Merge branch 'rc'

phonopy · Mar 20, 2024 · e8cdd5e · e8cdd5e
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -19,7 +19,7 @@ repos:
     - "--ignore=E203,W503"
 
 - repo: https://github.com/psf/black
-  rev: 24.1.1
+  rev: 24.2.0
   hooks:
   - id: black
     args:

diff --git a/LICENSE b/LICENSE
@@ -1,5 +1,4 @@
-Copyright (c) 2014, Atsushi Togo
-All rights reserved.
+Copyright (c) 2015-2024, Phonopy. All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions

diff --git a/doc/changelog.md b/doc/changelog.md
@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Mar-20-2024: Version 2.10.0
+
+- Maintenance release
+
 ## Feb-2-2024: Version 2.9.2
 
 - `boundary_mfp` value is stored in `kappa-*.hdf5` file when it is specified.

diff --git a/doc/citation.md b/doc/citation.md
@@ -24,26 +24,27 @@ indeed helps the phono3py project to continue:
   }
   ```
 
-- "First-principles Phonon Calculations with Phonopy and Phono3py",
+- "Implementation strategies in phonopy and phono3py",
 
-  Atsushi Togo, J. Phys. Soc. Jpn., **92**, 012001-1-21 (2023)
+  Atsushi Togo, Laurent Chaput, Terumasa Tadano, and Isao Tanaka, J. Phys. Condens. Matter **35**, 353001-1-22 (2023)
 
-  https://doi.org/10.7566/JPSJ.92.012001 (Open access)
+  https://dx.doi.org/10.1088/1361-648X/acd831 (Open access)
 
   ```
-  @article{phonopy-phono3py-JPSJ,
-    author  = {Togo ,Atsushi},
-    title   = {First-principles Phonon Calculations with Phonopy and Phono3py},
-    journal = {J. Phys. Soc. Jpn.},
-    volume  = {92},
-    number  = {1},
-    pages   = {012001},
+  @article{phonopy-phono3py-JPCM,
+    author  = {Togo, Atsushi and Chaput, Laurent and Tadano, Terumasa and Tanaka, Isao},
+    title   = {Implementation strategies in phonopy and phono3py},
+    journal = {J. Phys. Condens. Matter},
+    volume  = {35},
+    number  = {35},
+    pages   = {353001},
     year    = {2023},
-    doi     = {10.7566/JPSJ.92.012001}
+    doi     = {10.1088/1361-648X/acd831}
   }
   ```
 
 (citation_direct_solution_lbte)=
+
 ## Citation of direct solution of LBTE (`--lbte`)
 
 If you have used direct solution of LBTE in phono3py, please cite the
@@ -75,8 +76,9 @@ If you have used the solution of the Wigner transport equation in phono3py, plea
 following articles:
 
 (citation_unified_theory)=
+
 - "Unified theory of thermal transport in crystals and glasses"
-  Michele Simoncelli, Nicola  Marzari, and Francesco Mauri, Nat. Phys., **15**, 809 (2019)
+  Michele Simoncelli, Nicola Marzari, and Francesco Mauri, Nat. Phys., **15**, 809 (2019)
 
   ```
   @article{NatPhys.15.809,
@@ -92,9 +94,11 @@ following articles:
     url = {https://www.nature.com/articles/s41567-019-0520-x}
   }
   ```
-(citation_wigner_formulation)=
+
+  (citation_wigner_formulation)=
+
 - "Wigner formulation of thermal transport in solids"
-  Michele Simoncelli, Nicola  Marzari, and Francesco Mauri, Physical Review X **12**, 041011 (2022)
+  Michele Simoncelli, Nicola Marzari, and Francesco Mauri, Physical Review X **12**, 041011 (2022)
 
   ```
   @article{PhysRevX.12.041011,

