From chemistry-request@server.ccl.net Tue Apr 17 07:02:03 2001 Received: from linus.imcm.cas.cz ([147.231.77.250]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3HB21C17711 for ; Tue, 17 Apr 2001 07:02:02 -0400 Received: from thales (thales.imcm.cas.cz [147.231.77.130]) by linus.imcm.cas.cz (8.9.3/8.9.3) with ESMTP id NAA08150 for ; Tue, 17 Apr 2001 13:02:00 +0200 Message-Id: <200104171102.NAA08150@linus.imcm.cas.cz> From: "Petr Toman" To: chemistry@ccl.net Date: Tue, 17 Apr 2001 13:02:10 +0200 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: G98 and atomic coordinates printing Reply-to: toman@imc.cas.cz X-Confirm-Reading-To: toman@imc.cas.cz X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12a) Dear CCLers, Gaussian 98 prints the atomic coordinates in input (Z-matrix) orientation by default only if the number of atoms is less or equal 20. Does anybody know how can I force G98 to print the coordinates in all cases. Thanks in advance, Petr Toman From chemistry-request@server.ccl.net Mon Apr 16 19:51:13 2001 Received: from web13408.mail.yahoo.com ([216.136.175.66]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f3GNpCC14995 for ; Mon, 16 Apr 2001 19:51:13 -0400 Message-ID: <20010416235112.58020.qmail@web13408.mail.yahoo.com> Received: from [169.232.140.207] by web13408.mail.yahoo.com; Mon, 16 Apr 2001 16:51:12 PDT Date: Mon, 16 Apr 2001 16:51:12 -0700 (PDT) From: eric hu Subject: Re: CCL:molscript Makefile.complete for redhat 7.0 To: Andrew Dalke Cc: chemistry@ccl.net In-Reply-To: <008c01c0c4bc$a3223e40$0301a8c0@josiah> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="0-1303455736-987465072=:57623" --0-1303455736-987465072=:57623 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Here is my Makefile.complete as an attachment file. --- Andrew Dalke wrote: > >I'm trying to compile molscript 2.1.2 on the redhat > >7.0. There's always an error about clib/clib.a. I > >wonder if any of you have the Makefile. Thanks! > > I can't help you with that since I don't have > molscript. > However, as a point for future reference, if you had > included the error message in your mail you might > have gotten a response from people who know how to > solve the problem in the general sense, since it > might not be a molscript specific error. > > Andrew > dalke@acm.org > > __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! 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from citrin.chemie.uni-dortmund.de ([127.0.0.1]) by pluto.chemie.uni-dortmund.de (8.10.2/8.10.2/SuSE Linux 8.10.0-0.3) with ESMTP id f3HCow513149; Tue, 17 Apr 2001 14:50:58 +0200 X-Authentication-Warning: pluto.chemie.uni-dortmund.de: Host [127.0.0.1] claimed to be citrin.chemie.uni-dortmund.de Sender: tobbes@pluto.chemie.uni-dortmund.de Message-ID: <3ADC3C32.F8270E6C@citrin.chemie.uni-dortmund.de> Date: Tue, 17 Apr 2001 14:50:58 +0200 From: Tobias =?iso-8859-1?Q?Br=FCggemann?= X-Mailer: Mozilla 4.74 [de] (X11; U; Linux 2.2.16 i686) X-Accept-Language: de, en MIME-Version: 1.0 To: Petr Toman CC: chemistry@ccl.net Subject: Re: CCL:G98 and atomic coordinates printing References: <200104171102.NAA08150@linus.imcm.cas.cz> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f3HCw6C18243 Petr Toman wrote: > > Dear CCLers, > Gaussian 98 prints the atomic coordinates in input (Z-matrix) orientation > by default only if the number of atoms is less or equal 20. > Does anybody know how can I force G98 to print the coordinates in all > cases. > > Thanks in advance, > Petr Toman > > -= 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 Hi, try the IOP(99/14=1). It shuld print the final z-matrix at the end of the output. Tobias Brüggemann From chemistry-request@server.ccl.net Tue Apr 17 12:38:45 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3HGcjC19422 for ; Tue, 17 Apr 2001 12:38:45 