deploy: b0a5193

_sources/index.md

@@ -32,6 +32,7 @@ workflow
 phelel-command
 velph-command
 velph-init
+velph-init-template
 velph-subcommands
 velph-example
 changelog

_sources/velph-command.md

@@ -5,23 +5,22 @@ The `velph` command is a convenient tool for systematically performing
 electron-phonon interaction calculations using the VASP code and for analyzing
 the resulting data.
 
-## What does the `velph` command do?
-
 The `velph` command orchestrates the electron-phonon (el-ph) calculation
 workflow {ref}`workflow <workflow>` by running a series of subcommands in a
-specific sequence. These subcommands can:
+specific sequence.
 
-- Execute `phelel`.
-- Generate VASP input files for:
-  - Dielectric constant calculations
-  - Born effective charge calculations
-  - Electronic band structure and density of states calculations
-  (all of which are required for subsequent electron-phonon interaction calculations)
-- Generate VASP input files for phonon and lattice thermal conductivity calculations using phonopy and phono3py.
+## `velph` subcommands
 
-## Listing `velph` subcommands
+The `velph` command includes a variety of subcommands. To initiate an
+electron–phonon (el-ph) calculation, run `velph init` to generate the
+`velph.toml` file. Command options for `velph init` are detailed in
+{ref}`velph_init`. Once the `velph.toml` file is prepared, other `velph`
+subcommands generate VASP input files, post-process VASP calculation results,
+and calculate derivatives of the local potential and PAW strengths with respect
+to atomic displacement, resulting in the `phelel_params.hdf5` file. Most of the
+`velph` subcommands are explained in {ref}`velph_subcommands`.
 
