exercises:2018_uzh_cmest:basic_electronic_structure

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 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 First Login page.

Create a new directory for this exercise and run a CP2K calculation with the following (commented) input file (look at the first exercise again to figure out how to run a simulation):

- 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 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

If the calculation was performed correctly, a number of new files should have been written:

$ 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

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:

- Compare the new input file with the one from the previous exercise: which keywords changed? which section is missing, respectively new? Lookup the description of the changed keywords and sections in the 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.

- 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 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.

exercises/2018_uzh_cmest/basic_electronic_structure.txt · Last modified: 2020/08/21 10:15 (external edit)

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