From owner-chemistry@ccl.net Thu Aug 21 04:33:01 2008 From: "Ioan SILAGHI-DUMITRESCU isi|,|chem.ubbcluj.ro" To: CCL Subject: CCL: MP2 calculation Message-Id: <-37589-080820135428-23733-F5DxofajEjGzAi8JTnEpcw .. server.ccl.net> X-Original-From: Ioan SILAGHI-DUMITRESCU Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 20 Aug 2008 20:31:25 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Ioan SILAGHI-DUMITRESCU [isi^chem.ubbcluj.ro] Hi Ashwini It is most probable that the scratch file (rwf) has extended over the 2Gb limit, in that case the solution is to split this file in units of less then 2Gb: %rwf=rwf00,1999Mb,rwf01,1999Mb,rwf03,1999Mb,rwf04,1999Mb,rwf05,1999Mb,rwf06,1999Mb,rwf07,1999Mb Best regards, isi --------------------------------------------------------------------- Prof.dr. Ioan Silaghi-Dumitrescu Department of Chemistry | Facultatea de Chimie si Inginerie Chimica Babes-Bolyai University | Universitatea Babes-Bolyai 1, Kogalniceanu str. | str. Kogalniceanu, nr.1 RO-400084 Cluj-Napoca, | RO-400084 Cluj-Napoca Roumania | Romania e-mail: isi|,|chem.ubbcluj.ro Fax: +40-264-590818 Tel: +40-264-593833 ext.5665 On Wed, 20 Aug 2008, Ashwini Phukan ashwini_phukan=yahoo.com wrote: > > Sent to CCL by: Ashwini Phukan [ashwini_phukan{}yahoo.com] > Dear All, > > I was trying to run a MP2/6-31+G* calculation for a system with 232 basis functions using the following route card: > > #mp2(maxdisk=40GB)/6-31+g* fopt freq geom=check guess=read > > Before starting the calculation, I checked the disk space and found that 55GB is available. > > Filesystem Size Used Avail Use% Mounted on > /dev/mapper/VolGroup00-LogVol00 > 73G 14G 55G 21% / > /dev/sda1 99M 12M 82M 13% /boot > none 247M 0 247M 0% /dev/shm > > However, after running the calculation, I got the following message. > > **** Warning!!: The largest alpha MO coefficient is 0.60503943D+02 > > Disk-based method using ON**2 memory for 30 occupieds at a time. > Estimated scratch disk usage= 594240712 words. > Actual scratch disk usage= 593732296 words. > Erroneous write during file extend. write 28671 instead of 4096 > Probably out of disk space. > Write error in NtrExt1: Success > Erroneous write during file extend. write 28671 instead of 4096 > Probably out of disk space. > Write error in NtrExt1 > > But, when I checked the disk space again, the available space was still 53GB. > > I shall be very much obliged if some one can help me out. > > Regards, > > A. K. Phukan> > From owner-chemistry@ccl.net Thu Aug 21 09:52:01 2008 From: "Anatoli Korkin a_korkin[A]yahoo.com" To: CCL Subject: CCL:G: Transition State question Message-Id: <-37590-080820123625-13279-fV4R8CxEwlVrfle3iJseDw:+:server.ccl.net> X-Original-From: Anatoli Korkin Content-Type: text/plain; charset=us-ascii Date: Wed, 20 Aug 2008 09:36:12 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Anatoli Korkin [a_korkin,,yahoo.com] Si(n)H(m) molecules, electron deficient molecules, such as B(n)H(m) and mixed species, e.g. B(l)Si(n)H(m) with multiple Si-Si, B-B, Si-B bonds and H-bridging tendency can create very exotic potential surfaces - fun computational chemistry game, particularly if you use many "official tricks" in Gaussian and add your own recipes based on chemistry knowledge (such partial freeze of some coordinates) and symmetry. If you have time to kill, you may check these papers and references cited therein: Korkin, A.A.; Schleyer, P.v.R.; McKee, M.L. Theoretical Ab Initio Study of Neutral and Charged B3Hn Species. The Importance of Aromaticity in Determining the Structural Preferences. Inorg. Chem. 1995, 34, 961-977. Korkin, A.A.; Murashov, V.; Leszczynski, J.; Schleyer, P.v.R. Theoretical Study of Cyclic Si5H5+ Structural Isomers. Is There Any Analogy with the Corresponding Carbon Species? J. Phys. Chem. 1995, 99, 17742-17747. Jemmis, E.D.; Subramanian, G.; Korkin, A.A.; Hofmann, M.; Schleyer, P.v.R. The Exotic Structures of Si2B2H4. J. Phys. Chem. 1997, 101, 919-925. Srinavas, G.N.; Jemmis, E.D.; Korkin, A.A.; Scheleyer, P.v.R. An ab initio study of the Diverse Si3H3+ Isomers. J. Phys. Chem. 1999, 103, 11034-11039 --- On Tue, 8/19/08, Dr.Wolfgang Quapp quappa/rz.uni-leipzig.de wrote: > From: Dr.Wolfgang Quapp quappa/rz.uni-leipzig.de > Subject: CCL: Transition State question > To: "Korkin, Anatoli " > Date: Tuesday, August 19, 2008, 2:43 AM > Sent to CCL by: "Dr.Wolfgang Quapp" > [quapp-x-rz.uni-leipzig.de] > Zitat von "Mark Zottola mzottola^^gmail.com" > : > > > In examining a potential energy surface of a species > of interest, I have > > come across something unique to my experience. I > have, apparently, run > > across a system which an intermediate connects to a > transition state via > > *another* transition state. The IRC calculations > validate this connection. > > The second transition state connects two other > species. In other words > > > > A ----> B (TS_1) -----> C (TS_2) ; > > > > D ----> C (TS_2) -----> F > > > > The second TS (TS_2) is a first order saddle point. > Has anyone run across > > this before? Or am I missing something fundamental in > these calculations? > > I have come across a Schlegel reference where a > transition state connects > > three different species. Yet this communication was > for an open-shell > > system. > > > > Thanks for any helpful comments, references, etc. > > > > > > Mark > > > > Hallo Mark, > > see, for example, model surfaces for your problem in: > > Theoret Chem Acc 112 (2004) 40-51, or > J Molec struct 695-696 (2004) 95-101 > > Greetings > Dr.Wolfgang Quapp > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging > Program. > > > > -= This is automatically added to each message by the > mailing script =- > To recover the email address of the author of the message, > please change > the strange characters on the top line to the () sign. You > can also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search) From owner-chemistry@ccl.net Thu Aug 21 14:35:00 2008 From: "Antonio G. De Crisci antonio.decrisci(a)utoronto.ca" To: CCL Subject: CCL:G: when NOT to use guess=read? Message-Id: <-37591-080821143315-19457-tTBiu8+PbhqMtVLQJtnA+g]|[server.ccl.net> X-Original-From: "Antonio G. De Crisci" Date: Thu, 21 Aug 2008 14:33:11 -0400 Sent to CCL by: "Antonio G. De Crisci" [antonio.decrisci:-:utoronto.ca] Hello All, In Gaussian 03, when is it NOT a good idea to use the guess=read option? For example, when performing several calculations on the same molecule, which may including tweaking of the grids, changing the threshold criteria, level of theory or from check files of a failed/crashed/incomplete calculation. I guess im just wondering how smart that guess=read option is when you use it and whether you should start the guess from scratch instead (no puns intended). Thanks in advance for your time. Antonio De Crisci University of Toronto From owner-chemistry@ccl.net Thu Aug 21 19:29:02 2008 From: "Alvaro Vazquez vama*o*xanum.uam.mx" To: CCL Subject: CCL:G: how G03 builds promolecule density for Hirshfeld population analysis? Message-Id: <-37592-080821192607-10043-f4LV2Dbs3gGyu38QZflnmg**server.ccl.net> X-Original-From: "Alvaro Vazquez" Content-Type: multipart/alternative; boundary="----=_Part_44074_27447007.1219361155923" Date: Fri, 22 Aug 2008 01:25:55 +0200 MIME-Version: 1.0 Sent to CCL by: "Alvaro Vazquez" [vama]*[xanum.uam.mx] ------=_Part_44074_27447007.1219361155923 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCL readers, I found the option IOP(6/79=1) to get Hirshfeld charges in Gaussian03. I cannot notice the atomic calculations, how the promolecule density is build? Is there a specific basis set to work with that? Thanks in advance Alvaro ------=_Part_44074_27447007.1219361155923 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCL readers,

