PyPI - yu-mcal - Versions diffs - 0.1.4__tar.gz → 0.1.6__tar.gz - Mend

yu-mcal 0.1.4tar.gz → 0.1.6tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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{yu_mcal-0.1.4 → yu_mcal-0.1.6}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: yu-mcal
-Version: 0.1.4
+Version: 0.1.6
 Summary: Program for the calculation of mobility tensor for organic semiconductor crystals
 Author: Koki Ozawa
 Author-email: Hiroyuki Matsui <h-matsui@yz.yamagata-u.ac.jp>

{yu_mcal-0.1.4 → yu_mcal-0.1.6}/docs/_modules/mcal/mcal.html RENAMED Viewed

@@ -377,7 +377,7 @@
     <span class="n">cif_path_without_ext</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">directory</span><span class="si">}</span><span class="s1">/</span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s1">&#39;</span>
     <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;----------------------------------------&#39;</span><span class="p">)</span>
-    <span class="nb">print</span><span class="p">(</span><span class="s1">&#39; mcal 0.1.4 (2026/01/20) by Matsui Lab. &#39;</span><span class="p">)</span>
+    <span class="nb">print</span><span class="p">(</span><span class="s1">&#39; mcal 0.1.6 (2026/01/29) by Matsui Lab. &#39;</span><span class="p">)</span>
     <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;----------------------------------------&#39;</span><span class="p">)</span>
     <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">read_pickle</span><span class="p">:</span>
@@ -720,8 +720,8 @@
 <span class="sd">    Tuple[NDArray[np.float64], NDArray[np.float64]]</span>
 <span class="sd">        Eigenvalue(mobility value) and eigenvector(mobility vector)</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">value</span><span class="p">,</span> <span class="n">vector</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">eig</span><span class="p">(</span><span class="n">mobility_tensor</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">value</span><span class="p">,</span> <span class="n">vector</span></div>
+    <span class="n">value</span><span class="p">,</span> <span class="n">vector</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">eigh</span><span class="p">(</span><span class="n">mobility_tensor</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">value</span><span class="p">[::</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">vector</span><span class="p">[:,</span> <span class="p">::</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span></div>

{yu_mcal-0.1.4 → yu_mcal-0.1.6}/docs/_modules/mcal/utils/cif_reader.html RENAMED Viewed

