mirror of https://github.com/phonopy/phonopy.git
497 lines
16 KiB
Markdown
497 lines
16 KiB
Markdown
(examples_link)=
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# Examples
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Phonopy supports various external force calculators (mainly for abinitio codes).
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The examples below are given for the default system that is equivalent to VASP
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style. Most of usage is universal among the force calculators. So it is also
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useful for non-VASP users to see the examples below. The list of the force
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calculators and the links to their specific usages are shown at
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{ref}`calculator_interfaces`.
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Example files are found at
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https://github.com/phonopy/phonopy/tree/master/example. The same are found in
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the example directory of the phonopy package downloaded at
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https://github.com/phonopy/phonopy/archive/master.zip. The followings show how
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some of those examples work. Note that sometimes the followings are outdated
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than the examples in the phonopy package. So the results or displace outputs can
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be different.
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## Si
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### `FORCE_SETS` file creation for VASP
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~~~
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% phonopy -f vasprun.xml
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_
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_ __ | |__ ___ _ __ ___ _ __ _ _
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| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
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| |_) | | | | (_) | | | | (_) || |_) | |_| |
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| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
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|_| |_| |___/
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2.26.6
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Compiled with OpenMP support (max 10 threads).
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Python version 3.12.4
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Spglib version 2.4.0
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Displacements were read from "phonopy_disp.yaml".
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counter (file index): 1
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"FORCE_SETS" has been created.
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_
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___ _ __ __| |
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/ _ \ '_ \ / _` |
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| __/ | | | (_| |
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\___|_| |_|\__,_|
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~~~
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where `vasprun.xml` is the VASP output.
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### DOS
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~~~
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% phonopy-load --mesh 31 31 31 -p
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_
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_ __ | |__ ___ _ __ ___ _ __ _ _
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| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
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| |_) | | | | (_) | | | | (_) || |_) | |_| |
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| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
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|_| |_| |___/
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2.26.6
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Compiled with OpenMP support (max 10 threads).
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Running in phonopy.load mode.
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Python version 3.12.4
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Spglib version 2.4.0
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Crystal structure was read from "phonopy_disp.yaml".
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Unit of length: angstrom
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Mesh sampling mode
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Settings:
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Sampling mesh: [31 31 31]
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Supercell: [2 2 2]
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Primitive matrix:
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[1. 0. 0.]
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[0. 1. 0.]
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[0. 0. 1.]
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Spacegroup: Fd-3m (227)
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Number of symmetry operations in supercell: 384
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Use -v option to watch primitive cell, unit cell, and supercell structures.
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Force sets were read from "FORCE_SETS".
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Displacements were overwritten by "FORCE_SETS".
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Max drift of force constants: -0.000001 (zz) -0.000001 (zz)
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Max drift after symmetrization by translation: -0.000000 (xx) -0.000000 (xx)
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Mesh numbers: [31 31 31]
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Number of irreducible q-points on sampling mesh: 816/29791
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Calculating phonons on sampling mesh...
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Calculating DOS...
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Summary of calculation was written in "phonopy.yaml".
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_
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___ _ __ __| |
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/ _ \ '_ \ / _` |
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| __/ | | | (_| |
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\___|_| |_|\__,_|
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~~~
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```{image} Si-DOS.png
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:width: 50%
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```
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### Thermal properties
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~~~
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% phonopy-load --mesh 31 31 31 -t -p
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_
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_ __ | |__ ___ _ __ ___ _ __ _ _
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| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
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| |_) | | | | (_) | | | | (_) || |_) | |_| |
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| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
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|_| |_| |___/
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2.26.6-rdev26+g1f6a3f81
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Compiled with OpenMP support (max 10 threads).
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Running in phonopy.load mode.
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Python version 3.12.4
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Spglib version 2.4.0
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Crystal structure was read from "phonopy_disp.yaml".
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Unit of length: angstrom
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Mesh sampling mode
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Settings:
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Sampling mesh: [31 31 31]
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Supercell: [2 2 2]
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Primitive matrix:
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[1. 0. 0.]
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[0. 1. 0.]
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[0. 0. 1.]
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Spacegroup: Fd-3m (227)
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Number of symmetry operations in supercell: 384
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Use -v option to watch primitive cell, unit cell, and supercell structures.
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Force sets were read from "FORCE_SETS".
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Displacements were overwritten by "FORCE_SETS".
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Max drift of force constants: -0.000001 (zz) -0.000001 (zz)
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Max drift after symmetrization by translation: -0.000000 (xx) -0.000000 (xx)
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Mesh numbers: [31 31 31]
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Number of irreducible q-points on sampling mesh: 816/29791
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Calculating phonons on sampling mesh...
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Calculating thermal properties...
