CHEM 408 – Sp06 3/15/2006 Using Gaussian03 The main electronic structure program we will use is Gaussian03. The Gaussian series of programs was created in the early 1970s by John Pople and coworkers at Carnegie Mellon University. The company Gaussian, Inc. was set up in the 1980s to distribute the program. The current version, Gaussian03 (G03), which reflects contributions from over 60 scientists, is an extremely powerful tool consisting of over 106 lines of FORTRAN code. It is currently the most popular program for electronic structure calculations available and is used by a large fraction of the chemical community. (There has been some controversy surrounding the distribution of Gaussian programs to workers developing related software. If you are interested in such matters see http://www.bannedbygaussian.org/ and http://www.gaussian.com/libel.htm.) User Environment: In order for G03 to function correctly, you must have the proper path and scratch space properly configured in your environment. For this purpose, you should have already added the lines: export PATH=${PATH}:/usr/global/bin:./ export GAUSS_SCRDIR="/tmp" to your .bashrc file. If these lines are absent or incorrect, G03 will not function properly. Users interact with G03 is either through a graphical user interface (GUI) called “GaussView” or by creating and submitting input files manually. Independent of how jobs are formulated, the actual computations are always run in the background. G03 run “Manually”: Interacting with the program manually involves the following steps: 1. Creating an input file: Create a file “file_name.com” containing essential information on the geometry of the molecule(s) of interest and the type of calculation to be performed. The structure of G03 input files is briefly described in the G03 manual pages I handed out and in more detail in the Exploring Chemistry text. Especially useful are the many example input and output files described in Exploring Chemistry. Electronic versions of these files are available on the course web site (Topics Materials page) and on hammer in the directory /home2/chem408/exploring_files. 2. Submitting the job: Run a G03 job using the command: nice g03 file_name.com & where file_name.com is whatever you called your input file. The “nice” preceding the g03 command tells the operating system to run the program at a reduced priority in order to cause less interference with foreground jobs (such as editting, etc.). 3. Monitoring the job: Most of the jobs we will run will only require seconds or minutes for completion. If you are logged in when the job is complete, the operating system notifies you with the a message something like: [1]+ Done nice g03 file_name.com If you want to check on the status of a background job that is still running, use the ps (process status) command, for example: ps -al which lists all of the background processes running you or other users of the computer initiated from tty devices.CHEM 408 – Sp05 3/15/2006 22Another way of checking whether a particular G03 job has completed successfully is to look at the end of the output file file_name.log which is automatically created during execution of the program. You can do so using the command: tail file_name.log which will type the last 10 lines of the file. If the job has completed successfully, the last line of the file will be something like: Normal termination of Gaussian 03 at Mon Jan 3 18:39:34 2005. If it says anything else, either the job is still running or the job failed for some reason. If something is wrong with a job you have submitted and you want to abort it, use the command: kill job_ID# where job_ID# is the identification number associated with the job, which is found using the ps command. 4. Analyzing the results: Many results of the calculation are output in the output file file_name.log. Depending on the problem, these files can become quite long, and you will need to be able to work with an editor as well as string search commands such as: grep ‘search_string’ file_name.log in order to find the information desired. For example, to find the energy obtained from an RHF calculation one can use the search command: grep ‘SCF Done: E(RHF) =’ file_name.log The log file is not always easy to interpret and the Exploring Chemistry text provides many examples of how to find what you are looking for. The output of jobs run manually can also be inspected using the visual editor. Using the Graphical User Interface GaussView: GaussView is a relatively recent addition to Gaussian that allows the user to graphically construct and manipulate molecules, create and submit G03 jobs, and view various aspects of the output in graphical formats. GaussView is accessed using the command: gview & Once executed in this fashion the GUI starts up a number of windows on your monitor. (If you get an error message related to opening the display, you probably forgot to use the –X option when initiating your connection to hammer.) The “&” means that GaussView will run in the background so that your original xterm is still available for use. The use of GaussView is best learned by a combination of trial-and-error and working through the tutorials provided in the Help menu of GaussView. Note on Computer Use: Remember that hammer is really a collection of “nodes” (i.e. computers). If your interactions with the computer seem sluggish it may be because several people are logged onto the same machine (check using the who command) and or multiple background jobs (check with ps –a) are running. You can try one of the other nodes of hammer to seek better performance. The particular “node” on which you are running is indicated by the initial portion of the command