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Phonon calculations with phonopy

Phonon calculations with phonopy#

The phonopy code can calculate a range of harmonic and quasi-harmonic vibrational properties and from version 2.0 onwards supports DFTB+. Information about how to install phonopy is available, it is also available on conda-forge:

mamba install -c conda-forge phonopy

The below examples were tested with phonopy v2.14.0.

Phonon band structure#

[Input: recipes/properties/phononbs/]

The diamond lattice has very high symmetry, hence a phonon band structure can be obtained with a single calculation. A conventional unit cell with relaxed lattice constant is provided in geo.gen (the phonopy input assumes this is the name of the supplied starting geometry).

The DFTB+ input needs to calculate the atomic forces and also to write a results tag file, hence the dftb_in.hsd input contains lines including:

Analysis = {
  # required option for phonopy
  CalculateForces = Yes
}
Options = {
  # Required options for storing data needed by phonopy
  WriteResultsTag = Yes
}

The (single) distorted geometry and the required phonopy_disp.yaml file is then generated with the command

phonopy -d --dim="4 4 4" --dftb+

This constructs a 4x4x4 supercell of the primitive cell and saves the undistorted and distorted supercells as geo.genS and geo.genS-001 respectively. Note that you should test the phonon band structure is converged with respect to the number of repeats used in making the supercell (and likewise for any other properties of interest), as well as the number of k-points used in the DFTB+ calculation.

For the single (in this case) generated geo.genS-* file, calculate the forces on the atoms, using DFTB+ and retaining the resulting results.tag file

dftb+

Then create the required FORCE_SETS file

phonopy -f results.tag --dftb+

This assumes that the results.tag and phonopy_disp.yaml files are in the same directory (for more complex cases this stage of the phonopy calculation should be run in the same directory as phonopy_disp.yaml file and paths given to directories containing the DFTB+ output results.tag files).

Then specify the path in the Brillouin zone you are interested in in band.conf (see the phonopy documentation), and post-process the phonopy data, again providing the dimensions of the the supercell repeat. This can either be on the command line or in the settings file (a DIM file):

phonopy -p band.conf --dim="4 4 4" --dftb+

Finally, you can save the band structure data in gnuplot format

phonopy-bandplot --gnuplot band.yaml > band.dat

The resulting band structure for the mio carbon model is shown in Figure 24.

Phonon band structure for diamond.

Figure 24 The phonon band structure for diamond.#

Lower symmetry structures#

For lower symmetry geometries, multiple geo.genS-* files will be generated.

Assuming the dftb_in.hsd file expects the geometry to be called geo.gen and knows an absolute path to the Slater-Koster data, a simple bash shell loop to run these calculations could look like

for struct in geo.genS-*
do
  export dir=$(echo $struct | sed 's/geo.genS-//g')
  echo "Processing $dir"
  mkdir $dir
  cp $struct $dir/geo.genS-001
  cp dftb_in.hsd $dir
  cd $dir
  dftb+
  cd ..
done

In practice, the separate DFTB+ calculations could be submitted to a queueing system.

As separate calculation outputs are then in sub-directories, phonopy processing of the multiple results.tag files would be done with

phonopy -f [0-9][0-9][0-9]/results.tag --dftb+
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