CCL:G: ODP: CCL:G: Gaussian output problem

Dear Maciek,
I would try making a python, perl, or bash script that:
1) open the output file
2) search for the first line of the structure and step you're interested in (or a line with some "keyword" next to the beginning of the structure)
3) read the structure line by line counting the atom number in a variable and when the "****" appears change them by the following variable number i.e. 10000 and so on writing each line to a log/output file

In python, step 3 would by something like this:

n_at= 15000 #total number of atoms of your structure
i=1
while i<=n_at:
 line=file_in.readline()
 subline=line.split()
 if i<9999:
ÂÂÂ file_out.write(line)
 else:
ÂÂÂ subline[0]=str(i)
ÂÂÂ file_out.write("%s "*len(subline)%tuple(subline))
 i=i+1


(NOTE: please, check spelling and identation)


Best

Esteban G Vega-Hissi
UNSL Argentina

--
2010/11/24 Close, David M. CLOSED{=}mail.etsu.edu <owner-chemistry:ccl.net>

Sent to CCL by: "Close, David M." [CLOSED*mail.etsu.edu]
Maciej:
ÂThat's easy. ÂOne can purchase a program that is already compiled for a specific operating system. ÂIf you look at the Gaussian homepage you can select LINUX, WINDOWS, and a variety of parallel versions. ÂThese programs can be installed with simple instructions on specific machines. ÂThese packages are called machine language binaries. ÂAs such you cannot read the code.
ÂThe other option is to purchase the actual program code (as in Fortran). ÂThese programs have to be compiled (or converted into binary code), and then installed on the computer. ÂThis option is for people who are developing code, or who are impatient with the numerous bugs that are in most programs.
ÂTherefore my original suggestion to your problem was to look at the Fortran code and find the line that prints the output. ÂMost likely it calls for the atom number to be printed in fixed 4 space field (I4), that you could easily try to fix. ÂAs someone else pointed out, in another subroutine that used this output, you could cause a new problem with this altered format.
ÂRegards, Dave Close.

-----Original Message-----
> From: owner-chemistry+closed==etsu.edu[a]ccl.net [mailto:owner-chemistry+closed==etsu.edu[a]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]
WysÅano: 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. ÂHowever, there's a relatively easy fix (I think) unless your atom count exceeds 9999 by a lot. ÂJust go into the output file with an editor, and replace the **** by the actual atom number. ÂThat 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: Â804-289-8248
Fax: Â804-287-1897
E-mail: Âsabrash]|[richmond.edu
Web-page: Âhttp://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. ÂAfter 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:
ÂDo you own the source code? ÂIf so, look at the print command. ÂThe program is most likely trying to print a 5 digit number in a fix field (something like I4). ÂMuch of Gaussian code is in Fortran with fixed formats. ÂThe **** just mean that you have tried to print something that doesn't fix in the space allowed.
ÂRegards, 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 ÂMaslyk" [maciejmarcin.maslyk-,-http://ceu.es" target="_blank">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:
Â9995 Â Â Â Â Â1 Â Â Â20001030 Â Â Â-12.655571 Â 46.600810 Â 32.540627
Â9996 Â Â Â Â Â1 Â Â Â20001030 Â Â Â-12.533484 Â 47.134581 Â 33.952118
Â9997 Â Â Â Â Â8 Â Â Â20001021 Â Â Â Â2.441067 Â-19.529269 Â 31.331119
Â9998 Â Â Â Â Â1 Â Â Â20001030 Â Â Â Â2.813824 Â-19.307495 Â 32.184450
Â9999 Â Â Â Â Â1 Â Â Â20001030 Â Â Â Â1.933916 Â-20.325103 Â 31.491166
Â**** Â Â Â Â Â8 Â Â Â20001021 Â Â Â 37.587292 Â-11.572024 Â 28.812192
Â**** Â Â Â Â Â1 Â Â Â20001030 Â Â Â 37.333847 Â-11.927328 Â 27.960694
Â**** Â Â Â Â Â1 Â Â Â20001030 Â Â Â 38.095189 Â-12.272395 Â 29.221488
Â**** Â Â Â Â Â8 Â Â Â20001021 Â Â Â 23.735956 Â-43.072924 Â 13.135294
Â**** Â Â Â Â Â1 Â Â Â20001030 Â Â Â 23.388276 Â-42.182008 Â 13.115359
Â**** Â Â Â Â Â1 Â Â Â20001030 Â Â Â 22.974070 Â-43.624340 Â 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.shtml=http://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


-= This is automatically added to each message by the mailing script =-
E-mail to subscribers: CHEMISTRY:ccl.net or use:
  Âhttp://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST:ccl.net or use
  Âhttp://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
  Âhttp://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
  Âhttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/