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--- exercises:2017_ethz_mmm:stm [2017/05/25 11:58] – created dpasserone
+++ exercises:2017_ethz_mmm:stm [2017/05/25 12:25] – dpasserone
@@ Line 18: / Line 18: @@
 and copy there the tar file of the exercise:
 <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>
+</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>
+  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>