Update documentation

Author: masato1122

_sources/params_ak.rst.txt

@@ -2,6 +2,17 @@
 Parameters for auto-kappa
 ==========================
 
+.. contents:: Table of Contents
+   :local:
+   :depth: 1
+
+
+.. _sec_params_ak_recommendations:
+
+Recommendations for parameters
+================================
+
+
 .. _sec_params_ak_brief:
 
 Brief description
@@ -77,6 +88,7 @@ Others
 
 .. _sec_params_ak_detailed:
 
+
 Detailed description
 =====================
 

auto-kappa/auto_kappa.alamode.compat.html

@@ -181,24 +181,6 @@
 <dd><p>Get already calculated structures with displacement.</p>
 </dd></dl>
 
-<dl class="py function">
-<dt class="sig sig-object py" id="auto_kappa.alamode.compat.inverse_transformation">
-<span class="sig-prename descclassname"><span class="pre">auto_kappa.alamode.compat.</span></span><span class="sig-name descname"><span class="pre">inverse_transformation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">supercell</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sc_mat</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#auto_kappa.alamode.compat.inverse_transformation" title="Link to this definition"></a></dt>
-<dd><p>Get the small cell (e.g. unitcell) from the supercell and the transformation matrix
-from the small cell to the supercell.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>supercell</strong> (<em>ase.Atoms</em>) – The supercell structure.</p></li>
-<li><p><strong>sc_mat</strong> (<em>array-like</em>) – The transformation matrix from the small cell to the supercell with the Phonopy representation.</p></li>
-</ul>
-</dd>
-<dt class="field-even">Return type<span class="colon">:</span></dt>
-<dd class="field-even"><p><em>Atoms</em></p>
-</dd>
-</dl>
-</dd></dl>
-
 <dl class="py function">
 <dt class="sig sig-object py" id="auto_kappa.alamode.compat.was_primitive_changed">
 <span class="sig-prename descclassname"><span class="pre">auto_kappa.alamode.compat.</span></span><span class="sig-name descname"><span class="pre">was_primitive_changed</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct_tmp</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol_prev</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol_new</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#auto_kappa.alamode.compat.was_primitive_changed" title="Link to this definition"></a></dt>

auto-kappa/auto_kappa.alamode.html

@@ -210,7 +210,6 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <li class="toctree-l2"><a class="reference internal" href="auto_kappa.alamode.compat.html#auto_kappa.alamode.compat.check_previous_structures"><code class="docutils literal notranslate"><span class="pre">check_previous_structures()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="auto_kappa.alamode.compat.html#auto_kappa.alamode.compat.get_number_of_same_structures"><code class="docutils literal notranslate"><span class="pre">get_number_of_same_structures()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="auto_kappa.alamode.compat.html#auto_kappa.alamode.compat.get_previously_calculated_structure"><code class="docutils literal notranslate"><span class="pre">get_previously_calculated_structure()</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="auto_kappa.alamode.compat.html#auto_kappa.alamode.compat.inverse_transformation"><code class="docutils literal notranslate"><span class="pre">inverse_transformation()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="auto_kappa.alamode.compat.html#auto_kappa.alamode.compat.was_primitive_changed"><code class="docutils literal notranslate"><span class="pre">was_primitive_changed()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="auto_kappa.alamode.compat.html#auto_kappa.alamode.compat.was_tolerance_changed"><code class="docutils literal notranslate"><span class="pre">was_tolerance_changed()</span></code></a></li>
 </ul>

auto-kappa/auto_kappa.html

@@ -130,7 +130,6 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.alamode.compat.html#auto_kappa.alamode.compat.check_previous_structures"><code class="docutils literal notranslate"><span class="pre">check_previous_structures()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.alamode.compat.html#auto_kappa.alamode.compat.get_number_of_same_structures"><code class="docutils literal notranslate"><span class="pre">get_number_of_same_structures()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.alamode.compat.html#auto_kappa.alamode.compat.get_previously_calculated_structure"><code class="docutils literal notranslate"><span class="pre">get_previously_calculated_structure()</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="auto_kappa.alamode.compat.html#auto_kappa.alamode.compat.inverse_transformation"><code class="docutils literal notranslate"><span class="pre">inverse_transformation()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.alamode.compat.html#auto_kappa.alamode.compat.was_primitive_changed"><code class="docutils literal notranslate"><span class="pre">was_primitive_changed()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.alamode.compat.html#auto_kappa.alamode.compat.was_tolerance_changed"><code class="docutils literal notranslate"><span class="pre">was_tolerance_changed()</span></code></a></li>
 </ul>
@@ -499,7 +498,6 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.io.vasp.html#auto_kappa.io.vasp.read_incar"><code class="docutils literal notranslate"><span class="pre">read_incar()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.io.vasp.html#auto_kappa.io.vasp.read_kpoints"><code class="docutils literal notranslate"><span class="pre">read_kpoints()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.io.vasp.html#auto_kappa.io.vasp.read_outcar"><code class="docutils literal notranslate"><span class="pre">read_outcar()</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="auto_kappa.io.vasp.html#auto_kappa.io.vasp.read_poscar"><code class="docutils literal notranslate"><span class="pre">read_poscar()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.io.vasp.html#auto_kappa.io.vasp.wasfinished"><code class="docutils literal notranslate"><span class="pre">wasfinished()</span></code></a></li>
 </ul>
 </li>
@@ -558,7 +556,6 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 </ul>
 </li>
 <li class="toctree-l3"><a class="reference internal" href="auto_kappa.structure.crystal.html">auto_kappa.structure.crystal module</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="auto_kappa.structure.crystal.html#auto_kappa.structure.crystal.convert_primitive_to_unitcell"><code class="docutils literal notranslate"><span class="pre">convert_primitive_to_unitcell()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.structure.crystal.html#auto_kappa.structure.crystal.get_atomic_distance_list"><code class="docutils literal notranslate"><span class="pre">get_atomic_distance_list()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.structure.crystal.html#auto_kappa.structure.crystal.get_automatic_kmesh"><code class="docutils literal notranslate"><span class="pre">get_automatic_kmesh()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.structure.crystal.html#auto_kappa.structure.crystal.get_commensurate_points"><code class="docutils literal notranslate"><span class="pre">get_commensurate_points()</span></code></a></li>
@@ -567,7 +564,11 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.structure.crystal.html#auto_kappa.structure.crystal.get_spg_number"><code class="docutils literal notranslate"><span class="pre">get_spg_number()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.structure.crystal.html#auto_kappa.structure.crystal.get_standardized_structure"><code class="docutils literal notranslate"><span class="pre">get_standardized_structure()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.structure.crystal.html#auto_kappa.structure.crystal.get_standardized_structure_spglib"><code class="docutils literal notranslate"><span class="pre">get_standardized_structure_spglib()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="auto_kappa.structure.crystal.html#auto_kappa.structure.crystal.get_supercell"><code class="docutils literal notranslate"><span class="pre">get_supercell()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="auto_kappa.structure.crystal.html#auto_kappa.structure.crystal.get_symmetry_dataset"><code class="docutils literal notranslate"><span class="pre">get_symmetry_dataset()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="auto_kappa.structure.crystal.html#auto_kappa.structure.crystal.inverse_transformation"><code class="docutils literal notranslate"><span class="pre">inverse_transformation()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="auto_kappa.structure.crystal.html#auto_kappa.structure.crystal.transform_prim2unit"><code class="docutils literal notranslate"><span class="pre">transform_prim2unit()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="auto_kappa.structure.crystal.html#auto_kappa.structure.crystal.transform_unit2prim"><code class="docutils literal notranslate"><span class="pre">transform_unit2prim()</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l3"><a class="reference internal" href="auto_kappa.structure.supercell.html">auto_kappa.structure.supercell module</a><ul>

