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exercises:2016_ethz_mmm:simple_stm [2016/02/03 09:54] – external edit 127.0.0.1exercises:2016_ethz_mmm:simple_stm [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 </code> </code>
  
-There will be an output file with the unoccupied energy levels and the last "**EIG**" file with occupied energy levels. +There will a lot of "**EIG**" files, but only the last ("**EIG-1_0.MOLog**") file is of use for the energy level diagram plotting. Remove the other "**EIG**" files by using the command "** rm *EIG-1_0_*.MOLog**". To plot the energy level diagram, extract the energies from the eigenvalues file, and copy them (single column) into a file with the same shape as the provided example **energy_ref.dat**. Copy and paste following lines into the python script **eldplot.py**. The file **energy_ref.dat** contains the energy eigenvalues (in a.u.) in one column from the last "**EIG**" file (you can also use two names for the two molecules). The Fermi energy (**Ef** [a.u], is the energy of the highest occupied level) must be entered in the **eldplot.py** script. Use the command **python eldplot.py** to get the energy level diagram as a png image. (use display command to visualize it). Identify the occupied and unoccupied energy levels and name them. Feel free to change the png image name.
-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** in a.u., is the energy of the highest occupied value) must be entered in the **eldplot.py** script. Use the command **python eldplot.py** to get the energy level diagram as a postscript image. (use gs to visualize it). Identify the occupied and unoccupied energy levels and name them. Feel free to change the png image names.+
 <code> <code>
 import matplotlib.pyplot as plt import matplotlib.pyplot as plt
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 # Open file # Open file
  
-f = open('energy.dat', 'r')+f = open('energy_ref.dat', 'r')
  
 lines = f.readlines() lines = f.readlines()
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 # save plot in a eps file # save plot in a eps file
-plt.savefig('ELD.eps')+plt.savefig('ELD.png')
  
 </code> </code>
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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 Comment on the distribution of the states.
 </note> </note>
  
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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, it integrates all the density of states with energies between Fermi energy and the Bias potential: this energy interval is involved in the tunnel current.  +The section ** &STM ** shown above produces STM images at different bias voltages (feel free to change), meaning, using the Tersoff-Hamann approximation, it integrates all the density of states with energies between Fermi energy and the bias voltage: this energy interval is involved in the tunnel current.  
-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 a 2D map of the height of a given isosurface.+The program ** stm.py ** allows to extracting a 2D map of the height of a given isosurface.
  
 <code> <code>
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 </code>  </code> 
  
-For more options use command **stm.py -h**. The resulting .dat files contain the z profile (in angstrom) and may for example be plotted by gnuplot: +For more options use command **stm.py -h**. The resulting .dat files contain the z-profile (in angstrom).
- +
-<code> +
-gnuplot +
-set pm3d map +
-set size square +
-set xrange [...... +
-set yrange [..... +
- +
-splot "mystm.dat" matrix using 2:1:3 +
- +
-</code>  +
- +
-Where instead of "mystm" you use an appropriate filename. +
  
 <note important>  <note important> 
exercises/2016_ethz_mmm/simple_stm.1454493256.txt.gz · Last modified: 2020/08/21 10:15 (external edit)