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--- exercises:2016_ethz_mmm:simple_stm [2016/05/20 08:08] – [1. Task: Running the job and looking at the orbitals] pshinde
+++ exercises:2016_ethz_mmm:simple_stm [2016/05/30 11:41] – dpasserone
@@ Line 48: / Line 48: @@
 </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 gs 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>
 import matplotlib.pyplot as plt
@@ Line 59: / Line 59: @@
 # Open file
-f = open('energy.dat', 'r')
+f = open('energy_ref.dat', 'r')
 lines = f.readlines()
@@ Line 111: / Line 111: @@
 <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 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>