exercises:2017_uzh_cmest:phonon_calculation
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exercises:2017_uzh_cmest:phonon_calculation [2017/10/31 17:07] – created tmueller | exercises:2017_uzh_cmest:phonon_calculation [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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<code bash> | <code bash> | ||
pip install --user https:// | pip install --user https:// | ||
+ | # plus some tools required to handle CP2K input files: | ||
+ | pip install --user cp2k_tools | ||
</ | </ | ||
Line 16: | Line 18: | ||
<code bash> | <code bash> | ||
- | echo ' | + | echo ' |
</ | </ | ||
Line 32: | Line 34: | ||
====== Using Phonopy ====== | ====== Using Phonopy ====== | ||
- | Phonopy | + | A typical |
- | - 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 |
- 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 | - 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 | - 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 | - 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 | ||
+ | | ||
+ | | ||
+ | | ||
+ | &END GLOBAL | ||
+ | |||
+ | & | ||
+ | | ||
+ | & | ||
+ | BASIS_SET_FILE_NAME | ||
+ | POTENTIAL_FILE_NAME | ||
+ | |||
+ | & | ||
+ | | ||
+ | &END POISSON | ||
+ | |||
+ | &SCF | ||
+ | | ||
+ | | ||
+ | | ||
+ | & | ||
+ | ALGORITHM STANDARD | ||
+ | EPS_ADAPT 0.01 | ||
+ | & | ||
+ | & | ||
+ | METHOD FERMI_DIRAC | ||
+ | ELECTRONIC_TEMPERATURE [K] 300 | ||
+ | & | ||
+ | |||
+ | & | ||
+ | METHOD BROYDEN_MIXING | ||
+ | ALPHA 0.2 | ||
+ | BETA 1.5 | ||
+ | NBROYDEN 8 | ||
+ | & | ||
+ | |||
+ | &END SCF | ||
+ | &XC | ||
+ | & | ||
+ | & | ||
+ | &END XC | ||
+ | |||
+ | & | ||
+ | |||
+ | & | ||
+ | &CELL | ||
+ | ABC [angstrom] 5.4661639157319968 5.4661639157319968 5.4661639157319968 | ||
+ | | ||
+ | &END CELL | ||
+ | &COORD | ||
+ | | ||
+ | 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 | ||
+ | | ||
+ | | ||
+ | | ||
+ | &END KIND | ||
+ | |||
+ | & | ||
+ | &END FORCE_EVAL | ||
+ | </ | ||
+ | |||
+ | Now let Phonopy parse the CP2K input file and have it generate a 2x2x2 supercell with one displacement, | ||
+ | |||
+ | <code bash> | ||
+ | phonopy --cp2k -c Si.inp -d --dim=" | ||
+ | </ | ||
+ | |||
+ | which should give you the following additional files: | ||
+ | |||
+ | < | ||
+ | $ ls | ||
+ | disp.yaml | ||
+ | </ | ||
+ | |||
+ | '' | ||
+ | |||
+ | You therefore have to extend '' | ||
+ | |||
+ | After running CP2K, you should get the following output file in addition to the usual CP2K output: '' | ||
+ | |||
+ | Now run Phonopy on this output file to generate the force set (afterwards found in a file called '' | ||
+ | |||
+ | <code bash> | ||
+ | phonopy --cp2k -f Si-supercell-001-forces-1_0.xyz | ||
+ | </ | ||
+ | |||
+ | ... and run Phonopy again to get the band structure: | ||
+ | |||
+ | <code bash> | ||
+ | phonopy --cp2k -c Si.inp -p --dim=" | ||
+ | </ | ||
+ | |||
+ | 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 '' | ||
+ | |||
+ | 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:// |
exercises/2017_uzh_cmest/phonon_calculation.1509469669.txt.gz · Last modified: 2020/08/21 10:15 (external edit)