CP2K & phonopy calculation

CP2K & phonopy calculation#

Supported CP2K configuration options#

All CP2K input file features like unit prefixes ([rad] or [Bohr]) or preprocessor variables are supported, except for the functionality to load cell information or coordinates from external/referenced files (CIF, XYZ).

The cell information has to be provided using one of the following options.

Either by specifying the A, B and C cell vectors directly:

         A 11.452705822048308 0.0 0.0
         B 0.0 11.452705822048308 0.0
         C 0.0 0.0 11.452705822048308
      &END CELL

or by using the ABC scalings and ALPHA_BETA_GAMMA angles (the latter is optional, the cell is assumed to be orthorombic if no angles are specified):

         ALPHA_BETA_GAMMA 11.452705822048308 11.452705822048308 11.452705822048308
         ! ALPHA_BETA_GAMMA 90. 90. 90
      &END CELL

The coordinates have to be specified in a coordinate section and can be either specified as scaled coordinates (in cell vector coordinates) or as absolute coordinates (Angstrom if not otherwise specified):

         Na  0   0   0
         Na  0  1/2 1/2
         Na 1/2  0  1/2
         Na 1/2 1/2  0
         Cl 1/2 1/2 1/2
         Cl 1/2  0   0
         Cl  0  1/2  0
         Cl  0   0  1/2
      &END COORD

Please note:

  • The cell information in the generated (supercell) configuration files will always be using the A, B, C configuration options.

  • All other configuration options will be forwarded to the generated supercell configurations and all preprocessor options will be resolved prior to it.

  • Multiple &FORCE_EVAL sections are not allowed.

  • A &CELL_REF section and the MULTIPLE_UNIT_CELL will not be read or modified but simply forwarded to the generated configurations.

How to run#

A procedure of CP2K-phonopy calculation is as follows:

  1. Read a CP2K input file and create supercells with the --cp2k option:

    % phonopy --cp2k -d --dim="2 2 2" -c NaCl.inp

    In this example, 2x2x2 supercells are created. NaCl-supercell.inp and NaCl-supercell-xxx.inp (xxx are numbers) give the perfect supercell and supercells with displacements, respectively. Almost all other options will be copied from the original input NaCl.inp, except for the following:

    • the PROJECT_NAME will be suffixed to avoid name clashes of output files

    • additional &PRINT sections will be added to generate separate output files containing the forces

    • the RUN_TYPE is set to ENERGY_FORCE

    The phonopy_disp.yaml will also be created containing the Phonopy configuration.

  2. Calculate forces on atoms in the supercells with displacements.

    In this example there are two supercells with displacements to run. Using mpirun and an MPI-enabled CP2K this would simply be:

    % mpirun -np 16 cp2k.popt NaCl-supercell-001.inp
    % mpirun -np 16 cp2k.popt NaCl-supercell-002.inp

    Please do not change any options in the NaCl-supercell-002.inp which would require a re-relaxation of the cell parameters/structure. Also do not relax the generated supercells with displacements, because atomic forces induced by a small atomic displacement are what is need for phonon calculation.

  3. Create FORCE_SETS by running:

    % phonopy --cp2k -f NaCl-supercell-001-forces-1_0.xyz NaCl-supercell-002-forces-1_0.xyz  ...

    To run this command, phonopy_disp.yaml has to be located in the current directory. More information about the configuration options can be found in CP2K interface. The example outputs are located in example/NaCl-CP2K.

  4. Run post-process of phonopy with the original CP2K main input file for the unit cell used in step 1:

    % phonopy --cp2k -c NaCl.inp -p band.conf


    % phonopy --cp2k -c NaCl.inp --dim="2 2 2" [other-OPTIONS] [setting-file]