Examples#
Phonopy supports various external force calculators (mainly for abinitio codes). The examples below are given for the default system that is equivalent to VASP style. Most of usage is universal among the force calculators. So it is also useful for non-VASP users to see the examples below. The list of the force calculators and the links to their specific usages are shown at Interfaces to calculators.
Example files are found at phonopy/phonopy. The same are found in the example directory of the phonopy package downloaded at phonopy/phonopy. The followings show how some of those examples work. Note that sometimes the followings are outdated than the examples in the phonopy package. So the results or displace outputs can be different.
Si#
FORCE_SETS file creation for VASP#
% phonopy -f vasprun.xml
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.7.0
Python version 3.7.6
Spglib version 1.14.1
Displacements were read from "phonopy_disp.yaml".
counter (file index): 1
FORCE_SETS has been created.
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
where vasprun.xml is the VASP output.
DOS#
% phonopy -p mesh.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.7.0
Python version 3.7.6
Spglib version 1.14.1
Crystal structure was read from "phonopy_disp.yaml".
Unit of length: angstrom
Mesh sampling mode
Settings:
Sampling mesh: [31 31 31]
Supercell: [2 2 2]
Primitive matrix:
[1. 0. 0.]
[0. 1. 0.]
[0. 0. 1.]
Spacegroup: Fd-3m (227)
Use -v option to watch primitive cell, unit cell, and supercell structures.
Force sets were not found in "phonopy_disp.yaml".
Forces and displacements were read from "FORCE_SETS".
Computing force constants...
Max drift of force constants: -0.000001 (yy) -0.000001 (yy)
Mesh numbers: [31 31 31]
Number of irreducible q-points on sampling mesh: 816/29791
Calculating phonons on sampling mesh...
Calculating DOS...
Summary of calculation was written in "phonopy.yaml".
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
Thermal properties#
% phonopy -t -p mesh.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.12.0
Python version 3.9.6
Spglib version 1.16.2
Phonopy configuration was read from "mesh.conf".
Crystal structure was read from "phonopy_params.yaml".
Unit of length: angstrom
Mesh sampling mode
Settings:
Sampling mesh: [31 31 31]
Supercell: [2 2 2]
Primitive matrix:
[1. 0. 0.]
[0. 1. 0.]
[0. 0. 1.]
Spacegroup: Fd-3m (227)
Use -v option to watch primitive cell, unit cell, and supercell structures.
Forces and displacements were read from "phonopy_params.yaml".
Computing force constants...
Max drift of force constants: -0.000001 (zz) -0.000001 (zz)
Mesh numbers: [31 31 31]
Number of irreducible q-points on sampling mesh: 816/29791
Calculating phonons on sampling mesh...
Calculating thermal properties...
Cutoff frequency: 0.00000
Number of phonon frequencies less than cutoff frequency: 3/178746
# T [K] F [kJ/mol] S [J/K/mol] C_v [J/K/mol] E [kJ/mol]
0.000 11.7110491 0.0000000 0.0000000 11.7110491
10.000 11.7110004 0.0207133 0.0652014 11.7112076
20.000 11.7101706 0.1826665 0.5801980 11.7138239
30.000 11.7063148 0.6494417 1.9566658 11.7257980
40.000 11.6959680 1.4755146 3.9391312 11.7549886
50.000 11.6758626 2.5838026 6.0729959 11.8050528
60.000 11.6436849 3.8753235 8.1398561 11.8762043
70.000 11.5979858 5.2789840 10.1081937 11.9675147
80.000 11.5378706 6.7536681 12.0151391 12.0781640
90.000 11.4627490 8.2777067 13.8988296 12.2077426
100.000 11.3721917 9.8393078 15.7763730 12.3561224
...
NaCl#
Band structure#
% phonopy -p band.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.12.0
Python version 3.9.6
Spglib version 1.16.2
Phonopy configuration was read from "band.conf".
Crystal structure was read from "phonopy_disp.yaml".
Unit of length: angstrom
Band structure mode
Settings:
Supercell: [2 2 2]
Primitive matrix (Auto):
[0. 0.5 0.5]
[0.5 0. 0.5]
[0.5 0.5 0. ]
Spacegroup: Fm-3m (225)
Use -v option to watch primitive cell, unit cell, and supercell structures.
Force sets were not found in "phonopy_disp.yaml".
Forces and displacements were read from "FORCE_SETS".
Computing force constants...
Max drift of force constants: 0.040159 (yy) 0.000009 (xx)
Reciprocal space paths in reduced coordinates:
[ 0.000 0.000 0.000] --> [ 0.500 0.000 0.000]
[ 0.500 0.000 0.000] --> [ 0.500 0.500 0.000]
[ 0.500 0.500 0.000] --> [ 0.000 0.000 0.000]
[ 0.000 0.000 0.000] --> [ 0.500 0.500 0.500]
Summary of calculation was written in "phonopy.yaml".
