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transport Choose transport options.
```

(velph_hints)=
## `velph hints`

This command provides a quick reference of calculation steps.
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(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>`.

Expand All @@ -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`
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2 changes: 1 addition & 1 deletion velph-command.html
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Expand Up @@ -349,7 +349,7 @@ <h2><code class="docutils literal notranslate"><span class="pre">velph</span></c
</div>
</section>
<section id="velph-hints">
<h2><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">hints</span></code><a class="headerlink" href="#velph-hints" title="Link to this heading">#</a></h2>
<span id="id2"></span><h2><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">hints</span></code><a class="headerlink" href="#velph-hints" title="Link to this heading">#</a></h2>
<p>This command provides a quick reference of calculation steps.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">velph</span> <span class="n">hints</span>
</pre></div>
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Expand Up @@ -345,10 +345,64 @@ <h2> Contents </h2>

<section class="tex2jax_ignore mathjax_ignore" id="velph-subcommands">
<span id="id1"></span><h1><code class="docutils literal notranslate"><span class="pre">velph</span></code> subcommands<a class="headerlink" href="#velph-subcommands" title="Link to this heading">#</a></h1>
<p><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code> is</p>
<p>The <code class="docutils literal notranslate"><span class="pre">velph</span></code> subcommands, except for <a class="reference internal" href="velph-init.html#velph-init"><span class="std std-ref">velph init</span></a> and <a class="reference internal" href="velph-command.html#velph-hints"><span class="std std-ref">velph hints</span></a>,
are explained on this page.</p>
<p>The following subcommands must be executed in the directory containing the
<code class="docutils literal notranslate"><span class="pre">velph.toml</span></code> file. This ensures that the directories and files generated are
properly organized relative to the current directory where <code class="docutils literal notranslate"><span class="pre">velph.toml</span></code> is
located.</p>
<p>In the following example, two <code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code> command operations generate two
different directories. The first operation performs crystal structure relaxation
in the <code class="docutils literal notranslate"><span class="pre">relax</span></code> directory. The second operation, using the relaxed crystal
structure, carries out additional calculations required for electron-phonon
interactions in the <code class="docutils literal notranslate"><span class="pre">calc</span></code> directory. Details about <code class="docutils literal notranslate"><span class="pre">velph-tmpl.toml</span></code> are
described in <a class="reference internal" href="velph-init-template.html#velph-init-template"><span class="std std-ref">velph init template</span></a>.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>% 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 &quot;nac&quot;.
% ls
POTCAR nac/ velph.toml
...
# Run NAC calculation
...
% velph phelel init
Found &quot;nac&quot; directory. Read NAC params.
&quot;phelel/phelel_disp.yaml&quot; was generated.
VASP input files will be generated by &quot;velph phelel generate&quot;.
% velph phelel generate
VASP input files were generated in &quot;phelel/disp-000&quot;.
VASP input files were generated in &quot;phelel/disp-001&quot;.
VASP input files were generated in &quot;phelel/disp-002&quot;.
VASP input files were generated in &quot;phelel/disp-003&quot;.
VASP input files were generated in &quot;phelel/disp-004&quot;.
% ls
POTCAR nac/ phelel/ velph.toml
% velph phelel init
Found &quot;nac&quot; directory. Read NAC params.
&quot;phelel/phelel_disp.yaml&quot; was generated.
VASP input files will be generated by &quot;velph phelel generate&quot;.
...
