Merge branch 'doc' into publish-gh-pages

doc/command-options.md

@@ -605,7 +605,9 @@ 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
@@ -635,7 +637,11 @@ 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
@@ -826,7 +832,9 @@ $$
 
 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)=
 
@@ -890,7 +898,7 @@ $$
  \int_0^\infty \frac{d\omega}{2\pi} A_\lambda(\omega) = 1.
 $$
 
-See also reference {cite}`Togo-JPCM-2022`.
+See also {ref}`reference papers <spectral_function_reference>`.
 
 ### `--spf` (`SPECTRAL_FUNCTION = .TRUE.`)
 
@@ -944,7 +952,7 @@ $$
 \end{align}
 $$
 
-(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"
@@ -970,7 +978,7 @@ $$
 \end{align}
 $$
 
-(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
@@ -1247,8 +1255,8 @@ This modifies default input and output file names.
 
 This is equivalent to setting `-i` and `-o` simultaneously.
 
-## References
+<!-- ## References
 
 ```{bibliography}
 :filter: docname in docnames
-```
+``` -->

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
-```
+``` -->

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`
@@ -17,14 +17,6 @@ the supercell approach. For example, the following physical values are obtained:
 - API is prepared to operate phono3py from Python
   ([example](https://github.com/phonopy/phono3py/blob/master/example/Si-PBEsol/Si.py)).
 
-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).
-- Introduction to phono3py application:
-  https://doi.org/10.1103/PhysRevB.97.224306 (open access).
-
 ```{image} Si-kaccum.png
 :width: 20%
 ```
@@ -58,6 +50,7 @@ phono3py-api
 phono3py-load
 tips
 citation
+reference
 changelog
 ```
 

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

phono3py/phonon3/interaction.py

@@ -846,13 +846,13 @@ def delete_interaction_strength(self):
 
     def _set_fc3(self, fc3):
         if (
-            type(fc3) == np.ndarray
+            isinstance(fc3, np.ndarray)
             and fc3.dtype == np.dtype("double")
             and fc3.flags.aligned
             and fc3.flags.owndata
             and fc3.flags.c_contiguous
             and self._frequency_scale_factor is None
-        ):  # noqa E129
+        ):
             self._fc3 = fc3
         elif self._frequency_scale_factor is None:
             self._fc3 = np.array(fc3, dtype="double", order="C")