diff --git a/doc/command-options.md b/doc/command-options.md
@@ -174,7 +174,7 @@ created from `FORCES_FC2` and `phono3py_disp.yaml` instead of `FORCES_FC3` and
 % phono3py --cfs --dim-fc2="x x x"
 ```
 
-## Supercell and primitive cell
+## Supercell, primitive cell, masses, magnetic moments
 
 (dim_option)=
 
@@ -237,6 +237,16 @@ http://phonopy.github.io/phonopy/setting-tags.html#primitive-axis. When a proper
 `phono3py_disp.yaml` exists in the current directory, this is unnecessary to be
 specified.
 
+### `--mass` (`MASS`)
+
+Atomic masses of **primitive cell** are overwritten. See more details in
+[phonopy web page](https://phonopy.github.io/phonopy/setting-tags.html#mass).
+
+### `--magmom` (`MAGMOM`)
+
+Magnetic moments of **unit cell** are specified. This information is used to find crystal symmetry. See more details in [phonopy
+web page](https://phonopy.github.io/phonopy/setting-tags.html#magmom).
+
 ## Displacement creation
 
 (create_displacements_option)=
@@ -597,7 +607,9 @@ where $N$ is the number of grid points on the sampling mesh.
 $\Phi_{\lambda \lambda' \lambda''} \equiv 0$ unless
 $\mathbf{q} + \mathbf{q}' + \mathbf{q}'' = \mathbf{G}$.
 
-See also references {cite}`Togo-PRB-2015,Mizokami-PRB-2018`.
+<!-- See also references {cite}`Togo-PRB-2015,Mizokami-PRB-2018`. -->
+
+See also {ref}`reference papers <ave_pp_reference>`.
 
 This option works only when `--read-gamma` and `--br` options are activated
 where the averaged phonon-phonon interaction that is read from
@@ -627,8 +639,11 @@ constant value and $|\Phi_{\lambda \lambda'
 {ref}`--ave-pp <ave_pp_option>` for thermal conductivity calculation. This
 option works only when `--br` options are activated. Therefore third-order force
 constants are not necessary to input. The physical unit of the value is
-$\text{eV}^2$. See also references {cite}`Togo-PRB-2015,Mizokami-PRB-2018`.
+$\text{eV}^2$.
 
+<!-- See also references {cite}`Togo-PRB-2015,Mizokami-PRB-2018`. -->
+
+See also {ref}`reference papers <ave_pp_reference>`.
 
 ```bash
 % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --const-ave-pp=1e-10
@@ -819,7 +834,9 @@ $$
 
 respectively. In the above formulae, angular frequency $\omega$ is used, but in
 the calculation results, ordinal frequency $\nu$ is used. Be careful about
-$2\pi$ treatment. See also references {cite}`Togo-PRB-2015,Togo-JPCM-2022`.
+$2\pi$ treatment.
+
+See also {ref}`reference papers <spectral_function_reference>`.
 
 (ise_option)=
 
@@ -883,7 +900,7 @@ $$
  \int_0^\infty \frac{d\omega}{2\pi} A_\lambda(\omega) = 1.
 $$
 
-See also reference {cite}`Togo-JPCM-2022`.
+See also {ref}`reference papers <spectral_function_reference>`.
 
 ### `--spf` (`SPECTRAL_FUNCTION = .TRUE.`)
 
@@ -910,12 +927,10 @@ file, where $A_{\mathrm{q}j}$ is normalied as given above, i.e., numerical
 sum of stored value for each band should become roughly 1.
 ```
 
-
 (jdos_option)=
 
 ## Joint density of states (JDOS) and weighted-JDOS
 
-
 ### `--jdos` (`JOINT_DOS = .TRUE.`)
 
 Two classes of joint density of states (JDOS) are calculated. The result is
@@ -939,7 +954,7 @@ $$
 \end{align}
 $$
 
-(See also references {cite}`Togo-PRB-2015,Togo-JPCM-2022`.)
+See also {ref}`reference papers <spectral_function_reference>`.
 
