Remote submission to Spartan

You can set up and submit jobs without using the graphic interface.  However, you must be comfortable with running from the command line (e.g., via ssh).

First, create an input file.  This can be prepared in Spartan, or imported from another program (e.g., Hyperchem) and converted to the file input using Babel (format: Spartan).

Next, check the first line of input using a text editor.

 OPT PM3

0 1
 1  -0.681334584  -2.119548712  -1.020234099
 6   0.558184023  -0.387082181  -1.303256706
 6   0.776800296   1.041543294   0.745919314
 6  -0.932289382  -0.815893987   0.704648542
 6  -0.700451699   0.676373287   1.040295355
 6  -0.712075475  -1.037259502  -0.813547461

.....

ENDCART

Several things must be present. There must be a single space at the beginning of the first line. If you want to optimize the geometry, use the OPT keyword, or else a single-point calculation will be performed.  The method is next (SYBYL, MM2, AM1, PM3, HF).   If you are doing an ab initio calculation, the basis set must be specified.   The file shown above has a geometry optimization at the PM3 (semiempirical) level.

You may add keywords to this line as needed; the list of available keywords is in the files in the  "Commonly Used Program Options" under the Help menu, or in the Spartan Manual.

The following line has space for a title if you want.  The third line has the charge and spin multiplicity, and subsequent lines have the atom number and cartesian coordinates.  After the coordinates, the word ENDCART must appear.  (There are additional sections that may be specified, but these are not necessary unless you wish to freeze atoms or do other specialized operations.)

The input file must be in a proper Spartan directory.  If the file _spartan does not yet exist, type

touch _spartan

to create it.

Then, knowing the directory name (I'll use molname), from inside this directory type

spartan -x submit molname &

This calls Spartan, with no graphic interface, tells it to submit the job molname from the input file molname/input.  The ampersand at the end tells the system to run the job in the background, so you can log off and it will keep running.  To check its progress you can read the output file.

To a limit, you can submit several jobs at a time; they go into a job queue and execute in sequence.  Three jobs at a time can run simultaneously, 2 from any one person, and the job queue advances as jobs finish.

Last updated: 12/15/2005