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Cutoff frequency: 0.00000
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Number of phonon frequencies less than cutoff frequency: 1/178746
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# T [K] F [kJ/mol] S [J/K/mol] C_v [J/K/mol] E [kJ/mol]
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0.000 11.7110492 0.0000000 0.0000000 11.7110492
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10.000 11.7109211 0.0292204 0.0657586 11.7112133
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20.000 11.7100041 0.1915595 0.5807546 11.7138352
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30.000 11.7060581 0.6585603 1.9572223 11.7258149
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40.000 11.6956193 1.4847934 3.9396878 11.7550111
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50.000 11.6754205 2.5932055 6.0735527 11.8050808
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60.000 11.6431482 3.8848280 8.1404132 11.8762379
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70.000 11.5973537 5.2885744 10.1087510 11.9675539
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80.000 11.5371421 6.7633329 12.0156965 12.0782088
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90.000 11.4619236 8.2874371 13.8993871 12.2077929
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100.000 11.3712686 9.8490970 15.7769306 12.3561783
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...
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~~~
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```{image} Si-props.png
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:width: 50%
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```
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## NaCl
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### Band structure
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This requires to prepare `BORN` file.
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~~~
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% 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
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_
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_ __ | |__ ___ _ __ ___ _ __ _ _
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| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
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| |_) | | | | (_) | | | | (_) || |_) | |_| |
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| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
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|_| |_| |___/
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2.26.6
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Compiled with OpenMP support (max 10 threads).
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Running in phonopy.load mode.
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Python version 3.12.4
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Spglib version 2.4.0
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Crystal structure was read from "phonopy_disp.yaml".
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Unit of length: angstrom
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Band structure mode
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Settings:
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Supercell: [2 2 2]
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Primitive matrix (Auto):
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[0. 0.5 0.5]
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[0.5 0. 0.5]
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[0.5 0.5 0. ]
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Spacegroup: Fm-3m (225)
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Number of symmetry operations in supercell: 1536
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Use -v option to watch primitive cell, unit cell, and supercell structures.
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NAC params were read from "BORN".
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Force sets were read from "FORCE_SETS".
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Displacements were overwritten by "FORCE_SETS".
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Max drift of force constants: 0.040159 (xx) 0.000009 (xx)
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Max drift after symmetrization by translation: 0.000000 (zz) 0.000000 (zz)
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Reciprocal space paths in reduced coordinates:
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[ 0.000 0.000 0.000] --> [ 0.500 0.000 0.000]
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[ 0.500 0.000 0.000] --> [ 0.500 0.500 0.000]
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[ 0.500 0.500 0.000] --> [ 0.000 0.000 0.000]
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[ 0.000 0.000 0.000] --> [ 0.500 0.500 0.500]
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Summary of calculation was written in "phonopy.yaml".
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_
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___ _ __ __| |
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/ _ \ '_ \ / _` |
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| __/ | | | (_| |
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\___|_| |_|\__,_|
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~~~
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```{image} NaCl-band-NAC.png
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:width: 50%
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```
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(example_pdos)=
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### PDOS
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~~~
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% phonopy-load --mesh 41 41 41 --pdos "1, 2" -p
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_
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_ __ | |__ ___ _ __ ___ _ __ _ _
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| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
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| |_) | | | | (_) | | | | (_) || |_) | |_| |
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| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
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|_| |_| |___/
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2.26.6
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Compiled with OpenMP support (max 10 threads).
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Running in phonopy.load mode.
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Python version 3.12.4
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Spglib version 2.4.0
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Crystal structure was read from "phonopy_disp.yaml".
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Unit of length: angstrom
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Mesh sampling mode
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Settings:
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Sampling mesh: [41 41 41]
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Supercell: [2 2 2]
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Primitive matrix (Auto):
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[0. 0.5 0.5]
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[0.5 0. 0.5]
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[0.5 0.5 0. ]
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Spacegroup: Fm-3m (225)
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Number of symmetry operations in supercell: 1536
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Use -v option to watch primitive cell, unit cell, and supercell structures.
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NAC params were read from "BORN".
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Force sets were read from "FORCE_SETS".
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Displacements were overwritten by "FORCE_SETS".
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Max drift of force constants: 0.040159 (xx) 0.000009 (xx)
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Max drift after symmetrization by translation: 0.000000 (zz) 0.000000 (zz)
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Mesh numbers: [41 41 41]
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Number of q-points on sampling mesh: 68921
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Calculating phonons on sampling mesh...
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Calculating projected DOS...
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Summary of calculation was written in "phonopy.yaml".
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_
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___ _ __ __| |
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/ _ \ '_ \ / _` |
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| __/ | | | (_| |
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\___|_| |_|\__,_|
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~~~
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```{image} NaCl-PDOS-nac.png
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:width: 50%
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```
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### Plot band structure and DOS at once
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Band structure and DOS or PDOS can be plotted on one figure together by
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~~~
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% 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
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_
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_ __ | |__ ___ _ __ ___ _ __ _ _
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| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
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| |_) | | | | (_) | | | | (_) || |_) | |_| |
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| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
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2.26.6
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Compiled with OpenMP support (max 10 threads).
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Running in phonopy.load mode.
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Python version 3.12.4
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Spglib version 2.4.0
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Crystal structure was read from "phonopy_disp.yaml".
