Tips and Tricks for Working with SPARTAN

Submitting a Job from the Command Line

SPARTAN jobs can be run from the command line, either directly at the console or over a telnet connection. Create the input file in the usual way within Builder, select your options for surfaces, properties, etc., save the file, and close SPARTAN. Then, from within the molecule directory so created, or in the directory immediately above it, enter in a shell window:

spartan -x <molecule_name>

where <molecule_name> is the name of the molecule and hence its directory.

Restarting a SPARTAN job

If a SPARTAN job has failed by running out of cycles, or other reason not connected with loss of system power, it can be restarted by using vi or jot to add the following keywords to the first line of the input file:

guess=read hess=arch

Then resubmit the job from the command line, as above.

If a power failure has occurred, the molecule directory should contain a file named 'fort.12', which actually is the archive file for the last cycle completed before the power failure. Rename 'fort.12' to 'archive'.

A file called '_inuse' should also be in the molecule directory. This is a tag file that tells SPARTAN a calculation is in progress. Normally, it is removed automatically by SPARTAN when a calculation finishes. In the event of a power failure, you will need to remove it "by hand".

Finally, use the graphical interface to open the molecule file. The geometry will be the latest from the calculation. Select the appropriate setup dialog, and click the 'wavefunction' and 'Hessian' buttons. If the calculation being restarted is a single point frequency calculation (the only kind of single point calculation that can be restarted), add the keyword 'RESTART' to the keyword box (after the FREQ). You also may need to add the 'ACCEPT' keyword to instruct SPARTAN to ignore differences in symmetry between the displayed structure and the archive file. Click save, and submit the calculation.

Suspending a Calculation

A calculation can be suspended, for later resumption, as follows. Find out the process id (pid) for the job by finding it in the output list from the

ps -ef or top -d 5

commands. Then issue the command:

kill -STOP <pid>

where <pid> is the numerical process id of the calculation. To resume, use the command:

kill -CONT <pid>

and calculation should pick up from the most recent completed cycle.

Obtaining High-Quality Print Images

First, select high-resolution graphics when you set up your calculations of surfaces, rather than the default medium resolution.

Now click the Spartan icon in the top left of the window. Choose Print Setup from the menu, and then Print to File. Provide a name for the file.

• Create the display you want, with the size and orientation you prefer.

• Then select Print from the File menu; a jpeg image of the window will be created in the active directory

• FTP the image file to your PC and print it or embed it in a Windows file.

How Can I Make Spartan Print the Total Energy in Semi-Empirical Output ?

Damn the crappy Spartan manual. The manual for the old version is much better. When you set up the semi-empirical calculation, type in the box at the bottom of the pop up form: PRINTLEV=2.

You will automatically get a more verbose output, including the electronic energy, the core repulsions, and the total energy, all in hartrees.