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01K2I8XGZ5MS0061K5@trentu.ca> for chemistry@ccl.net; Tue, 17 Apr 2001 12:38:30 EDT Date: Tue, 17 Apr 2001 12:44:16 -0400 From: elewars Subject: SUMMARY: POTENTIAL E SURFACE, MARCELIN To: chemistry@ccl.net Message-id: <3ADC72E0.830A875A@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2001 April 17 Here are the answers to this question: ========= In his textbook "Physical Chemistry", Fourth Ed. (1972), on page 377, Walter J. Moore (author of the definitive biography of Erwin Schroedinger, 1989) says: "The idea that a chemical reaction can be represented by [a potential energy surface] was suggested by Marcelin in 1915..." and gives this reference: Marcelin, Ann. Phys., 3, 158 (1915). (1) Who was Marcelin, and what was his initial(s) (A. Marcelin, B. Marcelin, ...)? (2) What was Ann. Phys. in 1915--Annalen der Physik, or Annales de Physique, or what? If anyone.... ========= THE ANSWERS: I thank those who responded: Matt Thompson, Adam Hixson, and Konrad Hinsen. I summarize the answers here and give the responses below. R. Marcelin published in Annales de Physique, 1915, 3, 120-231 (!) a very long paper (perhaps a dissertation) which evidently created much of transition-state theory about 20 years before the much-better-known work of Eyring and coworkers. The section most relevant to potential energy surfaces seems to start on page 158. Rudolph Marcus, in his Nobel Prize (1992) speech recognizes Marcelin's work as a milestone: "...Marcelin's classic 1915 theory which came within one small step of the Transition State Theory of 1935." Marcelin was apparently killed in 1915, in World War I. Thanks again to all (below) who responded. E. Lewars ----- ----- #1 Matt Thompson: Dr. Lewars, here is some info on R. Marcelin, Ann. Phys., 3, 152 (1915). It is R. Marcelin from "Annales de Physique" and the paper is titled (sorry for no accents): "Contribution a l'etude de la cinetique physico-chimique" It spans pp. 120 - 231. Page 152 is in Chapter II, Section IV. The chapter is titled: "La formule synthetique precedemment obtenue se presente comme une consequence tres directe de la theorie de l'equipartition." The section is: "La formule synthetique obtenue dans le Chapitre precedent est une consequence du theoreme de Boltzmann-Gibbs." Essentially, the paper just about had all of transition state theory correct. Almost. I know Rudy Marcus feels it is a very important paper, see his Nobel biography at http://www.nobel.se/chemistry/laureates/1992/marcus-autobio.html Matt Thompson -- ****************************************************************** "And isn't sanity really just a one-trick pony, anyway? I mean, all you get is one trick, rational thinking, but when you're good and crazy, ooh ooh ooh, the sky's the limit!" -- The Tick ****************************************************************** The Matt Thompson -- thompsma@colorado.edu http://ucsub.colorado.edu/~thompsma/Home.html ======= #2 Adam Hixson The reference is R. Marcelin Annales de physique 3 120-231 1915. It is the length of a dissertation, but there is a footnote on the first page: Tue' a` l'ennemi en sept 1914. Died in WWI, apparently. Apparently a student of P. Duhem, of Gibbs-Duhem fame. Adam Hixson Department of Chemistry and Biochemistry The University of Oklahoma chixson@chemdept.chem.ou.edu 620 Parrington Oval hixsonc@yahoo.com Norman, OK 73069 ========== #3 Konrad Hinsen [This clears up the journal name (Annales ...), but Google seems to have got the initial wrong--EL] Just typing the reference into Google yielded a page with a more complete reference: A. Marcelin, Ann. Phys. (Paris), 3, 158 (1915). -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- ===================== ============== ======== ========= From chemistry-request@server.ccl.net Tue