Some of the calculations you will be doing in the latter part of the course are too time and resource consuming for our local workstations. Such calculations are usually performed on large supercomputers, such as NCSA's SGI Altix that you will be using. Your NCSA allocation sheet contains your login_name and password. Connect to this computer using ssh -X login_name@cobalt.ncsa.uiuc.edu.
You will rin a quick test calculation that involves calculation of the vibrational spectrum of formaldehyde. Locate the output file for the formaldehyde optimization job from few weeks ago. Examine that file and copy the optimized geometry ("Final structure in terms of initial Z-matrix:" from the end of the file into a new file. Add the following Gaussian input:
%NProc=32 %Mem=48MW # HF/6-31+G(d,p) Freq MaxDisk=1GW Formaldehyde vibrational analysis at ther HF/6-31+G(d,p) geometry 0 1
Save the file as and transfer it to the supercomputer. On the supercomputer shell, type scp chem226@ccl##.chem.ucsb.edu:/home/chem226/PERM/formaldehyde_HFF.dat . . Jobs on the supercomputer are submitted to queues. To submit your gaussian job, use command qg03. Enter the name of your input file when prompted, and enter 00:01:00 (1 minute) for the wall time. Hit enter to accept the default directory. If all went well, your job should finish in about 30 seconds (but it may wait in the queue for some time. Use ls -l to check if an output file was created.
If you see an output file, examine it with Unix command more formaldehyde_HFF.out. You should see only positive frequencies and converged forces. Then open the structure in MOLDEN: molden formaldehyde_HFF.out Cick on Norm. Mode. button to see the IR spectrum. Click on each of the normal modes in the Molden Frequency Select window to visualize each of the vibrations. Identify the carbonyl stretch.