Use bibtex style reference in document

doc/command-options.md

@@ -814,7 +814,7 @@ $$
 
 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.
+$2\pi$ treatment. See also {cite}`Togo-PRB-2015,Togo-JPCM-2022`.
 
 (ise_option)=
 
@@ -878,6 +878,8 @@ $$
  \int_0^\infty \frac{d\omega}{2\pi} A_\lambda(\omega) = 1.
 $$
 
+See also {cite}`Togo-JPCM-2022`.
+
 ### `--spf` (`SPECTRAL_FUNCTION = .TRUE.`)
 
 Spectral function of self energy $A_\lambda(\omega)$ is calculated with respect
@@ -903,13 +905,12 @@ 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.
 ```
 
-An example of application of spectral function calculation is found at
-{ref}`spectral_function_reference`.
 
 (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
@@ -933,6 +934,8 @@ $$
 \end{align}
 $$
 
+(See also {cite}`Togo-PRB-2015,Togo-JPCM-2022`.)
+
 ```bash
 % phono3py --fc2 --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0  8 8 8"
 ```
@@ -957,6 +960,8 @@ $$
 \end{align}
 $$
 
+(See also {cite}`Togo-PRB-2015,Mizokami-PRB-2018,Togo-JPCM-2022`.)
+
 ```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
 ```
@@ -1231,3 +1236,9 @@ This rule is applied to
 This modifies default input and output file names.
 
 This is equivalent to setting `-i` and `-o` simultaneously.
+
+
+## References
+```{bibliography}
+:filter: docname in docnames
+```

doc/conf.py

@@ -25,7 +25,11 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 # extensions = ['sphinx.ext.imgmath']
-extensions = ["sphinx.ext.mathjax", "myst_parser"]
+extensions = [
+    "sphinx.ext.mathjax",
+    "myst_parser",
+    "sphinxcontrib.bibtex",
+]
 myst_enable_extensions = ["linkify", "dollarmath", "amsmath"]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -34,6 +38,10 @@ templates_path = ["_templates"]
 # The suffix of source filenames.
 source_suffix = ".rst"
 
+# https://pypi.org/project/sphinxcontrib-bibtex/
+bibtex_bibfiles = ["references.bib"]
+bibtex_default_style = "unsrt"
+
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
 

doc/index.md

@@ -58,7 +58,6 @@ phono3py-api
 phono3py-load
 tips
 citation
-reference
 changelog
 ```
 

doc/references.bib

@@ -0,0 +1,41 @@
+@article{Togo-PRB-2015,
+  title = {Distributions of phonon lifetimes in Brillouin zones},
+  author = {Togo, Atsushi and Chaput, Laurent and Tanaka, Isao},
+  journal = {Phys. Rev. B},
+  volume = {91},
+  issue = {9},
+  pages = {094306},
+  numpages = {31},
+  year = {2015},
+  month = {Mar},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevB.91.094306},
+  url = {https://link.aps.org/doi/10.1103/PhysRevB.91.094306}
+}
+@article{Togo-JPCM-2022,
+  doi = {10.1088/1361-648X/ac7b01},
+  url = {https://dx.doi.org/10.1088/1361-648X/ac7b01},
+  year = {2022},
+  month = {jul},
+  publisher = {IOP Publishing},
+  volume = {34},
+  number = {36},
+  pages = {365401},
+  author = {Atsushi Togo and Hiroyuki Hayashi and Terumasa Tadano and Satoshi Tsutsui and Isao Tanaka},
+  title = {LO-mode phonon of KCl and NaCl at 300 K by inelastic x-ray scattering measurements and first principles calculations},
+  journal = {J. Phys. Condens. Matter},
+}
+@article{Mizokami-PRB-2018,
+  title = {Lattice thermal conductivities of two ${\mathrm{SiO}}_{2}$ polymorphs by first-principles calculations and the phonon Boltzmann transport equation},
+  author = {Mizokami, Keiyu and Togo, Atsushi and Tanaka, Isao},
+  journal = {Phys. Rev. B},
+  volume = {97},
+  issue = {22},
+  pages = {224306},
+  numpages = {10},
+  year = {2018},
+  month = {Jun},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevB.97.224306},
+  url = {https://link.aps.org/doi/10.1103/PhysRevB.97.224306}
+}