HOW TO USE GAUSSIAN 03 FOR WINDOWS

S. AragonChemistry Spring 07

G03W is a standalone program that runs under the Windows operating system on Intel compatible CPUs. In order to run a calculation with G03W, one must first prepare and input file, then run the calculation, and finally analyse/visualize the results. Please visit the following site to learn about the general capabilities of G03:http://www.gaussian.com/g_brochures/g03_intro.htmThe full manual for G03 can be found at:http://www.gaussian.com/g_ur/g03mantop.htm

The CCV Lab computers also have the previous version of Gaussian, G98W (manual zip file available at: http://www.gaussian.com/tech_top_level.htm). If your calculation can be done with that version, a simpler process than that described below is available for visualization of your results. Essentially, to submit jobs and to visualize your results you can use GaussView 2.1 directly because G98W output is compatible with GaussView 2.1. Unfortunately, the output of G03W is not compatible with GaussView 2.1 and we must use the work-around described below.

Please visit the following site to learn about what’s new in G03W: http://www.gaussian.com/g_brochures/g03_new.htm

I. Preparing the Input File:

The Gaussian job file (.gfj) can be typed in directly into G03W, but because it contains geometrical information on your structure, it is most easily prepared using the program GaussView. It is also possible to prepare the structure in Spartan and export it so that the file can be read by GaussView (see below). The Gaussian job file format is the same for all versions of the gaussian program, so both G03W and G98W can read and execute with the same gjf file. This is also true of the G03W for Linux that runs on the Aragon Cluster.

Input File Naming Recommendations:It is a good idea to use long file names containing suitable information about your calculation. For example: molecule_method_basis.gjf,where “molecule” is your molecule name, “method” identifies the type of calculation such as HF, DFT, MP2, etc., and “basis” identifies the basis set that you used in the calculation. Other names can be added to identify further aspects of the calculation such as single point energy, NMR, vibrations, etc. For example:

Cl2Sitmtaa_B3LYP_LanL2DZ_IR.gjf

Please consult your instructor or the GaussView manual in order to learn how to prepare an input file for Gaussian.

II. Running G03W

On your PC, find the icon that looks like: G03w.lnk

Double click it. When the program starts, use the File/Open menu choice to browse for your gjf file and select it. This action generates a new window called “Existing File Job Edit”. Type any modifications to the %Section and the Route section of the file as needed. For example, you will almost always want to include the statement:

%chk = molecule_method_basis.chkIn the % Section. This will cause the “checkpoint” file to be written to the Scratch directory within the G03W directory of your computer. Now, in the File menu of the edit window, select “Exit & Run”. This will cause another window to come up asking you to name the Gaussian output file. The default will be your molecule_method_basis.out, so save it. The program will now start printing its output on the main G03W window until it finishes. At the end of the run, G03W will print a summary of the timing of the calculation after a “saying or quote” from its internal database. At this point you can exit the program.

III. Analysis/Visualization of Output

The .out file is a text file and it is identical to what was printed on the screen while the computer ran. You can read this file with any editor or word processor at your disposal. An example of the final lines of output follows:

TIME IS IN FACT THE HERO OF THE PLOT. THE TIME WITH WHICH WE HAVE TO DEAL IS OF THE ORDER OF TWO BILLION YEARS...GIVEN SO MUCH TIME, THE "IMPOSSIBLE" BECOMES POSSIBLE, THE POSSIBLE PROBABLE, THE PROBABLE VIRTUALLY CERTAIN. ONE HAS ONLY TO WAIT, TIME ITSELF PERFORMS THE MIRACLES. "ORIGIN OF LIFE" LECTURES, GEORGE WALD, 1954 Job cpu time: 0 days 0 hours 0 minutes 27.0 seconds. File lengths (MBytes): RWF= 12 Int= 0 D2E= 0 Chk= 7 Scr= 1 Normal termination of Gaussian 03 at Tue Feb 20 12:00:01 2007.