 ```bash
 % phono3py --fc2 --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0  8 8 8"
@@ -965,7 +980,7 @@ $$
 \end{align}
 $$
 
-(See also references {cite}`Togo-PRB-2015,Mizokami-PRB-2018,Togo-JPCM-2022`.)
+See also {ref}`reference papers <spectral_function_reference>`.
 
 ```bash
 % phono3py --fc2 --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0  8 8 8" --ts=300
@@ -1242,8 +1257,8 @@ This modifies default input and output file names.
 
 This is equivalent to setting `-i` and `-o` simultaneously.
 
+<!-- ## References
 
-## References
 ```{bibliography}
 :filter: docname in docnames
-```
+``` -->
diff --git a/doc/conf.py b/doc/conf.py
@@ -58,9 +58,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "2.9"
+version = "2.10"
 # The full version, including alpha/beta/rc tags.
-release = "2.9.2"
+release = "2.10.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/cutoff-pair.md b/doc/cutoff-pair.md
@@ -1,8 +1,13 @@
 (command_cutoff_pair)=
+
 # Force constants calculation with cutoff pair-distance
 
 Here the detail of the command option {ref}`--cutoff_pair <cutoff_pair_option>`
-is explained. See also reference {cite}`Mizokami-PRB-2018`.
+is explained.
+
+<!-- See also reference {cite}`Mizokami-PRB-2018`. -->
+
+See also {ref}`a reference paper <cutoff_pair_reference>`.
 
 ```{contents}
 :depth: 2
@@ -270,7 +275,6 @@ if data2['distance'] < 5.0:  # 5.0 is cutoff-pair distance
 we can find the supercell IDs almost equivalent to those obtained
 above for `--cutoff-pair="5.0"`.
 
-
 ## Tests
 
 ### Si-PBE
@@ -429,7 +433,7 @@ number_of_pairs_in_cutoff: 1248
   300.0     235.728    235.728    219.102      0.000     -0.000     -0.000
 ```
 
-## References
+<!-- ## References
 ```{bibliography}
 :filter: docname in docnames
-```
+``` -->
diff --git a/doc/index.md b/doc/index.md
@@ -4,8 +4,8 @@ This software calculates phonon-phonon interaction and related properties using
 the supercell approach. For example, the following physical values are obtained:
 
 - {ref}`Lattice thermal conductivity by relaxation time approximation
-  and direct-solution of phonon Boltzmann equation and
-  the Wigner transport equation <LTC_options>`
+and direct-solution of phonon Boltzmann equation and
+the Wigner transport equation <LTC_options>`
 - {ref}`Cummulative lattice thermal conductivity and related properties <auxiliary_tools_kaccum>`
 - {ref}`self_energy_options` (Phonon lifetime/linewidth)
 - {ref}`jdos_option`
@@ -20,10 +20,10 @@ the supercell approach. For example, the following physical values are obtained:
 Papers that may introduce phono3py:
 
 - Theoretical background is summarized in this paper:
-  http://dx.doi.org/10.1103/PhysRevB.91.094306 (arxiv
-  http://arxiv.org/abs/1501.00691).
+  <http://dx.doi.org/10.1103/PhysRevB.91.094306> (arxiv
+  <http://arxiv.org/abs/1501.00691>).
 - Introduction to phono3py application:
-  https://doi.org/10.1103/PhysRevB.97.224306 (open access).
+  <https://doi.org/10.1103/PhysRevB.97.224306> (open access).
 