@@ -233,13 +233,14 @@
         </div>
         <article role="main" id="furo-main-content">
           <h1>Source code for mcal.utils.cif_reader</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;CifReader beta (2025/10/30)&quot;&quot;&quot;</span>
+<span></span><span class="sd">&quot;&quot;&quot;CifReader beta (2026/01/29)&quot;&quot;&quot;</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">re</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">warnings</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">collections</span><span class="w"> </span><span class="kn">import</span> <span class="n">deque</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">itertools</span><span class="w"> </span><span class="kn">import</span> <span class="n">product</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Literal</span><span class="p">,</span> <span class="n">Tuple</span>
-<span class="kn">import</span><span class="w"> </span><span class="nn">warnings</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>
@@ -304,13 +305,26 @@
         <span class="bp">self</span><span class="o">.</span><span class="n">_make_adjacency_mat</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_split_mols</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_put_unit_cell</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_unwrap_molecules</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_put_unit_cell</span><span class="p">()</span>
+        <span class="c1"># Remove duplicates again as they may occur when moving atoms into the unit cell</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">sym_symbols</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sym_coords</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_duplicates</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sym_symbols</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sym_coords</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_make_adjacency_mat</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_split_mols</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_calc_z_value</span><span class="p">()</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ref_z_value</span> <span class="o">!=</span> <span class="mi">0</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">z_value</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ref_z_value</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">ZValueIsNotMatchError</span><span class="p">(</span><span class="s1">&#39;Z value is not match.&#39;</span><span class="p">)</span>
+            <span class="k">raise</span> <span class="n">ZValueIsNotMatchError</span><span class="p">(</span>
+                <span class="sa">f</span><span class="s1">&#39;Z value is not match. Z value in cif file is </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_ref_z_value</span><span class="si">}</span><span class="s1">, but calculated Z value is </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">z_value</span><span class="si">}</span><span class="s1">.&#39;</span>
+            <span class="p">)</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">_apply_minimum_image</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Apply minimum image convention.&quot;&quot;&quot;</span>
+        <span class="n">frac_diff</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sym_coords</span><span class="p">[:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,</span> <span class="p">:]</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">sym_coords</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,</span> <span class="p">:,</span> <span class="p">:]</span>
+        <span class="n">frac_diff</span> <span class="o">=</span> <span class="n">frac_diff</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">round</span><span class="p">(</span><span class="n">frac_diff</span><span class="p">)</span>
+        <span class="n">cart_diff</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">frac_diff</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">lattice</span><span class="p">)</span>
+        <span class="n">distance</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">norm</span><span class="p">(</span><span class="n">cart_diff</span><span class="p">,</span> <span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">distance</span>
     <span class="k">def</span><span class="w"> </span><span class="nf">_calc_lattice</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Calculate lattice.&quot;&quot;&quot;</span>
@@ -365,7 +379,7 @@
         <span class="n">num_atoms</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sym_symbols</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">adjacency_mat</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="n">num_atoms</span><span class="p">,</span> <span class="n">num_atoms</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">bool</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">cart_coords</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sym_coords</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">lattice</span><span class="p">)</span>
+        <span class="n">distance</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_apply_minimum_image</span><span class="p">()</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="n">covalent_distance</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">COVALENT_RADII</span><span class="p">[</span><span class="n">symbol</span><span class="p">]</span> <span class="k">for</span> <span class="n">symbol</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">sym_symbols</span><span class="p">])</span> \
@@ -373,7 +387,6 @@
         <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
             <span class="k">raise</span> <span class="n">ElementPropertiesIsNotDefinedError</span><span class="p">(</span><span class="s1">&#39;Element properties is not defined.&#39;</span><span class="p">)</span>
-        <span class="n">distance</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">norm</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">cart_coords</span><span class="p">[:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,</span> <span class="p">:]</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">cart_coords</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,</span> <span class="p">:,</span> <span class="p">:],</span> <span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">adjacency_mat</span><span class="p">[(</span><span class="n">distance</span> <span class="o">&lt;=</span> <span class="n">covalent_distance</span> <span class="o">*</span> <span class="mf">1.3</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">distance</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">)]</span> <span class="o">=</span> <span class="mi">1</span>
     <span class="k">def</span><span class="w"> </span><span class="nf">_operate_sym</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
@@ -530,10 +543,11 @@
                         <span class="k">if</span> <span class="s1">&#39;?&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">tmp_atom_data</span><span class="p">[</span><span class="n">atom_data_index</span><span class="p">[</span><span class="s1">&#39;_atom_site_label&#39;</span><span class="p">]]:</span>
                             <span class="k">if</span> <span class="n">atom_data_index</span><span class="p">[</span><span class="s1">&#39;_atom_site_type_symbol&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
                                 <span class="n">symbol_label</span> <span class="o">=</span> <span class="n">tmp_atom_data</span><span class="p">[</span><span class="n">atom_data_index</span><span class="p">[</span><span class="s1">&#39;_atom_site_label&#39;</span><span class="p">]]</span>
-                                <span class="n">symbol</span> <span class="o">=</span> <span class="n">symbol_label</span>
-                                <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;A&#39;</span><span class="p">,</span> <span class="s1">&#39;B&#39;</span><span class="p">,</span> <span class="s1">&#39;C&#39;</span><span class="p">]:</span>
