====== 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]]
&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
==== 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.
**** **** ****** ** 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 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.