Merge branch 'doc' into publish-gh-pages

phonopy · Oct 19, 2023 · 2fced3a · 2fced3a
2 parents c356189 + b0af413
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: trailing-whitespace
   - id: end-of-file-fixer
@@ -19,7 +19,7 @@ repos:
     - "--ignore=E203,W503"
 
 - repo: https://github.com/psf/black
-  rev: 23.7.0
+  rev: 23.9.1
   hooks:
   - id: black
     args:
@@ -37,7 +37,7 @@ repos:
       name: isort (python)
 
 - repo: https://github.com/Takishima/cmake-pre-commit-hooks
-  rev: v1.9.2
+  rev: v1.9.4
   hooks:
     - id: clang-format
       args:

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)=
@@ -627,7 +637,6 @@ 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`.
 
-
 ```bash
 % phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --const-ave-pp=1e-10
 ```
@@ -908,12 +917,10 @@ 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
@@ -1240,8 +1247,8 @@ This modifies default input and output file names.
 
 This is equivalent to setting `-i` and `-o` simultaneously.
 
-
 ## References
+
 ```{bibliography}
 :filter: docname in docnames
 ```