Merge branch 'develop' into publish-gh-pages

phonopy · Jan 7, 2025 · 70ce205 · 70ce205
2 parents b0a5193 + d90751d
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -10,7 +10,7 @@ repos:
   - id: check-added-large-files
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.8.4
+  rev: v0.8.6
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

diff --git a/doc/velph-command.md b/doc/velph-command.md
@@ -46,6 +46,7 @@ Commands:
   transport   Choose transport options.
 ```
 
+(velph_hints)=
 ## `velph hints`
 
 This command provides a quick reference of calculation steps.

diff --git a/doc/velph-subcommands.md b/doc/velph-subcommands.md
@@ -1,11 +1,68 @@
 (velph_subcommands)=
 # `velph` subcommands
 
-`velph init` is
+The `velph` subcommands, except for {ref}`velph_init` and {ref}`velph_hints`,
+are explained on this page.
+
+The following subcommands must be executed in the directory containing the
+`velph.toml` file. This ensures that the directories and files generated are
+properly organized relative to the current directory where `velph.toml` is
+located.
+
+In the following example, two `velph init` command operations generate two
+different directories. The first operation performs crystal structure relaxation
+in the `relax` directory. The second operation, using the relaxed crystal
+structure, carries out additional calculations required for electron-phonon
+interactions in the `calc` directory. Details about `velph-tmpl.toml` are
+described in {ref}`velph_init_template`.
+
+```
+% ls
+POSCAR-unitcell  POTCAR  velph-tmpl.toml
+% velph init --template-toml velph-tmpl.toml POSCAR-unitcell relax
+...
+% cd relax
+% velph relax generate
+...
+# Run VASP relaxation calculation
+...
+% cd ..
+% ls
+POSCAR-unitcell  POTCAR  relax/  velph-tmpl.toml
+% velph init --template-toml velph-tmpl.toml `ls relax/relax/iter*/CONTCAR|tail -n 1` calc
+...
+% cd calc
+% ls
+POTCAR  velph.toml
+% velph nac generate
+VASP input files were made in "nac".
+% ls
+POTCAR  nac/  velph.toml
+...
+# Run NAC calculation
+...
+% velph phelel init
+Found "nac" directory. Read NAC params.
+"phelel/phelel_disp.yaml" was generated.
+VASP input files will be generated by "velph phelel generate".
+% velph phelel generate
+VASP input files were generated in "phelel/disp-000".
+VASP input files were generated in "phelel/disp-001".
+VASP input files were generated in "phelel/disp-002".
+VASP input files were generated in "phelel/disp-003".
+VASP input files were generated in "phelel/disp-004".
+% ls
+POTCAR  nac/  phelel/  velph.toml
+% velph phelel init
+Found "nac" directory. Read NAC params.
+"phelel/phelel_disp.yaml" was generated.
+VASP input files will be generated by "velph phelel generate".
+...
+```
 
 ## `velph phelel`
 
-This command calculates the derivatives of local potentials and PAW strengths
+This subcommand calculates the derivatives of local potentials and PAW strengths
 with respect to displacement, performing similar operations as steps 1 and 3
 carried out by the `phelel` command in the {ref}`workflow <workflow_minimal>`.
 
@@ -25,10 +82,51 @@ carried out by the `phelel` command in the {ref}`workflow <workflow_minimal>`.
 
 ## `velph relax`
 
+It is recommended to create a project directory secific for relaxation
+calculation, e.g., by
+
+```
+% ls
+POSCAR-unitcell  POTCAR  velph-tmpl.toml
+% velph init --template-toml velph-tmpl.toml POSCAR-unitcell relax
+...
+% cd relax
+% ls
+POTCAR  velph.toml
+% velph relax generate
+...
+```
+
 ### `velph relax generate`
 
+This subcommand prepares VASP input files and a job script for crystal structure
+relaxation. Multiple relaxation calculations can be performed. In such cases,
+the `CONTCAR` from the previous calculation is used as the `POSCAR` for the next
+calculation to generate a new set of VASP input files.
+
+```
+% ls
+POTCAR  velph.toml
+% velph relax generate
+VASP input files were made in "relax/iter1".
+...
+# Run VASP calculation in relax/iter1
+...
+% ls
+POTCAR  relax/  velph.toml
+% velph relax generate
+"relax/iter1" exists.
+"relax/iter1/CONTCAR" will be as new "POSCAR".
+VASP input files were made in "relax/iter2".
+...
+```
+
 ## `velph nac`
 
+This subcommand is used to calculate dielectric constant and Born effective
+charges that are used for non-analytical term correction of phonon calculation
+and treatment of long range term of electron phonon interaction.
+
 ### `velph nac generate`
 
 ## `velph el_bands`