From owner-chemistry@ccl.net Mon Mar 5 08:19:00 2012 From: "Ananda Gopal Sarkar aas14d%gmail.com" To: CCL Subject: CCL:G: chk file not opening in GV Message-Id: <-46420-120305023913-6963-hrfNMfZCsEKmIOksq6l77w]=[server.ccl.net> X-Original-From: "Ananda Gopal Sarkar" Date: Mon, 5 Mar 2012 02:39:12 -0500 Sent to CCL by: "Ananda Gopal Sarkar" [aas14d#%#gmail.com] Hi, I got a problem regarding check point file. I have run a Gaussian job and tried the job.chk file to be opened in Gauss View. The message coming is as follows: CConnectionGFCHK::ReadFile() Cannot find file The job was run in g09 and GV 5.0.8 was used to open the job.chk file. My system contains only 25 atoms. While doing trial and error, once I removed some of the atoms and run the job. This time the job.chk file opened successfully. does this signify a memory related issue? I am not familiar with this kind of problem. Then I tried %mem and maxdisk keywords to increase memory. Nothing could help me. If anybody is aware of the remedy of such a problem, please let me know the remedy. thanks in advance regards, Ananda Gopal Sarkar aas14d#,#gmail.com From owner-chemistry@ccl.net Mon Mar 5 08:53:00 2012 From: "rv solo rvsolo*gmail.com" To: CCL Subject: CCL:G: free ware for ONIOM input preparations Message-Id: <-46421-120305083632-17405-6Mj04FZzRYxIeYJsYOQxXw^server.ccl.net> X-Original-From: "rv solo" Date: Mon, 5 Mar 2012 08:36:29 -0500 Sent to CCL by: "rv solo" [rvsolo^gmail.com] dear cclrs, i would like to perform some ONIOM calculations using Gaussian 09. It is very difficult to find the active site and then cut that within 5 amstrong distance and so on using Gauss View . is there any supporting freewares available for the input preparation? thanks in advance R. V.solo From owner-chemistry@ccl.net Mon Mar 5 09:53:00 2012 From: "Laidig, Bill laidig.wd]^[pg.com" To: CCL Subject: CCL: A simple way to determine row and column indices for symmetric matrices? Message-Id: <-46422-120305095137-3830-R6JHXCXeuJQIGKrTkF2gdg(~)server.ccl.net> X-Original-From: "Laidig, Bill" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Mon, 5 Mar 2012 14:51:25 +0000 MIME-Version: 1.0 Sent to CCL by: "Laidig, Bill" [laidig.wd:pg.com] I would do it do creating 2 arrays of length IJMAX. Fill the arrays so IOfIJ(IJ)=I and JOfIJ=J once and you can look up very fast. Bill -----Original Message----- > From: owner-chemistry+laidig.wd==pg.com:ccl.net [mailto:owner-chemistry+laidig.wd==pg.com:ccl.net] On Behalf Of Jussi Lehtola jussi.lehtola- -helsinki.fi Sent: Sunday, March 04, 2012 5:46 AM To: Laidig, Bill Subject: CCL: A simple way to determine row and column indices for symmetric matrices? Sent to CCL by: Jussi Lehtola [jussi.lehtola-*-helsinki.fi] Hi, does anyone know if there is an efficient and numerically stable way to determine row and column indices of an element of a symmetric matrix, for which only the storage index is known? That is, the symmetric matrix A(i,j)=A(j,i) is stored in memory as A(i,j) = v[i*(i+1)/2 + j], i >= j and now I'd like to determine what are i and j if I only know the index in v. This has to do with improving parallel scaling of the direct formation of the (Hartree-)Fock matrix in ERKALE. -- -------------------------------------------------------- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.lehtola*helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland -------------------------------------------------------- Jussi Lehtola, FM Tohtorikoulutettava jussi.lehtola*helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 --------------------------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Mar 5 12:19:00 2012 From: "benoit lefevre bonoit_10 ~ yahoo.fr" To: CCL Subject: CCL: CBS-4M Message-Id: <-46423-120305121737-29171-QFVkWDEHn2hdPvFzobcALA++server.ccl.net> X-Original-From: "benoit lefevre" Date: Mon, 5 Mar 2012 12:17:05 -0500 Sent to CCL by: "benoit lefevre" [bonoit_10 ~~ yahoo.fr] Dear CCLer's, I would like to know what are the factor scales used in CBS-4M method. Any help will be appreciated Sincerely, Benoit From owner-chemistry@ccl.net Mon Mar 5 14:02:00 2012 From: "Wojciech Kolodziejczyk dziecial!