</pre></div>
</div>
<section id="velph-phelel">
<h2><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">phelel</span></code><a class="headerlink" href="#velph-phelel" title="Link to this heading">#</a></h2>
<p>This command calculates the derivatives of local potentials and PAW strengths
<p>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 <code class="docutils literal notranslate"><span class="pre">phelel</span></code> command in the <a class="reference internal" href="workflow.html#workflow-minimal"><span class="std std-ref">workflow</span></a>.</p>
<section id="velph-phelel-init">
Expand All @@ -375,12 +429,48 @@ <h3><code class="docutils literal notranslate"><span class="pre">velph</span> <s
</section>
<section id="velph-relax">
<h2><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">relax</span></code><a class="headerlink" href="#velph-relax" title="Link to this heading">#</a></h2>
<p>It is recommended to create a project directory secific for relaxation
calculation, e.g., by</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">ls</span>
<span class="n">POSCAR</span><span class="o">-</span><span class="n">unitcell</span> <span class="n">POTCAR</span> <span class="n">velph</span><span class="o">-</span><span class="n">tmpl</span><span class="o">.</span><span class="n">toml</span>
<span class="o">%</span> <span class="n">velph</span> <span class="n">init</span> <span class="o">--</span><span class="n">template</span><span class="o">-</span><span class="n">toml</span> <span class="n">velph</span><span class="o">-</span><span class="n">tmpl</span><span class="o">.</span><span class="n">toml</span> <span class="n">POSCAR</span><span class="o">-</span><span class="n">unitcell</span> <span class="n">relax</span>
<span class="o">...</span>
<span class="o">%</span> <span class="n">cd</span> <span class="n">relax</span>
<span class="o">%</span> <span class="n">ls</span>
<span class="n">POTCAR</span> <span class="n">velph</span><span class="o">.</span><span class="n">toml</span>
<span class="o">%</span> <span class="n">velph</span> <span class="n">relax</span> <span class="n">generate</span>
<span class="o">...</span>
</pre></div>
</div>
<section id="velph-relax-generate">
<h3><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">relax</span> <span class="pre">generate</span></code><a class="headerlink" href="#velph-relax-generate" title="Link to this heading">#</a></h3>
<p>This subcommand prepares VASP input files and a job script for crystal structure
relaxation. Multiple relaxation calculations can be performed. In such cases,
the <code class="docutils literal notranslate"><span class="pre">CONTCAR</span></code> from the previous calculation is used as the <code class="docutils literal notranslate"><span class="pre">POSCAR</span></code> for the next
calculation to generate a new set of VASP input files.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">ls</span>
<span class="n">POTCAR</span> <span class="n">velph</span><span class="o">.</span><span class="n">toml</span>
<span class="o">%</span> <span class="n">velph</span> <span class="n">relax</span> <span class="n">generate</span>
<span class="n">VASP</span> <span class="nb">input</span> <span class="n">files</span> <span class="n">were</span> <span class="n">made</span> <span class="ow">in</span> <span class="s2">&quot;relax/iter1&quot;</span><span class="o">.</span>
<span class="o">...</span>
<span class="c1"># Run VASP calculation in relax/iter1</span>
<span class="o">...</span>
<span class="o">%</span> <span class="n">ls</span>
<span class="n">POTCAR</span> <span class="n">relax</span><span class="o">/</span> <span class="n">velph</span><span class="o">.</span><span class="n">toml</span>
<span class="o">%</span> <span class="n">velph</span> <span class="n">relax</span> <span class="n">generate</span>
<span class="s2">&quot;relax/iter1&quot;</span> <span class="n">exists</span><span class="o">.</span>
<span class="s2">&quot;relax/iter1/CONTCAR&quot;</span> <span class="n">will</span> <span class="n">be</span> <span class="k">as</span> <span class="n">new</span> <span class="s2">&quot;POSCAR&quot;</span><span class="o">.</span>
<span class="n">VASP</span> <span class="nb">input</span> <span class="n">files</span> <span class="n">were</span> <span class="n">made</span> <span class="ow">in</span> <span class="s2">&quot;relax/iter2&quot;</span><span class="o">.</span>
<span class="o">...</span>
</pre></div>
</div>
</section>
</section>
<section id="velph-nac">
<h2><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">nac</span></code><a class="headerlink" href="#velph-nac" title="Link to this heading">#</a></h2>
<p>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.</p>
<section id="velph-nac-generate">
<h3><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">nac</span> <span class="pre">generate</span></code><a class="headerlink" href="#velph-nac-generate" title="Link to this heading">#</a></h3>
</section>
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