-You can see a list of supported subcommands by simply typing:
+A list of supported subcommands is displayed by typing:
 
 ```
 % velph

_sources/velph-init-template.md

@@ -0,0 +1,104 @@
+(velph_init_template)=
+# `velph init` template
+
+`velph init` is the command to prepare `velph.toml`. Without specifying a
+velph-toml-template, the default template is used. Custom template can be
+specified as follows:
+
+```
+% velph init [OPTIONS] CELL_FILENAME PROJECT_FOLDER --template-toml velph-tmpl.toml
+```
+
+The `velph-tmpl.toml` (arbitrary file name) is almost like the `velph.toml`
+file. It means that the `velph-tmpl.toml` may be created modifying
+`velph.toml`. The sections that exist only in the `velph-tmpl.toml` but not in
+`velph.toml` is `[init.options]`. This can be used as alternatives of command
+options of `velph-init`, e.g.,
+
+```toml
+[init.options]
+kspacing = 0.2
+kspacing_dense = 0.1
+max_num_atoms = 120
+```
+
+These `[init.options]` keywords can be found along with the list of the command
+options by
+
+```
+% velph init --help
+```
+
+## Settings in sections of `velph.toml`
+
+Note that the same can be applied to `velph-tmpl.toml`.
+
+### Default INCAR settings
+
+The default INCAR settins are written in `[vasp.incar]`. These settings are
+overwritten by `[vasp.CALC_TYPE.incar]` (`CALC_TYPE` can be `phelel`, `relax`,
+`nac`, `transport`, `phono3py`, `phono3py.phonon`, etc).
+
+### Scheduler settings
+
+The parameters used for generating the job submission script are specified as
+strings in `[scheduler]`. If `[vasp.CALC_TYPE.scheduler]` is
+specified, `[scheduler]` settings are overwritten by the settings for
+`[vasp.CALC_TYPE]`. The content in this section operates through [Python string
+formatting](https://docs.python.org/3/library/stdtypes.html#str.format), using
+replacement fields named after keyword arguments. Each parameter line in the
+`[scheduler]` section is treated as a keyword argument, which is then inserted
+into the string format.
+
+In the `[scheduler]` section, the parameters `scheduler_name` and
+`scheduler_template` have special roles:
+
+- `scheduler_name`: Specifies the template type, with options `slurm`, `sge`, or
+  `custom`. For `slurm` and `sge`, the template string (i.e.,
+  `scheduler_template`) is
+  [hard-coded](https://github.com/phonopy/phelel/blob/develop/src/phelel/velph/utils/scheduler.py).
+  If `custom` is selected, the string provided by `scheduler_template` is used,
+  into which the parameters are inserted.
+- `scheduler_template`: The string template where parameters defined in this
+  section are inserted.
+
+An example is shown below.
+
+```toml
+[scheduler]
+scheduler_name = "sge"
+job_name = "PbTe"
+mpirun_command = "mpirun"
+vasp_binary = "/usr/local/cluster-1/bin/vasp_std"
+pe = "vienna 32"
+prepend_text = '''
+source /opt/intel/oneapi/setvars.sh --config="/home/togo/.oneapi-config"
+'''
+
+...
+[vasp.phelel.scheduler]
+pe = "paris 24"
+
+...
+[vasp.phonopy.scheduler]
+scheduler_template = '''#!/bin/bash
+#QSUB2 core 192
+#QSUB2 mpi 192
+#QSUB2 smp 1
+#QSUB2 wtime 48:00:00
+#PBS -N {job_name}
+cd $PBS_O_WORKDIR
+
+{prepend_text}
+{mpirun_command} {vasp_binary} | tee vasp_output
+{append_text}
+'''
+job_name = "PbTe"
+mpirun_command = "mpijob"
+vasp_binary = "/usr/local/cluster-2/bin/vasp_std"
+prepend_text = '''
+. /etc/profile.d/modules.sh
+module load inteloneapi22u3
+'''
+append_text = ""
+```

_sources/velph-init.md

@@ -1,3 +1,4 @@
+(velph_init)=
 # `velph init`
 
 `velph init` with command options will generate modified `velph.toml` from the
@@ -10,7 +11,7 @@ template.
 be specified, POSCAR-format crystal structure and directory name that is created
 where `velph.toml` is stored. The available options are explained below. Some
 options can be specified in `[init.options]` section of the velph-toml template
-file (see {ref}`velph-init-template`).
+file (see {ref}`velph_init_template`).
 
 ## `velph init` options
 
@@ -79,109 +80,3 @@ String corresponding to INCAR MAGMOM tag value for unit cell, e.g., "24*1" or "0
 0 1". This is similar to `MAGMOM` tag in phonopy, see
 https://phonopy.github.io/phonopy/setting-tags.html#magmom. In velph, the
 asterisk symbol (`*`) is supported.
-
-
-(velph-init-template)=
-## `velph init` template
-
-`velph init` is the command to prepare `velph.toml`. Without specifying a
-velph-toml-template, the default template is used. Custom template can be
-specified as follows:
-
-```
-% velph init [OPTIONS] CELL_FILENAME PROJECT_FOLDER --template-toml velph-tmpl.toml
-```
-
-The `velph-tmpl.toml` (arbitrary file name) is almost like the `velph.toml`
-file. It means that the `velph-tmpl.toml` may be created modifying
-`velph.toml`. The sections that exist only in the `velph-tmpl.toml` but not in
-`velph.toml` is `[init.options]`. This can be used as alternatives of command
-options of `velph-init`, e.g.,
-
-```toml
-[init.options]
-kspacing = 0.2
-kspacing_dense = 0.1
-max_num_atoms = 120
-```
-
-These `[init.options]` keywords can be found along with the list of the command
-options by
-
-```
-% velph init --help
-```
-
-## Settings in sections of `velph.toml`
-
-Note that the same can be applied to `velph-tmpl.toml`.
-
-### Default INCAR settings
-
-The default INCAR settins are written in `[vasp.incar]`. These settings are
-overwritten by `[vasp.CALC_TYPE.incar]` (`CALC_TYPE` can be `phelel`, `relax`,
-`nac`, `transport`, `phono3py`, `phono3py.phonon`, etc).
-
-### Scheduler settings
-
-The parameters used for generating the job submission script are specified as
-strings in `[scheduler]`. If `[vasp.CALC_TYPE.scheduler]` is
-specified, `[scheduler]` settings are overwritten by the settings for
-`[vasp.CALC_TYPE]`. The content in this section operates through [Python string
-formatting](https://docs.python.org/3/library/stdtypes.html#str.format), using
-replacement fields named after keyword arguments. Each parameter line in the
-`[scheduler]` section is treated as a keyword argument, which is then inserted
-into the string format.
-
-In the `[scheduler]` section, the parameters `scheduler_name` and
-`scheduler_template` have special roles:
-
-- `scheduler_name`: Specifies the template type, with options `slurm`, `sge`, or
-  `custom`. For `slurm` and `sge`, the template string (i.e.,
-  `scheduler_template`) is
-  [hard-coded](https://github.com/phonopy/phelel/blob/develop/src/phelel/velph/utils/scheduler.py).
-  If `custom` is selected, the string provided by `scheduler_template` is used,
-  into which the parameters are inserted.
