exercises:2014_ethz_mmm:simple_stm
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exercise:simple_stm [2014/05/09 09:21] – dpasserone | exercises:2014_ethz_mmm:simple_stm [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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We will show how a simple change in the termination (1 vs. 2 Hydrogens) changes the state structure completely. | We will show how a simple change in the termination (1 vs. 2 Hydrogens) changes the state structure completely. | ||
- | {{ :exercise:2rib.jpg? | + | {{ 2rib.jpg? |
<note tip> | <note tip> | ||
You should run these calculations on 16 nodes with '' | You should run these calculations on 16 nodes with '' | ||
- | Copy, as usual, the files from the directory **/ | + | Download, as usual, the files from the media manager: {{exercise_10.2.tar.gz|}}. The 1h.1.5.inp file is **commented**). |
</ | </ | ||
Line 20: | Line 20: | ||
< | < | ||
+ | ! controls the printing of cubes for the generation of STM images. | ||
&STM | &STM | ||
+ | ! set of sample bias | ||
+ | ! negative for occupied states and positive for unoccupied states | ||
BIAS -2.0 -1.0 1.0 2.0 | BIAS -2.0 -1.0 1.0 2.0 | ||
+ | ! orbital symmetry of the tip | ||
+ | ! The change in the tip symmetry can radically alter the contrast of the topographic | ||
+ | ! image due to changes in tip-surface overlap | ||
TH_TORB S | TH_TORB S | ||
&END STM | &END STM | ||
+ | ! print molecular orbitals | ||
& | & | ||
+ | ! 10 occupied orbitals | ||
NHOMO 10 | NHOMO 10 | ||
+ | ! 10 unoccupied orbitals | ||
NLUMO 10 | NLUMO 10 | ||
+ | ! limit the size of cube files | ||
| | ||
| | ||
&END | &END | ||
+ | ! a cube file with eletrostatic potential generated by the total density (electrons+ions). | ||
& | & | ||
&END | &END | ||
&MO | &MO | ||
+ | ! molecular orbitals eigenvalues and molecular ocuupations after each scf | ||
| | ||
+ | ! add the last iteration with description | ||
| | ||
+ | ! printing of eigenvalues of molecular orbitals | ||
| | ||
+ | ! also print occupation of the molecular orbitals | ||
| | ||
&END | &END | ||
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- | <note tip> | + | <note tip> |
+ | Hitting ** ls -ltr ** will allow you to see on the last lines of the screen the most recent files. | ||
+ | </ | ||
- | + | <note important> | |
- | <note important> | + | - Draw the energy level diagram for the two molecules. What is the energy gap in the two cases? What are the differences? |
- | - Look with vmd at the cube files corresponding to the most interesting levels (close to Fermi...). Comment on the distribution of the states.</ | + | - Look with vmd at the cube files corresponding to the most interesting levels (close to Fermi...). Comment on the distribution of the states. |
+ | </ | ||
===== 2. Task: Producing a simple STM image ===== | ===== 2. Task: Producing a simple STM image ===== | ||
Line 60: | Line 78: | ||
< | < | ||
Run the program in the following way: | Run the program in the following way: | ||
- | > stm -c 2h*STM*.cube --isovalues 1E-5 > stm.out | + | $ module load boost/ |
+ | $ module load mkl | ||
+ | $ stm -c 2h*STM*.cube --isovalues 1E-5 > stm.out | ||
</ | </ | ||
The resulting .igor files contain the z profile (in bohr) and may for example be plotted by gnuplot: | The resulting .igor files contain the z profile (in bohr) and may for example be plotted by gnuplot: | ||
+ | < | ||
+ | gnuplot | ||
+ | set pm3d map | ||
+ | set size square | ||
+ | set xrange [...... | ||
+ | set yrange [..... | ||
+ | splot " | ||
+ | </ | ||
+ | |||
+ | Where instead of " | ||
+ | |||
+ | <note important> | ||
+ | - In the output file of cp2k, the program tells you how many states have contributed to each STM image. Discuss the images that you see in the two cases. | ||
+ | - What makes the 1h* case particular with respect to the 2h*? | ||
+ | - Change the isosurface and look at the z-range. Discuss the changes in the range. | ||
+ | - Would you define the differences between 1h and 2h in the STM images as more of structural origin or electronic origin? | ||
+ | </ |
exercises/2014_ethz_mmm/simple_stm.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1