exercises:2015_ethz_mmm:surface_au
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exercises:2015_ethz_mmm:surface_au [2015/03/06 02:37] – dpasserone | exercises:2015_ethz_mmm:surface_au [2015/03/19 22:18] – yakutovich | ||
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Take the above table as reference for the orders of magnitude of surface energies. | Take the above table as reference for the orders of magnitude of surface energies. | ||
- | You can download the ** commented ** | + | |
+ | <code bash> | ||
+ | you@eulerX ~$ wget http://www.cp2k.org/ | ||
+ | you@eulerX ~$ unzip exercises: | ||
+ | you@eulerX ~$ cd exercise_3.2 | ||
+ | </ | ||
In principle all reconstructed phases should be with a lower surface energy, but this EAM potential fails for some of them. | In principle all reconstructed phases should be with a lower surface energy, but this EAM potential fails for some of them. | ||
The input files are: | The input files are: | ||
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- 111.inp for the unreconstructed (111). | - 111.inp for the unreconstructed (111). | ||
- | Before, however, to be able to run the cp2k program, we need to build the **xyz** files for all cases. | + | Before, however, to be able to run the cp2k program, we need to build the **xyz** files for all cases. |
First, we build the slabs, using this chain of commands (**First assignment**). | First, we build the slabs, using this chain of commands (**First assignment**). | ||
Use for the following: | Use for the following: | ||
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</ | </ | ||
+ | <note important> | ||
+ | Substitute the LX LY LZ (but **ADD SOME VACUUM IN THE Z DIRECTION**) in the **ABC** section of the *inp files. | ||
+ | Check with vmd that the cell is ok. | ||
Run the cp2k code as | Run the cp2k code as | ||
- | < | + | < |
- | you@eulerxx $ cp2k.popt -i 100_unr.inp | + | you@eulerxx $ bsub cp2k.popt -i 100_unr.inp |
- | you@eulerxx $ cp2k.popt -i 110_unr.inp | + | you@eulerxx $ bsub cp2k.popt -i 110_unr.inp |
- | you@eulerxx $ cp2k.popt -i 111_unr.inp | + | you@eulerxx $ bsub cp2k.popt -i 111_unr.inp |
</ | </ | ||
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- | < | + | < |
- | you@eulerxx $ cp2k.popt -i 100_rec.inp | + | you@eulerxx $ bsub cp2k.popt -i 100_rec.inp |
- | you@eulerxx $ cp2k.popt -i 110_rec.inp | + | you@eulerxx $ bsub cp2k.popt -i 110_rec.inp |
</ | </ | ||
+ | <note tip> | ||
Assignments: | Assignments: | ||
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- Try to color the surfaces in vmd in a way that makes the height evident (ask the assistant) and produce snapshots (render) | - Try to color the surfaces in vmd in a way that makes the height evident (ask the assistant) and produce snapshots (render) | ||
- Comment on the (2x1) reconstruction: | - Comment on the (2x1) reconstruction: | ||
- | - Copy the 100_unr.xyz into a new file 110_my_rec.xyz | + | - Copy the 110_unr.xyz into a new file 110_my_rec.xyz |
- Edit the file and remove one line each two on the two surfaces | - Edit the file and remove one line each two on the two surfaces | ||
- Check that the result is the same as in 110_rec.xyz | - Check that the result is the same as in 110_rec.xyz | ||
- Plot the same slabs, but adding periodic images in vmd: remember pbc set { a b c 90 90 90 }. | - Plot the same slabs, but adding periodic images in vmd: remember pbc set { a b c 90 90 90 }. | ||
- | + | </ | |
- | < | + | < |
exercises/2015_ethz_mmm/surface_au.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1