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--- how_to_prepare_the_new_tip_and_sample_for_stm_simulations [2009/11/25 14:26]
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+++ how_to_prepare_the_new_tip_and_sample_for_stm_simulations [2011/02/18 13:13]
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- \\
-==== I. The geometry ====
-First of all we need the “*.bas” file of the tip and sample geometry
-(separately). We can use the Jmol to view the “*.xyz” file. Tip should have tip
-apex at 0.0 0.0 xy position.
-We have even to prepare the “Fdata” of given properties of elements of tip
-and sample we will use.
-For followings we should run the fireball to relax these structures. If you
-are using new FIREBALL input format, set up followings at the “fireball.in” file:
-__&OPTION__ part
-‐ basisfile = <filename> \\
-‐ lvsfile = <filename> \\
-‐ kptpreference = <filename> \\
-‐ nstepf = 1 \\
-Than you have the “CHARGES” of both the systems tip and sample
- \\
-==== II. The files we need ====
-We need several files before we can simulate the STM scanning for both
-tip and sample. For sample it is “Atomo_i” and "struc.inp files", hopping file
-“tip_sample_i_j.inp” (“interaction_i_j.dat”), “tip_e_str.inp” and “tip_g_str.inp” with
-the densities and geometry of the tip.
- \\
-=== II.I. Atomo_i, struc.inp ===
-Once we have the “CHARGES” we can produce the "Atomo_i" files by the
-FIREBALL. “CHARGES” file has to be at the same directory when you are running
-the FIREBALL. To the “fireball.in” we will write:
-__&OPTION__ part
-‐ nstepf = 1 \\
-‐ ifixcharge = 1 \\
-__&OUTPUT__ part
-‐ iwrtatom = 1
-Than you obtained “Atomo_i” files and the “struc.inp” file, which should be
-modified to work properly when you run the STM simulation. How to do that:
-The “struc.inp” file contains some information about the sample:
-                                 !number. of atoms in unit cell \\
-                                 !initial and final atom which is contributing to the tunneling current \\
-                                ! number maximum of neighbours \\
-//!! you have to modify this upper part//
-.000000 0.000000 0.000000 1      ! coordinates and type of each atom \\
-. \\
-. \\
-. \\
-//!! Next part (up to the lattice vectors) must be added// \\
-                                 !number of orbitals in each type of atom (in a row) \\
-                                 !number of shells of each atom type (in a row) \\
-1                               !l of each shell type atom=1 (each atom type in a row) \\
-                                !nkprl: no. of k's in one row (nk=nkprl2), =0 read a samplek.kpts file \\
-1                               !index_cell1, index_cell2 (ncell = (2*index_cell1+1)*(2*index_cell1+1) \\
-.866025 , 0.5 , 0.               !Horizontal lattice vector (x‐axis) \\
-.866025 , ‐0.5 , 0.              !Horizontal lattice vector (y‐axis) \\
-//!! We have to delete the last row of Lattice vector//
-The fixing the "nkprl" value to 0 and using the fireball k-points (with the
-opposite to complete the Brouilloin) is strongly reccomended.
-The "index_cell1" and "index_cell2" are relative to the number of cells we
-need in each direction x and y to avoid the border problems. The product of them
-gives us number of repetition unit which influence is involved to the
-computation.
- \\
-=== II.II. tip_sample_i_j.inp file ===
-In our approximation, we use a dimer formed by one kind of atom from
-the tip and another kind from the sample. We have to generate a
-"tip_sample_i_j.inp" (or "interaction_i_j.dat") for each pair of kinds. As we want
-interactions for bigger distances than we have in a crystal relaxation, we need to
-generate these wave-functions by the **BEGIN** with a cut‐off radius of about 10‐15 au.
-When we have the wave‐functions we generate the interactions (Fdata) with
-**CREATE**. After that, we run with **FIREBALL** the dimer, mentioned before, for
-several distances (normally from 2 au to 20 or 30 au). To obtain the hoppings in
-the STM format we need (“fireball.in”):
-__&OPTION__ part \\
-‐ ifixcharges = 1 \\
-‐ nstepf = 1
-__&OUTPUT__ part \\
-‐ iwrthop = 1
-To do this, we can use the script “run_hops.com” which is necessary to
-modify in dependence what output format you expect (read the “README” file of
-this script).
