From chemistry-request@ccl.net Fri Jun 25 03:27:25 2004 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5P8RO5d020277 for ; Fri, 25 Jun 2004 03:27:24 -0500 Received: from [136.206.86.70] by hawk.dcu.ie with HTTP; Fri, 25 Jun 2004 09:32:17 +0100 Date: Fri, 25 Jun 2004 09:32:17 +0100 Message-ID: <406A6C3900073D46-.at.-hawk.dcu.ie> In-Reply-To: <000501c459fc$b8caddf0$abcd6981@chief> From: "Noel O'Boyle" Subject: RE: CCL:Gaussian 03 PES results To: "Jim Pfaendtner" Cc: chemistry-.at.-ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.3 required=7.5 tests=MY_HTML_OBFU autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i5P8RP5d020281 Hello Jim, I think you should look at Python (www.python.org) - available for free for Windows and Linux. I have used Python to automate a lot of the common tasks I do - the results are available as GaussSum (gausssum.sourceforge.net). Warren DeLano's PyMol is a much more advanced example of what's possible with Python. A more everyday example - let's say you want the energies given by the lines containing "SCF Done": input=open("myoutput.out","r") # open file for 'r'eading line=input.readline() # Get the first line from the input file while len(line)>0: # Loop through every line in the file if line.find("SCF Done")>=0: # If the line contains the phrase "SCF Done" splitup=line.strip().split() # Creates a list of 'words' using spaces as separators energy=splitup[4] # The energy is the 5th item in the list print energy # Write the energy on the screen (or into an outputfile) line=input.readline() # Get the next line input.close() # Tidy up (Of course, in Linux you can do this particular job quicker with 'grep' and 'cut' - but this is not true for more complicated jobs, which is what you want to do - to get the values of the variables and create a table) I have never done a scan, so I don't have any example output files here. If you try this, you can also read in the values of the variables and create a table yourself at the end of program. The Windows version of Python comes with a simple GUI for writing and running programs, but you can also run programs at the command line: e.g. python myprog.py myinputfile.out If you need any help, please let me know. Noel >-- Original Message -- >From: "Jim Pfaendtner" >To: >Subject: CCL:Gaussian 03 PES results >Date: Thu, 24 Jun 2004 10:05:43 -0500 > > >Hi all, > >I have performed a potential energy scan over two coordinates with >geometry optimization at each point. From what I could gather from the >G03 manual and trying to get the simulations running, the way to do this >is like this: > > ># ... opt(addredundant,..) .. > > > >X Y S <#steps >W Z S <#steps > > >Where X,Y,W,Z are my coordinates of interest. > > >The calculation ran and completed geometry optimization at each step. >But I don't get a nice table like the Gaussian manual says I should by >using the scan keyword. I don't want to just use the scan keyword, >because I want geometry optimization at each step. > >Is there a way to get my results out of my log file? I know they are in >there, but I have done post-processing w/Excel and it's not that fun and >prone to errors. > > >Thanks! > > > From chemistry-request@ccl.net Fri Jun 25 04:06:31 2004 Received: from vwall.nc.kyushu-u.ac.jp (vwall.nc.kyushu-u.ac.jp [133.5.6.