-                                    <span class="n">symbol</span> <span class="o">=</span> <span class="n">symbol</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
-                                <span class="n">symbol</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">symbol</span><span class="p">)</span>
+                                <span class="n">symbol</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[A-Z][a-z]?&#39;</span><span class="p">,</span> <span class="n">symbol_label</span><span class="p">)</span>
+                                <span class="k">if</span> <span class="n">symbol</span><span class="p">:</span>
+                                    <span class="n">symbol</span> <span class="o">=</span> <span class="n">symbol</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+                                <span class="k">else</span><span class="p">:</span>
+                                    <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Symbol label </span><span class="si">{</span><span class="n">symbol_label</span><span class="si">}</span><span class="s1"> is not valid.&#39;</span><span class="p">)</span>
                             <span class="k">else</span><span class="p">:</span>
                                 <span class="n">symbol_label</span> <span class="o">=</span> <span class="n">tmp_atom_data</span><span class="p">[</span><span class="n">atom_data_index</span><span class="p">[</span><span class="s1">&#39;_atom_site_label&#39;</span><span class="p">]]</span>
                                 <span class="n">symbol</span> <span class="o">=</span> <span class="n">tmp_atom_data</span><span class="p">[</span><span class="n">atom_data_index</span><span class="p">[</span><span class="s1">&#39;_atom_site_type_symbol&#39;</span><span class="p">]]</span>
@@ -547,11 +561,10 @@
                     <span class="c1"># get symmetry operation information</span>
                     <span class="k">elif</span> <span class="n">is_read_sym</span><span class="p">:</span>
                         <span class="k">if</span> <span class="s2">&quot;&#39;&quot;</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
-                            <span class="n">line</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">),</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;&#39;&quot;</span><span class="p">)))</span>
-                            <span class="bp">self</span><span class="o">.</span><span class="n">symmetry_pos</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">symmetry_data_index</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span>
+                            <span class="n">line</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;&#39;&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">),</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span>
                         <span class="k">else</span><span class="p">:</span>
                             <span class="n">line</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">),</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span>
-                            <span class="bp">self</span><span class="o">.</span><span class="n">symmetry_pos</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">symmetry_data_index</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">symmetry_pos</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">symmetry_data_index</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">symbols</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">symbols</span><span class="p">)</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">)</span>
@@ -596,6 +609,35 @@
             <span class="n">sub_matrix</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">adjacency_mat</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ix_</span><span class="p">(</span><span class="n">index_group</span><span class="p">,</span> <span class="n">index_group</span><span class="p">)]</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">sub_matrices</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sub_matrix</span><span class="p">)</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">_unwrap_molecules</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Unwrap molecules using the adjacency matrix based on the minimum image convention.&quot;&quot;&quot;</span>
+        <span class="k">for</span> <span class="n">atom_group</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonded_atoms</span><span class="p">:</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">atom_group</span><span class="p">)</span> <span class="o">&lt;=</span> <span class="mi">1</span><span class="p">:</span>
+                <span class="k">continue</span>
+            <span class="n">criterion_idx</span> <span class="o">=</span> <span class="n">atom_group</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="c1"># Depth-first search</span>
+            <span class="n">visited</span> <span class="o">=</span> <span class="p">{</span><span class="n">criterion_idx</span><span class="p">}</span>
+            <span class="n">stack</span> <span class="o">=</span> <span class="n">deque</span><span class="p">([</span><span class="n">criterion_idx</span><span class="p">])</span>
+            <span class="k">while</span> <span class="n">stack</span><span class="p">:</span>
+                <span class="n">current_idx</span> <span class="o">=</span> <span class="n">stack</span><span class="o">.</span><span class="n">popleft</span><span class="p">()</span>
+                <span class="n">current_coord</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sym_coords</span><span class="p">[</span><span class="n">current_idx</span><span class="p">]</span>
+                <span class="k">for</span> <span class="n">neighbor_idx</span> <span class="ow">in</span> <span class="n">atom_group</span><span class="p">:</span>
+                    <span class="k">if</span> <span class="n">neighbor_idx</span> <span class="ow">in</span> <span class="n">visited</span><span class="p">:</span>
+                        <span class="k">continue</span>
+                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">adjacency_mat</span><span class="p">[</span><span class="n">current_idx</span><span class="p">,</span> <span class="n">neighbor_idx</span><span class="p">]:</span>
+                        <span class="c1"># Minimum image convention</span>
+                        <span class="n">frac_diff</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sym_coords</span><span class="p">[</span><span class="n">neighbor_idx</span><span class="p">]</span> <span class="o">-</span> <span class="n">current_coord</span>
+                        <span class="n">frac_diff</span> <span class="o">=</span> <span class="n">frac_diff</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">round</span><span class="p">(</span><span class="n">frac_diff</span><span class="p">)</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">sym_coords</span><span class="p">[</span><span class="n">neighbor_idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">current_coord</span> <span class="o">+</span> <span class="n">frac_diff</span>
+                        <span class="n">visited</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">neighbor_idx</span><span class="p">)</span>
+                        <span class="n">stack</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">neighbor_idx</span><span class="p">)</span>
 <div class="viewcode-block" id="CifReader.calc_cen_of_weight">
 <a class="viewcode-back" href="../../../mcal.utils.html#mcal.utils.cif_reader.CifReader.calc_cen_of_weight">[docs]</a>
     <span class="k">def</span><span class="w"> </span><span class="nf">calc_cen_of_weight</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">coordinates</span><span class="p">:</span> <span class="n">NDArray</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">NDArray</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">]:</span>