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
Band structure with non-analytical term correction#
This requires to prepare BORN file.
% phonopy -p --nac band.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.12.0
Python version 3.9.6
Spglib version 1.16.2
Phonopy configuration was read from "band.conf".
Crystal structure was read from "phonopy_disp.yaml".
Unit of length: angstrom
Band structure mode
Settings:
Non-analytical term correction (NAC): on
Supercell: [2 2 2]
Primitive matrix (Auto):
[0. 0.5 0.5]
[0.5 0. 0.5]
[0.5 0.5 0. ]
Spacegroup: Fm-3m (225)
Use -v option to watch primitive cell, unit cell, and supercell structures.
Force sets were not found in "phonopy_disp.yaml".
Forces and displacements were read from "FORCE_SETS".
Computing force constants...
Max drift of force constants: 0.040159 (yy) 0.000009 (xx)
NAC parameters were not found in "phonopy_disp.yaml".
NAC parameters were read from "BORN".
Use NAC by Gonze et al. (no real space sum in current implementation)
PRB 50, 13035(R) (1994), PRB 55, 10355 (1997)
G-cutoff distance: 1.16, Number of G-points: 307, Lambda: 0.19
Reciprocal space paths in reduced coordinates:
[ 0.000 0.000 0.000] --> [ 0.500 0.000 0.000]
[ 0.500 0.000 0.000] --> [ 0.500 0.500 0.000]
[ 0.500 0.500 0.000] --> [ 0.000 0.000 0.000]
[ 0.000 0.000 0.000] --> [ 0.500 0.500 0.500]
Summary of calculation was written in "phonopy.yaml".
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
PDOS#
% phonopy -p pdos.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.12.0
Python version 3.9.6
Spglib version 1.16.2
Phonopy configuration was read from "pdos.conf".
Crystal structure was read from "phonopy_disp.yaml".
Unit of length: angstrom
Mesh sampling mode
Settings:
Sampling mesh: [41 41 41]
Supercell: [2 2 2]
Primitive matrix (Auto):
[0. 0.5 0.5]
[0.5 0. 0.5]
[0.5 0.5 0. ]
Spacegroup: Fm-3m (225)
Use -v option to watch primitive cell, unit cell, and supercell structures.
Force sets were not found in "phonopy_disp.yaml".
Forces and displacements were read from "FORCE_SETS".
Computing force constants...
Max drift of force constants: 0.040159 (yy) 0.000009 (xx)
Mesh numbers: [41 41 41]
Number of q-points on sampling mesh: 68921
Calculating phonons on sampling mesh...
Calculating projected DOS...
Summary of calculation was written in "phonopy.yaml".
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
With non-analytical term correction, the PDOS may not change very much because it mainly affects phonon modes in the reciprocal region close to \(\Gamma\) point.
% phonopy --nac -p pdos.conf
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.12.0
Python version 3.9.6
Spglib version 1.16.2
Phonopy configuration was read from "pdos.conf".
Crystal structure was read from "phonopy_disp.yaml".
Unit of length: angstrom
Mesh sampling mode
Settings:
Non-analytical term correction (NAC): on
Sampling mesh: [41 41 41]
Supercell: [2 2 2]
Primitive matrix (Auto):
[0. 0.5 0.5]
[0.5 0. 0.5]
[0.5 0.5 0. ]
Spacegroup: Fm-3m (225)
Use -v option to watch primitive cell, unit cell, and supercell structures.
Force sets were not found in "phonopy_disp.yaml".
Forces and displacements were read from "FORCE_SETS".
Computing force constants...
Max drift of force constants: 0.040159 (yy) 0.000009 (xx)
NAC parameters were not found in "phonopy_disp.yaml".
NAC parameters were read from "BORN".
Use NAC by Gonze et al. (no real space sum in current implementation)
PRB 50, 13035(R) (1994), PRB 55, 10355 (1997)
G-cutoff distance: 1.16, Number of G-points: 307, Lambda: 0.19
Mesh numbers: [41 41 41]
Number of q-points on sampling mesh: 68921
Calculating phonons on sampling mesh...
Calculating projected DOS...
Summary of calculation was written in "phonopy.yaml".
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
Plot band structure and DOS at once#
Band structure and DOS or PDOS can be plotted on one figure together by
% phonopy band-pdos.conf --nac -p
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.12.0
Python version 3.9.6
Spglib version 1.16.2
Phonopy configuration was read from "band-pdos.conf".
Crystal structure was read from "phonopy_disp.yaml".