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5P96T5d021563 for ; Fri, 25 Jun 2004 04:06:30 -0500 Received: from vwall.nc.kyushu-u.ac.jp (localhost [127.0.0.1]) by vwall.nc.kyushu-u.ac.jp (8.12.11/8.12.11) with ESMTP id i5P9BPvK004625; Fri, 25 Jun 2004 18:11:25 +0900 (JST) Received: from yuuki5 (yuuki5.scc.kyushu-u.ac.jp [133.5.167.18]) by vwall.nc.kyushu-u.ac.jp (8.12.11/8.12.11) with ESMTP id i5P9BL93004592; Fri, 25 Jun 2004 18:11:25 +0900 (JST) To: chezbowlus^at^goldrush.com, chemistry^at^ccl.net Subject: CCL: Orient molecule From: Masahiko Suenaga Message-Id: <200406251810.JEG93853.MDBBIDTP^at^mbox.nc.kyushu-u.ac.jp> X-Mailer: Winbiff [Version 2.34PL1] X-Accept-Language: ja,en Date: Fri, 25 Jun 2004 18:10:09 +0900 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Bowlus, Facio 8.3.1 can do this. Please visit Facio's web site. http://hb6.seikyou.ne.jp/home/zzzfelis/Facio.html Best regards, Masahiko Suenaga, Ph.D. Department of Chemistry, Faculty of Sciences, Kyushu University, Japan. ********************************************* -----Original Message----- I am frantically searching for a simple piece of code that will allow me to: Read a standard file (mol, pdb, Sybyl ...) select an atom to put at the Cartesian origin select an atom to put on the X axis select an atom to put in the XY plane Do a rigid rotation Do sequential rigid rotations about Cartesian axes Freeze the molecule in the new orientation Output the NEW, transformed coordinates. This is equivalent to the Sybyl "orient" command, plus rigid rotations, plus "Freeze molecule". But I have not found a free (or even cheap) package that $B!! (Bwill freeze a molecule in the new coordinates before output. Thanks in advance for any pointers, Steve From chemistry-request@ccl.net Fri Jun 25 04:41:57 2004 Received: from mailservice.tudelft.nl (mailservice.tudelft.nl [130.161.131.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5P9fuEd022983 for ; Fri, 25 Jun 2004 04:41:57 -0500 Received: from localhost (localhost [127.0.0.1]) by rav.antivirus (Postfix) with ESMTP id CECA4266B9 for ; Fri, 25 Jun 2004 11:46:53 +0200 (MEST) Received: from mail.dct.tudelft.nl (mail.dct.tudelft.nl [130.161.196.201]) by mx3.tudelft.nl (Postfix) with ESMTP id DD2B4266B5 for ; Fri, 25 Jun 2004 11:46:52 +0200 (MEST) Received: from TNW-DCT1/SpoolDir by mail.dct.tudelft.nl (Mercury 1.48); 25 Jun 04 11:46:53 +0200 Received: from SpoolDir by TNW-DCT1 (Mercury 1.48); 25 Jun 04 11:46:51 +0200 From: "Martijn Zwijnenburg" Organization: Delft University of Technology (TNW-DCT) To: chemistry^at^ccl.net Date: Fri, 25 Jun 2004 11:46:49 +0200 MIME-Version: 1.0 Subject: ccl: G98 Unable to match L and R vectors in BiOrth. Message-ID: <40DC1095.32335.57DBBADF@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.12a) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body X-Virus-Scanned: by amavisd-new at tudelft.nl X-Spam-Status: No, hits=1.8 required=7.5 tests=BAD_X_HEADERS, FVGT_s_SINGLE_LETTER,IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, I'm running a TDDFT calc (using the TD keyword in G98, for input file see below) on a small silica cluster. I've done similar calcs for similar systems which always worked nicely, but this one fails with the following error message: Iteration 7 Dimension 96 CISAX: IP= 1 NPass= 4 NMax= 3. CISAX will form 3 AO SS matrices at one time. NMat= 3 NSing= 3. NMat= 3 NSing= 3. NMat= 3 NSing= 0. NMat= 3 NSing= 0. CISAX: IP= 1 NPass= 4 NMax= 3. CISAX will form 3 AO SS matrices at one time. NMat= 3 NSing= 3. NMat= 3 NSing= 3. NMat= 3 NSing= 0. NMat= 3 NSing= 0. Unable to match L and R vectors in BiOrth. Error termination via Lnk1e in /opt/g98/g98/l914.exe. Job cpu time: 0 days 19 hours 9 minutes 51.6 seconds. File lengths (MBytes): RWF= 530 Int= 0 D2E= 0 Chk= 37 Scr= 1 Could somebody please explain me what is going wrong? Thanks in advance Martijn Zwijnenburg ---------------------------------------------------------------------------------------------- input file: %chk=Si10O20_diamond_TD #P trackio # GFINPUT IOP(6/7=3) # B3LYP/6-31G* # TD(50-50) # geom=check # guess=check # density=current # fcheck=all # nosymm Gaussian job Si10O20_diamond_TD 0 1 From chemistry-request@ccl.net Fri Jun 25 09:22:21 2004 Received: from sal.ahpcrc.org (sal.ahpcrc.org [144.34.1.