exercises:2016_ethz_mmm:simple_stm
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exercises:2016_ethz_mmm:simple_stm [2016/05/19 13:27] – [1. Task: Running the job and looking at the orbitals] pshinde | exercises:2016_ethz_mmm:simple_stm [2016/05/30 11:41] – dpasserone | ||
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- | There will be an output file with the unoccupied energy levels and the last " | + | There will a lot of " |
- | To plot the energy level diagram, copy and paste following lines into the python script **eldplot.py**. The file **energy.dat** contains energy eigenvalues (in a.u.) in one column from the output file and from the EIG file. The Fermi energy (**Ef** | + | |
< | < | ||
import matplotlib.pyplot as plt | import matplotlib.pyplot as plt | ||
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# Open file | # Open file | ||
- | f = open('energy.dat', ' | + | f = open('energy_ref.dat', ' |
lines = f.readlines() | lines = f.readlines() | ||
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<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? | - 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 the WFN cube files corresponding to the most interesting levels (close to the Fermi energy). Use command e.g. vmd -e orbitals.vmd 2H-WFN_00094_1-1_0.cube |
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- | The section ** &STM ** shown above produces STM images at different bias (feel free to change), meaning, using the Tersoff-Hamann approximation, | + | The section ** &STM ** shown above produces STM images at different bias voltages |
- | The ** *STM* **cube files are 3D maps of the integrated density of states. Imagine that we have a microscope with a feedback that can keep constant current between tip and sample, by changing the height of the tip on the surface. Since the current is proportional to the density of states, we move the tip on ** isosurfaces ** of our cubefile. | + | The ** *STM* **cube files are 3D maps of the integrated density of states. Imagine that we have a microscope with a feedback that can keep constant current between tip and sample, by changing the height of the tip on the surface. Since the current is proportional to the density of states, we move the tip on ** isosurfaces ** of our cube file. |
- | The program ** stm.py ** allows to extract | + | The program ** stm.py ** allows to extracting |
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- | For more options use command **stm.py -h**. The resulting .dat files contain the z profile (in angstrom) | + | For more options use command **stm.py -h**. The resulting .dat files contain the z-profile (in angstrom). |
- | + | ||
- | < | + | |
- | gnuplot | + | |
- | set pm3d map | + | |
- | set size square | + | |
- | set xrange [...... | + | |
- | set yrange [..... | + | |
- | + | ||
- | splot " | + | |
- | + | ||
- | </ | + | |
- | + | ||
- | Where instead of " | + | |
<note important> | <note important> |
exercises/2016_ethz_mmm/simple_stm.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1