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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 [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ 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.
+{{:exercises:2015_ethz_mmm:lect2_surf.001.jpg?nolink&400|}}
+----
+{{:exercises:2015_ethz_mmm:lect2_surf.002.jpg?400|}}
+----
+{{:exercises:2015_ethz_mmm:lect2_surf.003.jpg?400|}}
+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?direct |}}
 Take the above table as reference for the orders of magnitude of surface energies.
-You can download the ** commented **  inputs by downloading from the wiki: {{exercise_3.2.zip|exercise_3.2.zip}}) the necessary files for computing the surface energies of all 3 high symmetry faces of gold.
+  * 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>
+you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_3.2.zip
+you@eulerX ~$ unzip exercises:2015_ethz_mmm:exercise_3.2.zip
+you@eulerX ~$ cd exercise_3.2
+</code>
 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:
@@ Line 14: / Line 33: @@
   - 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 = ????????  ????????  1.4142135 ; NX NY NZ = 4 5 5
+  - (110) surface: use (in first neighbor units) LX LY LZ = ????????  ????????  1.0000000 ; NX NY NZ = 6 4 5
+  - (111) surface: use (in first neighbor units) LX LY LZ = ????????  ????????  2.4494897 ; NX NY NZ = 4 3 3
+  - Find the correct values of lx ly for the three cases.
+  - use ** D = 2.885 ** (correct value for gold)
+</note>
+Example:
+<code>
+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  > 100_unr.xyz
+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  > 110_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
+</code>
+<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
+<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
+</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.
+<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
+</code>
+<note tip>
 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)
   - Comment on the (2x1) reconstruction: what do you see?
-  - Plot the same, but adding periodic images in vmd: remember pbc set { a b c 90 90 90 }.
+  - 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
-<note tip>Hint: you can save a configuration file in vmd and reuse it for a new sample! Ask the assistant!</note>
+  - 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 }.
+</note>
+<note important>Hint: you can save a configuration file in vmd and reuse it for a new sample! Ask the assistant!</note>