Apr 17 11:05:54 2001 Received: from chemistry.chem.utah.edu ([128.110.197.226]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3HF5rC19056 for ; Tue, 17 Apr 2001 11:05:53 -0400 Received: from scottsbox (anderson5.chem.utah.edu [128.110.196.158]) by chemistry.chem.utah.edu (Switch-2.0.1/Switch-2.0.1) with SMTP id f3HF5As10648 for ; Tue, 17 Apr 2001 09:05:10 -0600 (MDT) Message-ID: <030601c0c750$02b34cb0$9ec46e80@scottsbox> From: "Scott L. Anderson" To: Subject: visualization software Date: Tue, 17 Apr 2001 09:06:42 -0600 Version 2.0 of the gOpenMol visualization package has been released by Leif Laaksonen and can be downloaded at http://www.csc.fi/~laaksone/gopenmol/ Versions are available for Win 95/98/ME/2000, Linux, SGI Irix, and Compaq OSF1. gOpenMol is designed to allow visualization of molecules, MOs, densities, etc., as well as animations of vibrations, MD simulations etc. It can read results from a wide variety of quantum chemistry and simulation programs. gOpenMol also includes many tools for analyzing structures and trajectories. New features include: Handling up to 100,000 atoms Additional controls for trajectory/MD visualization and analysis (including variable animation speed) Ability to define clip planes to allow you to cut away part of a molecule or orbital to see the interior structure Ability to define arbitrarily oriented planes for displaying contours (of MOs, etc) Additional import filters for new quantum chemistry, MM, and MD programs (23 at last count) You can find a tutorial that illustrates the features and operations of the program at http://www.chem.utah.edu/chemistry/faculty/anderson/gopen.html The tutorial now includes a section on use of Tcl/Tk scripts to automate gOpenMol. The scripts can be used to deal with repeated tasks, and can also be used to produce animated presentations, etc. Prof. Scott L. Anderson / Chemistry Dept. 315 S. 1400 E. Rm 1216 / U. of Utah Salt Lake City, UT 84112 (801)585-7289 FAX: (801)581-8433 www.chem.utah.edu/chemistry/faculty/anderson/anderson.html From chemistry-request@server.ccl.net Tue Apr 17 11:41:01 2001 Received: from kanga.INS.cwru.edu (root@[129.22.8.32]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3HFf1C19190 for ; Tue, 17 Apr 2001 11:41:01 -0400 Received: from gavin (chem51286.CHEM.CWRU.Edu [129.22.129.217]) by kanga.INS.cwru.edu with SMTP (8.8.8+cwru/CWRU-3.8) id LAA24994; Tue, 17 Apr 2001 11:41:00 -0400 (EDT) (from hxt10@po.cwru.edu for ) Message-ID: <004201c0c755$62e81b60$d9811681@cwru.edu> Reply-To: "Hui-Hsu \(Gavin\) Tsai" From: "Hui-Hsu \(Gavin\) Tsai" To: Subject: "all electron" basis set for second row transition metal Date: Tue, 17 Apr 2001 11:45:10 -0400 Hi CCLers, I have searched different sources for an "all electron" basis set higher than 3-21G for second row transition metal and Ce. I mainly focused on Zr and Ce so far. If they do exist, I would appreciate knowing where to find it? Any comment is welcome. Gavin From chemistry-request@server.ccl.net Tue Apr 17 13:47:34 2001 Received: from mercury.chem.nwu.edu (fparnold@[129.105.116.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3HHlYC19896 for ; Tue, 17 Apr 2001 13:47:34 -0400 Received: from localhost (fparnold@localhost) by mercury.chem.nwu.edu (8.11.3/8.11.3) with ESMTP id f3HHlXA00159; Tue, 17 Apr 2001 12:47:33 -0500 (CDT) Date: Tue, 17 Apr 2001 12:47:33 -0500 (CDT) From: "Fred P. Arnold" X-X-Sender: To: "Hui-Hsu (Gavin) Tsai" cc: Subject: Re: CCL:"all electron" basis set for second row transition metal In-Reply-To: <004201c0c755$62e81b60$d9811681@cwru.