{yu_mcal-0.1.4 → yu_mcal-0.1.6}/docs/mcal.utils.html RENAMED Viewed

@@ -246,7 +246,7 @@
 </section>
 <section id="module-mcal.utils.cif_reader">
 <span id="mcal-utils-cif-reader-module"></span><h2>mcal.utils.cif_reader module<a class="headerlink" href="#module-mcal.utils.cif_reader" title="Link to this heading">¶</a></h2>
-<p>CifReader beta (2025/10/30)</p>
+<p>CifReader beta (2026/01/29)</p>
 <dl class="py class">
 <dt class="sig sig-object py" id="mcal.utils.cif_reader.CifReader">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mcal.utils.cif_reader.</span></span><span class="sig-name descname"><span class="pre">CifReader</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cif_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/mcal/utils/cif_reader.html#CifReader"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mcal.utils.cif_reader.CifReader" title="Link to this definition">¶</a></dt>

{yu_mcal-0.1.4 → yu_mcal-0.1.6}/docs/searchindex.js RENAMED Viewed

	@@ -1 +1 @@
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{yu_mcal-0.1.4 → yu_mcal-0.1.6}/pyproject.toml RENAMED Viewed

@@ -1,6 +1,6 @@
 [project]
 name = "yu-mcal"
-version = "0.1.4"
+version = "0.1.6"
 description = "Program for the calculation of mobility tensor for organic semiconductor crystals"
 requires-python = ">=3.9"
 dependencies = [

{yu_mcal-0.1.4 → yu_mcal-0.1.6}/src/mcal/mcal.py RENAMED Viewed

@@ -140,7 +140,7 @@ def main():
     cif_path_without_ext = f'{directory}/{filename}'
     print('----------------------------------------')
-    print(' mcal 0.1.4 (2026/01/20) by Matsui Lab. ')
+    print(' mcal 0.1.6 (2026/01/29) by Matsui Lab. ')
     print('----------------------------------------')
     if args.read_pickle:
@@ -471,8 +471,8 @@ def cal_eigenvalue_decomposition(mobility_tensor: NDArray[np.float64]) -> Tuple[
     Tuple[NDArray[np.float64], NDArray[np.float64]]
         Eigenvalue(mobility value) and eigenvector(mobility vector)
     """
-    value, vector = np.linalg.eig(mobility_tensor)
-    return value, vector
+    value, vector = np.linalg.eigh(mobility_tensor)
+    return value[::-1], vector[:, ::-1]
 def cal_min_distance(

