exercises:2017_ethz_mmm:mo_ethene
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— | exercises:2017_ethz_mmm:mo_ethene [2020/08/21 10:15] (current) – created - 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 the calculation ===== | ||
+ | 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 | ||
+ | |||
+ | & | ||
+ | METHOD Quickstep | ||
+ | &DFT | ||
+ | |||
+ | & | ||
+ | NHOMO 5 | ||
+ | NLUMO 5 | ||
+ | &END MO_CUBES | ||
+ | & | ||
+ | NLUMO 5 | ||
+ | &END | ||
+ | &END PRINT | ||
+ | & | ||
+ | PERIODIC NONE | ||
+ | PSOLVER | ||
+ | &END POISSON | ||
+ | & | ||
+ | METHOD GAPW ! Method: gaussian and augmented plane waves | ||
+ | &END QS | ||
+ | |||
+ | & | ||
+ | MAX_ITER_LUMOS 10000 | ||
+ | EPS_SCF 1.0E-6 | ||
+ | SCF_GUESS ATOMIC | ||
+ | MAX_SCF 60 | ||
+ | EPS_LUMOS | ||
+ | & | ||
+ | EPS_SCF 1.0E-6 | ||
+ | MAX_SCF 6 | ||
+ | &END | ||
+ | &END SCF | ||
+ | |||
+ | & | ||
+ | & | ||
+ | &END XC_FUNCTIONAL | ||
+ | & | ||
+ | & | ||
+ | EPS_SCHWARZ 1.0E-10 | ||
+ | &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 | ||
+ | & | ||
+ | & | ||
+ | &END | ||
+ | &END | ||
+ | &COORD | ||
+ | C | ||
+ | C | ||
+ | H | ||
+ | H | ||
+ | H | ||
+ | H | ||
+ | &END COORD | ||
+ | &KIND H ! Basis set and potential for H | ||
+ | & | ||
+ | 2 | ||
+ | 1 0 0 3 1 | ||
+ | | ||
+ | 2.82539370 | ||
+ | 0.64012170 | ||
+ | 1 0 0 1 1 | ||
+ | 0.16127780 | ||
+ | & | ||
+ | | ||
+ | & | ||
+ | | ||
+ | | ||
+ | & | ||
+ | &END KIND | ||
+ | &KIND C ! Basis set and potential for C | ||
+ | & | ||
+ | 4 | ||
+ | 1 0 0 6 1 | ||
+ | | ||
+ | 457.36951000 | ||
+ | 103.94869000 | ||
+ | | ||
+ | 9.28666300 | ||
+ | 3.16392700 | ||
+ | 1 0 1 3 1 1 | ||
+ | 7.86827240 | ||
+ | 1.88128850 | ||
+ | 0.54424930 | ||
+ | 1 0 1 1 1 1 | ||
+ | 0.16871440 | ||
+ | 1 2 2 1 1 | ||
+ | 0.80000000 | ||
+ | & | ||
+ | | ||
+ | & | ||
+ | | ||
+ | | ||
+ | & | ||
+ | &END KIND | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | </ | ||
+ | |||
+ | |||
+ | ===== 2. Step ===== | ||
+ | |||
+ | If the calculation was performed correctly, a number of new files should have been written: | ||
+ | < | ||
+ | $ ls *.pdos *.cube | ||
+ | ethene-k1-1.pdos | ||
+ | ethene-k2-1.pdos | ||
+ | </ | ||
+ | |||
+ | First have a look at the *.pdos files. PDOS stands for Projected Density of States. These files list the energies and occupation of the MOs. Furthermore, | ||
+ | |||
+ | ===== 3. Step ===== | ||
+ | |||
+ | Now look at the *.cube files. | ||
+ | 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 '' | ||
+ | |||
+ | Use VMD to visualize the cube-files: | ||
+ | - To run '' | ||
+ | - To visualize the molecule (sometimes it's not visible by default): | ||
+ | - 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, | ||
+ | - 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 ===== | ||
+ | - Quickly sketch the energy distribution of the MOs. | ||
+ | - What's the energy of the HOMO, LUMO, and the band-gap? | ||
+ | - Use VMD to identify the shape and energy of the $\pi$ and $\pi^*$ orbitals. | ||
+ | |
exercises/2017_ethz_mmm/mo_ethene.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1