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input_parameters [2017/05/05 14:38] krejcio |
input_parameters [2017/05/05 15:38] (current) |
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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 PP. | ||
+ | |||
+ | **px=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //px// orbital on the PP. | ||
+ | |||
+ | **py=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //py// orbital on the PP. | ||
+ | |||
+ | **pz=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //pz// orbital on the PP. | ||
+ | |||
+ | **dxz=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //dxz// orbital on the PP. | ||
+ | |||
+ | **dyz=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //dyz// orbital on the PP. | ||
+ | |||
+ | **dz2=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //dz2// orbital on the PP. | ||
+ | |||
+ | === dI/dV with tilting orbitals (as PP relaxes) === | ||
+ | |||
+ | **__dIdV_tilt( V, WF, eta ,eig, R, R0, Rat, coes, orbs='sp', pz=0.0, pxy =0.0, dz2=0.0, dxyz=0.0, len_R=4.0, al=1.0)__** | ||
+ | |||
+ | # **V-coes**: no change | ||
+ | |||
+ | **orbs='sp'** # only 'sp' works here | ||
+ | |||
+ | **pz=0.0** # <0.0,1.0> -- contribution to the tunneling to/from tilting //pz// orbital on the PP. | ||
+ | |||
+ | **pxy=0.0** # <0.0,1.0> -- contribution to the tunneling to/from tilting //px// and //py// orbitals on the PP. | ||
+ | |||
+ | **dz2=0.0** # <0.0,1.0> -- contribution to the tunneling to/from //dz2// orbital on the PP. | ||
+ | |||
+ | **dxyz=0.0** # <0.0,1.0> -- contribution to the tunneling to/from tilting //dxz// and //dyz// orbitals on the PP. | ||
+ | |||
+ | **len_R=4.0** # length of the PP-tip "bond"; 4 Å is an standard length in PPAFM calculations | ||
+ | |||
+ | **al=1.0** # (0.0,2.0> -- rescalling constants of the tilting; 1.0 -- tilts with the same angle as the PP; 2.0 -- tilts twice as fast; 0.5 -- tilts twice as slow. | ||
+ | |||
+ | === STM (no tilting of orbitals) === | ||
+ | |||
+ | **__STM( V, nV, 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, WF_decay=1.0)__** | ||
+ | |||
+ | # note: everything the same as dI/dV except for: | ||
+ | |||
+ | **nV** # number of dI/dV steps - should be approx. V/eta +1 ; STM is rectangular integrated from the dI/dV; | ||
+ | |||
+ | **WF_decay=1.0** # How the Workfunction (barrier and therefore tunneling decay) is changing with increasing/decreasing voltage for each dI/dV step; 1.0 -- the change of the tunneling decay scales with the voltage (at V=1.0 is WF=4.0 eV); 0.0 -- no change with the voltage. | ||
+ | |||
+ | |||
+ | === IETS (no tilting of orbitals) === | ||
+ | |||
+ | **//__UNDER DEVELOPMENT__//** |