From owner-chemistry- at -ccl.net Fri Nov 26 04:14:00 2010 From: "MASLYK, MACIEJ MARCIN maciejmarcin.maslyk__ceu.es" To: CCL Subject: CCL:G: ODP: CCL:G: ODP: CCL:G: Gaussian output problem Message-Id: <-43230-101126035906-21118-zx+w+ZUe5URv62Rqd1oWAg+*+server.ccl.net> X-Original-From: "MASLYK, MACIEJ MARCIN" Content-Language: pl-PL Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Fri, 26 Nov 2010 10:03:15 +0100 MIME-Version: 1.0 Sent to CCL by: "MASLYK, MACIEJ MARCIN" [maciejmarcin.maslyk]_[ceu.es] Thanks Olli, the script is working. The thing is that in my input I have 200 sections with coordinates and this script changes stars for appropriate numbers in section 1 but in the second it doesn't change again from 10000 but continues from section 1. And so on. Do you know how to modify this script? Example: 9998 1 20001030 2.813824 -19.307495 32.184450 9999 1 20001030 1.933916 -20.325103 31.491169 **** 8 20001021 37.587292 -11.572024 28.812192 **** 1 20001030 37.333847 -11.927328 27.960694 **** 1 20001030 38.095189 -12.272395 29.221488 ble ble ble 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 ble cble ble 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 ....... more then 200 times So in every section of the file I want to have numbers from 10000 to ...... thanks regards Maciek Dr. Maciej Maslyk Universidad San Pablo CEU Urb. Montepríncipe, Ctra. Boadilla del Monte, Km. 5.300, 28668 Madrid, España Tel.- 91.372.64.31 - FAX.- 91.351.04.75 ________________________________________ Od: owner-chemistry+maciejmarcin.maslyk==ceu.es[*]ccl.net [owner-chemistry+maciejmarcin.maslyk==ceu.es[*]ccl.net] w imieniu Olli Lehtonen olehtone]~[chem.helsinki.fi [owner-chemistry[*]ccl.net] Wysłano: 24 listopada 2010 13:12 Do: MASLYK, MACIEJ MARCIN Temat: CCL:G: ODP: CCL:G: Gaussian output problem Sent to CCL by: Olli Lehtonen [olehtone . chem.helsinki.fi] Hi, Apparently you are using linux so with scripting language awk you can write BEGIN {atom=10000} { if (/^\ \*\*\*\*/) { sub("^\\ \\*\\*\\*\\*",atom); atom++; } print $0; } Assuming that script is contained in file called stars.awk you then give a command (output follows) awk -f stars.awk test.out 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 10000 8 20001021 37.587292 -11.572024 28.812192 10001 1 20001030 37.333847 -11.927328 27.960694 10002 1 20001030 38.095189 -12.272395 29.221488 10003 8 20001021 23.735956 -43.072924 13.135294 10004 1 20001030 23.388276 -42.182008 13.115359 10005 1 20001030 22.974070 -43.624340 13.312930 where test.out contains your sample output. Just be aware that the script changes all **** (in the beginning of line with one extra space) with the running number so if you have the same problem someplace else in the output file it will change it there too. Hope it helps, Olli Oe Wed, Nov 24, 2010 at 10:20:47AM +0100, MASLYK, MACIEJ MARCIN maciejmarcin.maslyk^-^ceu.es wrote: > > 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 > > -----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 advancehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt