From chemistry-request@server.ccl.net Tue Apr 3 20:07:59 2001 Received: from mail.dulug.duke.edu (IDENT:mail@[152.3.142.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3407xD18010 for ; Tue, 3 Apr 2001 20:07:59 -0400 Received: from teton.dulug.duke.edu (teton.dulug.duke.edu [152.3.142.11]) by mail.dulug.duke.edu (Postfix) with ESMTP id EB3D63B74 for ; Tue, 3 Apr 2001 19:34:18 -0400 (EDT) Received: by teton.dulug.duke.edu (Postfix, from userid 99) id 8ED6B7EA8; Tue, 3 Apr 2001 20:05:40 -0400 (EDT) To: chemistry@ccl.net Subject: summary:Gram-Schmidt orthogonalization Message-ID: <986342740.3aca6554704f2@webmail.dulug.duke.edu> Date: Tue, 03 Apr 2001 20:05:40 -0400 (EDT) From: Hong Jiang MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.2 Thanks for those who gave me helpful information and instructions about orthogonalization algorithm. Here I give a summary of them. And I hope it will be helpful to some others. Hong Jiang PS: Car and Parrenello (PRL55, 2471, 1985) used an iterative algorithm. **************************Summary of Gram-Schmidt orthogonalization********* 1. Hi Hong, I found that the book "Matrix computations" (2nd edition) G. H. Golub, C. F. van Loan (Johns Hopkins University Press, Baltimore, 1993) ISBN 0-8018-3772-3 ISBN 0-8018-3739-2 (paperback) gives a good description of orthogonalisation methods in chapter 5. In particular it explains on pages 218-220 why Gram-Schmidt is inaccurate if the basis you are trying to orthogonalize is (nearly) linear dependent. In those cases Householder works much better as far as my experience goes. The Householder approach is discussed in at the beginning of chapter 5, including pseudo-code for this algorithm. The pseudo-code is can easily be rewritten into an imperative computer language like Fortran, C, C++, Java, etc. I hope this helps. Kind regards, Huub -- ======================================================================== Huub van Dam E-mail: h.j.j.vandam@dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603362 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK WA4 4AD ======================================================================== 2. Hello, In Ostlund-Szabo "Modern Quantum Mechanics" you will find the symmetric orthogonalization (Lowdin) the canonical orthogonalization (modified Lowdin to remove linear dependencies) the Schmidt orthogonalization. The two first methods are straightforward to implement in any QM code. Hope this helps. -- ...Xav WARNING! NEW E-MAIL ADDRESS ! (u-nancy changed to uhp-nancy) Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr 3. From zdenko tomasic To Hong Jiang Reply-To ztomasic@austin.rr.com Subject Re: CCL:Gram-Schmidt orthogonalization algorithms Parts Message Source in a nutshell, classical GS fails to properly orthogonalize a set of vectors, modified GS is only slightly better but fails strict orthogonality too, the thing to do is classical GS + iterative refinement if you deal with dense matrices, LAPACK package should give you all you need. From chemistry-request@server.ccl.net Wed Apr 4 00:21:57 2001 Received: from po.cwru.edu (root@[129.22.4.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f344LvD19810 for ; Wed, 4 Apr 2001 00:21:57 -0400 Received: from gavin (chem51286.CHEM.CWRU.Edu [129.22.129.217]) by po.cwru.edu with SMTP (8.8.8+cwru/CWRU-3.6) id AAA26385; Wed, 4 Apr 2001 00:21:56 -0400 (EDT) (from hxt10@po.cwru.edu for ) Message-ID: <002701c0bcbf$5b55d0e0$d9811681@cwru.edu> Reply-To: "Hui-Hsu \(Gavin\) Tsai" From: "Hui-Hsu \(Gavin\) Tsai" To: Subject: symmetry change Date: Wed, 4 Apr 2001 00:26:02 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0024_01C0BC9D.D4229F20" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 This is a multi-part message in MIME format. ------=_NextPart_000_0024_01C0BC9D.D4229F20 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi CClers: I have a question about symmetry change in gaussian calculation. The molecule I studied can have different possible point groups due = to its different conformations. By using G98 to do the geometry optimization, I start from one = symmetric geometry and the poing group will be changed late during the geometry optimization. The G98 just terminated = the job when the molecular point group is changed and says "change in = poing group or standard orientation, job terminated" Becasue the molecule is symmetric at different conformations even the = geometry is changed. I know the calculation will be ok=20 if I use C1 poing group by slightly changing the symmetric cartesian = coordinates, but the job will take a long time to finish. Becasue Gaussian job is very fast when symmetry option is turned on. Is it possible to "force" G98 to keep on running by using "new" = symmetric wavefunction and geometry?=20 any comment or advice is welcome and appreciated. Gavin ------=_NextPart_000_0024_01C0BC9D.D4229F20 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi CClers:
 
    I have a question = about symmetry=20 change in gaussian calculation.
 
    The molecule I = studied can=20 have different possible point groups due to its different=20 conformations.
 By using G98 to do the geometry = optimization,=20 I start from one symmetric geometry and the poing group will=20 be
changed late during the geometry=20 optimization.  The G98 just terminated the job when the molecular = point=20 group is changed and says "change in poing group or standard = orientation, job=20 terminated"
 
   Becasue the molecule is=20 symmetric at different conformations even the geometry is = changed. I=20 know the calculation will be ok
if I use C1 poing group by slightly = changing=20 the symmetric cartesian coordinates, = but the job=20 will take a long time to finish.
Becasue Gaussian job is very fast when = symmetry=20 option is turned on.
 
    Is it possible to = "force" G98 to=20 keep on running by using "new" symmetric wavefunction and geometry?=20
any comment or advice is welcome and=20 appreciated.
 
Gavin
------=_NextPart_000_0024_01C0BC9D.D4229F20-- From chemistry-request@server.ccl.net Wed Apr 4 02:27:53 2001 Received: from smtp.csc.fi ([193.166.0.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f346RrD20105 for ; Wed, 4 Apr 2001 02:27:53 -0400 Received: from isosirri (isosirri.csc.fi [193.166.1.218]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with SMTP id JAA27366 for ; Wed, 4 Apr 2001 09:27:51 +0300 From: "Leif Laaksonen" To: "Chemistry@Ccl. Net" Subject: gOpenMol version 2.0 available REVISITED! Date: Wed, 4 Apr 2001 09:31:12 +0300 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0018_01C0BCE9.FD52AE70" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 This is a multi-part message in MIME format. ------=_NextPart_000_0018_01C0BCE9.FD52AE70 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Hi, I'm very sorry but I already have to submit a correction to the new gOpenMol release. By mistake the new release contains the old utility routines and because some of them has gone through changes and corrections it is highly recommended that all gOpenMol users download the patches available on the page: http://www.csc.fi/~laaksone/gopenmol/distribute/ On this page you will find the pathes for all the platforms gOpenMol is supporting. My sincere thanks to Arlen Viste who spotted immediately the error! Regards, -leif laaksonen ------=_NextPart_000_0018_01C0BCE9.FD52AE70 Content-Type: text/x-vcard; name="Leif Laaksonen.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Leif Laaksonen.vcf" BEGIN:VCARD VERSION:2.1 N:Laaksonen;Leif FN:Leif Laaksonen ORG:Center for Scientific Computing;CSC New Technology Group TITLE:New Technology Group Manager NOTE:My personal Web page: http://www.csc.fi/~laaksone/ TEL;WORK;VOICE:+358 9 457 2378 TEL;CELL;VOICE:+358 +358400425203 TEL;WORK;FAX:+358 9 457 2302 ADR;WORK;ENCODING=QUOTED-PRINTABLE:;;Tekniikantie 15 a D=0D=0AP.O.Box 405;Espoo;;FIN-02101;Finland LABEL;WORK;ENCODING=QUOTED-PRINTABLE:Tekniikantie 15 a D=0D=0AP.O.Box 405=0D=0AEspoo FIN-02101=0D=0AFinland URL:http://laaksonen.csc.fi/ URL:http://www.csc.fi/ EMAIL;PREF;INTERNET:Leif.Laaksonen@csc.fi EMAIL;INTERNET:Leif.Laaksone@csc.fi REV:20000906T051522Z END:VCARD ------=_NextPart_000_0018_01C0BCE9.FD52AE70-- From chemistry-request@server.ccl.net Wed Apr 4 10:13:30 2001 Received: from mailhub1.shef.ac.uk ([143.167.1.9]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f34EDTD23886 for ; Wed, 4 Apr 2001 10:13:29 -0400 Received: from ramsley.shef.ac.uk ([143.167.103.254]) by mailhub1.shef.ac.uk with esmtp (Exim 3.22 #2) id 14ko2K-0003wb-00 for chemistry@ccl.net; Wed, 04 Apr 2001 15:13:28 +0100 Received: from RAMSLEY/SpoolDir by ramsley.shef.ac.uk (Mercury 1.48); 4 Apr 01 15:13:29 +0100 Received: from SpoolDir by RAMSLEY (Mercury 1.48); 4 Apr 01 15:13:20 +0100 From: "O.Nicolotti" To: "Chemistry@Ccl. Net" Date: Wed, 4 Apr 2001 15:13:19 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: simultaneous linear equations Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12a) Message-Id: Thanks to everybody for the very useful suggestions. By the way "Numerical Recipes in C" proved to be a very good book for such problems. I finally wrote a C routine solving simultaneous linear equations. Given a data set of predictors X and the corresponding responses Y (as quite frequently in QSAR), the routine finds out the best fitting curve coefficients. If anybody needs, feel free to contact me. Orazio From chemistry-request@server.ccl.net Wed Apr 4 10:31:39 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f34EVdD23991 for ; Wed, 4 Apr 2001 10:31:39 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id KAA00532; Wed, 4 Apr 2001 10:31:34 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Wed, 04 Apr 2001 09:31:19 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GB900F70UTNOR@lvlmail.unitedcatalysts.com>; Wed, 04 Apr 2001 10:27:23 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Wed, 04 Apr 2001 10:31:34 -0400 Content-return: allowed Date: Wed, 04 Apr 2001 10:31:33 -0400 From: "Shobe, Dave" Subject: RE: symmetry change To: "'Hui-Hsu (Gavin) Tsai'" , CHEMISTRY@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629DDAADDE@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Not only that, but sometimes Gaussian "error terminates" even when the point group does not change--because the standard orientation changed. Apparently Gaussian is too dumb to either rotate the molecule as needed, or continue with the original standard orientation. There is a "nosymm" keyword, but you lose the efficiency gains that result > from taking symmetry into account. -----Original Message----- From: Hui-Hsu (Gavin) Tsai [mailto:hxt10@po.cwru.edu] Sent: Wednesday, April 04, 2001 12:26 AM To: CHEMISTRY@ccl.net Subject: CCL:symmetry change Hi CClers: I have a question about symmetry change in gaussian calculation. The molecule I studied can have different possible point groups due to its different conformations. By using G98 to do the geometry optimization, I start from one symmetric geometry and the poing group will be changed late during the geometry optimization. The G98 just terminated the job when the molecular point group is changed and says "change in poing group or standard orientation, job terminated" Becasue the molecule is symmetric at different conformations even the geometry is changed. I know the calculation will be ok if I use C1 poing group by slightly changing the symmetric cartesian coordinates, but the job will take a long time to finish. Becasue Gaussian job is very fast when symmetry option is turned on. Is it possible to "force" G98 to keep on running by using "new" symmetric wavefunction and geometry? any comment or advice is welcome and appreciated. Gavin From chemistry-request@server.ccl.net Wed Apr 4 11:05:12 2001 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f34F5CD24160 for ; Wed, 4 Apr 2001 11:05:12 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.11.2/8.11.2/Guy-12-01-2001) with ESMTP id f34F5AB00156; Wed, 4 Apr 2001 17:05:10 +0200 (METDST) Received: from lctn.uhp-nancy.fr (host23.lctn.uhp-nancy.fr [193.50.239.30]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id RAA22248; Wed, 4 Apr 2001 17:06:14 +0200 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3ACB3694.A075CF73@lctn.uhp-nancy.fr> Date: Wed, 04 Apr 2001 16:58:29 +0200 From: Xavier ASSFELD Organization: Chimie Theorique X-Mailer: Mozilla 4.51i [en] (X11; I; AIX 4.3) X-Accept-Language: en MIME-Version: 1.0 To: "Shobe, Dave" , hxt10@po.cwru.edu, CCL Subject: Re: CCL:symmetry change References: <157A51F55AAAD3119CD70008C7B1629DDAADDE@lvlxch01.unitedcatalysts.