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5PEMLoZ030465 for ; Fri, 25 Jun 2004 09:22:21 -0500 Received: from mycroft.ahpcrc.org (mycroft.ahpcrc.org [144.34.9.34]) by sal.ahpcrc.org (Postfix) with ESMTP id 41D2B13C57; Fri, 25 Jun 2004 09:27:19 -0500 (CDT) Received: from localhost (localhost [127.0.0.1]) by mycroft.ahpcrc.org (Postfix) with ESMTP id 7BB6917800A; Fri, 25 Jun 2004 09:27:18 -0500 (CDT) Received: from ahpcrc.org (GULL.dhcp.famu.ahpcrc.org [144.34.131.114]) by mycroft.ahpcrc.org (Postfix) with ESMTP id 6B6A8178009; Fri, 25 Jun 2004 09:27:10 -0500 (CDT) Message-ID: <40DC35F9.98E169BE..at..ahpcrc.org> Date: Fri, 25 Jun 2004 10:26:01 -0400 From: Genzo Tanaka X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: Jim Pfaendtner Cc: chemistry..at..ccl.net Subject: Gaussian 03 PES results Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS snapshot-20020222 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Jim, Your desired results are in your output (log) file. Extracting the eigenvalues and the corresponding interested coordinates yield a similar table as in the Gaussian manual (but in a row form). You can get your optimized energy for each scan step by prompt> grep "EIGENVALUES" your output The optimized coordinates in Z-matrix format ( R1 R2... A1 A2... D1 D2 ...) follow the eigenvalue rows. Your interested coordinates are rows in this table. In some cases, you may not get this table due to some kind errors. In this case, you need to do some elaborate work. Let me know if you need more information. Genzo From chemistry-request@ccl.net Fri Jun 25 13:08:19 2004 Received: from calmail-cr.berkeley.edu (mailfarm.Berkeley.EDU [128.32.61.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5PI8IsF004717 for >ccl.net>; Fri, 25 Jun 2004 13:08:18 -0500 Received: from [128.32.198.91] (account shaji<>calmail.berkeley.edu HELO berkeley.edu) by calmail-cr.berkeley.edu (CommuniGate Pro SMTP 4.1.8) with ESMTP-TLS id 43546271; Fri, 25 Jun 2004 11:13:12 -0700 Message-ID: <40DC6B38.4040403<>berkeley.edu> Date: Fri, 25 Jun 2004 11:13:12 -0700 From: Shaji Chempath >berkeley.edu> User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.1) Gecko/20031114 X-Accept-Language: en-us, en MIME-Version: 1.0 To: ccl >ccl.net> CC: Kathy Durkin >cchem.berkeley.edu> Subject: open-new-file problem with Gaussian Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, CCLers I am running my gaussian jobs an a cluster (g03 on Linux 2.4.18-14smp) many of my runs now are stopping with open-new-file written at the end of file. A sample of gaussian output is given here (last two lines) ------------------------------------------------- fname=/scr/shaji/Gau-29993.d2e fd = -1 open-new-file ------------------------------------------------- but this happens with almost 50% of my gaussian jobs, with all kinds of runs (optimization, frequency... ). They usually runs for a day and then dies. This did not use to happen before. I have been using G03 for 6 months, but the problems started last month. So it is not something with gaussian itself, but maybe something to do with NFS file handling, or something else with the linux cluster.. If anybody has seen this before and solved it please let me know Thanks a lot Shaji