The Jaguar Input File: A quick primer

Here's a quick primer of the Jaguar input file. More details, including all the keywords, can be found in the Jaguar manual which is located in my directory.
~jkua/manuals/j60_user_manual.pdf

All Jaguar input files have the suffix .in

The input file must have at least two sections (gen, zmat). Each section is delimited with &'s in the following way:
&gen
general info here
&
&zmat
geometry info here
&

The gen section contains keywords to run your Jaguar job. For example,
&gen
dftname=b3lyp    [Use the density functional theory (DFT) method with the B3LYP flavour]
igeopt=1               [Do a geometry optimization]
maxit=99              [Set the max number of SCF iterations for converging the wavefunction to 99]
maxitg=99            [Set the max number of geometry iterations to 99]
basis=6-311+g*  [Use the 6-311+g* basis set]
ip11=2                  [List bond distances, angles, dihedrals in the output file]
icfit=1                    [Calculate and list electrostatic potential charges in the output file]
&

The zmat section contains the geometry of your molecule either in Z-matrix form or in Cartesian form. The Z-matrix form gives you exact geometric control when building your molecule. It's fairly easy to use for small molecules but much harder for larger molecules. Cartesian coordinates are generated by most molecule-building programs such as Spartan. You can do this from ST383 following these instructions. An example for the water molecule in both forms are:

&zmat
O
H1  O  0.964
H2  O  0.964  H1  107.0
&

&zmat
O1  0.0000  0.0000  0.0000
H1  0.0000  0.7747  0.5088
H2  0.0000 -0.7747  0.5088
&

If you are calculating a reaction energy curve and need to set constraints, you can do it by adding a coord section.

When your calculation is completed, Jaguar generates a file with the suffix .01.in
This file will contain the same gen section, and if you did a geometry optimization, the zmat section will have the new geometry. The file will also contain two other sections: the converged wavefunction (guess section) and the Hessian matrix (hess section). This file is sometimes also called the "restart" file because you can now use it as a starting point for other calculations.