From owner-chemistry@ccl.net Wed Nov 24 07:48:00 2010 From: "Close, David M. CLOSED{=}mail.etsu.edu" To: CCL Subject: CCL:G: ODP: CCL:G: Gaussian output problem Message-Id: <-43210-101124074653-1381-HRt02wi6rU1oYmJTjOJirw.@.server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-2" Date: Wed, 24 Nov 2010 12:46:47 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED*mail.etsu.edu] Maciej: That's easy. One can purchase a program that is already compiled for a specific operating system. If you look at the Gaussian homepage you can select LINUX, WINDOWS, and a variety of parallel versions. These programs can be installed with simple instructions on specific machines. These packages are called machine language binaries. As such you cannot read the code. The other option is to purchase the actual program code (as in Fortran). These programs have to be compiled (or converted into binary code), and then installed on the computer. This option is for people who are developing code, or who are impatient with the numerous bugs that are in most programs. Therefore my original suggestion to your problem was to look at the Fortran code and find the line that prints the output. Most likely it calls for the atom number to be printed in fixed 4 space field (I4), that you could easily try to fix. As someone else pointed out, in another subroutine that used this output, you could cause a new problem with this altered format. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu _ ccl.net [mailto:owner-chemistry+closed==etsu.edu _ ccl.net] On Behalf Of MASLYK, MACIEJ MARCIN maciejmarcin.maslyk^-^ceu.es Sent: Wednesday, November 24, 2010 4:21 AM To: Close, David M. Subject: CCL:G: ODP: CCL:G: Gaussian output problem Sent to CCL by: "MASLYK, MACIEJ MARCIN" [maciejmarcin.maslyk!A!ceu.es] Thanks for help but I'm completely begginer in gaussian and also in linux so can you guys explain this thing with source code more precisely, please? Sam, I got 15 k atoms and 250 steps so it will kill me if I start changing stars to numbers manually :) regards Maciek ________________________________________ Od: owner-chemistry+maciejmarcin.maslyk==ceu.es-x-ccl.net [owner-chemistry+maciejmarcin.maslyk==ceu.es-x-ccl.net] w imieniu Abrash, Sam sabrash:_:richmond.edu [owner-chemistry-x-ccl.net] Wysłano: 23 listopada 2010 19:09 Do: MASLYK, MACIEJ MARCIN Temat: CCL:G: Gaussian output problem Sent to CCL by: "Abrash, Sam" [sabrash**richmond.edu] Hi, I think David is correct. However, there's a relatively easy fix (I think) unless your atom count exceeds 9999 by a lot. Just go into the output file with an editor, and replace the **** by the actual atom number. That should fix the problem of not being able to read structures (unless the program you're using for the structures has the same problem). Sam Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-287-1897 E-mail: sabrash]|[richmond.edu Web-page: http://www.richmond.edu/~sabrash "In 1893 Charles Hinton left Japan to become a mathematics instructor at Princeton University, where he invented a baseball-pitching machine that used gunpowder to propel the balls, like a cannon. After several accidents, the device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian Steward and Jack Cohen, The Science of Diskworld III -----Original Message----- > From: owner-chemistry+sabrash==richmond.edu]|[ccl.net [mailto:owner-chemistry+sabrash==richmond.edu]|[ccl.net] On Behalf Of Close, David M. CLOSED _ mail.etsu.edu Sent: Tuesday, November 23, 2010 11:18 AM To: Abrash, Sam Subject: CCL:G: Gaussian output problem Sent to CCL by: "Close, David M." [CLOSED..mail.etsu.edu] Maciej: Do you own the source code? If so, look at the print command. The program is most likely trying to print a 5 digit number in a fix field (something like I4). Much of Gaussian code is in Fortran with fixed formats. The **** just mean that you have tried to print something that doesn't fix in the space allowed. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu__ccl.net [mailto:owner-chemistry+closed==etsu.edu__ccl.net] On Behalf Of Maciej Maslyk maciejmarcin.maslyk .. ceu.es Sent: Tuesday, November 23, 2010 8:45 AM To: Close, David M. Subject: CCL:G: Gaussian output problem Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] Hi everyone, could you help me with one problem, please? Every time I'm running G03 job I got problem with outputs. The problem is that I cannot extract structures because there are stars **** instead of atom numbers higher than 9999. Have you ever had this problem in your calculation if you had more than 9999 atoms in the system? It looks like this in output: 9995 1 20001030 -12.655571 46.600810 32.540627 9996 1 20001030 -12.533484 47.134581 33.952118 9997 8 20001021 2.441067 -19.529269 31.331119 9998 1 20001030 2.813824 -19.307495 32.184450 9999 1 20001030 1.933916 -20.325103 31.491166 **** 8 20001021 37.587292 -11.572024 28.812192 **** 1 20001030 37.333847 -11.927328 27.960694 **** 1 20001030 38.095189 -12.272395 29.221488 **** 8 20001021 23.735956 -43.072924 13.135294 **** 1 20001030 23.388276 -42.182008 13.115359 **** 1 20001030 22.974070 -43.624340 13.312930 Do you have any suggestions? Thanks in advance Maciekhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt