Quantum ESPRESSO (QE) & phonopy calculation

Quantum ESPRESSO (QE) & phonopy calculation#

Quantum ESPRESSO package itself has a set of the phonon calculation system. But the document here explains how to calculate phonons using phonopy, i.e., using the finite displacement and supercell approach.

Supported QE-PW tags#

Currently QE-PW tags that phonopy can read are shown below. Only ibrav = 0 type representation of crystal structure is supported. More tags may be supported on request.

nat, ntyp, celldm(1), ATOMIC_SPECIES, ATOMIC_POSITIONS, CELL_PARAMETERS

Chemical symbols with natural number for ATOMIC_SPECIES like Xn (n>0), e.g.. Fe1, can be used. The formats of X_* and X-* are not supported. When this extended symbol is used, masses of all atoms including usual chemical symbols are read from QE structure file. Otherwise, masses of respective chemical symbols implemented in phonopy are used. Note that when using the extended symbol, if the unit cell of QE structure file is not a primitive cell, and the primitive cell is defined by the transformation matrix (PRIMITIVE_AXES tag or --pa option), atoms with the extended symbols in the unit cell have to be mapped properly to those in the primitive cell.

How to run#

The procedure of QE-phonopy calculation is shown below using the NaCl example found in example/NaCl-QE directory.

  1. Read a QE-PW input file and create supercells with --qe option:

    % phonopy --qe -d --dim="2 2 2" -c NaCl.in

    In this example, 2x2x2 supercells are created. supercell.in and supercell-xxx.in (xxx are numbers) give the perfect supercell and supercells with displacements, respectively. In the case of the NaCl example, two files supercell-001.in and supercell-002.in are created. In these supercell files, lines only relevant to crystal structures are given. phonopy_disp.yaml is also generated, which contains information about supercell and displacements.

  2. To make QE-PW input files, necessary setting information is added to supercell-xxx.in files, e.g., by:

    % for i in {001,002};do cat header.in supercell-$i.in >| NaCl-$i.in; done

    where header.in is specially made for this NaCl example and this file is found in example/NaCl-QE directory. This setting is of course dependent on systems and has to be written for each interested system. 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.

    Then QE-PW supercell calculations are executed to obtain force on atoms, e.g., as follows:

    % mpirun pw.x -i NaCl-001.in |& tee NaCl-001.out
% mpirun pw.x -i NaCl-002.in |& tee NaCl-002.out

  3. To create FORCE_SETS, that is used by phonopy, the following phonopy command is executed:

    % phonopy -f NaCl-001.out NaCl-002.out

    Here .out files are the saved text files of standard outputs of the QE-PW calculations. If more supercells with displacements were created in the step 1, all .out files are 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 Quantum ESPRESSO interface.

  4. Now post-process of phonopy is ready to run. The unit cell file used in the step 1 has to be specified but FORCE_SETS is automatically read. Examples of post-process are shown below.

    % phonopy --qe -c NaCl.in -p band.conf
        _
  _ __ | |__   ___  _ __   ___   _ __  _   _
 | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
 | |_) | | | | (_) | | | | (_) || |_) | |_| |
 | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
 |_|                            |_|    |___/
                                      1.13.0

Python version 2.7.14
Spglib version 1.10.3
Calculator interface: qe
Band structure mode
Settings:
  Supercell: [2 2 2]
  Primitive axis:
    [ 0.   0.5  0.5]
    [ 0.5  0.   0.5]
    [ 0.5  0.5  0. ]
Spacegroup: Fm-3m (225)
Computing force constants...
max drift of force constants: -0.001194 (zz) -0.000000 (zz)
Reciprocal space paths in reduced coordinates:
[ 0.00  0.00  0.00] --> [ 0.50  0.00  0.00]
[ 0.50  0.00  0.00] --> [ 0.50  0.50  0.00]
[ 0.50  0.50  0.00] --> [-0.00 -0.00  0.00]
[ 0.00  0.00  0.00] --> [ 0.50  0.50  0.50]
...
    _images/NaCl-pwscf-band.png

    --qe -c NaCl.in is specific for the QE-phonopy calculation but the other settings are totally common among calculator interfaces such as

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

    For settings and command options, see Setting tags and Command options, respectively, and for examples, see Examples.

Non-analytical term correction (Optional)#

To activate non-analytical term correction, BORN (optional) is required. This file contains the information of Born effective charge and dielectric constant. These physical values are also obtained from the PW (pw.x) & PH (ph.x) codes in Quantum ESPRESSO package. There are two steps. The first step is usual self-consistent field (SCF) calculation by and the second step is running its response function calculations under DFPT.

For the SCF calculation, the input file NaCl.in looks like:

 &control
    calculation = 'scf'
    tprnfor = .true.
    tstress = .true.
    pseudo_dir = '/home/togo/espresso/pseudo/'
 /
 &system
    ibrav = 0
    nat = 8
    ntyp = 2
    ecutwfc = 70.0
 /
 &electrons
    diagonalization = 'david'
    conv_thr = 1.0d-9
 /
ATOMIC_SPECIES
 Na  22.98976928 Na.pbe-spn-kjpaw_psl.0.2.UPF
 Cl  35.453      Cl.pbe-n-kjpaw_psl.0.1.UPF
ATOMIC_POSITIONS crystal
 Na   0.0000000000000000  0.0000000000000000  0.0000000000000000
 Na   0.0000000000000000  0.5000000000000000  0.5000000000000000
 Na   0.5000000000000000  0.0000000000000000  0.5000000000000000
 Na   0.5000000000000000  0.5000000000000000  0.0000000000000000
 Cl   0.5000000000000000  0.5000000000000000  0.5000000000000000
 Cl   0.5000000000000000  0.0000000000000000  0.0000000000000000
 Cl   0.0000000000000000  0.5000000000000000  0.0000000000000000
 Cl   0.0000000000000000  0.0000000000000000  0.5000000000000000
CELL_PARAMETERS angstrom
 5.6903014761756712 0 0
 0 5.6903014761756712 0
 0 0 5.6903014761756712
K_POINTS automatic
 8 8 8 1 1 1

where more the k-point mesh numbers are specified. This may be exectued as:

% mpirun ~/espresso/bin/pw.x -i NaCl.in |& tee NaCl.out

Many files whose names stating with pwscf should be created. These are used for the next calculation. The input file for the response function calculations, NaCl.ph.in, is created as follows:

 &inputph
  tr2_ph = 1.0d-14,
  epsil = .true.
 /
0 0 0

Similary ph.x is executed:

% mpirun ~/espresso/bin/ph.x -i NaCl.ph.in |& tee NaCl.ph.out

Finally the Born effective charges and dielectric constant are obtained in the output file NaCl.ph.out. The BORN file has to be created following the BORN format (BORN (optional)). The BORN file for this NaCl calculation would be something like below:

default value
2.472958201 0 0 0 2.472958201 0 0 0 2.472958201
1.105385 0 0 0 1.105385 0 0 0 1.105385
-1.105385 0 0 0 -1.105385 0 0 0 -1.105385

This BORN file can be made using phonopy-qe-born command.

% phonopy-qe-born NaCl.in  | tee BORN

Once this is made, the non-analytical term correction is included just adding the --nac option as follows:

% phonopy --qe --nac -c NaCl.in -p band.conf
_images/NaCl-pwscf-band-NAC.png

Using q2r.x to create phonopy force constants file#

Experimental

A parser of q2r.x output is implemented experimentally. Currently command-line user interface is not prepared. Using the following script, the force constants file readable by phonopy is created. Probably thus obtained force constants are required to be symmetrized by the translational invariance condition using FC_SYMMETRY = .TRUE..

#!/usr/bin/env python

import sys
from phonopy.interface.qe import read_pwscf, PH_Q2R

primcell_filename = sys.argv[1]
q2r_filename = sys.argv[2]
cell, _ = read_pwscf(primcell_filename)
q2r = PH_Q2R(q2r_filename)
q2r.run(cell)
q2r.write_force_constants()

Saving this script as make_fc_q2r.py, this is used as, e.g.,

% python make_fc_q2r.py NaCl.in NaCl.fc

This gives force_constants.hdf5 file in the compact format (see FORCE_CONSTANTS and force_constants.hdf5). From version 1.13.2, full supercell force constants can be written by q2r.run(cell, is_full_fc=True) instead of q2r.run(cell) in the above script. FORCE_CONSTANTS file instead of force_constants.hdf5 can be obtained by q2r.write_force_constants(fc_format='text').

Non-analytical term correction#

Treatment of non-analytical term correction (NAC) is different between phonopy and QE. For insulator, QE automatically calculate dielectric constant and Born effective charges at PH calculation when q-point mesh sampling mode (ldisp = .true.), and these data are written in the Gamma point dynamical matrix file (probably in .dyn1 file). When running q2r.x, these files are read including the dielectric constant and Born effective charges, and the real space force constants where QE-NAC treatment is done are written to the q2r output file. This is not that phonopy expects. Therefore the dielectric constant and Born effective charges data have to be removed manually from the Gamma point dynamical matrix file before running q2r.x. Alternatively Gamma point only PH calculation with ‘epsil = .false.’ can generate the dynamical matrix file without the dielectric constant and Born effective charges data. So it is possible to replace the Gamma point file by this Gamma point only file to run q2r.x for phonopy.

Creating BORN file#

If the q2r.x output contains dielectric constant and Born effective charges, the following script can generate BORN format text.

#!/usr/bin/env python

import sys
import numpy as np
from phonopy.structure.symmetry import elaborate_borns_and_epsilon
from phonopy.interface.qe import read_pwscf, PH_Q2R

primcell_filename = sys.argv[1]
q2r_filename = sys.argv[2]
cell, _ = read_pwscf(primcell_filename)
q2r = PH_Q2R(q2r_filename)
q2r.run(cell, parse_fc=False)
if q2r.epsilon is not None:
    borns, epsilon, _ = elaborate_borns_and_epsilon(
        cell,
        q2r.borns,
        q2r.epsilon,
        supercell_matrix=np.diag(q2r.dimension),
        symmetrize_tensors=True)
    print("default")
    print(("%13.8f" * 9) % tuple(epsilon.ravel()))
    for z in borns:
        print(("%13.8f" * 9) % tuple(z.ravel()))

Saving this script as make_born_q2r.py,

% python make_born_q2r.py NaCl.in NaCl.fc > BORN

NaCl example#

NaCl example is found at phonopy/phonopy.

% phonopy --qe -c NaCl.in --dim="8 8 8" --band="0 0 0  1/2 0 0  1/2 1/2 0  0 0 0  1/2 1/2 1/2" --readfc --readfc-format=hdf5 --fc-symmetry --nac -p
_images/NaCl-q2r-band-NAC.png