Simple Visualization of Geometry after a G03W run

Once a calculation is finished, you can proceed to visualize the geometry and view the output file using GaussView 2.1. Simply use GV to open the *.out file for the computation and a new view window will appear that will show you the structure obtained after minimization. GV has no problem reading *.out files produced by G03 because they are simple text files. You will not be able to visualize MO’s however without the extra steps detailed below.

The visualization of MO’s requires a bit more work for the following reason. We have GaussView 2.1, and this version is not capable of reading the format of the checkpoint files generated by G03W, only those of G98W. The instructions below tell you how to generate a checkpoint file that is compatible with GaussView 2.1.

Generation of a chk file compatible with GaussView 2.1

Gaussian comes with several utilities to enable files to be transferred to different computer architectures. We will use these utilities to achieve our objective. These utilities will run on the PC you are working with.

1. Generate a formatted text file in the G03W Scratch directory

Let's suppose you ran a G03W job from a file called molecule.gjf, and you requested a checkpoint file. Then molecule.chk exists in the Scratch directory. Start G03W again and select the Utilities->Formchk in the menu. A window will open that allows you to browse for checkpoint files. Select the file of interest and hit the “open” button. The utility will start a Command Window, and generate the file “molecule.fch” in the Scratch directory. This file is a formatted checkpoint file. When it’s done, you can quit the Command window.

Do this for as many files as you are interested in visualizing in GaussView 2.1, one by one. When you are finished, you can quit G03W.

2. Move the files to the G98W molecule directory

Using the Windows Explorer (not to be confused with the Internet Explorer), move each of the .fch files from G03W/Scratch to G98W/molecule directory.

3. Convert the .fch files to binary on the G98W molecule directory

Now start the G98W program. G98w.lnk Select the Utilities->Unfchk. A window will open that allows you to browse for .fch files. Select the file of interest and hit the “open” button. The utility will start a Command Window, and generate the file “molecule.chk” in the molecule directory. This file is a binary checkpoint file in G98W format. When it’s done, you can quit the Command window.

Repeat this for each of your .fch files. When you are finished, you can quit G98W.

IV. Visualize the Structure with GaussView/Generate MO pictures

Start GaussView 2.1 on your PC. gview.exe.lnk In the File menu, select Open, choose the file type .chk, and select the checkpoint file of interest in the G98W directories. The structure you selected should be opened in a new View window. You can now examine the geometry, measure bond lengths, angles, and animate vibrational modes, among other things.

MO Visualization:Gaussian does not allow you to choose MO’s to be visualized until a calculation is first completed (unlike Spartan, which does). After your calculation is complete, then the information for computing a visual picture of the MO’s is extracted from the checkpoint file. To visualize orbitals, do the following.

Select the structure of interest in a View window, then select "Surfaces" from the Results menu.

[If the "Surfaces" entry is greyed out, then there is no wavefunction information in the checkpoint file or there is some other problem. Make sure the calculation actually finished! Consult with your instructor if you need assistance.

When you select "Surfaces" a new box will appear called "Cubes and Surfaces". Press the Generate button, to show the "Generate Cube" box. Select the MO you wish to generate from the pull down menu. Finish by pushing the "Apply button on the "Cubes and Surfaces" box. The program will open a new View to display the MO as it performs the calculation.

To generate MO's other than the HOMO and LUMO, select "Other" and indicate the desired MO by its number. The number of occupied (Occ) and virtual (Virt) MO's in the checkpoint file is indicated just below the MO selection button to assist you in the choice.

Repeat the above for as many MO's you wish to generate, save them (as *.cub files) for later printing or viewing.

V. Importing Spartan generated structures

Spartan and GaussView share one common file format, Brookhaven pdb format. Generate your molecule in Spartan and then Save being careful to select the *.pdb format in Spartan. The molecule should be named molecule.pdb.

GaussView can now be used to open the pdb file, and to finish preparing the gjf input file for a Gaussian calculation.