Update documentation

Author: masato1122

_sources/tutorial/alamode.rst.txt

@@ -2,6 +2,8 @@
 Preparation of ALAMODE input files
 ========================================
 
+The following Python scripts can be found in ``auto-kappa/examples/6_parser/alamode_inputs``.
+
 .. contents:: Table of contents
    :local:
    :depth: 1

_static/ak_logo.png

@@ -238,15 +238,12 @@ <h3>Others<a class="headerlink" href="#others" title="Link to this heading"><
 <span id="sec-params-ak-detailed"></span><h2><a class="toc-backref" href="#id4" role="doc-backlink"><span class="section-number">3.3. </span>Detailed description</a><a class="headerlink" href="#detailed-description" title="Link to this heading"></a></h2>
 <p><p>Parser for akrun command</p>
 </p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">auto</span><span class="o">-</span><span class="n">kappa</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">d</span> <span class="n">DIRECTORY</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">file_structure</span> <span class="n">FILE_STRUCTURE</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">outdir</span> <span class="n">OUTDIR</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">n</span> <span class="n">NPROCS</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">mpirun</span> <span class="n">MPIRUN</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">command_vasp</span> <span class="n">COMMAND_VASP</span><span class="p">]</span>
-                  <span class="p">[</span><span class="o">--</span><span class="n">command_vasp_gam</span> <span class="n">COMMAND_VASP_GAM</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">command_alm</span> <span class="n">COMMAND_ALM</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">command_anphon</span> <span class="n">COMMAND_ANPHON</span><span class="p">]</span>
-                  <span class="p">[</span><span class="o">--</span><span class="n">command_anphon_ver2</span> <span class="n">COMMAND_ANPHON_VER2</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">nonanalytic</span> <span class="n">NONANALYTIC</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">cutoff_cubic</span> <span class="n">CUTOFF_CUBIC</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">min_nearest</span> <span class="n">MIN_NEAREST</span><span class="p">]</span>
-                  <span class="p">[</span><span class="o">--</span><span class="n">nmax_suggest</span> <span class="n">NMAX_SUGGEST</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">frac_nrandom</span> <span class="n">FRAC_NRANDOM</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">frac_nrandom_higher</span> <span class="n">FRAC_NRANDOM_HIGHER</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">mag_harm</span> <span class="n">MAG_HARM</span><span class="p">]</span>
-                  <span class="p">[</span><span class="o">--</span><span class="n">mag_cubic</span> <span class="n">MAG_CUBIC</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">negative_freq</span> <span class="n">NEGATIVE_FREQ</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">volume_relaxation</span> <span class="n">VOLUME_RELAXATION</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">k_length</span> <span class="n">K_LENGTH</span><span class="p">]</span>
-                  <span class="p">[</span><span class="o">--</span><span class="n">max_natoms</span> <span class="n">MAX_NATOMS</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">analyze_with_larger_supercell</span> <span class="n">ANALYZE_WITH_LARGERSC</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">delta_max_natoms</span> <span class="n">DELTA_MAX_NATOMS</span><span class="p">]</span>
-                  <span class="p">[</span><span class="o">--</span><span class="n">max_loop_for_largesc</span> <span class="n">MAX_LOOP_FOR_LARGESC</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">nsw_params</span> <span class="n">NSW_PARAMS</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">calculate_forces</span> <span class="n">CALCULATE_FORCES</span><span class="p">]</span>
-                  <span class="p">[</span><span class="o">--</span><span class="n">harmonic_only</span> <span class="n">HARMONIC_ONLY</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">command_dfc2</span> <span class="n">COMMAND_DFC2</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">scph</span> <span class="n">SCPH</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">four</span> <span class="n">FOUR</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">frac_kdensity_4ph</span> <span class="n">FRAC_KDENSITY_4PH</span><span class="p">]</span>
-                  <span class="p">[</span><span class="o">--</span><span class="n">random_disp_temperature</span> <span class="n">RANDOM_DISP_TEMPERATURE</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">vasp_parameters</span> <span class="n">VASP_PARAMETERS</span><span class="p">]</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">auto</span><span class="o">-</span><span class="n">kappa</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">d</span> <span class="n">DIRECTORY</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">file_structure</span> <span class="n">FILE_STRUCTURE</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">outdir</span> <span class="n">OUTDIR</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">n</span> <span class="n">NPROCS</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">mpirun</span> <span class="n">MPIRUN</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">command_vasp</span> <span class="n">COMMAND_VASP</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">command_vasp_gam</span> <span class="n">COMMAND_VASP_GAM</span><span class="p">]</span>
+                  <span class="p">[</span><span class="o">--</span><span class="n">command_alm</span> <span class="n">COMMAND_ALM</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">command_anphon</span> <span class="n">COMMAND_ANPHON</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">command_anphon_ver2</span> <span class="n">COMMAND_ANPHON_VER2</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">nonanalytic</span> <span class="n">NONANALYTIC</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">cutoff_cubic</span> <span class="n">CUTOFF_CUBIC</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">min_nearest</span> <span class="n">MIN_NEAREST</span><span class="p">]</span>
+                  <span class="p">[</span><span class="o">--</span><span class="n">nmax_suggest</span> <span class="n">NMAX_SUGGEST</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">frac_nrandom</span> <span class="n">FRAC_NRANDOM</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">frac_nrandom_higher</span> <span class="n">FRAC_NRANDOM_HIGHER</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">mag_harm</span> <span class="n">MAG_HARM</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">mag_cubic</span> <span class="n">MAG_CUBIC</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">negative_freq</span> <span class="n">NEGATIVE_FREQ</span><span class="p">]</span>
+                  <span class="p">[</span><span class="o">--</span><span class="n">volume_relaxation</span> <span class="n">VOLUME_RELAXATION</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">k_length</span> <span class="n">K_LENGTH</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">max_natoms</span> <span class="n">MAX_NATOMS</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">analyze_with_larger_supercell</span> <span class="n">ANALYZE_WITH_LARGERSC</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">delta_max_natoms</span> <span class="n">DELTA_MAX_NATOMS</span><span class="p">]</span>
+                  <span class="p">[</span><span class="o">--</span><span class="n">max_loop_for_largesc</span> <span class="n">MAX_LOOP_FOR_LARGESC</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">nsw_params</span> <span class="n">NSW_PARAMS</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">calculate_forces</span> <span class="n">CALCULATE_FORCES</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">harmonic_only</span> <span class="n">HARMONIC_ONLY</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">command_dfc2</span> <span class="n">COMMAND_DFC2</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">scph</span> <span class="n">SCPH</span><span class="p">]</span>
+                  <span class="p">[</span><span class="o">--</span><span class="n">four</span> <span class="n">FOUR</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">frac_kdensity_4ph</span> <span class="n">FRAC_KDENSITY_4PH</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">random_disp_temperature</span> <span class="n">RANDOM_DISP_TEMPERATURE</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">vasp_parameters</span> <span class="n">VASP_PARAMETERS</span><span class="p">]</span>
 </pre></div>
 </div>
 <section id="auto_kappa.cui.ak_parser-get_parser-named-arguments">

params_ak.html

@@ -98,6 +98,7 @@
 
   <section id="preparation-of-alamode-input-files">
 <h1><span class="section-number">5.1. </span>Preparation of ALAMODE input files<a class="headerlink" href="#preparation-of-alamode-input-files" title="Link to this heading"></a></h1>
+<p>The following Python scripts can be found in <code class="docutils literal notranslate"><span class="pre">auto-kappa/examples/6_parser/alamode_inputs</span></code>.</p>
 <nav class="contents local" id="table-of-contents">
 <p class="topic-title">Table of contents</p>
 <ul class="simple">