-- `scheduler_template`: The string template where parameters defined in this
-  section are inserted.
-
-An example is shown below.
-
-```toml
-[scheduler]
-scheduler_name = "sge"
-job_name = "PbTe"
-mpirun_command = "mpirun"
-vasp_binary = "/usr/local/cluster-1/bin/vasp_std"
-pe = "vienna 32"
-prepend_text = '''
-source /opt/intel/oneapi/setvars.sh --config="/home/togo/.oneapi-config"
-'''
-
-...
-[vasp.phelel.scheduler]
-pe = "paris 24"
-
-...
-[vasp.phonopy.scheduler]
-scheduler_template = '''#!/bin/bash
-#QSUB2 core 192
-#QSUB2 mpi 192
-#QSUB2 smp 1
-#QSUB2 wtime 48:00:00
-#PBS -N {job_name}
-cd $PBS_O_WORKDIR
-
-{prepend_text}
-{mpirun_command} {vasp_binary} | tee vasp_output
-{append_text}
-'''
-job_name = "PbTe"
-mpirun_command = "mpijob"
-vasp_binary = "/usr/local/cluster-2/bin/vasp_std"
-prepend_text = '''
-. /etc/profile.d/modules.sh
-module load inteloneapi22u3
-'''
-append_text = ""
-```

_sources/velph-subcommands.md

@@ -1,5 +1,8 @@
+(velph_subcommands)=
 # `velph` subcommands
 
+`velph init` is
+
 ## `velph phelel`
 
 This command calculates the derivatives of local potentials and PAW strengths

changelog.html

@@ -142,6 +142,7 @@
 <li class="toctree-l1"><a class="reference internal" href="phelel-command.html"><code class="docutils literal notranslate"><span class="pre">phelel</span></code> command</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-command.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> command</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-init.html"><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="velph-init-template.html"><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code> template</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-subcommands.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> subcommands</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-example.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> example</a></li>
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Change Log</a></li>

genindex.html

@@ -142,6 +142,7 @@
 <li class="toctree-l1"><a class="reference internal" href="phelel-command.html"><code class="docutils literal notranslate"><span class="pre">phelel</span></code> command</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-command.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> command</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-init.html"><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="velph-init-template.html"><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code> template</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-subcommands.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> subcommands</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-example.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> example</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Change Log</a></li>

index.html

@@ -144,6 +144,7 @@
 <li class="toctree-l1"><a class="reference internal" href="phelel-command.html"><code class="docutils literal notranslate"><span class="pre">phelel</span></code> command</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-command.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> command</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-init.html"><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="velph-init-template.html"><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code> template</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-subcommands.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> subcommands</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-example.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> example</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Change Log</a></li>

install.html

@@ -143,6 +143,7 @@
 <li class="toctree-l1"><a class="reference internal" href="phelel-command.html"><code class="docutils literal notranslate"><span class="pre">phelel</span></code> command</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-command.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> command</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-init.html"><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="velph-init-template.html"><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code> template</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-subcommands.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> subcommands</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-example.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> example</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Change Log</a></li>

phelel-command.html

@@ -143,6 +143,7 @@
 <li class="toctree-l1 current active"><a class="current reference internal" href="#"><code class="docutils literal notranslate"><span class="pre">phelel</span></code> command</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-command.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> command</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-init.html"><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="velph-init-template.html"><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code> template</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-subcommands.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> subcommands</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-example.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> example</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Change Log</a></li>

search.html

@@ -144,6 +144,7 @@
 <li class="toctree-l1"><a class="reference internal" href="phelel-command.html"><code class="docutils literal notranslate"><span class="pre">phelel</span></code> command</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-command.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> command</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-init.html"><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="velph-init-template.html"><code class="docutils literal notranslate"><span class="pre">velph</span> <span class="pre">init</span></code> template</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-subcommands.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> subcommands</a></li>
 <li class="toctree-l1"><a class="reference internal" href="velph-example.html"><code class="docutils literal notranslate"><span class="pre">velph</span></code> example</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Change Log</a></li>