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exercises:2017_ethz_mmm:stm [2017/05/25 11:59]
dpasserone
exercises:2017_ethz_mmm:stm [2017/05/25 12:27] (current)
dpasserone
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 and copy there the tar file of the exercise: and copy there the tar file of the exercise:
 <​code>​ <​code>​
-cp /home/cpi/exercise_11.tar ./ +cp /home/cpi/exercise_12.tar ./ 
-tar -xvf exercise_11.tar +tar -xvf exercise_12.tar 
-cd exercise_11+cd exercise_12
 </​code>​ </​code>​
-</note important>​+</note> 
 + 
 +We consider two possible chemical terminations for a finite size 7-AGNR. 
 +In TASK_1 the ribbon is terminated with a C-H2 bonding while in TASK_2 the termination is C-H 
 +The additional H atom present at the termini of the ribbon of TASK_1 will suppress the spin polarized 
 +edge states that are evident in the ribbon of TASK_2 
 + 
 + 
 +===TASK_1=== 
 +Have a look to the cp2k input file cp2k.inp 
 +used to obtain quickly the optimized geometry of a ribbon adsorbed on a Au substrate. 
 +The ribbon is modelled within DFTB (similar to tight binding) while the substrate is modelled 
 +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>​ 
 +submit the geometry optimization run 
 +<​code>​ 
 +qsub run 
 +</​code>​ 
 + 
 +After completion of the optimization you should extract the final coordinates of the molecule 
 +and copy them in the STM directory to compute the KS orbitals and to ocmpute the STM images 
 +you can extract the coordinates running the following script: 
 +<​code>​ 
 +./pos.sc 
 +</​code>​ 
 +</​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.1495713555.txt.gz · Last modified: 2017/05/25 11:59 by dpasserone