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "Shobe, Dave" wrote: > > Not only that, but sometimes Gaussian "error terminates" even when the point > group does not change--because the standard orientation changed. Apparently > Gaussian is too dumb to either rotate the molecule as needed, or continue > with the original standard orientation. > > There is a "nosymm" keyword, but you lose the efficiency gains that result > > from taking symmetry into account. > Instead of the NOSYM keyword, and loosing the efficiency..., you can use the keyword IOP(2/16=N) which keeps all advantages of symmetry and keep going if the point group change. If N=1 : keep going N=2 : keep going and leave symmetry on, using the old symmetry N=3 : keep going and leave symmetry on, using the new symmetry. Another point: is the number of degrees of freedom equal to the number of internal coordinates you define? If not, bad surprises may arise. Hope this helps. -- ...Xav WARNING! NEW E-MAIL ADDRESS ! (u-nancy changed to uhp-nancy) Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Wed Apr 4 12:13:53 2001 Received: from sunflare.ccs.yorku.ca ([130.63.236.128]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f34GDqD24805 for ; Wed, 4 Apr 2001 12:13:53 -0400 Received: from sunlight.ccs.yorku.ca (sunlight.ccs.yorku.ca [130.63.236.85]) by sunflare.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id MAA07269; Wed, 4 Apr 2001 12:13:50 -0400 (EDT) Received: from localhost (serge@localhost) by sunlight.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id MAA29947; Wed, 4 Apr 2001 12:13:50 -0400 (EDT) X-Authentication-Warning: sunlight.ccs.yorku.ca: serge owned process doing -bs Date: Wed, 4 Apr 2001 12:13:50 -0400 (EDT) From: "S.I.Gorelsky" X-X-Sender: To: "Shobe, Dave" cc: "'Hui-Hsu (Gavin) Tsai'" , Subject: Re: CCL:symmetry change In-Reply-To: <157A51F55AAAD3119CD70008C7B1629DDAADDE@lvlxch01.unitedcatalysts.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII You can use IOp(2/16=3) to avoid this problem. The job will continue with a new symmetry. Best wishes, Serge Gorelsky > There is a "nosymm" keyword, but you lose the efficiency gains that result > > from taking symmetry into account. > > -----Original Message----- > From: Hui-Hsu (Gavin) Tsai [mailto:hxt10@po.cwru.edu] > Sent: Wednesday, April 04, 2001 12:26 AM > To: CHEMISTRY@ccl.net > Subject: CCL:symmetry change > > > Hi CClers: > > I have a question about symmetry change in gaussian calculation. > > The molecule I studied can have different possible point groups due to > its different conformations. > By using G98 to do the geometry optimization, I start from one symmetric > geometry and the poing group will be > changed late during the geometry optimization. The G98 just terminated the > job when the molecular point group is changed and says "change in poing > group or standard orientation, job terminated" > > Becasue the molecule is symmetric at different conformations even the > geometry is changed. I know the calculation will be ok > if I use C1 poing group by slightly changing the symmetric cartesian > coordinates, but the job will take a long time to finish. > Becasue Gaussian job is very fast when symmetry option is turned on. > > Is it possible to "force" G98 to keep on running by using "new" > symmetric wavefunction and geometry? > any comment or advice is welcome and appreciated. > > Gavin > > > -= 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 > > > > > ________________________________________________________________ Sergey I. Gorelsky, M.Sc. Department of Chemistry, York University 4700 Keele Street, Toronto, Ontario M3J 1P3 phone: 416-736-2100 ext#77720 and ext#70131 fax: 416-736-5936 http://www.chem.yorku.ca/grad/SG/ ________________________________________________________________ From chemistry-request@server.ccl.net Wed Apr 4 12:56:37 2001 Received: from web13401.mail.yahoo.com ([216.136.175.59]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f34GubD25097 for ; Wed, 4 Apr 2001 12:56:37 -0400 Message-ID: <20010404165626.5943.qmail@web13401.mail.yahoo.com> Received: from [169.232.140.246] by web13401.mail.yahoo.com; Wed, 04 Apr 2001 09:56:26 PDT Date: Wed, 4 Apr 2001 09:56:26 -0700 (PDT) From: eric hu Subject: ways to detect transition state To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, all I posted a message earlier asking for the DFT transition search. Maybe it's a little bit long. Now here it is the short one. How many ways are there available in G98 to find a transition state (especially for a diradical) ? Guess from reactant or product, Coordinate driving.... Eric __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! Mail. http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Wed Apr 4 14:32:50 2001 Received: from cascara.UVic.CA (root@[142.104.5.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f34IWoD25663 for ; Wed, 4 Apr 2001 14:32:50 -0400 Received: from unix4.uvic.ca (unix4.uvic.ca [142.104.5.112]) by cascara.UVic.CA (8.11.2/8.11.2) with ESMTP id f34IWnf105610; Wed, 4 Apr 2001 11:32:49 -0700 Date: Wed, 4 Apr 2001 11:32:48 -0700 (PDT) From: Roy Jensen To: Subject: Re: CCL:symmetry change Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have not been able to get this IOP to work in G98W. Gaussian is aware of the error; I have sent them a simple input file that fails. No response yet... Roy Jensen > Instead of the NOSYM keyword, and loosing the efficiency..., you can use > the > keyword IOP(2/16=N) which keeps all advantages of symmetry and keep > going if the point group change. > If N=1 : keep going > N=2 : keep going and leave symmetry on, using the old symmetry > N=3 : keep going and leave symmetry on, using the new symmetry. From chemistry-request@server.ccl.net Wed Apr 4 14:46:15 2001 Received: from gordon.chem.wayne.edu (root@[141.217.26.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f34IkFD25790 for ; Wed, 4 Apr 2001 14:46:15 -0400 Received: from chem.wayne.edu (dyn27-199.chem.wayne.edu [141.217.27.199] (may be forged)) by gordon.chem.wayne.edu (8.9.3+Sun/8.9.3) with ESMTP id OAA15666 for ; Wed, 4 Apr 2001 14:46:12 -0400 (EDT) Message-ID: <3ACB6BF4.BDB22147@chem.wayne.edu> Date: Wed, 04 Apr 2001 14:46:14 -0400 From: "Prof. Kihyung Song" Reply-To: ksong@chem.wayne.edu Organization: Korea Nat'l Univ. of Education X-Mailer: Mozilla 4.76C-CCK-MCD {C-UDP; EBM-APPLE} (Macintosh; U; PPC) X-Accept-Language: ko,en,pdf MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: CCL: Stationary point search Content-Type: text/plain; charset=EUC-KR; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Hello everyone, I am looking for a routine for saddle point (and/or minimum energy) structure search routine, preferably in fortran. I am specifically looking for a public domain. I can not use a routine in numerical recipes book, because of the legal problem. The routine will be included in a program which we will distribute, and the numerical recipe routine can not be distributed. Is there any library to look for? I tried www.netlib.org but not successful. Thank you for your help. Truly, Kihyung Song From chemistry-request@server.ccl.net Wed Apr 4 17:43:20 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 f34LhKD26777 for ; Wed, 4 Apr 2001 17:43:20 -0400 Received: from clusterf.urz.uni-halle.de by mlucom8.urz.uni-halle.de with lsmtp with ESMTP; Wed, 4 Apr 2001 23:43:09 +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 XAA48734 for ; Wed, 4 Apr 2001 23:43:08 +0200 From: Bernd Schubert To: Chemistry Subject: Re: CCL:symmetry change Date: Wed, 4 Apr 2001 23:43:07 +0200 X-Mailer: KMail [version 1.2] References: In-Reply-To: Message-Id: <01040423430701.00680@bathl> MIME-version: 1.0 Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 8bit On Wednesday 04 April 2001 20:32, you wrote: > I have not been able to get this IOP to work in G98W. Gaussian is > aware of the error; I have sent them a simple input file that fails. > No response yet... > > Roy Jensen All my tryings to get IOP(2/16=3) working in G98A3 (on Linux and Irix machines) failed, too. Instead of the complainment about changed symmetry it complained about a file input/output error (missing file). I haven't already tried with G98A7 or newer, so I would be interested if some already had success to use this keyword. Bernd From chemistry-request@server.ccl.net Wed Apr 4 19:12:59 2001 Received: from cougar.it.wsu.edu (root@[134.121.1.