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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__//​**
input_parameters.1493987937.txt.gz · Last modified: 2017/05/05 14:38 (external edit)