CRYSTAL & phonopy calculation

CRYSTAL & phonopy calculation#

CRYSTAL program package has a robust built-in phonon calculation workflow. However, the Phonopy interface enables convenient access to many phonon-related properties, such as subsequent Phono3py calculations of lattice thermal conductivity.

Supported features#

The CRYSTAL interface reads the unit cell from a CRYSTAL output file (lattice vectors, conventional atomic numbers, fractional atomic positions). For optimization outputs, the final geometry in the file is read.

If dielectric tensor and effective Born charges are available, they can be read with phonopy-crystal-born script. The script creates a BORN file for NAC.

The recommended strategy is to carry out a Gamma-point frequency calculation with INTENS and INTCPHF and use this as input to Phonopy. This produces all required quantities and also confirms that the structure optimization has converged to a true local minimum.

If ATOMSPIN keyword is present, magnetic moments are read from it. There is very little experience on using this feature, so be careful.

How to run#

The workflow for a CRYSTAL-Phonopy calculation is outlined here using the Si example found in example/Si-CRYSTAL.

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

  1. Create supercells with --crystal option:

    % phonopy --crystal -d --dim="4 4 4"

    In this example, 4x4x4 supercells are created. For every supercell file, the interface creates a .d12 input file and an .ext structure file. The files supercell.d12/.ext contain the perfect supercell. The files supercell-xxx.d12/.ext (xxx are numbers) contain the supercells with displacements. File phonopy_disp.yaml is also generated, containing information about the supercell and the displacements.

    In the case of the Si example, files supercell-001.d12 and supercell-001.ext will be created.

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

    1. Manually: modify the generated supercell-xxx.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 a file named TEMPLATE in the current directory. This file should contain the basis sets and computational parameters for CRYSTAL (see the Si example). When phonopy finds this file, 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:

    % runcry17 supercell-001.d12

  3. To create FORCE_SETS file required by phonopy, the following command is executed:

    % phonopy --crystal -f supercell-001.o

    Here .o files are the CRYSTAL output files from the force calculations. All .o files corresponding to the generated supercell-xxx.d12 files have to be given in the above command. To run this command, phonopy_disp.yaml has to be located in the current directory because the information on atomic displacements stored in phonopy_disp.yaml are used to generate FORCE_SETS. See some more detail at CRYSTAL interface.

  4. Now, Phonopy post-prcessing commands can be run. FORCE_SETS is automatically read in. Create phonon dispersion plot with:

    % phonopy --crystal --dim="4 4 4" -p -s band.conf
        _
  _ __ | |__   ___  _ __   ___   _ __  _   _
 | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
 | |_) | | | | (_) | | | | (_) || |_) | |_| |
 | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
 |_|                            |_|    |___/
                                      1.13.0


Python version 2.7.3
Spglib version 1.10.3
Calculator interface: crystal
Band structure mode
Settings:
  Supercell: [4 4 4]
Spacegroup: Fd-3m (227)
Computing force constants...
max drift of force constants: 0.000000 (xx) 0.000000 (zz)
Reciprocal space paths in reduced coordinates:
[ 0.00  0.00  0.00] --> [ 0.50  0.00  0.50]
[ 0.50  0.00  0.50] --> [ 0.50  0.25  0.75]
[ 0.50  0.25  0.75] --> [ 0.37  0.38  0.75]
[ 0.38  0.38  0.75] --> [ 0.00  0.00  0.00]
[ 0.00  0.00  0.00] --> [ 0.50  0.50  0.50]
[ 0.50  0.50  0.50] --> [ 0.63  0.25  0.63]
[ 0.62  0.25  0.62] --> [ 0.50  0.25  0.75]
[ 0.50  0.25  0.75] --> [ 0.50  0.50  0.50]
[ 0.50  0.50  0.50] --> [ 0.37  0.37  0.75]
[ 0.62  0.25  0.62] --> [ 0.50 -0.00  0.50]
                 _
   ___ _ __   __| |
  / _ \ '_ \ / _` |
 |  __/ | | | (_| |
  \___|_| |_|\__,_|

    crystal-band

    For further settings and command options, see the general Phonopy documentation Setting tags and Command options, respectively, and for examples, see Examples.

Non-analytical term correction (Optional)#

The workflow for a CRYSTAL-Phonopy calculation with NAC is outlined here using the NaCl example found in example/NaCl-CRYSTAL.

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

To activate non-analytical term correction, BORN (optional) is required. This file contains the Born effective charges and the dielectric tensor. They can be calculated with CRYSTAL. The recommended strategy is to carry out a Gamma-point frequency calculation with INTENS and INTCPHF. This produces all required quantities and also confirms that the structure optimization has converged to a true local minimum. (see the FREQCALC-INTENS-INTCPHF block in the beginning of crystal.o)

The workflow is very similar to the Si example below:

  1. Create displaced supercells:

    phonopy --crystal --dim="4 4 4" -d

    Note that now the CRYSTAL interface automatically creates the BORN file. It should look like this:

    default
1.8126 0.0000 0.0000 0.0000 1.8126 0.0000 0.0000 0.0000 1.8126
1.0238 -0.0000 -0.0000 -0.0000 1.0238 0.0000 -0.0000 0.0000 1.0238
-1.0238 0.0000 0.0000 0.0000 -1.0238 0.0000 0.0000 0.0000 -1.0238

    However, if you don’t want to run a FREQCALC-INTENS-INTCPHF calculation, but have the necessary data from some other source, you can create the BORN file manually following the BORN format (BORN (optional)).

  2. Create BORN file with phonopy-crystal-born script:

    phonopy-crystal-born > BORN

    By default, phonopy-crystal-born looks for a file called crystal.o. File with some other name can be given as an argument to the script. The BORN file created by the script should look like this:

    default
1.8126 0.0000 0.0000 0.0000 1.8126 0.0000 0.0000 0.0000 1.8126
1.0238 0.0000 0.0000 0.0000 1.0238 0.0000 0.0000 0.0000 1.0238
-1.0238 -0.0000 -0.0000 -0.0000 -1.0238 0.0000 -0.0000 0.0000 -1.0238

    If you don’t want to run a FREQCALC-INTENS-INTCPHF calculation, but have the necessary data from some other source, you can create the BORN file manually following the BORN format (BORN (optional)).

  3. Run the supercell inputs with CRYSTAL as in the Si example above.

  4. Collect forces:

    phonopy --crystal -f supercell-*o

  5. Calculate phonon dispersion data into band.yaml and save band.pdf, using non-analytical correction --nac:

    phonopy --crystal --dim="4 4 4" -p -s --nac band.conf

    crystal-band-nac