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f34NCxD27195 for ; Wed, 4 Apr 2001 19:12:59 -0400 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cougar.it.wsu.edu (8.9.3/8.9.3) with SMTP id QAA05050; Wed, 4 Apr 2001 16:12:56 -0700 (PDT) Message-ID: <000d01c0bd5c$c78be950$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "Bernd Schubert" , "Chemistry" References: <01040423430701.00680@bathl> Subject: Re: CCL:symmetry change Date: Wed, 4 Apr 2001 16:12:54 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hi, In G98W A.7 (SCAN job changing Cs to C2v to Cs for H2O): IOP(2/16=3) -> crashes on "Operation on file out of range." IOP(2/16=2) -> crashes on "Error in generated initial guess." IOP(2/16=1) -> crashes on "Operation on file out of range." In G98 A.7 (SCAN job changing Cs to C2v to Cs for H2O): IOP(2/16=3) -> crashes on "Operation on file out of range." IOP(2/16=2) -> crashes on "Error in generated initial guess." IOP(2/16=1) -> crashes on "Operation on file out of range." It does not appear to matter with rev A.7 whether you employ the windows version or the linux version of G98, the generated errors are identical. I guess we're stuck with the nosymm option... Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "Bernd Schubert" To: "Chemistry" Sent: Wednesday, April 04, 2001 2:43 PM Subject: CCL:symmetry change > On Wednesday 04 April 2001 20:32, you wrote: > > I have not been able to get this IOP to work in G98W. Gaussian is > > aware of the error; I have sent them a simple input file that fails. > > No response yet... > > > > Roy Jensen > > All my tryings to get IOP(2/16=3) working in G98A3 (on Linux and Irix > machines) failed, too. Instead of the complainment about changed symmetry it > complained about a file input/output error (missing file). > I haven't already tried with G98A7 or newer, so I would be interested if some > already had success to use this keyword. > > Bernd > > > -= 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 > > > > > From chemistry-request@server.ccl.net Wed Apr 4 18:28:50 2001 Received: from deimos.email.Arizona.EDU (IDENT:root@[128.196.133.166]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f34MSoD26999 for ; Wed, 4 Apr 2001 18:28:50 -0400 Received: from u.arizona.edu (128.196.184.158) by deimos.email.Arizona.EDU (5.1.056) (authenticated as mcafiero@email.arizona.edu) id 3AB8AE9800131570 for chemistry@ccl.net; Wed, 4 Apr 2001 15:28:44 -0700 Sender: mcafiero@ccl.net Message-ID: <3ACBA013.2A6FA28E@u.arizona.edu> Date: Wed, 04 Apr 2001 22:28:35 +0000 From: Maurice Cafiero X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.13-7mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: basis for Tl Content-Type: multipart/alternative; boundary="------------7F4E82259AB8FC67EB58FDA1" --------------7F4E82259AB8FC67EB58FDA1 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit hello: I was wondering if anyone can suggest a basis for Tl. In gaussian, I have only been able to use sdd. Are there any others? Thanks, -- Mauricio Cafiero Doctoral Candidate : Theoretical and Computational Quantum Chemistry Department of Chemistry University of Arizona --------------7F4E82259AB8FC67EB58FDA1 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit hello:
    I was wondering if anyone can suggest a basis for Tl. In gaussian, I have only been able to use
sdd. Are there any others?

