exercises:2016_ethz_mmm:surface_au
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exercises:2016_ethz_mmm:surface_au [2016/02/03 09:54] – external edit 127.0.0.1 | exercises:2016_ethz_mmm:surface_au [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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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. | + | <note warning> |
+ | TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | ||
- | {{: | + | you@eulerX ~$ module load courses mmm vmd |
+ | |||
+ | you@eulerX ~$ mmm-init | ||
+ | </ | ||
- | ---- | ||
- | {{: | + | 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. | Figure out what is (in nearest neighbor units) the length of the three vectors Lx, Ly, Lz for the three high-symmetry surfaces. | ||
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* Download all the necessary files for computing the surface energies of all 3 high symmetry faces of gold from from the wiki: {{exercise_3.2.zip|exercise_3.2.zip}} (**all inputs are commented**) in your home directory and unzip it: | * Download all the necessary files for computing the surface energies of all 3 high symmetry faces of gold from from the wiki: {{exercise_3.2.zip|exercise_3.2.zip}} (**all inputs are commented**) in your home directory and unzip it: | ||
<code bash> | <code bash> | ||
- | you@eulerX ~$ wget http:// | + | you@eulerX ~$ wget http:// |
- | you@eulerX ~$ unzip exercises:2015_ethz_mmm: | + | you@eulerX ~$ unzip exercises:2016_ethz_mmm: |
you@eulerX ~$ cd exercise_3.2 | you@eulerX ~$ cd exercise_3.2 | ||
</ | </ | ||
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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 | 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 | ||
</ | </ | ||
+ | |||
+ | |||
+ | Substitute the LX LY LZ NX NY NZ and D by their appropriate values. As a result of the command execution you will obtain several slab structures. Open them with a text editor and get the unit cell parameters from the second line of each XYZ file. Use this parameters in the ABC section of the *inp files. Do not forget to **ADD SOME VACUUM IN THE Z DIRECTION**. Check with vmd that the cell is OK. | ||
<note important> | <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 | ||
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you@eulerxx $ bsub cp2k.popt -i 110_unr.inp -o 110_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 | you@eulerxx $ bsub cp2k.popt -i 111_unr.inp -o 111_unr.out | ||
+ | you@eulerxx $ bsub cp2k.popt -i 100_bulk.inp -o 100_bulk.out | ||
</ | </ | ||
The compute_surf* scripts give an idea how to compute the surface energies. | 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. | + | In the next step, we work with 2 reconstructed surfaces |
exercises/2016_ethz_mmm/surface_au.1454493256.txt.gz · Last modified: 2020/08/21 10:15 (external edit)