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Unit of length: angstrom
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Band structure and mesh sampling mode
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Settings:
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Sampling mesh: [41 41 41]
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Supercell: [2 2 2]
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Primitive matrix (Auto):
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[0. 0.5 0.5]
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[0.5 0. 0.5]
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[0.5 0.5 0. ]
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Spacegroup: Fm-3m (225)
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Number of symmetry operations in supercell: 1536
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Use -v option to watch primitive cell, unit cell, and supercell structures.
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NAC params were read from "BORN".
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Force sets were read from "FORCE_SETS".
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Displacements were overwritten by "FORCE_SETS".
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Max drift of force constants: 0.040159 (xx) 0.000009 (xx)
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Max drift after symmetrization by translation: 0.000000 (zz) 0.000000 (zz)
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Reciprocal space paths in reduced coordinates:
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[ 0.000 0.000 0.000] --> [ 0.500 0.000 0.000]
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[ 0.500 0.000 0.000] --> [ 0.500 0.500 0.000]
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[ 0.500 0.500 0.000] --> [ 0.000 0.000 0.000]
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[ 0.000 0.000 0.000] --> [ 0.500 0.500 0.500]
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Mesh numbers: [41 41 41]
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Number of q-points on sampling mesh: 68921
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Calculating phonons on sampling mesh...
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Calculating projected DOS...
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Summary of calculation was written in "phonopy.yaml".
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_
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___ _ __ __| |
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/ _ \ '_ \ / _` |
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| __/ | | | (_| |
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\___|_| |_|\__,_|
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~~~
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```{image} NaCl-band-PDOS-NAC.png
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:width: 50%
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```
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## MgB2 characters of ireducible representations
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~~~bash
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% phonopy-load --irreps 0 0 0
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_
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_ __ | |__ ___ _ __ ___ _ __ _ _
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| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
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| |_) | | | | (_) | | | | (_) || |_) | |_| |
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| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
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|_| |_| |___/
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2.26.6-rdev26+g1f6a3f81
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Compiled with OpenMP support (max 10 threads).
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Running in phonopy.load mode.
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Python version 3.12.4
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Spglib version 2.4.0
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Crystal structure was read from "phonopy_disp.yaml".
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Unit of length: angstrom
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Ir-representation mode
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Settings:
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Supercell: [3 3 2]
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Spacegroup: P6/mmm (191)
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Number of symmetry operations in supercell: 432
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Use -v option to watch primitive cell, unit cell, and supercell structures.
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Force sets were read from "FORCE_SETS".
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Displacements were overwritten by "FORCE_SETS".
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Max drift of force constants: -0.039930 (zz) -0.000007 (zz)
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Max drift after symmetrization by translation: 0.000000 (yy) 0.000000 (yy)
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-------------------------------
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Irreducible representations
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-------------------------------
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q-point: [0. 0. 0.]
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Point group: 6/mmm
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Original rotation matrices:
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1 2 3 4 5 6
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-------- -------- -------- -------- -------- --------
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1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0
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0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0
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0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1
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7 8 9 10 11 12
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-------- -------- -------- -------- -------- --------
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-1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0
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0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0
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0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1
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13 14 15 16 17 18
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-------- -------- -------- -------- -------- --------
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0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0
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-1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0
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0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1
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19 20 21 22 23 24
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-------- -------- -------- -------- -------- --------
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0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0
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1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0
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0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1
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Transformation matrix:
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1.000 -0.000 0.000
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0.000 1.000 0.000
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0.000 0.000 1.000
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Rotation matrices by transformation matrix:
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E i C6 S3 C3 S6
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-------- -------- -------- -------- -------- --------
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1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0
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0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0
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0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1
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C2 sgh C3 S6 C6 S3
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-------- -------- -------- -------- -------- --------
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-1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0
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0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0
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0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1
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C2'' sgv C2' sgd C2'' sgv
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-------- -------- -------- -------- -------- --------
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0 -1 0 0 1 0 -1 0 0 1 0 0 -1 1 0 1 -1 0
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-1 0 0 1 0 0 -1 1 0 1 -1 0 0 1 0 0 -1 0
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0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1
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C2' sgd C2'' sgv C2' sgd
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-------- -------- -------- -------- -------- --------
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0 1 0 0 -1 0 1 0 0 -1 0 0 1 -1 0 -1 1 0
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1 0 0 -1 0 0 1 -1 0 -1 1 0 0 -1 0 0 1 0
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0 0 -1 0 0 1 0 0 -1 0 0 1 0 0 -1 0 0 1
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Character table:
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1 ( -0.000): Not found. Try adjusting tolerance value in IRREPS.
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( 3, 0.0) ( 3, 180.0) ( 2, 0.0) ( 2, 180.0) ( 0, 0.0) ( 0, 0.0)
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( 1, 180.0) ( 1, 0.0) ( 0, 0.0) ( 0, 0.0) ( 2, 0.0) ( 2, 180.0)
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( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0)
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( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0)
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4 ( 9.953): E1u
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( 2, 0.0) ( 2, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 180.0) ( 1, 0.0)
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( 2, 180.0) ( 2, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 0.0) ( 1, 180.0)
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( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
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( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0) ( 0, 0.0)
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6 ( 11.975): A2u
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( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0)
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( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0)
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( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0) ( 1, 180.0) ( 1, 0.0)
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( 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`.
|