exercises:2015_ethz_mmm:surface_au
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exercises:2015_ethz_mmm:surface_au [2015/02/06 17:49] – external edit 127.0.0.1 | exercises:2015_ethz_mmm:surface_au [2015/03/19 22:18] – yakutovich | ||
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====== Calculation of surface energies of Au ====== | ====== Calculation of surface energies of Au ====== | ||
+ | |||
+ | In this exercise, we will build three small slabs based on the following figures; the cell is an **orthorombic** cell with repetition along z. | ||
+ | |||
+ | {{: | ||
+ | |||
+ | ---- | ||
+ | |||
+ | {{: | ||
+ | |||
+ | ---- | ||
+ | |||
+ | {{: | ||
+ | |||
+ | Figure out what is (in nearest neighbor units) the length of the three vectors Lx, Ly, Lz for the three high-symmetry surfaces. | ||
{{ screen_shot_2014-03-07_at_8.47.53_am.png? | {{ screen_shot_2014-03-07_at_8.47.53_am.png? | ||
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: | ||
Line 14: | Line 33: | ||
- 111.inp for the unreconstructed (111). | - 111.inp for the unreconstructed (111). | ||
- | The compute_surf scripts give an idea how to compute the surface energies. | + | 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**). | ||
+ | Use for the following: | ||
+ | <note important> | ||
+ | - (100) surface: use (in first neighbor units) LX LY LZ = ???????? | ||
+ | - (110) surface: use (in first neighbor units) LX LY LZ = ???????? | ||
+ | - (111) surface: use (in first neighbor units) LX LY LZ = ???????? | ||
+ | - Find the correct values of lx ly for the three cases. | ||
+ | - use ** D = 2.885 ** (correct value for gold) | ||
+ | </ | ||
+ | |||
+ | Example: | ||
+ | < | ||
+ | you@eulerxx $ m_lattice LX LY LZ NX NY NZ < 100.unit | m_xyzrescale D | m_xyzrefold 1 1 1 | m_xyzcenter 1 1 1 | m_xyzsort | ||
+ | you@eulerxx $ m_lattice LX LY LZ NX NY NZ < 110.unit | m_xyzrescale D | m_xyzrefold 1 1 1 | m_xyzcenter 1 1 1 | m_xyzsort | ||
+ | you@eulerxx $ m_lattice LX LY LZ NX NY NZ < 111.unit | m_xyzrescale D | m_xyzrefold 1 1 1 | m_xyzcenter 1 1 1 | m_xyzsort | ||
+ | </ | ||
+ | |||
+ | <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 | ||
+ | |||
+ | <code bash> | ||
+ | you@eulerxx $ bsub cp2k.popt -i 100_unr.inp -o 100_unr.out | ||
+ | you@eulerxx $ bsub cp2k.popt -i 110_unr.inp -o 110_unr.out | ||
+ | you@eulerxx $ bsub cp2k.popt -i 111_unr.inp -o 111_unr.out | ||
+ | </ | ||
+ | |||
+ | The compute_surf* scripts give an idea how to compute the surface energies. | ||
+ | |||
+ | In the next step, we work also with 2 reconstructed surfaces: the 110_rec.xyz and the 100_rec.xyz. | ||
+ | |||
+ | |||
+ | <code bash> | ||
+ | you@eulerxx $ bsub cp2k.popt -i 100_rec.inp -o 100_rec.out | ||
+ | you@eulerxx $ bsub cp2k.popt -i 110_rec.inp -o 110_rec.out | ||
+ | </ | ||
+ | <note tip> | ||
Assignments: | Assignments: | ||
Line 20: | Line 77: | ||
- 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: | ||
- | - Plot the same, but adding periodic images in vmd: remember pbc set { a b c 90 90 90 }. | + | |
- | + | - 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 |
+ | | ||
+ | </ | ||
+ | < |
exercises/2015_ethz_mmm/surface_au.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1