Unit of length: angstrom
Band structure and mesh sampling mode
Settings:
Non-analytical term correction (NAC): on
Sampling mesh: [41 41 41]
Supercell: [2 2 2]
Primitive matrix (Auto):
[0. 0.5 0.5]
[0.5 0. 0.5]
[0.5 0.5 0. ]
Spacegroup: Fm-3m (225)
Use -v option to watch primitive cell, unit cell, and supercell structures.
Force sets were not found in "phonopy_disp.yaml".
Forces and displacements were read from "FORCE_SETS".
Computing force constants...
Max drift of force constants: 0.040159 (yy) 0.000009 (xx)
NAC parameters were not found in "phonopy_disp.yaml".
NAC parameters were read from "BORN".
Use NAC by Gonze et al. (no real space sum in current implementation)
PRB 50, 13035(R) (1994), PRB 55, 10355 (1997)
G-cutoff distance: 1.16, Number of G-points: 307, Lambda: 0.19
Reciprocal space paths in reduced coordinates:
[ 0.000 0.000 0.000] --> [ 0.500 0.000 0.000]
[ 0.500 0.000 0.000] --> [ 0.500 0.500 0.000]
[ 0.500 0.500 0.000] --> [ 0.000 0.000 0.000]
[ 0.000 0.000 0.000] --> [ 0.500 0.500 0.500]
Mesh numbers: [41 41 41]
Number of q-points on sampling mesh: 68921
Calculating phonons on sampling mesh...
Calculating projected DOS...
Summary of calculation was written in "phonopy.yaml".
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
MgB2 characters of ireducible representations#
% phonopy -f vasprun.xml-{001,002}
% phonopy --dim="3 3 2" --irreps="0 0 0"
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.12.0
Python version 3.9.6
Spglib version 1.16.2
Crystal structure was read from "phonopy_disp.yaml".
Unit of length: angstrom
Ir-representation mode
Settings:
Supercell: [3 3 2]
Primitive matrix (Auto):
[1. 0. 0.]
[0. 1. 0.]
[0. 0. 1.]
Spacegroup: P6/mmm (191)
Use -v option to watch primitive cell, unit cell, and supercell structures.
Force sets were not found in "phonopy_disp.yaml".
Forces and displacements were read from "FORCE_SETS".
Computing force constants...
Max drift of force constants: -0.039930 (zz) -0.000007 (zz)
-------------------------------
Irreducible representations
-------------------------------
q-point: [0. 0. 0.]
Point group: 6/mmm
Original rotation matrices:
1 2 3 4 5 6
-------- -------- -------- -------- -------- --------
1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0
0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0
0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1
7 8 9 10 11 12
-------- -------- -------- -------- -------- --------
-1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0
0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0
0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1
13 14 15 16 17 18
-------- -------- -------- -------- -------- --------
0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0
-1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0
0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1
19 20 21 22 23 24
-------- -------- -------- -------- -------- --------
0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0
1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0
0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1
Transformation matrix:
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
Rotation matrices by transformation matrix:
E i C6 S3 C3 S6
-------- -------- -------- -------- -------- --------
1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0
0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0
0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1
C2 sgh C3 S6 C6 S3
-------- -------- -------- -------- -------- --------
-1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0
0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0
0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1
C2'' sgv C2' sgd C2'' sgv
-------- -------- -------- -------- -------- --------
0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0
-1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0
0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1
C2' sgd C2'' sgv C2' sgd
-------- -------- -------- -------- -------- --------
0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0
1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0
0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1
Character table:
1 ( -0.019): A2u
( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0)
( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0)
( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0)
( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0)
2 ( 0.004): E1u
( 2, 0.0) ( 2, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0)
( 2, 180.0) ( 2, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0)
( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
4 ( 9.953): E1u
( 2, 0.0) ( 2, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0)
( 2, 180.0) ( 2, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0)
( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
6 ( 11.982): A2u
( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0)
( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0)
( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0)
( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0)
7 ( 17.269): E2g
( 2, 0.0) ( 2, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0)
( 2, 0.0) ( 2, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0) ( 1, 180.0)
( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
9 ( 20.565): B1g
( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0)
( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0)
( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0)
( 1, 0.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0)
Summary of calculation was written in "phonopy.yaml".
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
Al-QHA#
% phonopy-qha e-v.dat thermal_properties.yaml-{-{5..1},{0..5}} --sparse=50 -p
# Vinet EOS
# T E_0 B_0 B'_0 V_0
0.000000 -14.814330 75.358945 4.746862 66.684166
2.000000 -14.814330 75.358944 4.746862 66.684166
4.000000 -14.814330 75.358934 4.746864 66.684167
6.000000 -14.814330 75.358891 4.746869 66.684169
8.000000 -14.814330 75.358779 4.746883 66.684174
10.000000 -14.814331 75.358553 4.746911 66.684185
...
