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Starting up GaussView on a Mac

Our version of GaussViewM allows the user to do computer visualization of molecules and to set up the parameters for calculations. This version on the Macs is not capable of completing the calculations. The .com files must be transferred to a linux computer which has Gaussian running on it. In the Chemistry Department, our cluster, ted, has Gaussian installed. Members of the Chemistry Department should get an account on our cluster by emailing Margaret Doll.

To install GaussViewM on a Brown-owned Mac or Gaussian on a Brown-owned linux computer, contact Margaret Doll for the distribution cds. Installation instructions for Macs.

The user of GaussViewW or Gaussian agree to acknowledge the use of the software in any papers resulting from work with the software. View the Citation Requirements.

Running GaussViewM

I am assuming in this documentation that the user will be starting up GaussView by clicking on the gview icon on their desktop.

If GaussView was installed exactly per the web instructions, your directory structure would look like:

Your GaussDirRoot would be Gauss3E.01.

Now we are ready to start the program.

Go to Applications -> Gauss3E.01 -> gv where Gauss3E.01 should be changed to the root directory where GaussView was installed. You will see two gview entries. Double click on the gview with an icon in front of it.

If you are going to be using GaussView a lot, you will want to drag the icon to your desktop dock.

If the program starts with the following error message, the Gaussian variables have not been defined for your account. Link to installation notes to set up your variables. After the .login file and my_login files have been created in your home directory, restart GaussView M.

The program will come up with an error indicating that this version of GaussViewM does not contain the executables to do the Gaussian calculations. This is ok.

A title screen will then appear, followed by a grey screen, a blue screen and a helpful hints screen.

To eliminate job execution error message the next time that you startup GaussViewM, go to GaussView on the top menu, then to Preferences. On the lefthand side, chose Job Setup. Click on the second choice - Execute indirectly through script using default command line.

Create your molecule in the grey screen. Transfer it to the blue screen by just dragging it over. Once the molecule is in the blue screen, you can set up the calculations that you want to do on the molecule.

Click on the Calculate tab on the grey screen and set up your calculations.

Save your requests by going to File -> Save. A window requesting where you would like to save your file will appear.

Be sure to move to your home directory or desktop before saving the file.

You will now see your saved results in a file ending with .com.

Double clicking on this .com file will startup GaussView.

We will transfer the .com file to the unix cluster for the calculation.

  1. Open a terminal window by going clicking on Terminal.app in the Utilites folder. Again if you are using Gaussian a lot, you will want to drag the Terminal.app to your desktop dock.

  2. Change in the terminal window to the location of the .com file. If you saved the .com in your home directory, skip this step. I am assuming that you saved the .com in your desktop. In the terminal window, type cd Desktop Following is an example from my computer.

  3. Transfer your .com file(s).
  4. In the terminal window following the example below where you must

    • type the words that appear in bold type as is and
    • substitute words appropriate to your setup for the words that appear in Bold-Italic.
    • Standard and standard italic typed words indicate the system's output.

    sftp youraccount@ted.chem.brown.edu
    Connecting to ted ...
    youraccountname@ted's password: yourpassword
    sftp> put yourfile.com
    Uploading yourfile.com to /home/youraccount/yourfile.com
    yourfile.com 100% ...
    sftp>exit

Next read: Directions for a user on the Chemistry cluster