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Simulation of STM and AFM images for two short graphene nanoribbons with different chemical termination
download from the tar file exercise_10.tar, move the file to your exercise directory, and extract the content
tar -xvf exercise_10.tar cd exercise_10
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===
cd 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 the form of C6/R^6 plus a Pauli repulsion term are added to couple the adsorbate/substrate systems.
Two geometry fiels are present: mol.xyz and all.xyz The cp2k program will need both of them.
Have a look at the geometry of the system using ASE or vmd for both all.xyz and mol.xyz:
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()
./run
Have a look at the final geometry optained (you can extract the last frame from the file PROJ-pos-1.xyz) After completion of the optimization you should extract the final coordinates of the molecule (first 80 atoms) and copy them in the STM directory (call them p.xyz) to compute the KS orbitals and to compute the STM images
tail -442 PROJ-pos-1.xyz | head -82 > p.xyz mv p.xyz STM
Now go to the directorySTM
cd STM
and have a look to the input file cp2k.inp used to converge the wavefunction of the system and to plot the cube files for the KS orbitals. Execute the program
cd STM ./run
The program will compute the 4 highest occupied and 4 lowest unoccupied KS orbitals. 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:
./run_sumbias
you will then obtain a cube file for each desired bias voltage (see the script run_sumbias)
Now you can compute a constant current STM image running the script
./run_stm
Please note that we are simulating a molecule, we do not include the electrons of the substrate thus we have a discrete spectrum of energies
Now we can simulate for teh same ribbon a nc-AFM image: Go the the AFM directory of TASK_1 copy there the p.xyz file that you have in the STM directory and execute:
./run_PP
It will take ~ 5 minutes, then you will find a dir containing the AFM simulated image.
===TASK_2=== Modify the geometry of TASK_1 removing one H atom from each C-H2 at the termini of the ribbon. Create the corresponding mol.xyz and all.xyz files, optimize the geometry, compute STM and nc-AFM images repeating all the instructions of TASK_1 for the scripts present in the dir TASK_2
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
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