-The “run_hops.com” script:
-#!/bin/bash
-#mv -f interactions.dat interactions.dat.old
-echo 1 > lockfile
-tipo1="`cat lista`"
-for i in $tipo1; do
-tipo2="`cat lockfile`"
-if [ $tipo2 == "2" ]; then
-echo 1 > lockfile
-name2="`echo $i`";
-sed "s/AAAAAAA/$name2/g" tip_sample_aux >>
-interactions.dat;
-echo $i
-else
-echo 2 > lockfile
-name1="`echo $i`";
-sed "s/AAAAAAA/$name1/g" model.bas > tmp.bas;
-./fireball.k.x > out_tmp;
-fi
-done
-cat header.dat > interaction_X_Y.dat
-cat interactions.dat >> interaction_X_Y.dat
-rm -f lockfile
-rm -f inter_aux.dat
-rm -f tip_sample_aux
-The “README” file:
-************a short description how to generate hopping data
-files we need:
-fireball.in
-model.bas
-lista
-header.dat
-=======A. edit:
-CHARGES
-model.bas
-=======B. edit run_hops.com
-if you need the fireball output format, than to the
-interactions.dat you have to write
-the inter_aux.dat
-if you need the STM code output format, than to the
-interactions.dat you have to write
-the tip_sample_aux
-*****The difference is amount of some writen informations at
-the header of interaction (hopping) file,*****
-*****number of interactions and even the length units. For
-STM format it is a.u. when for the fireball*****
-*****format it is Angstroms.
-*****
-=======C. launch
-./run_hop.com
-=======D. modify header of interacti_X_Y.dat file
-***************** Interactions for W(spd)-C(sp) using
-FIREBALL program *******
-!number of distances
-.00000 30.00000 !dist_min dist_max
-!number of interactions
-in the case you choose the STM output format, don't forget
-to remove duplicate (symmetric) interactions
-from the interactions_X_Y.inp file. You have to write there
-even the line of 3 more numbers (2 3 10)
-which gives us the number of the shells of the tip and
-sample respectively.
-***************** Interactions for W(spd)-C(sp) using
-FIREBALL program *******
-!number of distances
-.00000 30.00000 !dist_min dist_max
-3 10 !number of shells of the tip, of the
-sample, number of interactions
-If we put the hoppings for all the distances in a file, we will have the basis
-for the tip_sample_i_j.inp (or interaction_i_j.dat) files (see the example in the STM
-code). Then we have to complete the file with the parameters for the long
-distances approximation. See the header:
-* Interactions for W‐Tid using FIREBALL program *
-.000000 30.00000
-3 14
-0 0 ‐21.0000 1.0000 0.5738 1 1 14.5000
-1 0 95.0000 1.0000 0.5738 1 1 16.5000
-….
-where 57 is the number of distance steps, from 2 au to 30 ua. 3 and 3 are
-the number of shells for each kind of atom on the tip and the sample respectively.
-is the total number of interactions for each distance. Finally, the 14 next rows
-are related with the long‐range approximation. 0,0,0 means orbital s (0)in the tip
-and orbital s (0) in the sample and a interaction sigma (0). Orbitals p will be 1
-and d 2, the interaction pi will be 1 and delta 2.
-For long distances, we do the parallel planes approximation using
-the expression: . The A (4th value in the row) is the independent value we
-have to find. α (5th value) depends on the orbitals you have in the hoppings, the
-expression used is: α=l1+l2+1, but sometimes it could be changed depending on
-the fix conditions. Finally, the W (6th) is related with the work function of the
-materials in the hopping: where ω’s are the work function for
-each kind of atom. There is no function as BEGIN or CREATE to calculate these
-long‐distance parameters, but there is a tool in the XEO program made by Daniel
-Gonzalez. Here you have to change by hand the values of A till you “see” (with the
-eyes) a coincidence in the value and the derivative. Finally, let’s mention that the
-th and 8th values in the row are related with the simple basis or double basis
-case. When you have a double basis you need an extra parameter to differentiate
-from the simple basis orbital. The last value is the cut‐off radius.
-II.III. tip_g_str.inp
-Last thing which we have to do is to write the “tip_g_str.inp” file. This file
-contains the geometrical structure of the tip. The xyz atom coordinates should be
-written there at the same order as we used for the “tip_e_str.inp” file, with the
-apex atom at first position. The file could looks like this:
-5 ! natoms_tip_contributing, natoms_tip
-.000000 0.000000 0.400000 1 9 ! x, y, z, atomic type, # of orbitals
-.590800 1.590800 1.590800 1 9 ! x, y, z, atomic type, # of orbitals
-.590800 ‐1.59080 1.59080 1 9 ! x, y, z, atomic type, # of orbitals
-‐1.590800 1.59080 1.59080 1 9 ! x, y, z, atomic type, # of orbitals
-‐1.590800 ‐1.59080 1.59080 1 9 ! x, y, z, atomic type, # of orbitals
-! number of shells in each type of atom
-1 2 ! l for each shell in atom type=1
-‐2.0 4.0 81 ! energy initial, range and steps in dos file

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