exercises:2016_uzh_cmest:basic_electronic_structure
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exercises:2016_uzh_cmest:basic_electronic_structure [2016/09/29 08:52] – [1. Step: Run the calculation] tmueller | exercises:2016_uzh_cmest:basic_electronic_structure [2016/09/29 14:58] – [Questions] tmueller | ||
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===== 1. Step: Run the calculation ===== | ===== 1. Step: Run the calculation ===== | ||
- | Run a calculation with the following (commented) input file. | + | Create |
<code - ethene.inp > | <code - ethene.inp > | ||
Line 22: | Line 22: | ||
NLUMO 5 | NLUMO 5 | ||
&END MO_CUBES | &END MO_CUBES | ||
- | & | ||
- | NLUMO 5 | ||
- | &END | ||
&END PRINT | &END PRINT | ||
& | & | ||
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&CELL | &CELL | ||
ABC 10 10 10 | ABC 10 10 10 | ||
- | PERIODIC NONE ! Non periodic calculations. That's why the POISSON | + | PERIODIC NONE ! Non periodic calculations. That's why the POISSON |
&END CELL | &END CELL | ||
& | & | ||
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If the calculation was performed correctly, a number of new files should have been written: | If the calculation was performed correctly, a number of new files should have been written: | ||
< | < | ||
- | $ ls *.pdos | + | $ ls *.cube |
- | ethene-k1-1.pdos | + | ethene-WFN_00004_1-1_0.cube |
- | ethene-k2-1.pdos | + | ethene-WFN_00005_1-1_0.cube |
+ | ethene-WFN_00006_1-1_0.cube | ||
+ | ethene-WFN_00007_1-1_0.cube | ||
</ | </ | ||
- | 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 ===== | ===== 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 '' |
- | 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: | Use VMD to visualize the cube-files: | ||
- | | + | |
- | - To visualize the molecule (sometimes it's not visible by default): | + | |
+ | - To visualize the molecule (sometimes it's not visible by default): | ||
- Add a second representation by clicking on **Create Rep** | - Add a second representation by clicking on **Create Rep** | ||
- In this second representation set **Drawing Method=Isosurfaces** and **Draw=Wireframe** | - In this second representation set **Drawing Method=Isosurfaces** and **Draw=Wireframe** | ||
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What you get should look similar to this: | What you get should look similar to this: | ||
+ | |||
{{ ethene_pi_orbital.png |}} | {{ ethene_pi_orbital.png |}} | ||
===== Questions ===== | ===== Questions ===== | ||
- | | + | |
- | - What' | + | |
- | - Use VMD to identify the shape and energy | + | - From the output: |
- | | + | - Use VMD to identify the shape of the $\pi$ and $\pi^*$ orbitals |
+ | - Run the calculation again for Propene and find again the **HOMO**, **LUMO** and band-gap energies. | ||
+ | |||
+ | <note tip> | ||
+ | | ||
+ | - 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|http:// | ||
+ | </ |
exercises/2016_uzh_cmest/basic_electronic_structure.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1