deploy: 99b6548

_sources/index.md

@@ -35,5 +35,6 @@ velph-init
 velph-init-template
 velph-subcommands
 velph-example
+reference
 changelog
 ```

_sources/install.md

@@ -5,7 +5,7 @@
 * phonopy
 * phono3py
 * spglib
-* finufft
+* {ref}`reference_finufft`
 * click
 * tomli
 * tomli-w

_sources/phelel-command.md

@@ -8,7 +8,7 @@ phonon calculations.
 
 The following example demonstrates operations using the `phelel` command:
 
-```
+```bash
 % phelel -d --dim 2 2 2 -c POSCAR-unitcell --pa auto --pm
 
 # After running VASP calculations in directories corresponding to displacements:
@@ -21,7 +21,7 @@ The following example demonstrates operations using the `phelel` command:
 Supercells with displacements can be generated by combining the following
 command options. For example:
 
-```
+```bash
 % phelel -d --dim 2 2 2 -c POSCAR-unitcell --pa auto --pm
 ```
 
@@ -46,11 +46,11 @@ three values are given, they represent the diagonal elements of the supercell
 matrix, meaning each axis of the input unit cell is simply extended by the
 corresponding integer factor.
 
-```
+```bash
 % phelel --dim 2 2 2 [OPTIONS]
 ```
 
-```
+```bash
 % phelel --dim 0 1 1 1 0 1 1 1 0 [OPTIONS]
 ```
 
@@ -59,7 +59,7 @@ corresponding integer factor.
 
 Unit cell structure is specified.
 
-```
+```bash
 % phelel -c POSCAR-unitcell [OPTIONS]
 ```
 
@@ -70,7 +70,7 @@ symmetrically equivalent displacements in the opposite direction. With this
 option specified, both directions are included in the generated supercells with
 dispacements. Use of this option is recommended.
 
-```
+```bash
 % phelel --pm [OPTIONS]
 ```
 
@@ -81,7 +81,7 @@ under the configurations of displacements in supercells, those data are stored
 in cetain files. Those are read and then the derivatives are computed by the
 following command option, e.g.,
 
-```
+```bash
 % phelel --cd disp-000 disp-001 disp-002 disp-003 disp-004
 ```
 

_sources/velph-command.md

@@ -22,7 +22,7 @@ to atomic displacement, resulting in the `phelel_params.hdf5` file. Most of the
 
 A list of supported subcommands is displayed by typing:
 
-```
+```bash
 % velph
 Usage: velph [OPTIONS] COMMAND [ARGS]...
 
@@ -51,6 +51,6 @@ Commands:
 
 This command provides a quick reference of calculation steps.
 
-```
+```bash
 % velph hints
 ```

_sources/velph-init.md

@@ -3,7 +3,7 @@
 
 `velph init` with command options will generate modified `velph.toml` from the
 template.
-```
+```bash
 % velph init [OPTIONS] CELL_FILENAME PROJECT_FOLDER
 ```
 

_sources/velph-subcommands.md

@@ -16,7 +16,7 @@ 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`.
 
-```
+```bash
 % ls
 POSCAR-unitcell  POTCAR  velph-tmpl.toml
 % velph init --template-toml velph-tmpl.toml POSCAR-unitcell relax
@@ -68,8 +68,31 @@ carried out by the `phelel` command in the {ref}`workflow <workflow_minimal>`.
 
 ### `velph phelel init`
 
+This subcommand generates the `phelel_disp.yaml` file, which contains
+information about the supercell structure and displacements. It is recommended
+to generate `phelel_disp.yaml` after performing the NAC calculation (see
+{ref}`velph_nac_subcommand`). At this stage, the dielectric constant and Born
+effective charges are written to `phelel_disp.yaml`, and these values are
+ultimately stored in `phelel_params.hdf5` through the `phelel_disp.yaml` file.
+
+```bash
+% 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`
 
+```bash
+% 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".
+```
+
 ### `velph phelel differentiate`
 
 ### `velph phelel phonopy`
@@ -83,9 +106,9 @@ 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
+calculation, e.g., as
 
-```
+```bash
 % ls
 POSCAR-unitcell  POTCAR  velph-tmpl.toml
 % velph init --template-toml velph-tmpl.toml POSCAR-unitcell relax
@@ -96,15 +119,16 @@ 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.
+This subcommand generates VASP input files and a job script for crystal
+structure relaxation. Initially, these files are created in the `iter1`
+directory. The process supports multiple relaxation steps, where the `CONTCAR`
+file from the previous iteration is used as the `POSCAR` for the next step once
+the preceding VASP calculation is complete. Each subsequent set of input files
+is generated in directories named `iter2`, `iter3`, and so on.
 
-```
+```bash
 % ls
 POTCAR  velph.toml
 % velph relax generate
@@ -121,14 +145,26 @@ VASP input files were made in "relax/iter2".
 ...
 ```
 
+(velph_nac_subcommand)=
 ## `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.
+and treatment of long range term of electron-phonon interaction calculation.
 
 ### `velph nac generate`
 
+After the VASP calculation is complete, the dielectric constant and Born
+effective charges are extracted from the `vasprun.xml` file during the execution
+of `velph phelel init`, `velph phono3py init`, or `velph phonopy init`. The
+extracted values are then written to `phelel_disp.yaml`, `phono3py_disp.yaml`,
+or `phonopy_disp.yaml`, respectively.
+
+```bash
+% velph nac generate
+VASP input files were made in "nac".
+```
+
 ## `velph el_bands`
 
 ### `velph el_bands generate`