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exercises:2014_ethz_mmm:mo_ethene

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Molecular orbitals of Benzene

In this exercise, you will perform an electronic structure calculation to obtain the benzene 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

benzene.inp
&GLOBAL
  PROJECT benzene
  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 3                   ! Number of HOMOs to be printed (count starts from the highest occupied orbital. -1 = all). Here 3.
      NLUMO 3                   ! Number of LUMOs to be printed (count starts from the lowest unoccupied orbital). Here 3. 
      &END MO_CUBES            
    &END PRINT
    &POISSON                    ! Solver requested for non periodic calculations
      PERIODIC NONE
      PSOLVER  MT               ! 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 5000
      EPS_SCF 1.0E-6
      SCF_GUESS ATOMIC
      MAX_SCF 60
      EPS_LUMOS  0.0001
      &OUTER_SCF
        EPS_SCF 1.0E-6
        MAX_SCF 6
      &END
      &OT
          PRECONDITIONER FULL_ALL
          ENERGY_GAP 0.1
      &END OT
    &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     5.000000     6.382700     5.000000
C     6.197400     5.691300     5.000000
C     6.197400     4.308700     5.000000
C     5.000000     3.617300     5.000000
C     3.802600     4.308700     5.000000
C     3.802600     5.691300     5.000000
H     5.000000     7.456100     5.000000
H     7.127000     6.228000     5.000000
H     7.127000     3.772000     5.000000
H     5.000000     2.543900     5.000000
H     2.873000     3.772000     5.000000
H     2.873000     6.228000     5.000000
    &END COORD
    &KIND H                                  !Potential and basis sets for H
      &BASIS
  6
  1  0  0  4  1
         75.42300000          0.00240650
         11.35000000          0.01848700
          2.59930000          0.08974200
          0.73513000          0.28111000
  1  0  0  1  1
          0.23167000          1.00000000
  1  0  0  1  1
          0.07414700          1.00000000
  1  1  1  1  1
          1.60000000          1.00000000
  1  1  1  1  1
          0.45000000          1.00000000
  1  2  2  1  1
          1.25000000          1.00000000
      &END
      POTENTIAL ALL
      &POTENTIAL
          1    0    0
          0.20 0
      &END
    &END KIND
    &KIND C                                    !Potential and basis sets for C             
      &BASIS
  9
  1  0  0  8  2
       7857.10000000          0.00056825          0.00000000
       1178.70000000          0.00439150         -0.00000059
        268.32000000          0.02250400         -0.00006275
         75.94800000          0.08665300         -0.00075773
         24.55900000          0.24405000         -0.00733080
          8.62120000          0.44148000         -0.03893200
          3.12780000          0.35332000         -0.08890800
          0.82202000          0.00000000          0.21689000
  1  0  0  1  1
          0.33017000          1.00000000
  1  0  0  1  1
          0.11463000          1.00000000
  1  1  1  4  1
         33.77500000          0.00602940
          7.67660000          0.04322800
          2.23570000          0.16301000
          0.76447000          0.36504000
  1  1  1  1  1
          0.26232000          1.00000000
  1  1  1  1  1
          0.08463800          1.00000000
  1  2  2  1  1
          1.40000000          1.00000000
  1  2  2  1  1
          0.45000000          1.00000000
  1  3  3  1  1
          0.95000000          1.00000000
      &END
      POTENTIAL ALL
      &POTENTIAL
         4    2    0
         0.34883045    0
      &END
    &END KIND

  &END SUBSYS
&END FORCE_EVAL
this calculation can be fairly expensive, a run on multiple nodes is reccomended.

To run on multiple nodes:

bsub  -n 16 mpirun cp2k.popt -i benzene -o benz.out

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 benzene band gap (energy difference between HOMO and LUMO) is also printed.

  **** **** ******  **  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                   
Note that the eigenvalues are given in Eh , while the Band gap is given in eV.

3. Step

In addition to the list of eigenvalues ( printed directly in the output file) a series of *.cube files are generated.
The number and typology of cubes 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 benzene-WFN_00021_1-1_0.cube
  • To visualize the MO structure in VMD : Graphics > Representations > Draw style > Drawing Method: Isosurfaces
  • In Isosurfaces, set Isovalue to 0.1, 0.01 …

Questions

Quickly sketch the energy distribution for the 21 occupied MOs and the three unoccupied MOs.

exercises/2014_ethz_mmm/mo_ethene.1395817635.txt.gz · Last modified: 2020/08/21 10:14 (external edit)