Analysing the output file

  • the output of a simple optimisation of BH3 has been explained in the third year computational chemistry lab
  • use this information to explore your H2O optimisation
  • you should also examine the log file directly on cx1, using the terminal application open a new window, and open your water.log file in your favourite editor, I use vi so these instructions will relate to this editor
    [phunt@login-0]/work/phunt/liquids $ ls
    water.chk  water.com  water.log
    
  • vi water.log
    the following is a portion from the top and bottom of my water.log file
    I used the useful vi options [shift]g to get to the end of the file and 1[shift]g to go back to the begining of the file.
    Entering Gaussian System, Link 0=g09
    Input=/export3/work/phunt/liquids/water.com
    Output=/export3/work/phunt/liquids/water.log
    Initial command:
    /apps/gaussian/g09/g09/l1.exe /export3/work/phunt/liquids/Gau-25991.inp -scrdir=/export3/work/phunt/liquids/
    Entering Link 1 = /apps/gaussian/g09/g09/l1.exe PID=     25993.
    
    Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009, Gaussian, Inc.
    			  All Rights Reserved.
    ...
    ...
    ...
    YOU KNOW YOU'RE A TEACHER WHEN YOU SAY 2, WRITE 3, AND MEAN 4.
    -- RONALD ANSTROM, HIGH SCHOOL TEACHER, UNDERWOOD, N.D. 1974
    Job cpu time:  0 days  0 hours  0 minutes  5.6 seconds.
    File lengths (MBytes):  RWF=      5 Int=      0 D2E=      0 Chk=      1 Scr=      1
    Normal termination of Gaussian 09 at Sun Jan 23 11:51:49 2011.
    
  • for those with some experience in scripting some very usefull aliases to set up and put in your .bashrc file are shown below.
    #
    # alias
    #
       alias home="cd"
       alias work="cd \$WORK"
       alias tmp="cd \$TMPDIR"
       alias force="grep -i 'Maximum Force'"
       alias dist="grep -i 'Maximum Disp'"
       alias energy="grep -i 'SCF Done:'"
    
  • Alternatively you could just execute the whole command each time, for example the force script pulls out the maximum force on each step of an optimisation and allows you to examine the convergence quickly and easily without resorting to gaussview:
    [phunt@login-0]/work/phunt/liquids $ force water.log
     Maximum Force            0.014864     0.000450     NO 
     Maximum Force            0.002692     0.000450     NO 
     Maximum Force            0.000206     0.000450     YES
     [phunt@login-0]/work/phunt/liquids $ grep -i "Maximum Force" water.log
     Maximum Force            0.014864     0.000450     NO 
     Maximum Force            0.002692     0.000450     NO 
     Maximum Force            0.000206     0.000450     YES