet and legal issues briefing has been prepared for you and/or your organization at (www.factnet.org). Factnet’s Board of Directors urgently asks your help to promote both media coverage and a vigorous dialogue among netizens on the immediate and substantial threat this briefing discloses to the future of the Internet. To help understand the importance of this briefing to Internet costs, Internet slowdowns, Internet intellectual property and Internet free speech please find the following media quotes. 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No matter what they call it, free speech is the issue." --Wayne Langsen, "Raiding Free Speech," Boulder Weekly editorial. 8/24/95 PLEASE help protect our mutual Internet freedoms by appropriately forwarding this briefing to your personal or organizational network of individuals, newsgroups, listservs, net media, and net watch organizations where it hasn’t appeared yet. Your timely attention to this critical briefing is appreciated, The Directors of Factnet Boulder Colorado USA P.S. Factnet has been reconstructing its electronic files since they were sabotaged and returned to us by court order after the Scientology raid. Our original mailing lists consisted of individuals and organizations who had viewed materials or had an interest in Scientology’s Internet abuses and other human rights abuses. Because of the raid we are not fully certain that our reconstructed mailing lists contain what they originally contained or have been reassembled back into the proper lists. These reconstructed mailing lists are far to important to the battle for Internet free speech not to begin using again just because they were in Scientology's possession. If you have received this alert and you have not previously reviewed or been interested in any information on these issues let us know and we will immediately correct the situation. We ask your understanding if there has been an error or duplicate mailing. Try to imagine someone illegally seizing all of your computers and computer files then searching and altering and destroying parts of them. Finally you get it all back to you in boxes and pieces. That's what happened to Factnet. Over the last 12 months with minimal resources it has had to reconstruct 6 gigabits of its deliberately disordered returned libraries and files. From macrae@rikaxp.riken.go.jp Mon Mar 31 21:33:06 1997 Received: from ns.riken.go.jp for macrae@rikaxp.riken.go.jp by www.ccl.net (8.8.3/950822.1) id VAA03421; Mon, 31 Mar 1997 21:11:49 -0500 (EST) Received: from rikax1.riken.go.jp (rikax1.riken.go.jp [134.160.3.2]) by ns.riken.go.jp (8.8.5/8.8.5) with SMTP id LAA00643 for <@ns.riken.go.jp:CHEMISTRY@www.ccl.net>; Tue, 1 Apr 1997 11:11:48 +0900 (JST) Received: by rikaxp.riken.go.jp (MX V4.2 AXP) id 52; Tue, 01 Apr 1997 11:11:45 JST Date: Tue, 01 Apr 1997 11:11:45 JST From: "R. M. Macrae" To: CHEMISTRY@www.ccl.net Message-ID: <009B2215.F2A511D3.52@rikaxp.riken.go.jp> Subject: degenerate open shells Dear CCL subscribers Looking in the archive I saw some discussion from some considerable time back (around 1993) on the topic of G92 calculations on linear systems with x,y degenerate open shells, the point being that UHF gives the wrong result apparently even if nonstandard guess orbitals are used. (In some other programs apparently one can generate fractional occupancies with equally populated x and y components and this constraint will be retained throughout the calculation.) ROHF, on the other hand, will not of course give correct spin-dependent properties. There didn't seem to be a satisfactory outcome to this discussion at the time (unless, of course, i missed it). My question is, then: is there a satisfactory solution or workaround to this problem either in G92 or G94? Sincerely Rod * Rod Macrae * Muon Science Laboratory * macrae@rikaxp.riken.go.jp *