User Tools

Site Tools


exercises:2017_ethz_mmm:stm

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Next revision
Previous revision
exercises:2017_ethz_mmm:stm [2017/05/25 11:58]
dpasserone created
exercises:2017_ethz_mmm:stm [2017/05/25 12:27] (current)
dpasserone
Line 18: Line 18:
 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>​
 +
 +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.1495713519.txt.gz · Last modified: 2017/05/25 11:58 by dpasserone