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exercises:2017_ethz_mmm:stm [2017/05/25 12:05]
dpasserone
exercises:2017_ethz_mmm:stm [2017/05/25 12:27] (current)
dpasserone
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 The ribbon is modelled within DFTB (similar to tight binding) while the substrate is modelled The ribbon is modelled within DFTB (similar to tight binding) while the substrate is modelled
 via Embedded Atom Model. via Embedded Atom Model.
 +An empirical potential in teh form of C6/R^6 plus a pauli repulsion
 +is added to couple the adsorbate/​substrate systems.
 +
 +
 +Two geometry fiels are present: mol.xyz and all.xyz
 +The input needs both of them.
 +
 +Have a look at the geometry of the system using ASE:
 +
 +<​code>​
 +ipython
 +In [1]: from ase.io import read
 +
 +In [2]: from ase.visualize import view
 +
 +In [3]: s=read("​all.xyz"​)
 +
 +In [4]: view(s)
 +
 +In [5]: exit()
 +</​code>​
 +
 <note important>​ <note important>​
 submit the geometry optimization run submit the geometry optimization run
Line 45: Line 67:
 you can extract the coordinates running the following script: you can extract the coordinates running the following script:
 <​code>​ <​code>​
-./positions.sc+./pos.sc
 </​code>​ </​code>​
 </​note>​ </​note>​
 +
 +Now go to the STM directory andsubmit the run script
 +<​code>​
 +qsub run
 +</​code>​
 +The program will compute the 10 highest and 10 lowest KS orbitals.
 +You can produce a contour plot of each orbital on a plane ~2A above the ribbon running a pyhton script:
 +
 +<​code>​
 +./​plotorbitals.sc
 +</​code>​
 +I will also show you how to visualize the orbitals with VMD.
 +
 +To obtain teh stm images you have to combine different KS orbitals (depending on the bias voltage applied)
 +into a single cube file:
 +
 +<​code>​
 +qsub run_sumbias
 +</​code>​
 +you will then obtain a cube file for each desired bias voltage (see the script run_sumbias)
 +
 +Now you can compuyte a constant current STM image runnong the script
 +
 +<​code>​
 +qsub run_stm
 +</​code>​
 +
 +Please note that we are simulating a molecule, we do not include the electrons of the substrate
 +thus we have a disceret spectrum of energies and it is quite likely that for  values of the bias voltage
 +that fall in the HOMO-LUMO gap we will obtain an empty image
 +
 +Now we can simulate for teh same ribbon a AFM image:
 +Go the the AFM directory of TASK_1
 +copy there the p.xyz file that you find in the STM directory
 +and execute:
 +
 +<​code>​
 +./run_PP
 +</​code>​
 +It will take ~ 5 minutes, then you will find a dir containing the AFM simulated image.
 +
 +===TASK_2===
 +Repeat all the instructions of TASK_1 for the scripts present in the dir TASK_2
 +<note warning>
 +Be carefulhere we do a spin polarized simulation,
 +we have to distinguish the three C atoms of one terminus of the ribbon from the 
 +three of the opposite terminus calling them C1 and C2.
 +
 +When the file p.xyz is created in the STM dir (after running ./pos.sc)
 +copy it immediateli to the AFM dir.
 +Now, before executing the instructions for the STM dir
 +edit the file p.xyz and modify it in such a way that
 +the first three C atoms will be labelled as C1
 +and the C atoms from 4 to 6 will be labelled as C2
 +<​code>​
 +222
 +   
 +  C1        6.0848407282 ​       7.8280098155 ​      ​21.6125989354
 +  C1        6.0865671686 ​      ​12.7633436664 ​      ​21.6071222309
 +  C1        6.1020007836 ​      ​10.2957686990 ​      ​21.6036624306
 +  C2       ​56.3447906713 ​      ​10.2958157091 ​      ​21.6033852713
 +  C2       ​56.3619529363 ​       7.8280149623 ​      ​21.6128774460
 +  C2       ​56.3601930737 ​      ​12.7634261117 ​      ​21.6063533886
 +  H         ​4.9837063610 ​       7.8327959357 ​      ​21.5912164696
 +  H         ​4.9855872642 ​      ​12.7623732365 ​      ​21.5844580428
 +</​code>​
 +
 +</​note>​
 +
 +<note important>​
 +Notice the difference between the images in TASK_2 and the images in TASK_1
 +In TASK_2 we have KS states localised at the termini of the ribbon.
 +These states are suppressed by the addiitonal H atoms in TASK_1
 +</​note>​
 +
exercises/2017_ethz_mmm/stm.1495713951.txt.gz ยท Last modified: 2017/05/25 12:05 by dpasserone