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—exercises:2014_ethz_mmm:mo_ethene [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 +====== 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 oribital with VMD. 
 +
 + ==== 1. Step ====
 +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]]
 +
 +<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 the printing of the MOs in the output and in the *.cube files
 +      NHOMO 5                   ! Number of HOMOs to be printed (count starts from the highest occupied orbital. -1 = all). Here 5.
 +      NLUMO 5                   ! Number of LUMOs to be printed (count starts from the lowest unoccupied orbital). Here 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                        ! Parametes 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 scetion 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
 +     1    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
 +     4    2    0
 +     0.34883045    0   
 +     &END
 +    &END KIND
 +  &END SUBSYS
 +&END FORCE_EVAL
 +
 +</code>
 +
 +
 + ==== 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. \\
 +The ethene band gap (energy difference between HOMO and LUMO) is also printed. 
 +<code>
 +
 +  **** **** ******  **  PROGRAM STARTED AT               
 + ***** ** ***  *** **   PROGRAM STARTED ON                   
 + **    ****   ******    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>
 +
 +<note important> Note that the eigenvalues are given in Eh , while the Band gap is given in eV. </note>
 +
 +
 + ==== 3. Step ====
 +
 +In addition to the list of eigenvalues ( printed directly in the output file) a series of *.cube files is generated. \\
 +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.)  \\
 +∗.cube files report the structure of a given MO and can be visualized with VMD:
 +
 +  * To run vmd: vmd ethene-WFN_00008_1-1_0.cube
 +  * To visualize the molecule (sometimes the default settings are not visible with VMD in Brutus):\\    Graphics > Representations > Draw style > Drawing Method: CPK
 +  * To visualize the MO structure in VMD:\\    Graphics > Representations > Draw style > Drawing Method: Isosurfaces 
 +  * In  Isosurfaces, set Draw to "Wireframe" (other formats may not be visible with VMD in Brutus)
 +  * 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:
 +{{ 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. 
 +
 +
 +