CRYSTAL & phono3py calculation

CRYSTAL program package has a robust built-in phonon calculation workflow for harmonic phonon properties. However, combining CRYSTAL with Phono3py enables convenient access to anharmonic phonon properties.

An example for CRYSTAL is found in the example/Si-CRYSTAL directory.

To invoke the CRYSTAL interface, --crystal option has to be always specified:

% phono3py --crystal [options] [arguments]

When the file name of the unit cell is different from the default one (see Default unit cell file name), -c option is used to specify the file name. CRYSTAL unit cell file parser used in phono3py is the same as that in phonopy. It can read only limited number of keywords that are shown in the phonopy web site (


In this example (Si-CRYSTAL), the CRYSTAL output file is crystal.o. This is the default file name for the CRYSTAL interface, so the -c crystal.o parameter is not needed.

  1. Create supercells with displacements (4x4x4 for 2nd order FC, 2x2x2 for 3rd order FC)

    % phono3py --crystal --dim="2 2 2" --dim_fc2="4 4 4" -d

    57 supercell files (supercell-xxx.d12/.ext) for the third order force constants are created. In addition, one supercell file (supercell_fc2-00001.d12/.ext) is created for the second order force constants.

  2. To make valid CRYSTAL input files, there are two possible options:

    1. Manually: modify the generated supercell-xxx.d12 and supercell_fc2-xxxxx.d12 files by replacing the line Insert basis sets and parameters here with the basis set and computational parameters.
    2. Recommended option: before generating the supercells, include files named TEMPLATE and TEMPLATE3 in the current directory. These files should contain the basis sets and computational parameters for CRYSTAL (see the example). When phono3py finds these files it automatically generates complete CRYSTAL input files in the step 1.

    Note that supercells with displacements must not be relaxed in the force calculations, because atomic forces induced by a small atomic displacement are what we need for phonon calculation. To get accurate forces, TOLDEE parameter should be 10 or higher. Phonopy includes this parameter and the necessary GRADCAL keyword automatically in the inputs.

    Then, CRYSTAL supercell calculations are executed to obtain forces on atoms, e.g., as follows:

    % runcry14 supercell-001.d12
  3. Collect forces in FORCES_FC3 and FORCES_FC2:

    % phono3py --crystal --cf3 supercell-*o
    % phono3py --crystal --cf2 supercell_fc2-*o

    disp_fc3.yaml and disp_fc2.yaml are used to create FORCES_FC3 and FORCES_FC2, therefore they must exist in current directory.

  4. Calculate 3rd and 2nd order force constants in files fc3.hdf5 and fc2.hdf5:

    % phono3py --crystal --dim="2 2 2" --dim_fc2="4 4 4" --sym_fc3r --sym_fc2 --tsym

    --sym_fc2, --sym_fc3r, and --tsym are used to symmetrize second- and third-order force constants.

  5. Thermal conductivity calculation:

    % phono3py --crystal --fc3 --fc2 --dim="2 2 2" --dim_fc2="4 4 4" --mesh="20 20 20" --br

    --br invokes the Relaxation Time Approximation. Add --isotope for isotope scattering. Check the effect of --nac for polar systems. Carefully test the convergence with respect to --mesh!