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--- exercises:2016_ethz_mmm:surface_au [2016/03/09 22:55] – yakutovich
+++ exercises:2016_ethz_mmm:surface_au [2016/03/11 11:02] – yakutovich
@@ Line 1: / Line 1: @@
 ====== 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:
-{{:exercises:2016_ethz_mmm:lect2_surf.001.jpg?nolink&400|}}
+you@eulerX ~$ module load courses mmm vmd
+you@eulerX ~$ mmm-init
+</note>
-----
-{{:exercises:2016_ethz_mmm:lect2_surf.002.jpg?400|}}
+In this exercise, we will build three small slabs based on the following figures; the cell is an **orthorombic** cell with repetition along z.
-----
-{{:exercises:2016_ethz_mmm:lect2_surf.003.jpg?400|}}
+{{ :exercises:2016_ethz_mmm:fcc_surf_2.png?1000 |}}
 Figure out what is (in nearest neighbor units) the length of the three vectors Lx, Ly, Lz for the three high-symmetry surfaces.
@@ 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
 </code>
+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>For the bulk case, simply copy 100_unr.xyz into 100_bulk.xyz</note>
-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
@@ Line 60: / Line 62: @@
 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 100_bulk.inp -o 100_bulk.out
 </code>
 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 given in the 100_rec.xyz and 110_rec.xyz files. 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.