# Open SourceMolecular Dynamics

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exercises:2016_ethz_mmm:surface_au

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 exercises:2016_ethz_mmm:surface_au [2016/03/11 10:28]yakutovich exercises:2016_ethz_mmm:surface_au [2016/03/11 10:58]yakutovich Both sides previous revision Previous revision 2016/03/11 11:02 yakutovich 2016/03/11 10:58 yakutovich 2016/03/11 10:28 yakutovich 2016/03/10 09:52 yakutovich 2016/03/09 22:55 yakutovich 2016/02/03 09:54 external edit 2016/03/11 11:02 yakutovich 2016/03/11 10:58 yakutovich 2016/03/11 10:28 yakutovich 2016/03/10 09:52 yakutovich 2016/03/09 22:55 yakutovich 2016/02/03 09:54 external edit Last revision Both sides next revision Line 50: Line 50: you@eulerxx $m_lattice LX LY LZ NX NY NZ < 111.unit | m_xyzrescale D | m_xyzrefold 1 1 1 | m_xyzcenter 1 1 1 | m_xyzsort ​ > 111_unr.xyz you@eulerxx$ 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 ​ > 111_unr.xyz ​ + + + 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. ​For the bulk case, simply copy 100_unr.xyz into 100_bulk.xyz​For the bulk case, simply copy 100_unr.xyz into 100_bulk.xyz​ - 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 Line 60: Line 62: 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: the 110_rec.xyz and the 100_rec.xyz. For this calculations you will need to use the same unit cell parameters as for the corresponding unreconstracted surface structures that you have built previously.