exercises:2018_ethz_mmm:stm_2018
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exercises:2018_ethz_mmm:stm_2018 [2018/05/10 12:57] – 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> |
+ | In case you do not want to use the quantum-mobile VM, you will need to install the asetk and ProbeParticle packages: | ||
+ | < | ||
+ | git clone https:// | ||
+ | pip install -e asetk | ||
+ | </ | ||
+ | and | ||
+ | < | ||
+ | git clone https:// | ||
+ | cd ProbeParticleModel/ | ||
+ | git checkout dev | ||
+ | </ | ||
+ | |||
+ | </ | ||
+ | download from [[https:// | ||
- | connect to hypatia: | ||
< | < | ||
tar -xvf exercise_10.tar | tar -xvf exercise_10.tar | ||
Line 80: | Line 94: | ||
</ | </ | ||
The program will compute the 4 highest occupied and 4 lowest unoccupied KS orbitals. | The program will compute the 4 highest occupied and 4 lowest unoccupied KS orbitals. | ||
- | visualize | + | Visualize |
Line 108: | Line 122: | ||
Now we can simulate for the same ribbon a nc-AFM image: | Now we can simulate for the same ribbon a nc-AFM image: | ||
<note important> | <note important> | ||
- | Go the the AFM directory of TASK_1 | + | Go the the AFM directory of TASK_1 |
- | copy there the p.xyz file that you have in the STM directory | + | copy there the p.xyz file that you havein |
and execute: | and execute: | ||
Line 131: | Line 145: | ||
The file p.xyz in teh STM directory should look similar to: | The file p.xyz in teh STM directory should look similar to: | ||
< | < | ||
- | 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> | ||
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