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exercises:2018_uzh_cmest:basic_electronic_structure [2018/09/17 12:52]
exercises:2018_uzh_cmest:basic_electronic_structure [2020/08/21 10:15] (current)
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 +======= Basic electronic structure calculation =======
  
 +In this exercise, you will perform a first basic electronic structure calculation to obtain the molecular orbitals (**MO**s) of Ethene: 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//
 +
 +It is recommended to install and run //VMD// on your local machine. //VMD// can be [[http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD|downloaded free of charge]] after registering with your name and email address. To load and render the ''*.cube'' files on your local //VMD// you first have to transfer them from the server to your machine by using one of the transfer tools recommended on the [[exercises:2017_uzh_cmest:login|First Login]] page.
 +===== 1. Step: Run the calculation =====
 +
 +Create a new directory for this exercise and run a CP2K calculation with the following (commented) input file (look at the [[exercises:2017_uzh_cmest:first_simulation_run|first exercise again to figure out how to run a simulation]]):
 +
 +<code - ethene.inp >
 +&GLOBAL
 +  PROJECT ethene
 +  RUN_TYPE ENERGY
 +  PRINT_LEVEL MEDIUM
 +&END GLOBAL
 +
 +&FORCE_EVAL
 +  METHOD Quickstep              ! Electronic structure method (DFT,...)
 +  &DFT
 +    &PRINT
 +      &MO_CUBES                 ! Controls which MOs are written to cube-files.
 +        NHOMO 5
 +        NLUMO 5
 +      &END MO_CUBES
 +    &END PRINT
 +    &POISSON                    ! Solver requested for non periodic calculations
 +      PERIODIC NONE
 +      PSOLVER  WAVELET          ! Type of solver
 +    &END POISSON
 +    &QS                         ! Parameters needed to set up the Quickstep framework
 +      METHOD GAPW               ! Method: gaussian and augmented plane waves 
 +    &END QS
 +
 +    &SCF                        ! Parameters controlling the convergence of the scf. This section should not be changed. 
 +      MAX_ITER_LUMOS 10000
 +      EPS_SCF 1.0E-6
 +      SCF_GUESS ATOMIC
 +      MAX_SCF 60
 +      EPS_LUMOS  0.000001
 +      &OUTER_SCF
 +        EPS_SCF 1.0E-6
 +        MAX_SCF 6
 +      &END
 +    &END SCF
 +
 +    &XC                        ! Parameters needed to compute the electronic exchange potential 
 +      &XC_FUNCTIONAL NONE      ! No xc functional
 +      &END XC_FUNCTIONAL
 +      &HF                      ! Hartree Fock exchange. In this case is 100% (no fraction specified).   
 +        &SCREENING             ! Screening of the electronic repulsion up to the given threshold.               
 +          EPS_SCHWARZ 1.0E-10  ! Threshold specification
 +        &END SCREENING
 +      &END HF
 +    &END XC
 +  &END DFT
 +
 +  &SUBSYS
 +    &CELL
 +      ABC 10 10 10
 +      PERIODIC NONE              ! Non-periodic calculations. That's why the POISSON section is needed 
 +    &END CELL
 +    &TOPOLOGY                    ! Section used to center the atomic coordinates in the given box. Useful for big molecules
 +      &CENTER_COORDINATES
 +      &END
 +    &END
 +    &COORD
 +    C         -2.15324        3.98235        0.00126
 +    C         -0.83403        4.16252       -0.00140
 +    H         -0.25355        3.95641        0.89185
 +    H         -0.33362        4.51626       -0.89682
 +    H         -2.65364        3.62861        0.89669
 +    H         -2.73371        4.18846       -0.89198
 +    &END COORD
 +    &KIND H                    ! Basis set and potential for H
 +     &BASIS
 +  2
 +  1  0  0  3  1
 +         18.73113700          0.03349460
 +          2.82539370          0.23472695
 +          0.64012170          0.81375733
 +  1  0  0  1  1
 +          0.16127780          1.00000000
 +     &END
 +     POTENTIAL ALL
 +     &POTENTIAL
 +        0    0
 +     0.20000000    0
 +     &END
 +    &END KIND
 +    &KIND C                    ! Basis set and potential for C
 +     &BASIS
 +  4
 +  1  0  0  6  1
 +       3047.52490000          0.00183470
 +        457.36951000          0.01403730
 +        103.94869000          0.06884260
 +         29.21015500          0.23218440
 +          9.28666300          0.46794130
 +          3.16392700          0.36231200
 +  1  0  1  3  1  1
 +          7.86827240         -0.11933240          0.06899910
 +          1.88128850         -0.16085420          0.31642400
 +          0.54424930          1.14345640          0.74430830
 +  1  0  1  1  1  1
 +          0.16871440          1.00000000          1.00000000
 +  1  2  2  1  1
 +          0.80000000          1.00000000
 +     &END
 +     POTENTIAL ALL
 +     &POTENTIAL
 +        2    0
 +     0.34883045    0   
 +     &END
 +    &END KIND
 +  &END SUBSYS
 +&END FORCE_EVAL
 +</code>
 +
 +
 +===== 2. Step =====
 +
 +If the calculation was performed correctly, a number of new files should have been written:
 +<code>
 +$ ls *.cube
 +ethene-WFN_00004_1-1_0.cube  ethene-WFN_00008_1-1_0.cube  ethene-WFN_00012_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>
 +
 +
 +===== 3. Step =====
 +
 +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:
 +
 +  - Open one ''.cube'' file at a time in //VMD//
 +  - 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**
 +  - In this second representation set **Drawing Method=Isosurfaces** and **Draw=Wireframe**
 +  - Finally set the **Isovalue** of to a reasonable value, eg. 0.1 .
 +  - 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 .
 +  - To give the two representations different colors, set their **Coloring Method=ColorID** and choose different ids.
 +
 +What you get should look similar to this:
 +
 +{{ ethene_pi_orbital.png |}}
 +
 +===== Questions =====
 +
 +  - 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]]
 +  - 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 optimized using a Hartree-Fock calculation and the ''6-311+G(3df,2pd)'' basis set.
 +</note>
exercises/2018_uzh_cmest/basic_electronic_structure.txt ยท Last modified: 2020/08/21 10:15 (external edit)