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII This is becoming a FAQ, but the two main sources: http://www.emsl.pnl.gov:2080/forms/basisform.html Gaussian Basis Set Order Form. Huzinaga WTBS, Partridge Uncontracted, etc. "Gaussian Basis Sets for Molecular Calculations" Huzinaga, S. (ed). Otherwise known as the "Green Book". -fred Frederick P. Arnold, Jr. NUIT, Northwestern U. f-arnold@northwestern.edu From chemistry-request@server.ccl.net Tue Apr 17 17:18:24 2001 Received: from mlucom8.urz.uni-halle.de ([141.48.10.118]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3HLINC21250 for ; Tue, 17 Apr 2001 17:18:23 -0400 Received: from clusterf.urz.uni-halle.de by mlucom8.urz.uni-halle.de with lsmtp with ESMTP; Tue, 17 Apr 2001 23:18:02 +0200 Received: from bathl ([141.48.223.39]) by clusterf.urz.uni-halle.de (AIX4.3/8.9.3/8.8.8) with SMTP id XAA57444; Tue, 17 Apr 2001 23:18:01 +0200 From: Bernd Schubert To: chemistry@ccl.net Subject: Re: CCL:gaussian and hollerith string Summury Date: Tue, 17 Apr 2001 23:18:00 +0200 X-Mailer: KMail [version 1.2] References: In-Reply-To: Cc: Stefan Fau Message-Id: <01041723180000.00318@bathl> MIME-version: 1.0 Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 8bit On Monday 9 April 2001 I asked how to define the maximum allowed symmetry in Gaussian. I got two replies to my answer and the problem is completely solved (thanks both for their reply). The maximum allowed symmetry might be specified by using the undocumented keyword symm(pg=pointgroup). For example: symm(pg=cs) If someone wants to use iop(2/19) for defining then the required number can be determinated by using the following procedure: 1.) The hollerith string is a 4 byte string 2.) the string must be written from the right to the left, unused characters are replaced by space for example for the cs group: 3.) The characters are replaced by hexadecimal numbers of the ascii table for my example giving: 20 20 53 43 4.) The resulting hex. number (20205343) is translated into a decimal number giving: 538989379 5.) This decimal number can be used for iop(2/19) for my example: iop(2/19=538989379) By using a lower symmetry than the molecule has there might be several equal symmetry planes possible to use as main symmetry plane. IOP(2/20) is needed to define which one is the main symmetry plane. -------------------------------------------------------------------------- Here are the 2 answers I got: From: Stefan Fau Hi Bernd, I ran across the problem of Hollerith strings in connection with symmetry in Gaussian some years ago. Unfortunately I lost access to the handbook in which I wrote down the solution ... As far as I remember, the Hollerith string is a hexadecimal representation of the characters in the symmetry label. I think it went like this: " C2v", characters 32, 67, 50 and 118 of the ASCII character table. In hexadecimal this corresponds to 20, 43, 32, 76 giving the Hollerith string "20433276". This string depends on which character set is default on your computer. You can find out using the FORTRAN command char('C'). I'm not sure anymore if the Hollerith string expects 8 hexadecimal numbers and about small or capital characters. If it doesn't work at first, better look into the source code ... Stefan P.S.: please post the final solution to CCL when you find it, so it gets into the archives. ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 ------------------------------------------------------------------------------ From: "Cust. Service Jim" Dear Bernd, There is an undocumented feature that will get around your iop(2/19=2HCS) problem, and that is to use something like "symm=(pg=cs)". This will read in the point group you requested. As for opt(2/20), this is necessary when it is ambiguous how the symmetry will be reduced. For example, if your initial structure is C4V and you request a reduction of symmetry to CS, the program wants to know which of the symmetry planes in the C4V point group you'd like as the CS plane. Regards, Jim Hess ------------------------------------------------------------------------------