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(examples_link)=
# 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
{ref}`calculator_interfaces`.
Example files are found at
https://github.com/phonopy/phonopy/tree/master/example. The same are found in
the example directory of the phonopy package downloaded at
https://github.com/phonopy/phonopy/archive/master.zip. 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 Note that sometimes the followings are outdated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
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.26.6
Compiled with OpenMP support (max 10 threads).
Python version 3.12.4
Spglib version 2.4.0
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-load --mesh 31 31 31 -p
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.26.6
Compiled with OpenMP support (max 10 threads).
Running in phonopy.load mode.
Python version 3.12.4
Spglib version 2.4.0
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)
Number of symmetry operations in supercell: 384
Use -v option to watch primitive cell, unit cell, and supercell structures.
Force sets were read from "FORCE_SETS".
Displacements were overwritten by "FORCE_SETS".
Max drift of force constants: -0.000001 (zz) -0.000001 (zz)
Max drift after symmetrization by translation: -0.000000 (xx) -0.000000 (xx)
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".
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
~~~
```{image} Si-DOS.png
:width: 50%
```
### Thermal properties
~~~
% phonopy-load --mesh 31 31 31 -t -p
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.26.6-rdev26+g1f6a3f81
Compiled with OpenMP support (max 10 threads).
Running in phonopy.load mode.
Python version 3.12.4
Spglib version 2.4.0
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)
Number of symmetry operations in supercell: 384
Use -v option to watch primitive cell, unit cell, and supercell structures.
Force sets were read from "FORCE_SETS".
Displacements were overwritten by "FORCE_SETS".
Max drift of force constants: -0.000001 (zz) -0.000001 (zz)
Max drift after symmetrization by translation: -0.000000 (xx) -0.000000 (xx)
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: 1/178746
# T [K] F [kJ/mol] S [J/K/mol] C_v [J/K/mol] E [kJ/mol]
0.000 11.7110492 0.0000000 0.0000000 11.7110492
10.000 11.7109211 0.0292204 0.0657586 11.7112133
20.000 11.7100041 0.1915595 0.5807546 11.7138352
30.000 11.7060581 0.6585603 1.9572223 11.7258149
40.000 11.6956193 1.4847934 3.9396878 11.7550111
50.000 11.6754205 2.5932055 6.0735527 11.8050808
60.000 11.6431482 3.8848280 8.1404132 11.8762379
70.000 11.5973537 5.2885744 10.1087510 11.9675539
80.000 11.5371421 6.7633329 12.0156965 12.0782088
90.000 11.4619236 8.2874371 13.8993871 12.2077929
100.000 11.3712686 9.8490970 15.7769306 12.3561783
...
~~~
```{image} Si-props.png
:width: 50%
```
## NaCl
### Band structure
This requires to prepare `BORN` file.
~~~
% phonopy-load --band "0.0 0.0 0.0 0.5 0.0 0.0 0.5 0.5 0.0 0.0 0.0 0.0 0.5 0.5 0.5" -p
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.26.6
Compiled with OpenMP support (max 10 threads).
Running in phonopy.load mode.
Python version 3.12.4
Spglib version 2.4.0
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)
Number of symmetry operations in supercell: 1536
Use -v option to watch primitive cell, unit cell, and supercell structures.
NAC params were read from "BORN".
Force sets were read from "FORCE_SETS".
Displacements were overwritten by "FORCE_SETS".
Max drift of force constants: 0.040159 (xx) 0.000009 (xx)
Max drift after symmetrization by translation: 0.000000 (zz) 0.000000 (zz)
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".
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
~~~
```{image} NaCl-band-NAC.png
:width: 50%
```
(example_pdos)=
### PDOS
~~~
% phonopy-load --mesh 41 41 41 --pdos "1, 2" -p
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.26.6
Compiled with OpenMP support (max 10 threads).
Running in phonopy.load mode.
Python version 3.12.4
Spglib version 2.4.0
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)
Number of symmetry operations in supercell: 1536
Use -v option to watch primitive cell, unit cell, and supercell structures.
NAC params were read from "BORN".
Force sets were read from "FORCE_SETS".
Displacements were overwritten by "FORCE_SETS".
Max drift of force constants: 0.040159 (xx) 0.000009 (xx)
Max drift after symmetrization by translation: 0.000000 (zz) 0.000000 (zz)
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".
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
~~~
```{image} NaCl-PDOS-nac.png
:width: 50%
```
### Plot band structure and DOS at once
Band structure and DOS or PDOS can be plotted on one figure together by
~~~
% phonopy-load --band "0.0 0.0 0.0 0.5 0.0 0.0 0.5 0.5 0.0 0.0 0.0 0.0 0.5 0.5 0.5" --mesh 41 41 41 --pdos "1, 2" -p
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.26.6
Compiled with OpenMP support (max 10 threads).
Running in phonopy.load mode.
Python version 3.12.4
Spglib version 2.4.0
Crystal structure was read from "phonopy_disp.yaml".
Unit of length: angstrom
Band structure and 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)
Number of symmetry operations in supercell: 1536
Use -v option to watch primitive cell, unit cell, and supercell structures.
NAC params were read from "BORN".
Force sets were read from "FORCE_SETS".
Displacements were overwritten by "FORCE_SETS".
Max drift of force constants: 0.040159 (xx) 0.000009 (xx)
Max drift after symmetrization by translation: 0.000000 (zz) 0.000000 (zz)
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".
_
___ _ __ __| |
/ _ \ '_ \ / _` |
| __/ | | | (_| |
\___|_| |_|\__,_|
~~~
```{image} NaCl-band-PDOS-NAC.png
:width: 50%
```
## MgB2 characters of ireducible representations
~~~bash
% phonopy-load --irreps 0 0 0
_
_ __ | |__ ___ _ __ ___ _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
| |_) | | | | (_) | | | | (_) || |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
|_| |_| |___/
2.26.6-rdev26+g1f6a3f81
Compiled with OpenMP support (max 10 threads).
Running in phonopy.load mode.
Python version 3.12.4
Spglib version 2.4.0
Crystal structure was read from "phonopy_disp.yaml".
Unit of length: angstrom
Ir-representation mode
Settings:
Supercell: [3 3 2]
Spacegroup: P6/mmm (191)
Number of symmetry operations in supercell: 432
Use -v option to watch primitive cell, unit cell, and supercell structures.
Force sets were read from "FORCE_SETS".
Displacements were overwritten by "FORCE_SETS".
Max drift of force constants: -0.039930 (zz) -0.000007 (zz)
Max drift after symmetrization by translation: 0.000000 (yy) 0.000000 (yy)
-------------------------------
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 ( -0.000): Not found. Try adjusting tolerance value in IRREPS.
( 3, 0.0) ( 3, 180.0) ( 2, 0.0) ( 2, 180.0) ( 0, 0.0) ( 0, 0.0)
( 1, 180.0) ( 1, 0.0) ( 0, 0.0) ( 0, 0.0) ( 2, 0.0) ( 2, 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)
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 ( 11.975): 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
...
```
```{image} Al-QHA.png
:width: 50%
```
## Si-gruneisen
See {ref}`phonopy_gruneisen`.
|