Thanks, 

-- 
Mauricio Cafiero
Doctoral Candidate : Theoretical
                     and Computational
                     Quantum Chemistry
Department of Chemistry
University of Arizona
  --------------7F4E82259AB8FC67EB58FDA1-- From chemistry-request@server.ccl.net Wed Apr 4 19:50:26 2001 Received: from cranc02.cra.canon.com ([205.227.186.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f34NoQD27503 for ; Wed, 4 Apr 2001 19:50:26 -0400 Received: by cranc02.cra.canon.com with Internet Mail Service (5.5.2653.19) id ; Wed, 4 Apr 2001 16:50:25 -0700 Message-ID: <3FD2BCBD9153D41192B100C04F1FD832067E3D@cranc02.cra.canon.com> From: "Thoms, Travis" To: "Computational Chemistry List (E-mail)" Subject: Thanks and Summary was: Fluorescence and phosphorescence Date: Wed, 4 Apr 2001 16:50:24 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Thank you all for your responses to my inquiry. They were all very helpful. I have included the original question and responses below, as suggested by the rules of CCL. Thanks again, Travis Thoms Greetings: I hope this question is not too far off-topic; it does actually relate to my feeble attempts at modeling fluorescent and phosporescent materials. I have reviewed a couple of physical chemistry books concerning these two topics, and to be quite honest, either they have not explained it well, or I am missing the big picture. If you don't mind, I would like to explain to you what I think is going on, and then you could correct me, or refer me to some good sources to set me straight. Fluorescence: A photon comes in and excites a molecule in a ground state (are most ground states "singlet states"?) to an excited state (I am assuming that one cannot excite to a triplet state). There is a percentage or probability that this excited state will relax back down to the ground state by emissive means, emitting a photon of light that is smaller than the homo-lumo band gap of the ground state molecule. The molecule can also lose its energy through non-emissive means such as heat. The energy cannot move from the excited singlet state to a lower energy triplet state due to the need to conserve momentum. Phosphorescence: Exitation occurs as above, except energy in this case is allowed to move from the excited singlet state to a lower energy triplet state through intersystem crossing (which was forbidden in the previous scenario). The triplet state in turn can relax to the (singlet?) ground state via emission because of spin orbital coupleing with the heavy nucleus). Does this sound right? Have I left something out which is important? Thanks. Travis Thoms Reply 1: That's right. Experimentally, the difference between phosphorescence & fluorescence is that the decay time of the triplet is orders of magnitude longer than the decay time of a singlet because decay from the excited triplet to the ground state singlet is also a forbidden process. Irene Newhouse Reply 2: You seem to have the general idea. Most but not all ground states are singlet states. The percentage or probability of a specific process is usually referred to as a quantum yield, denote by a subscripted Greek phi (e.g., phi_sub_f for the probability that an absorbed photon will produce a fluorescent photon). A number of non-radiative relaxation pathways can be important including collisional quenching and static quenching in addition to 'heat'. I usually recommend R. Lakowicz's text to my students interseted in biological systems, but C.A. Parker's much older Photoluminescence in Solution may be closer to what you are looking for. First-principle modeling of fluorescence yields is more complex than the modeling of absorption probabilities (which is the first step). The actual quantum efficiency depends on the relative size of the different relaxation rates, which in turn are solvent and temperature dependent. Fluorescence yield (and wavelength dependence) is much more dependent on solvent composition and temperature than absorbance, and is also subject to quenching by solutes. Many (most?) fluorescent modellers use a more empirical approach based on model compounds. Reply 3: Dear Dr. Thoms; I recommend the book titled "Excited States