The atomic Section of the Jaguar Input File

The atomic section allows you to specify data for different atoms in a molecule. The data can include basis sets for each atom, or atomic masses for isotope calculations. You can also use the atomic section to define groups of atoms called “fragments”, where each fragment can then be converted to dummy atoms or counterpoise atoms or used to define a part of the system for which you want to compute a numerical Hessian. Restart files may include atomic sections as well, in order to keep information about charge fitting or other properties calculated previously.

In addition, atomic sections can be used to supply information about transition-metal-containing systems that is used to generate high-quality initial guesses for these systems. See Initial Guess Orbitals for Molecules Containing Transition Metals for more information on using atomic sections in this manner.