Workflow Gaussian Example

From Java CoG Kit

The aim of this example is to use the workflow to run gaussian examples. The examples will be run on the theory group cluster in the chemistry department and details regarding the creation of accounts and the examples of the basic gaussian files that are being run will be on this page.

Contents 1 Accounts 2 Gausssian 3 Testing 3.1 Input Files 3.2 Running the inputs 3.3 Input and Output Extensions 3.4 Outputs look like 4 Contacts

Accounts

Gaussian is setup in the chemistry department on the Theory Group cluster. An account on this will enable us to run gaussian jobs using CoGKit workflow on the cluster. TCG SSH server: anchil2.chm.anl.gov TCG head node: wahl.tcg.anl.gov

Gausssian

Basic Info

Information on running gaussian jobs

Testing

Theory Group Cluster: The environment variables to be defined on the cluster are the following.

 setenv g98root /tcghome/linux
 source $g98root/g98/bsd/g98.login
 setenv GAUSS_SCRDIR /s1/(your username should go here)

To run your job,

 g98  (input data file)  &

Note: The first time you use a node you need to create a scratch directory on that node /s1/(your username).

Input Files

• H2O_B3LYP_SP.gjf -- Water single point calc using one of the

density-functional electronic structure methods, B3LYP, and a modest basis set, 6-31G(d). Runs in about 15 secs or less of wall time on my PC

• H2O_B3LYP_Opt_Freq.gjf -- Water, geometry optimization to find the

structure corresponding to the bottom of the potential well, followed by calc. of vibrational frequencies. Both using the same method and basis set as the above single-point calculation. The geometry optimization and frequencies job runs in about 2 minutes of wall time on my PC.

Running the inputs

• Generally, in Windows you drag and drop the input.
• In Unix, there are usually two ways:

 g03 job-name 
 g03 <input-file >output-file 

Input and Output Extensions

Windows

The extension .gjf for input and .out for output is the default.

Unix

The defaults are .com for input and .log for output.

So, in the first case (g03 job-name) Gaussian will look for an input file job-name.com. With redirection via pipes the file extension does not matter, of course. The attached inputs will also run on older versions of Gaussian, such as g98 (in which case the Unix command is, of course, g98 job-name etc.)

Outputs look like

Once it runs, you want to retrieve the output files, of course -- that is the proof that it ran. The last line in the output should be " Normal termination of Gaussian 03 at <date and time>." The actual fine details of the output will differ from installation to installation...

These outputs are from gaussian 03 run on windows:

• File 1: Media:H2O_B3LYP_SP.txt
• File 2:

Contacts

Theory Group Cluster:

• Theory Group Cluster Incharge: Ron Shepard shepard@tcg.anl.gov
• Account Setup: George Beranek gberanek@anl.gov
• Info on formalising gaussian jobs on the cluster: Larry Harding harding@anl.gov

Gaussian Workflow tests:

• Deepti Kodeboyina dkodeboy@mcs.anl.gov