 ```{image} Si-kaccum.png
 :width: 20%
@@ -58,21 +58,28 @@ phono3py-api
 phono3py-load
 tips
 citation
+reference
 changelog
 ```
 
 ## Mailing list
 
 For questions, bug reports, and comments, please visit following mailing list:
 
-https://lists.sourceforge.net/lists/listinfo/phonopy-users
+<https://lists.sourceforge.net/lists/listinfo/phonopy-users>
 
 Message body including attached files has to be smaller than 300 KB.
 
 ## License
 
 BSD-3-Clause (New BSD)
 
-## Contact
+## Contributors
 
-- Author: [Atsushi Togo](http://atztogo.github.io/)
+- Atsushi Togo, National Institute for Materials Science
+
+## Acknowledgements
+
+Phono3py development is supported by:
+
+- National Institute for Materials Science
diff --git a/doc/install.md b/doc/install.md
@@ -161,7 +161,7 @@ wrong python libraries can be imported.
    For macOS ARM64 system, currently only openblas can be chosen:
 
    ```bash
-   % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler spglib cmake openblas="0.3.18"
+   % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler spglib cmake openblas
    ```
 
    Note that using hdf5 files on NFS mounted file system, you may have to disable

diff --git a/doc/reference.md b/doc/reference.md
@@ -1,9 +1,50 @@
 # References
 
+(reviews_reference)=
+
+## Reviews
+
+- "First-principles Phonon Calculations with Phonopy and Phono3py" Atsushi Togo,
+  J. Phys. Soc. Jpn. **92**, 012001-1-21 (2023)
+  [[doi](https://doi.org/10.7566/JPSJ.92.012001)] open access
+
+- "Implementation strategies in phonopy and phono3py" Atsushi Togo, Laurent
+  Chaput, Terumasa Tadano, Isao Tanaka, J. Phys.: Condens. Matter **35**,
+  353001-1-22 (2023) [[doi](https://doi.org/10.1088/1361-648x/acd831)] open
+  access
+
+(ave_pp_reference)=
+
+## Averaged phonon-phonon interaction strength
+
+- "Distributions of phonon lifetimes in Brillouin zones" Atsushi Togo, Laurent
+  Chaput, and Isao Tanaka, Phys. Rev. B, **91**, 094306-1-31 (2015).
+  [[doi](https://doi.org/10.1103/PhysRevB.91.094306)]
+
+- "Lattice thermal conductivities of two SiO2 polymorphs by first-principles
+  calculations and the phonon Boltzmann transport equation" Keiyu Mizokami,
+  Atsushi Togo, and Isao Tanaka, Phys. Rev. B **97**, 224306-1-10 (2018)
+  [[doi](https://doi.org/10.1103/PhysRevB.97.224306)] open access
+
+(cutoff_pair_reference)=
+
+## Cutoff-pair displacements
+
+- "Lattice thermal conductivities of two SiO2 polymorphs by first-principles
+  calculations and the phonon Boltzmann transport equation" Keiyu Mizokami,
+  Atsushi Togo, and Isao Tanaka, Phys. Rev. B **97**, 224306-1-10 (2018)
+  [[doi](https://doi.org/10.1103/PhysRevB.97.224306)] open access
+
 (spectral_function_reference)=
+
 ## Self-energy, spectral function, joint-density of states
 
-“LO-mode phonon of KCl and NaCl at 300 K by inelastic x-ray scattering
-measurements and first principles calculations” Atsushi Togo, Hiroyuki Hayashi,
-Terumasa Tadano, Satoshi Tsutsui, Isao Tanaka, J. Phys.: Condens. Matter 34,
-365401-1-15 (2022) [[doi]](https://doi.org/10.1088/1361-648X/ac7b01).
+- "LO-mode phonon of KCl and NaCl at 300 K by inelastic x-ray scattering
+  measurements and first principles calculations" Atsushi Togo, Hiroyuki
+  Hayashi, Terumasa Tadano, Satoshi Tsutsui, Isao Tanaka, J. Phys.: Condens.
+  Matter **34**, 365401-1-15 (2022)
+  [[doi](https://doi.org/10.1088/1361-648X/ac7b01)] open access
+
+- "First-principles Phonon Calculations with Phonopy and Phono3py" Atsushi Togo,
+  J. Phys. Soc. Jpn. **92**, 012001-1-21 (2023)
+  [[doi](https://doi.org/10.7566/JPSJ.92.012001)] open access
diff --git a/phono3py/other/isotope.py b/phono3py/other/isotope.py
@@ -256,7 +256,6 @@ def init_dynamical_matrix(
             nac_params=nac_params,
             frequency_scale_factor=frequency_scale_factor,
             decimals=decimals,
-            symprec=self._symprec,
         )
 
     def set_nac_q_direction(self, nac_q_direction=None):