exercises:2016_uzh_cmest:basic_electronic_structure
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exercises:2016_uzh_cmest:basic_electronic_structure [2016/09/29 09:16] – [2. Step] tmueller | exercises:2016_uzh_cmest:basic_electronic_structure [2016/09/29 14:50] – [Questions] tmueller | ||
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===== 1. Step: Run the calculation ===== | ===== 1. Step: Run the calculation ===== | ||
- | Run a CP2K calculation with the following (commented) input file: | + | Create a new directory for this exercise and run a CP2K calculation with the following (commented) input file: |
<code - ethene.inp > | <code - ethene.inp > | ||
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===== 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 run: '' | - To run: '' | ||
- | - 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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- Compare the new input file with the one from the [[first_simulation_run|previous exercise]]: which keywords changed? which section is missing, respectively new? Lookup the description of the changed keywords and sections in the [[https:// | - Compare the new input file with the one from the [[first_simulation_run|previous exercise]]: which keywords changed? which section is missing, respectively new? Lookup the description of the changed keywords and sections in the [[https:// | ||
- | - Quickly sketch | + | - From the output: |
- | - What' | + | - Use VMD to identify the shape of the $\pi$ and $\pi^*$ orbitals |
- | - Use VMD to identify the shape and energy | + | |
- | | + | <note tip> |
+ | | ||
+ | - Lookup the molecular orbital diagram of Ethen to identify which MOs and therefore which cube files you need to open. | ||
+ | </ |
exercises/2016_uzh_cmest/basic_electronic_structure.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1