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Reading parameters
fermi=None # or 0.0 – the Fermi level is taken from the DFT calculations; e.g. -0.5 – the Fermi level is shifted by -0.5 eV.
orbs = 'sp' # s and p orbitals of the sample – calculations approx. 4× faster than 'spd', more tip orbitals allowed (dz2, dxz and dyz) and tilting orbitals are allowed–; 'spd' – works fine for Fireball and FHI-AIMS, GPAW can do mistakes.
pbc=(0,0) # only the original geometry; (0.5,0.5) three more cells are added to the right and behind the original geometry; (1,1) 8 cells are added around the original geometry ; (2,2) 8+16 cells are added around the original geometry …
imaginary = False # do not change, only for possible future development.
cut_min=-15.0 # all molecular orbitals (eigen-states) with their eigen-energies lower than -15.0 eV bellow the Fermi level are excluded from the calculations.
cut_max=5.0 # all molecular orbitals (eigen-states) with their eigen-energies higher than 5.0 eV above the Fermi level are excluded from the calculations.
note - For a proper slab (more than 3 layers of substrate, big unit cell approx. >= 15 Å in x and y) the cut can be only twice eta (width of the Lorentzian used for calcultions) + extreme voltage used for in the dI/dV or STM calculations. For single molecules wider cut, so all important molecular orbitals are in the cut. If there is NO molecular orbital in the reading procedure, than the procedure will stop itself.
cut_at=-1 # all atoms of the substrate are taken into account; 50 - tunneling from only FIRST fifty atoms of the sample are taken into account – normally only the adsorbed molecule and/or the first layer of substrate are important for the calculations.
lvs = None # parameter only when Fireball inputs are read – lattice vector of the cell –, if periodic boundary conditions (PBC) are not stated – pbc=(0,0) – then None is fine;; if PBC are required, then 3×3 python/numpy array containing cell parameters is needed for Fireball input you can get them by e.g. np.loadtxt('input.lvs'); In the case of FHI-AIMS and GPAW this parameter is read automatically.
lower_atoms=[]
lower_coefs=[]
