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exercises:2015_ethz_mmm:mo_ethene [2015/04/17 09:34]
oschuett
exercises:2015_ethz_mmm:mo_ethene [2015/04/17 15:36]
oschuett
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-====== Molecular orbitals of Ethene ====== +======= Molecular orbitals of Ethene ​======= 
-In this exercise, you will perform an electronic structure calculation to obtain the ethene molecular orbitals (MOs). If performed correctly, your calculations will produce a list of occupied and non occupied MOs and a series of *.cube files, that allow the visualization of the orbitals ​with VMD. +In this exercise, you will perform an electronic structure calculation to obtain the ethene molecular orbitals (MOs). If performed correctly, your calculations will produce a list of occupied and non occupied MOs and a series of *.cube files, that allow the visualization of the oribital ​with VMD. 
  
- ==== 1. Step ====+===== 1. Step: Run the calculation =====
 Run a calculation with the following (commented) input file. \\ Run a calculation with the following (commented) input file. \\
 Note that the file contains explicit basis sets and potential for all-electron calculations. An explanation of the basis set formats is given here: [[basis_sets|Basis Sets]] Note that the file contains explicit basis sets and potential for all-electron calculations. An explanation of the basis set formats is given here: [[basis_sets|Basis Sets]]
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   &DFT   &DFT
     &PRINT     &PRINT
-      &​MO_CUBES ​                ! Controls ​the printing of the MOs in the output and in the *.cube files +      &​MO_CUBES ​                ! Controls ​which MOs are written to cube-files. 
-      NHOMO 5                   ! Number of HOMOs to be printed (count starts from the highest occupied orbital. -1 = all). Here 5. +        NHOMO 5 
-      NLUMO 5                   ! Number of LUMOs to be printed (count starts from the lowest unoccupied orbital). Here 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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   &END SUBSYS   &END SUBSYS
 &END FORCE_EVAL &END FORCE_EVAL
- 
 </​code>​ </​code>​
  
  
- ==== 2. Step ====+===== 2. Step =====
  
-If the calculation was performed correctly, a list of ALL the occupied MOs and 3 (as specified in the input) unoccupied MOs eigenvalues are printed in the output. \\ +If the calculation was performed correctly, a number ​of new files should have been written:
-The ethene band gap (energy difference between HOMO and LUMO) is also printed. ​+
 <​code>​ <​code>​
- +$ ls *.pdos *.cube 
-  ​**** **** ****** ​ **  PROGRAM STARTED AT                +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 
- ***** ** ***  *** **   ​PROGRAM STARTED ON                    +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
- ​** ​   ****   ​****** ​   PROGRAM STARTED BY                                +
- ***** **    ** ** **   ​PROGRAM PROCESS ID                                  +
-  **** **  ******* ​ **  PROGRAM STARTED IN                     +
- +
-..... +
-  Eigenvalues of the occupied subspace spin            1 +
- ​--------------------------------------------- +
-list of eigenvalues +
-.... +
- +
-  Lowest Eigenvalues of the unoccupied subspace spin            1 +
- ----------------------------------------------------- +
-list of eigenvalues +
-..... +
- +
- HOMO - LUMO gap [eV] :    +
-...... +
- +
- +
-  **** **** ****** ​ **  PROGRAM ENDED AT                  +
- ***** ** ***  *** **   ​PROGRAM RAN ON                        +
- ​** ​   ****   ​****** ​   PROGRAM RAN BY                                   +
- ***** **    ** ** **   ​PROGRAM PROCESS ID                                  +
-  **** **  ******* ​ **  PROGRAM STOPPED IN                    +
 </​code>​ </​code>​
  
-<note important>​ Note that the eigenvalues are given in Eh while the Band gap is given in eV</​note>​+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. Furthermorethey 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 =====
  
- ==== 3Step ====+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.
  
-In addition ​to the list of eigenvalues ( printed directly in the output file) a series of *.cube files is generated. \\ +Use VMD to visualize ​the cube-files: 
-The number of cubes strictly depends on what you have specified in the PRINT_MO section. No extra files are generated (while in the output a default list of all the occupied MOs eigenvalues is anyway produced.) ​ \\ +  ​To run ''​vmd ethene-WFN_00008_1-1_0.cube''​ 
-∗.cube files report the structure of a given MO and can be visualized with VMD: +  ​To visualize the molecule (sometimes ​it'​s ​not visible ​by default):\\    ​**Graphics > Representations > Draw style > Drawing Method=CPK** 
- +  ​- Add a second representation by clicking on **Create Rep** 
-  ​To run vmd: vmd ethene-WFN_00008_1-1_0.cube +  - In this second representation set **Drawing Method=Isosurfaces** and **Draw=Wireframe** 
-  ​To visualize the molecule (sometimes ​the default settings are not visible ​with VMD in Brutus):\\    Graphics > Representations > Draw style > Drawing MethodCPK +  ​- Finally ​set the **Isovalue** of to a reasonable value, eg. 0.1 . 
-  * To visualize the MO structure in VMD:​\\ ​   Graphics > Representations > Draw style > Drawing MethodIsosurfaces ​ +  ​To visualize the positive and the negative part of an orbital simultaneously, ​you will have to add a third representation with a negative **Isovalue**,​ e.g. -0.1 . 
-  ​In  Isosurfaces,​ set Draw to "Wireframe" (other formats may not be visible with VMD in Brutus) +  ​To give the two representations different colors, set their **Coloring Method=ColorID** and choose different ids.
-  ​* In Isosurfaces, ​set Isovalue to 0.1, 0.01 ..+
-  ​To visualize the positive and the negative part of an orbital simultaneously,​ add a second isosurface ​representation with isovalues ​-0.1, -0.01, ..+
-  ​To give the two representations different colors, set their "Coloring Method" to "ColorID" ​and choose different ids.+
  
 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 ==== 
- 
-- Quickly sketch the energy distribution for the occupied MOs and the  five unoccupied MOs. \\ 
-- By using VMD, identify the shape and energy of the π and π* orbitals. ​ 
- 
  
 +===== Questions =====
 +  - Quickly sketch the energy distribution of the MOs.
 +  - What's the energy of the HOMO, LUMO, and the band-gap?
 +  - Use VMD to identify the shape and energy of the $\pi$ and $\pi^*$ orbitals. ​
   ​   ​
- 
exercises/2015_ethz_mmm/mo_ethene.txt · Last modified: 2015/04/17 15:36 by oschuett