and Photochemistry of Organic Molecules" which seems to be me very good in terms of understanding excited state phenomena. For fluorescence, only internal conversion is occurred(Singlet-Singlet transition). For phosphorescence, intersystem crossing is important(singlet-triplet crossing) which takes more time than fluorescence. I hope it will be something helpful for you. Best regards, Ohyun Kwon Reply 4: Travis Thoms, in principle you meet the point; in addition to that, what you are writing: * F. and P.: light emission (luminescence), induced by absorbed photons. * F.: emission from the state, into which the molecule was excited; spin-allowed; short lifetimes; coupled vibrations reduce the energy (progressions ...); * P.: "intersystem crossing": spin-state changes from absorption to emission; longer lifetimes; (-> name "phosphorescence"); * singulett: -´||,- is the ground state in case of closed shell spin paired situations * triplett (excited state): -´|- -´|- at lower energies than singulett (excited state): -´| - -|,- Regards, Claudia From chemistry-request@server.ccl.net Wed Apr 4 21:37:23 2001 Received: from femail13.sdc1.sfba.home.com ([24.0.95.140]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f351bND28079 for ; Wed, 4 Apr 2001 21:37:23 -0400 Received: from C1353359A ([65.4.172.51]) by femail13.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with SMTP id <20010405013717.HGDV14036.femail13.sdc1.sfba.home.com@C1353359A>; Wed, 4 Apr 2001 18:37:17 -0700 Reply-To: From: "Mark Thompson" To: , "env chem" , "organic chem" , "nat prod" , "GAMESS" , "chem web" , , "chem ed2" , "chem ed" Subject: UFF Date: Wed, 4 Apr 2001 18:29:49 -0700 Message-ID: <000101c0bd6f$e7aba820$33ac0441@sttln1.wa.home.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Importance: Normal It was just pointed out to me that ArgusLab 2.0 probably has the only non-commercial implementation of the Universal Force Field (UFF). This force field covers the entire periodic table. ArgusLab 2.0 is free. http://www.planaria-software.com/ enjoy. ----------------------------------- Planaria Software LLC Seattle, WA. ----------------------------------- From chemistry-request@server.ccl.net Wed Apr 4 23:25:26 2001 Received: from mail.shcnc.ac.cn ([202.127.16.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f353PPD28575 for ; Wed, 4 Apr 2001 23:25:26 -0400 Received: from pc7 ([202.127.19.247]) by mail.shcnc.ac.cn (8.9.3/8.9.3) with SMTP id LAA28697 for ; Thu, 5 Apr 2001 11:24:36 +0800 (CST) Message-Id: <200104050324.LAA28697@mail.shcnc.ac.cn> Date: Thu, 5 Apr 2001 11:16:23 +0800 From: shen Lingling To: "chemistry@ccl.net" Subject: X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Hi, Everyone: I want to calculate the partial charge distribution of a small molecular, which has two Br atoms using keyword POP=CheloG. I am failed with error information that the program has no VDM radia of Br. Is there anyone can help me? Thanks Lingling Shen From chemistry-request@server.ccl.net Wed Apr 4 23:57:42 2001 Received: from smtp.csc.fi ([193.166.0.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f353vgD29027 for ; Wed, 4 Apr 2001 23:57:42 -0400 Received: from sampo.csc.fi (sampo.csc.fi [193.166.1.154]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id GAA17466 for ; Thu, 5 Apr 2001 06:57:41 +0300 Date: Thu, 5 Apr 2001 06:57:41 +0300 (EEST) From: Maija Lahtela To: chemistry@ccl.net Subject: units in Gaussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I would appreciate your help with this problem. As I get in Gaussian output following values for RMS Electrostatic Properties Using The MP2 Density ... Fitting point charges to eletrostatic potential Charges from ESP fit, RMS= 0.00226 RRMS= 0.17190: ... I am wondering that in what units are RMS and RRMS are presented. How could they be converted to electron volts eV's ? Yours Maija L.-K. ***************************************************** Maija Lahtela-Kakkonen, Application Scientist / Chemistry CSC-Scientific Computing Tekniikantie 15 a D, P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 E-MAIL mlahtela@csc.fi, Internet:www.csc.fi ****************************************************