exercises:2018_ethz_mmm:stm_2018
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exercises:2018_ethz_mmm:stm_2018 [2018/05/10 12:32] – dpasserone | exercises:2018_ethz_mmm:stm_2018 [2018/05/10 17:22] – dpasserone | ||
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=====Simulation of STM and AFM images for two short graphene nanoribbons with different chemical termination===== | =====Simulation of STM and AFM images for two short graphene nanoribbons with different chemical termination===== | ||
- | download from the tar file exercise_10.tar, | + | <note warning> |
- | <note important> | + | In case you do not want to use the quantum-mobile VM, you will need to install the asetk and ProbeParticle packages: |
- | connect to hypatia: | + | < |
+ | git clone https:// | ||
+ | pip install -e asetk | ||
+ | </ | ||
+ | and | ||
+ | < | ||
+ | git clone https:// | ||
+ | cd ProbeParticleModel/ | ||
+ | git checkout dev | ||
+ | </ | ||
+ | |||
+ | </ | ||
+ | download from [[https:// | ||
+ | |||
< | < | ||
tar -xvf exercise_10.tar | tar -xvf exercise_10.tar | ||
Line 68: | Line 82: | ||
- | Now go to the STM directory andsubmit the run script | + | Now go to the directorySTM |
< | < | ||
- | qsub run | + | cd STM |
</ | </ | ||
- | The program will compute | + | and have a look to the input file cp2k.inp used to converge the |
- | You can produce a contour plot of each orbital on a plane ~2A above the ribbon running a pyhton script: | + | wavefunction of the system |
+ | Execute | ||
< | < | ||
- | ./plotorbitals.sc | + | cd STM |
+ | ./run | ||
</ | </ | ||
- | I will also show you how to visualize | + | The program |
+ | Visualize | ||
+ | |||
- | To obtain | + | To obtain |
into a single cube file: | into a single cube file: | ||
< | < | ||
- | qsub run_sumbias | + | ./run_sumbias |
</ | </ | ||
you will then obtain a cube file for each desired bias voltage (see the script run_sumbias) | you will then obtain a cube file for each desired bias voltage (see the script run_sumbias) | ||
- | Now you can compuyte | + | Now you can compute |
< | < | ||
- | qsub run_stm | + | ./run_stm |
</ | </ | ||
Please note that we are simulating a molecule, we do not include the electrons of the substrate | Please note that we are simulating a molecule, we do not include the electrons of the substrate | ||
- | thus we have a disceret | + | thus we have a discrete |
- | that fall in the HOMO-LUMO gap we will obtain an empty image | + | |
- | Now we can simulate for teh same ribbon a AFM image: | + | <note warning> |
- | Go the the AFM directory of TASK_1 | + | why some of the STM images look empty? |
- | copy there the p.xyz file that you find in the STM directory | + | </ |
+ | </ | ||
+ | |||
+ | Now we can simulate for the same ribbon a nc-AFM image: | ||
+ | <note important> | ||
+ | Go the the AFM directory of TASK_1 | ||
+ | copy there the p.xyz file that you havein | ||
and execute: | and execute: | ||
Line 107: | Line 130: | ||
</ | </ | ||
It will take ~ 5 minutes, then you will find a dir containing the AFM simulated image. | It will take ~ 5 minutes, then you will find a dir containing the AFM simulated image. | ||
+ | </ | ||
===TASK_2=== | ===TASK_2=== | ||
- | Repeat | + | Modify the geometry of TASK_1 removing one H atom from each C-H2 at the termini of the ribbon (remove two H atoms in total). |
+ | Create the corresponding mol.xyz and all.xyz files, optimize the geometry, compute STM and nc-AFM images | ||
+ | repeating | ||
<note warning> | <note warning> | ||
- | Be carefulhere | + | Be careful: here we do a spin polarised |
we have to distinguish the three C atoms of one terminus of the ribbon from the | 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. | + | three of the opposite terminus calling them C1 and C2. For these atoms |
+ | we will define a guess electronic configuration with spin up on one side and spin down on the opposite side. | ||
+ | This is achieved defining a occupation unbalance in the alpha and beta orbitals (try to identify this section of the input | ||
+ | and note that the calculation is performed for a spin multiplicity of 1) | ||
- | When the file p.xyz is created | + | The file p.xyz in teh STM directory should look similar |
- | 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 | + | |
- | | + | i = 49, E = -140.2738100175 |
- | | + | |
- | | + | H 4.2778729017 |
- | C1 | + | |
- | | + | C |
- | C2 56.3619529363 | + | . |
- | C2 56.3601930737 | + | . |
- | | + | . |
- | H | + | C1 5.3788157746 |
+ | . | ||
+ | . | ||
+ | C1 | ||
+ | . | ||
+ | . | ||
+ | C1 5.3792136407 | ||
+ | . | ||
+ | . | ||
+ | . | ||
+ | C2 21.1530397078 | ||
+ | . | ||
+ | C2 21.1385072480 | ||
+ | . | ||
+ | C2 21.1533012965 | ||
+ | . | ||
+ | . | ||
+ | | ||
</ | </ | ||
</ | </ | ||
+ | <note important> | ||
+ | Look at the KS orbitals (especially HOMO and LUMO) for both spin UP and DOWN | ||
+ | </ | ||
<note important> | <note important> | ||
Notice the difference between the images in TASK_2 and the images in TASK_1 | 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. | 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 | These states are suppressed by the addiitonal H atoms in TASK_1 | ||
+ | </ | ||
+ | <note important> | ||
+ | why some STM images are remarkably asymmetric? Is this correct? | ||
</ | </ | ||
exercises/2018_ethz_mmm/stm_2018.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1