Let's assume we already obtained fully relaxed atomic and electronic structure of a desired system. To write down Hamiltonian into a file, we will run only one SCF cycle with fixed charges. In addition we need to switch on a flag iwrtatom in section &OUTPUT& in input file fireball in. To ensure this, the input file fireball.in should look like:
&OPTION basisfile = answer.bas nstepf = 1 ifixcharge = 1 &END &OUTPUT iwrtatom = 1 &END
The flag iwrtatom can be set to value 1 or 2. In case iwrtatom = 1 the Hamiltonian is written in Lowdin orthogonal representation, where blocks of Hamiltonian corresponding to each atom and its neighbors are stored to file Atomo_XX, where XX stands for atom number according to list of atoms in *.bas file. If iwrtatom = 2, then the Hamiltonian is written in Atomic Orbital (AO) basis set including the overlap matrix. Again, blocks of Hamiltonian and Overlap matrices corresponding to each atom and its neighbors are written down to file Hamilt_XX and Overlap_XX of given atom XX.
Once the iwratom flag is switched on, dos.optional file is also required. Basically only first line of the file is considered to control, in which units distance will be written (see explanation in the line).
dos.optional
This file defines basic parameters of the DOS calculation.
1.00000 ! ratio of lattice (for fractional coordinates, if xyz are in Angstroms maintain 1.000)
1 60 ! natom_beg,natom_end (initial and final atom for the DOS calculation)
151 ! number of energies (number of energies in the DOS calcuation)
-10.749617402457092 0.10 ! first energy (initial absolute energy (fireball's value is the Fermi Level) and energy step
0 ! 1/0 yes/no write the tip_e_str.inp file for the DOS
-4.00 4.00 ! minimun and maximum energy limit for writing the green function in the tip_e_str.inp file
0.05 ! imaginary part for the green function in the DOS calculation