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 of orbitals is 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. -> important for speeding up the simulations: see the note bellow.

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. -> important for speeding up the simulations: see the note bellow.

• note: For a proper slab (more than 3 layers of substrate, big unit cell approx. >= 15 Å in x and y, since only gamma point can be used now) the cut can be only twice eta (width of the Lorentzian curve 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 - tunnelling 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. -> For this it is important that the top-most atoms are as first in the geometry file, see here how to adjust the DFT input geometry files.

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=[] # normally doesn't do anything; In special cases -- in the molecule are elements with rather different barrier for tunnelling (like an elements with very low or high electronegativity and therefore charged in the molecule) -- some of the atoms needs to have different tunnelling than other. These atoms are named here, but BEWARE python numbering is applied here -- e.g. [0,1,2,3] means that 1st four atoms will have rescaled their tunnelling.

lower_coefs=[] # normally doesn't do anything; Here are written rescaling constants (lowering coefficients) for each atoms named in lower_atoms -- e.g. [0.5,0.5,0.25,0.25] means that 1st two atoms have lowered their contribution to tunnelling by factor of two and only one quarter of tunnelling is taken into account for atom 3 and 4 in the lower_atoms list.

• note: This was used e.g. for a TOAT molecule where oxygens have they rescaling constants (lowering coefficients) set to 0.5.

• note: Since d-orbitals have a faster decay, than s and p orbitals, then all tunnelling contributions from d orbitals are automatically decreased. A constant 0.2 is used -- it equals to a ratio between radial function of valence s and d at 4-7 Å above the atom.