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--- exercises:2017_uzh_cmest:phonon_calculation [2017/10/31 17:07] – created tmueller
+++ exercises:2017_uzh_cmest:phonon_calculation [2017/11/08 08:01] – tmueller
@@ 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 32: / Line 34: @@
 ====== Using Phonopy ======
-Phonopy works in 3 stages:
+A typical Phonopy workflow looks as follows:
-  - It takes a CP2K input file containing at least a cell specification plus coordinates for a crystal and generates a number of input file skeletons containing new cell definitions and new coordinates
+  - Phonopy takes a CP2K input file containing at least a cell specification plus coordinates for a crystal and generates a number of input file skeletons containing new cell definitions and new coordinates
   - You have to take these input file skeletons, complete them with the rest of the simulation parameters and run a energy+forces simulation. The input file skeleton will also contain an option for CP2K to write the forces into a separate file
   - Phonopy is then run a second time to parse these forces and generate a so-called force set out of it
   - The third time Phonopy is called, it is used to actually calculate and generate a plot of the phonon band structure for a given path
+====== Phonon band structure for bulk silicon ======
+As a first example we are going to reproduce the text book band structure for bulk silicon.
+Take the following CP2K input file:
+<code cp2k Si.inp>
+&GLOBAL
+   PROJECT Si
+   RUN_TYPE ENERGY_FORCE
+   PRINT_LEVEL MEDIUM
+&END GLOBAL
+&FORCE_EVAL
+   METHOD Quickstep
+   &DFT
+      BASIS_SET_FILE_NAME  BASIS_MOLOPT
+      POTENTIAL_FILE_NAME  POTENTIAL
+      &POISSON
+         PERIODIC XYZ
+      &END POISSON
+      &SCF
+         SCF_GUESS ATOMIC
+         MAX_SCF 300
+         ADDED_MOS 100
+         &DIAGONALIZATION
+            ALGORITHM STANDARD
+            EPS_ADAPT 0.01
+         &END DIAGONALIZATION
+         &SMEAR  ON
+            METHOD FERMI_DIRAC
+            ELECTRONIC_TEMPERATURE [K] 300
+         &END SMEAR
+         &MIXING
+            METHOD BROYDEN_MIXING
+            ALPHA 0.2
+            BETA 1.5
+            NBROYDEN 8
+         &END MIXING
+      &END SCF
+      &XC
+         &XC_FUNCTIONAL PBE
+         &END XC_FUNCTIONAL
+      &END XC
+   &END DFT
+   &SUBSYS
+      &CELL
+         ABC [angstrom] 5.4661639157319968 5.4661639157319968 5.4661639157319968
+         PERIODIC XYZ
+      &END CELL
+      &COORD
+         SCALED
+         Si 0.875  0.875  0.875
+         Si 0.875  0.375  0.375
+         Si 0.375  0.875  0.375
+         Si 0.375  0.375  0.875
+         Si 0.125  0.125  0.125
+         Si 0.125  0.625  0.625
+         Si 0.625  0.125  0.625
+         Si 0.625  0.625  0.125
+      &END COORD
+      &KIND Si
+         ELEMENT Si
+         BASIS_SET DZVP-MOLOPT-GTH
+         POTENTIAL GTH-PBE
+      &END KIND
+   &END SUBSYS
+&END FORCE_EVAL
+</code>
+Now let Phonopy parse the CP2K input file and have it generate a 2x2x2 supercell with one displacement, by running the following command:
+<code bash>
+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>