auto-kappa/auto_kappa.io.html

@@ -535,7 +535,6 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <li class="toctree-l2"><a class="reference internal" href="auto_kappa.io.vasp.html#auto_kappa.io.vasp.read_incar"><code class="docutils literal notranslate"><span class="pre">read_incar()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="auto_kappa.io.vasp.html#auto_kappa.io.vasp.read_kpoints"><code class="docutils literal notranslate"><span class="pre">read_kpoints()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="auto_kappa.io.vasp.html#auto_kappa.io.vasp.read_outcar"><code class="docutils literal notranslate"><span class="pre">read_outcar()</span></code></a></li>
-<li class="toctree-l2"><a class="reference internal" href="auto_kappa.io.vasp.html#auto_kappa.io.vasp.read_poscar"><code class="docutils literal notranslate"><span class="pre">read_poscar()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="auto_kappa.io.vasp.html#auto_kappa.io.vasp.wasfinished"><code class="docutils literal notranslate"><span class="pre">wasfinished()</span></code></a></li>
 </ul>
 </li>

auto-kappa/auto_kappa.io.vasp.html

@@ -153,13 +153,6 @@
 </dl>
 </dd></dl>
 
-<dl class="py function">
-<dt class="sig sig-object py" id="auto_kappa.io.vasp.read_poscar">
-<span class="sig-prename descclassname"><span class="pre">auto_kappa.io.vasp.</span></span><span class="sig-name descname"><span class="pre">read_poscar</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#auto_kappa.io.vasp.read_poscar" title="Link to this definition"></a></dt>
-<dd><p>Read filename
-filename : string, POSCAR filename</p>
-</dd></dl>
-
 <dl class="py function">
 <dt class="sig sig-object py" id="auto_kappa.io.vasp.wasfinished">
 <span class="sig-prename descclassname"><span class="pre">auto_kappa.io.vasp.</span></span><span class="sig-name descname"><span class="pre">wasfinished</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">directory</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'vasprun.xml'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tar</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#auto_kappa.io.vasp.wasfinished" title="Link to this definition"></a></dt>

auto-kappa/auto_kappa.structure.comparison.html

@@ -114,14 +114,14 @@
 
 <dl class="py function">
 <dt class="sig sig-object py" id="auto_kappa.structure.comparison.generate_mapping_s2p">
-<span class="sig-prename descclassname"><span class="pre">auto_kappa.structure.comparison.</span></span><span class="sig-name descname"><span class="pre">generate_mapping_s2p</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">supercell</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">primitive</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol_zero</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.001</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#auto_kappa.structure.comparison.generate_mapping_s2p" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">auto_kappa.structure.comparison.</span></span><span class="sig-name descname"><span class="pre">generate_mapping_s2p</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">supercell</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">primitive</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol_zero</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.001</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#auto_kappa.structure.comparison.generate_mapping_s2p" title="Link to this definition"></a></dt>
 <dd><p>Generate mapping from supercell to primitive cell.
 This function was made based on the function in an ALAMODE tool.</p>
 </dd></dl>
 
 <dl class="py function">
 <dt class="sig sig-object py" id="auto_kappa.structure.comparison.get_structure_matcher">
-<span class="sig-prename descclassname"><span class="pre">auto_kappa.structure.comparison.</span></span><span class="sig-name descname"><span class="pre">get_structure_matcher</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ltol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">angle_tol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">primitive_cell</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#auto_kappa.structure.comparison.get_structure_matcher" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">auto_kappa.structure.comparison.</span></span><span class="sig-name descname"><span class="pre">get_structure_matcher</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ltol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">angle_tol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">primitive_cell</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#auto_kappa.structure.comparison.get_structure_matcher" title="Link to this definition"></a></dt>
 <dd><p>Get a StructureMatcher object with the specified tolerances.</p>
 </dd></dl>