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--- exercises:2017_uzh_cmest:phonon_calculation [2017/10/31 17:23] – [Using Phonopy] tmueller
+++ exercises:2017_uzh_cmest:phonon_calculation [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 11: / Line 11: @@
 <code bash>
 pip install --user https://github.com/atztogo/phonopy/archive/develop.zip
+# plus some tools required to handle CP2K input files:
+pip install --user cp2k_tools
 </code>
@@ Line 16: / Line 18: @@
 <code bash>
-echo 'export PATH="${HOME}/.local/bin:${PATH}"' >> .bashrc
+echo 'export PATH="${HOME}/.local/bin:${PATH}"' >> ~/.bashrc
 </code>
@@ Line 114: / Line 116: @@
    &END SUBSYS
-  &PRINT
-      &FORCES
-        FILENAME forces
-      &END FORCES
-   &END PRINT
 &END FORCE_EVAL
 </code>
@@ Line 128: / Line 124: @@
 phonopy --cp2k -c Si.inp -d --dim="2 2 2"
 </code>
+which should give you the following additional files:
+<code>
+$ ls
+disp.yaml  phonopy_disp.yaml  Si.inp  supercell-001.inp  supercell.inp
+</code>
+''supercell.inp'' is a skeleton with only the newly generated supercell, but without the displacement, while ''supercell-001.inp'' also contains the displacement of one Silicon atom and is therefore the calculation we need to run.
+You therefore have to extend ''supercell-001.inp'' with the rest of the missing calculation parameters from the original input file ''Si.inp''. Also make sure that you change project name to ''Si-supercell-001''.
+After running CP2K, you should get the following output file in addition to the usual CP2K output: ''Si-supercell-001-forces-1_0.xyz''.
+Now run Phonopy on this output file to generate the force set (afterwards found in a file called ''FORCE_SETS''):
+<code bash>
+phonopy --cp2k -f Si-supercell-001-forces-1_0.xyz
+</code>
+... and run Phonopy again to get the band structure:
+<code bash>
+phonopy --cp2k -c Si.inp -p --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --band="1/2 1/2 1/2 0 0 0 1/2 0 1/2"
+</code>
+This command is supposed to open a window with the plot on your local machine. But this works only if you have setup the X11-Forwarding as described at the beginning of the lecture. Should this not work, then your best chance is to install the ''phonopy'' and ''cp2k-tools'' package on your local machine and run the last command on your local machine after having transferred all files in the current project folder to your local machine. Phonopy does not call CP2K directly so CP2K does not have to be installed.
+Compare the generated plot to plots usually found in literature. Which special points have been specified in the above command? Change them to plot the path $\Gamma-X-K-\Gamma-L$ instead.
+<note tip>Use [[https://www.sciencedirect.com/science/article/pii/S0927025610002697|this paper]] again to get the coordinates of special points in the reciprocal space.</note>