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exercises:2016_uzh_cmest:basic_electronic_structure [2016/09/29 08:52] – [1. Step: Run the calculation] tmuellerexercises:2016_uzh_cmest:basic_electronic_structure [2016/09/29 14:59] – [Questions] tmueller
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 ===== 1. Step: Run the calculation ===== ===== 1. Step: Run the calculation =====
  
-Run a calculation with the following (commented) input file.+Create a new directory for this exercise and run a CP2K calculation with the following (commented) input file:
  
 <code - ethene.inp > <code - ethene.inp >
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         NLUMO 5         NLUMO 5
       &END MO_CUBES       &END MO_CUBES
-      &PDOS                     ! Controls which MOs are included in the pdos-files. 
-         NLUMO 5 
-      &END 
     &END PRINT     &END PRINT
     &POISSON                    ! Solver requested for non periodic calculations     &POISSON                    ! Solver requested for non periodic calculations
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     &CELL     &CELL
       ABC 10 10 10       ABC 10 10 10
-      PERIODIC NONE              ! Non periodic calculations. That's why the POISSON scetion is needed +      PERIODIC NONE              ! Non periodic calculations. That's why the POISSON section is needed 
     &END CELL     &END CELL
     &TOPOLOGY                    ! Section used to center the atomic coordinates in the given box. Useful for big molecules     &TOPOLOGY                    ! Section used to center the atomic coordinates in the given box. Useful for big molecules
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 If the calculation was performed correctly, a number of new files should have been written: If the calculation was performed correctly, a number of new files should have been written:
 <code> <code>
-$ ls *.pdos *.cube +$ ls *.cube 
-ethene-k1-1.pdos  ethene-WFN_00004_1-1_0.cube  ethene-WFN_00006_1-1_0.cube  ethene-WFN_00008_1-1_0.cube  ethene-WFN_00010_1-1_0.cube  ethene-WFN_00012_1-1_0.cube +ethene-WFN_00004_1-1_0.cube  ethene-WFN_00008_1-1_0.cube  ethene-WFN_00012_1-1_0.cube 
-ethene-k2-1.pdos  ethene-WFN_00005_1-1_0.cube  ethene-WFN_00007_1-1_0.cube  ethene-WFN_00009_1-1_0.cube  ethene-WFN_00011_1-1_0.cube  ethene-WFN_00013_1-1_0.cube+ethene-WFN_00005_1-1_0.cube  ethene-WFN_00009_1-1_0.cube  ethene-WFN_00013_1-1_0.cube 
 +ethene-WFN_00006_1-1_0.cube  ethene-WFN_00010_1-1_0.cube 
 +ethene-WFN_00007_1-1_0.cube  ethene-WFN_00011_1-1_0.cube
 </code> </code>
  
-First have a look at the *.pdos files. PDOS stands for Projected Density of States. These files list the energies and occupation of the MOs. Furthermore, they show how the MOs are compose from basis-functions of different atoms (one pdos-file for each atomic kind) and angular momentum (s,p,d). Hence, these numbers always sum up to 1.0. 
  
 ===== 3. Step ===== ===== 3. Step =====
  
-Now look at the *.cube files.  +Each cube-file contains the electronic density of one MO mapped onto a regular 3D-grid. Not all MOs were written to a cube-file, this is controlled by the ''PRINT_MO'' section. Their filenames tell you to which MO a cube-file belongs. For example ''ethene-WFN_00005_1-1_0.cube'' contains the 5th orbital.
-Each cube-file contains the electronic density of one MO mapped onto a regular 3D-grid. Not all MOs were written to a cube-file, this is controlled by the PRINT_MO section. Their filenames tell you to which MO a cube-file belongs. For example ''ethene-WFN_00005_1-1_0.cube'' contains the 5th orbital.+
  
 Use VMD to visualize the cube-files: Use VMD to visualize the cube-files:
-  - To run ''vmd ethene-WFN_00008_1-1_0.cube'' + 
-  - To visualize the molecule (sometimes it's not visible by default):\\    **Graphics > Representations > Draw style > Drawing Method=CPK**+  - To run: ''$ vmd ethene-WFN_00008_1-1_0.cube'' 
 +  - To visualize the molecule (sometimes it's not visible by default):\\ go to **Graphics > Representations > Draw style** and set **Drawing Method** to **CPK**
   - Add a second representation by clicking on **Create Rep**   - Add a second representation by clicking on **Create Rep**
   - In this second representation set **Drawing Method=Isosurfaces** and **Draw=Wireframe**   - In this second representation set **Drawing Method=Isosurfaces** and **Draw=Wireframe**
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 What you get should look similar to this: What you get should look similar to this:
 +
 {{ ethene_pi_orbital.png |}} {{ ethene_pi_orbital.png |}}
  
 ===== Questions ===== ===== Questions =====
-  - Quickly sketch the energy distribution of the MOs. + 
-  - What's the energy of the HOMO, LUMO, and the band-gap? +  - Compare the new input file with the one from the [[first_simulation_run|previous exercise]]: which keywords changed? which section is missing, respectively new? Lookup the description of the changed keywords and sections in the [[https://manual.cp2k.org/|CP2K Manual]] 
-  - Use VMD to identify the shape and energy of the $\pi$ and $\pi^*$ orbitals.  +  - From the output: What are the energies of the Highest Occupied MO (**HOMO**), Lowest Unoccupied MO (**LUMO**), and the band-gap (in electronvolt)? 
-  +  - Use VMD to identify the shape of the $\pi$ and $\pi^*$ orbitals (submit images like the one from above) 
 +  - Repeat the calculation for Propene and find again the **HOMO**, **LUMO** and band-gap energies. 
 + 
 +<note tip> 
 +  - The eigenvalues are given in Hartree (//Eh//) while the band-gap is stated directly in electronvolt 
 +  - Lookup the molecular orbital diagram of Ethen to identify which MOs and therefore which cube files you need to open. 
 +  - Use the [[http://cccbdb.nist.gov/|Computational Chemistry Comparison and Benchmark DataBase]] to lookup the calculated geometry for Propene (CH2CHCH3), use the geometry made using a Hartree-Fock calculation and the ''6-311+G(3df,2pd)'' basis set. 
 +</note>
exercises/2016_uzh_cmest/basic_electronic_structure.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1