^!icnanotox.org" To: CCL Subject: CCL:G: chk file not opening in GV Message-Id: <-46424-120305135956-10235-oB4mxsLHohZUVKDDCjYRGw(0)server.ccl.net> X-Original-From: Wojciech Kolodziejczyk Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 5 Mar 2012 19:59:48 +0100 MIME-Version: 1.0 Sent to CCL by: Wojciech Kolodziejczyk [dziecial|a|icnanotox.org] Hi You can only open chk file if you use the same system for g09. Otherwise you have to format chk file into fchk with formchk program. It is available from gaussian directory on the machine you run you calculations. Formatted chk file you can open with any GV program Best regards W. 2012/3/5 Ananda Gopal Sarkar aas14d%gmail.com : > > Sent to CCL by: "Ananda Gopal Sarkar" [aas14d#%#gmail.com] > Hi, > I got a problem regarding check point file. I have run a Gaussian job and tried > the job.chk file to be opened in Gauss View. The message coming is as follows: > CConnectionGFCHK::ReadFile() > Cannot find file > The job was run in g09 and GV 5.0.8 was used to open the job.chk file. My > system contains only 25 atoms. While doing trial and error, once I removed some > of the atoms and run the job. This time the job.chk file opened successfully. > does this signify a memory related issue? I am not familiar with this kind of > problem. Then I tried %mem and maxdisk keywords to increase memory. Nothing > could help me. If anybody is aware of the remedy of such a problem, please let > me know the remedy. > thanks in advance > regards, > Ananda Gopal Sarkar > aas14d##gmail.com>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Mon Mar 5 19:54:00 2012 From: "James Mao xjamesmao*|*gmail.com" To: CCL Subject: CCL: Entropy calculations for condensed state Message-Id: <-46425-120305195228-17067-MusxCT+M0EJY1lqAFhqaWA(0)server.ccl.net> X-Original-From: "James Mao" Date: Mon, 5 Mar 2012 19:52:16 -0500 Sent to CCL by: "James Mao" [xjamesmao|a|gmail.com] Dear cclers, I am trying to evaluate the entropy change of a reaction (1,3-cyclohexadiene -> 1,4-cyclohexadiene). They both are liquid and the experimental data shows the entropy change is negative, which is reasonable since 1,4-cyclohexadiene has a higher symmetry. However calculations for gas phase all show 1,3-cyclohexadiene has a lower entropy than 1,4-cyclohexadiene (I tried different basis sets and methods). Is this due to the reason that symmetry factor is not included for a single molecule calculation in gas state? The arrangements of the molecules in liquid phase should contribute a large part of entropy, right? As to my problem, is there any way to evaluate entropy in liquid phase? Any suggestion will be greatly appreciated. Best, James From owner-chemistry@ccl.net Mon Mar 5 21:37:01 2012 From: "Billy McCann bwm0005^_^tigermail.auburn.edu" To: CCL Subject: CCL: CBS-4M Message-Id: <-46426-120305142745-16482-QUMMMr75MM7wzm02Pim1ig~!~server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 5 Mar 2012 19:27:20 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [bwm0005.:.tigermail.auburn.edu] Hi Benoit. Your best course of action would be to look into the original articles themselves. Searching for "CBS-4M" in Google Scholar yields [2] as the first result. [2] would naturally lead you to [1], which is where you'll find the data for which you're looking. I'm not sure which "factor scales" you're referring to, e.g. the scaling of the ZPE vibrational terms, empirical terms, etc. The relevant literature is below: [1] J. W. Ochterski, G. A. Petersson, and J. A. Montgomery Jr., "A complete basis set model chemistry. V. Extensions to six or more heavy atoms," J. Chem. Phys., 104 (1996) 2598-619. [2] J. A. Montgomery Jr., M. J. Frisch, J. W. Ochterski, and G. A. Petersson, "A complete basis set model chemistry. VII. Use of the minimum population localization method," J. Chem. Phys., 112 (2000) 6532-42. +++++++++++++++++++ Billy Wayne McCann Acevedo Research Auburn University, Alabama Office # = 334-844-6948 +++++++++++++++++++ -----Original Message----- > From: owner-chemistry+bwm0005==auburn.edu*_*ccl.net [mailto:owner-chemistry+bwm0005==auburn.edu*_*ccl.net] On Behalf Of benoit lefevre bonoit_10 ~ yahoo.fr Sent: Monday, March 05, 2012 11:17 AM To: Billy McCann Subject: CCL: CBS-4M Sent to CCL by: "benoit lefevre" [bonoit_10 ~~ yahoo.fr] Dear CCLer's, I would like to know what are the factor scales used in CBS-4M method. Any help will be appreciated Sincerely, Benoithttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Mar 5 22:12:01 2012 From: "benoit lefevre bonoit_10---yahoo.fr" To: CCL Subject: CCL:G: cbs calculation Message-Id: <-46427-120305162251-12234-bBbNVY0lrjEARmZSWNQiIQ,+,server.ccl.net> X-Original-From: "benoit lefevre" Date: Mon, 5 Mar 2012 16:22:44 -0500 Sent to CCL by: "benoit lefevre" [bonoit_10^_^yahoo.fr] Dear CCLers, I'm Benoit, i'm trying to do cbs-4m and cbs-qb3 calculations but i've some troubles with these methods. For cbs-4m: it stops at the fourth step (Route section from calculation 4 #N Geom=AllCheck Guess=Read SCRF=Check Test MP2/6-31+D** CBSExtrap=(NM) of calculation given this message: Error termination via Lnk1e in /share/apps/g03/l502.exe at Mon Mar 5 10:16:29 2012. For cbs-qb3: it stops at the first step of calculation given this message: Error termination via Lnk1e in /share/apps/g03/l9999.exe at Mon Mar 5 10:56:33 2012. Any help will be appreciated Best regards Benoit Lefevre