I found the option IOP(6/79=1) to get Hirshfeld charges in Gaussian03.
I cannot notice the atomic calculations, how the promolecule density is build?

Is there a specific basis set to work with that?

Thanks in advance
Alvaro

------=_Part_44074_27447007.1219361155923-- From owner-chemistry@ccl.net Thu Aug 21 21:47:00 2008 From: "Cherif Matta Cherif.Matta:_:dal.ca" To: CCL Subject: CCL:G: how G03 builds promolecule density for Hirshfeld population analysis? Message-Id: <-37593-080821213939-11899-5yEiJFSpWRD6xA5X8eka8w/./server.ccl.net> X-Original-From: Cherif Matta Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Thu, 21 Aug 2008 21:55:31 -0300 MIME-Version: 1.0 Sent to CCL by: Cherif Matta [Cherif.Matta . dal.ca] Dear Alvaro, In my opinion, your question is exactly why one have to think twice before relying on Hirshfeld charges, since the reference is arbitrary. For example, in the case of LiF should the reference be the isolated atoms or the ions? Cheers, Cherif ------------------------------------------- Cherif F. Matta, Ph.D., MCIC Assistant Professor of Chemistry Department of Chemistry and Physics Mount Saint Vincent University Halifax, NS, Canada B3M 2J6. & Adjunct Professor of Chemistry Dalhousie University Halifax, NS, Canada B3H 4J3. ------------------------------------------- Tel.: +1(902)457 6142 Fax: +1(902)457 6134 Web-site: http://chem.utoronto.ca/~cmatta/ ------------------------------------------- Quoting "Alvaro Vazquez vama*o*xanum.uam.mx" : > Dear CCL readers, > > I found the option IOP(6/79=1) to get Hirshfeld charges in Gaussian03. > I cannot notice the atomic calculations, how the promolecule density is > build? > > Is there a specific basis set to work with that? > > Thanks in advance > Alvaro >