input_parameters
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input_parameters [2017/05/05 14:38] krejcio |
input_parameters [2017/05/05 15:08] krejcio |
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| - | === Reading parameters === | + | ===== 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. | **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. | ||
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| **lower_atoms=[]** # normally doesn't do anything; In special cases -- in the molecule are elements with rather different barrier for tunneling (like an elements with very low or high electronegativity and therefore charged in the molecule) -- some of the atoms needs to have different tunneling 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 tunneling. | **lower_atoms=[]** # normally doesn't do anything; In special cases -- in the molecule are elements with rather different barrier for tunneling (like an elements with very low or high electronegativity and therefore charged in the molecule) -- some of the atoms needs to have different tunneling 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 tunneling. | ||
| - | **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 tunneling by factor of two and only one quarter of tunneling is taken into account for atom 3 and 4 in the **lower_atoms** list | + | **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 tunneling by factor of two and only one quarter of tunneling is taken into account for atom 3 and 4 in the **lower_atoms** list. |
| # note: So far this was used only for a TOAT molecule where oxygens have they rescaling constants (lowering coefficients) set to 0.5. | # note: So far this was used only for a TOAT molecule where oxygens have they rescaling constants (lowering coefficients) set to 0.5. | ||
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| # note2: Since //d//-orbitals have a faster decay, than //s// and //p// orbitals, then all tunelling 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. | # note2: Since //d//-orbitals have a faster decay, than //s// and //p// orbitals, then all tunelling 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. | ||
| + | ===== Running parameters ===== | ||
| + | |||
| + | === dI/dV (no tilting of orbitals) === | ||
| + | |||
| + | **__dIdV( V, WF, eta ,eig, R, Rat, coes, orbs='sp', s=0.0, px =0.0, py=0.0, pz=0.0, dxz=0.0, dyz=0.0, dz2=0.0)__** | ||
| + | |||
| + | **V** # applied sample bias = (energy vs. the Fermi Level in eV). | ||
| + | |||
| + | **WF** # the Work-function (normally ~5 eV gives reasonable results). | ||
| + | |||
| + | **eta** # Width of the Lorentzian function for energy smearing deppending on system it can reach various values: for single molecular orbital very low number -- 1e-6 eV; For standard slabs -- 0.05-0.1 eV; For low layered or small slabs -- 0.3-0.5 eV. | ||
| + | |||
| + | **eig** # eigenenergies of sample states (=molecular orbitals) (given by 1st output of 3 of the reading procedure). | ||
| + | |||
| + | **R** #input of points in which you calculate dI/dV (relaxed via PP-AFM -- you need to have linked PPAFM part and GridUtils of PPAFM to get them; or nonrelaxed via ReadSTM.mkSpaceGrid). | ||
| + | |||
| + | **Rat** # position of atoms of the sample (given by 3rdt output of 3 of the reading procedure). | ||
| + | |||
| + | **coes** # LCAO coefficients (given by 2nd output of 3 of the reading procedure). | ||
| + | |||
| + | **orbs='sp'** # the same as in Reading parameters | ||
| + | |||
| + | **s=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //s// orbital on the tip. | ||
| + | |||
| + | **px=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //px// orbital on the tip. | ||
| + | |||
| + | **py=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //py// orbital on the tip. | ||
| + | |||
| + | **pz=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //pz// orbital on the tip. | ||
| + | |||
| + | **dxz=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //dxz// orbital on the tip. | ||
| + | |||
| + | **dyz=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //dyz// orbital on the tip. | ||
| + | |||
| + | **dz2=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //dz2// orbital on the tip. | ||
input_parameters.txt · Last modified: 2017/05/05 15:38 (external edit)
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