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exercises:2016_ethz_mmm:simple_stm [2016/05/20 08:18]
pshinde [1. Task: Running the job and looking at the orbitals]
exercises:2016_ethz_mmm:simple_stm [2020/08/21 10:15] (current)
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 </code> </code>
  
-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, copy and paste following lines into the python script **eldplot.py**. The file **energy_ref.dat** contains energy eigenvalues (in a.u.) in one column from the last "**EIG**" file. 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 to visualize it). Identify the occupied and unoccupied energy levels and name them. Feel free to change the png image names.+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.
 <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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 <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 the WFN cube files corresponding to the most interesting levels (close to Fermi...). e.g. vmd -e orbitals.vmd 2H-WFN_00094_1-1_0.cube 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>
  
exercises/2016_ethz_mmm/simple_stm.1463732329.txt.gz ยท Last modified: 2020/08/21 10:15 (external edit)