31x Lab Manual Essay

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Chemistry Through Practice CHEM 31X Laboratory Manual

Charlie Cox, Ph.D. Marie Russo Fall 2012

Using Gaussian and GaussView at Stanford
Set-up Guide for Chem 31X, COX Gaussian and GaussView are accessible either over the network from your own computer (remotely), or directly in the 24hour Gates Computer Lab (Gates B08). In either case, you will be accessing your Stanford network storage space (so all of your calculations will be accessible wherever you connect). Follow the instructions below, depending on if you are using a PC, Mac, or the Gates Computer Lab. Whichever method you use, be sure to follow the instructions in *First Time Connecting to the Network*.

Connecting to the Network: Mac
Note: It is better to use a wired connection rather than the wireless, which can run slow. To connect using a Mac, you need to make sure X11 is installed (this is the case with most newer Macs). Go to Applications->Utilities and make sure it is there. If not, use your Mac OSX disk to install. To connect, have X11 running in the background, then start a Terminal (also under Applications->Utilities). Type the command “ssh –Y USERNAME@corn.stanford.edu” (without the quotes) and replace USERNAME with your SUNetID. Say ‘yes’ to any requests to continue connecting. The password is your regular SUNetID password. You’re done! Go to *First Time Connecting to the Network*

Connecting to the Network: PC
Note: It is better to use a wired connection rather than the wireless, which can run slow. To connect using a PC, you need two free programs: PuTTY SSH (for connecting to the cluster) and Xming X11 (for graphical programs like GaussView). Penn State has two excellent guides for installing the software. 1) Install PuTTY SSH following this guide: http://gears.aset.psu.edu/hpc/guides/putty/ hostname: corn.stanford.edu username: your SUNETID 2) Install Xming X11 following this guide: http://rcc.its.psu.edu/user_guides/remote_display/xming/ up until the section "Configure X11 Forwarding in SSH Clients," which you already did in #1 You should now be able, with Xming running the background, to run PuTTY SSH and bring up a terminal window asking you for your password to connect to corn. Your password is your SUNetID password. You’re done! Go to *First Time Connecting to the Network*

Connecting to the Network: Direct Access in Gates
The 24-hour Gates Computer Lab (Gates B08), named myth.stanford.edu, are Linux-based computers using the GNOME graphical interface which is very similar to PCs running Windows. Log on using your SUNet ID and password. You can access a terminal window with the toolbar. Important: Never shut down the computers – there are other users connected remotely. You’re done! Go to *First Time Connecting to the Network*

*First Time Connecting to the Network*
Whichever way you connect to the network, the first time you do so, you must make changes to your Stanford network .cshrc file (essentially a settings file). Once you have made this modification, you will be able to run the GaussView or Gaussian program regardless of how you are connected. 1. 2. In a terminal window, type “nano .cshrc” and press enter. This will open the file “.cshrc” in an editor Scroll down to the end of the file (using the down arrow or Ctrl+v), and at the end paste (Ctrl+u) the text below as indicated.

---------copy below this------------#Code added for Gaussian # setenv USE_MESAGL 1 setenv g03root /usr/sweet/apps/gaussian03-e01 source $g03root/g03/bsd/g03.login alias gview '/usr/sweet/bin/gview' alias gv '/usr/sweet/bin/gview' setenv LD_LIBRARY_PATH "${GV_DIR}/lib:${LD_LIBRARY_PATH}" if (! -e /tmp/${USER}) then mkdir /tmp/${USER} endif setenv GAUSS_SCRDIR /tmp/${USER} -----------copy above this-------------3. 4. Exit the editor and save the file (Ctrl-x, followed by yes). Log out of the cluster (exit).

That should be it! Next time you log-on, you can type “gview” or “gv” to load GaussView.

General Linux Commands (Terminal) ls pwd…