{yu_mcal-0.1.4 → yu_mcal-0.1.6}/src/mcal/utils/cif_reader.py RENAMED Viewed

@@ -1,10 +1,11 @@
-"""CifReader beta (2025/10/30)"""
+"""CifReader beta (2026/01/29)"""
 import os
 import re
+import warnings
+from collections import deque
 from itertools import product
 from pathlib import Path
 from typing import Dict, List, Literal, Tuple
-import warnings
 import numpy as np
 import pandas as pd
@@ -67,13 +68,26 @@ class CifReader:
         self._make_adjacency_mat()
         self._split_mols()
         self._put_unit_cell()
+        self._unwrap_molecules()
+        self._put_unit_cell()
+        # Remove duplicates again as they may occur when moving atoms into the unit cell
         self.sym_symbols, self.sym_coords = self.remove_duplicates(self.sym_symbols, self.sym_coords)
         self._make_adjacency_mat()
         self._split_mols()
         self._calc_z_value()
         if self._ref_z_value != 0 and self.z_value != self._ref_z_value:
-            raise ZValueIsNotMatchError('Z value is not match.')
+            raise ZValueIsNotMatchError(
+                f'Z value is not match. Z value in cif file is {self._ref_z_value}, but calculated Z value is {self.z_value}.'
+            )
+    def _apply_minimum_image(self):
+        """Apply minimum image convention."""
+        frac_diff = self.sym_coords[:, np.newaxis, :] - self.sym_coords[np.newaxis, :, :]
+        frac_diff = frac_diff - np.round(frac_diff)
+        cart_diff = np.dot(frac_diff, self.lattice)
+        distance = np.linalg.norm(cart_diff, axis=-1)
+        return distance
     def _calc_lattice(self):
         """Calculate lattice."""
@@ -128,7 +142,7 @@ class CifReader:
         num_atoms = len(self.sym_symbols)
         self.adjacency_mat = np.zeros((num_atoms, num_atoms), dtype=bool)
-        self.cart_coords = np.dot(self.sym_coords, self.lattice)
+        distance = self._apply_minimum_image()
         try:
             covalent_distance = np.array([self.COVALENT_RADII[symbol] for symbol in self.sym_symbols]) \
@@ -136,7 +150,6 @@ class CifReader:
         except KeyError:
             raise ElementPropertiesIsNotDefinedError('Element properties is not defined.')
-        distance = np.linalg.norm(self.cart_coords[:, np.newaxis, :] - self.cart_coords[np.newaxis, :, :], axis=-1)
         self.adjacency_mat[(distance <= covalent_distance * 1.3) & (distance != 0)] = 1
     def _operate_sym(self) -> None:
@@ -293,10 +306,11 @@ class CifReader:
                         if '?' not in tmp_atom_data[atom_data_index['_atom_site_label']]:
                             if atom_data_index['_atom_site_type_symbol'] is None:
                                 symbol_label = tmp_atom_data[atom_data_index['_atom_site_label']]
-                                symbol = symbol_label
-                                for s in ['A', 'B', 'C']:
-                                    symbol = symbol.replace(s, '')
-                                symbol = re.sub(r'\d+', '', symbol)
+                                symbol = re.match(r'[A-Z][a-z]?', symbol_label)
+                                if symbol:
+                                    symbol = symbol.group(0)
+                                else:
+                                    raise ValueError(f'Symbol label {symbol_label} is not valid.')
                             else:
                                 symbol_label = tmp_atom_data[atom_data_index['_atom_site_label']]
                                 symbol = tmp_atom_data[atom_data_index['_atom_site_type_symbol']]
@@ -310,11 +324,10 @@ class CifReader:
                     # get symmetry operation information
                     elif is_read_sym:
                         if "'" in line:
-                            line = list(map(lambda x: x.strip().replace(' ', ''), line.split("'")))
-                            self.symmetry_pos.append(line[symmetry_data_index].lower())
+                            line = list(map(lambda x: x.strip().replace(' ', '').replace("'", ""), line.split()))
                         else:
                             line = list(map(lambda x: x.strip().replace(' ', ''), line.split()))
-                            self.symmetry_pos.append(line[symmetry_data_index].lower())
+                        self.symmetry_pos.append(line[symmetry_data_index].lower())
             self.symbols = np.array(self.symbols)
             self.coordinates = np.array(self.coordinates)
@@ -359,6 +372,35 @@ class CifReader:
             sub_matrix = self.adjacency_mat[np.ix_(index_group, index_group)]
             self.sub_matrices.append(sub_matrix)
+    def _unwrap_molecules(self):
+        """Unwrap molecules using the adjacency matrix based on the minimum image convention."""
+        for atom_group in self.bonded_atoms:
+            if len(atom_group) <= 1:
+                continue
+            criterion_idx = atom_group[0]
+            # Depth-first search
+            visited = {criterion_idx}
+            stack = deque([criterion_idx])
+            while stack:
+                current_idx = stack.popleft()
+                current_coord = self.sym_coords[current_idx]
+                for neighbor_idx in atom_group:
+                    if neighbor_idx in visited:
+                        continue
+                    if self.adjacency_mat[current_idx, neighbor_idx]:
+                        # Minimum image convention
+                        frac_diff = self.sym_coords[neighbor_idx] - current_coord
+                        frac_diff = frac_diff - np.round(frac_diff)
+                        self.sym_coords[neighbor_idx] = current_coord + frac_diff
+                        visited.add(neighbor_idx)
+                        stack.append(neighbor_idx)
     def calc_cen_of_weight(self, coordinates: NDArray[np.float64]) -> NDArray[np.float64]:
         """Calculate center of weight.

{yu_mcal-0.1.4 → yu_mcal-0.1.6}/uv.lock RENAMED Viewed

@@ -1244,7 +1244,7 @@ wheels = [
 [[package]]
 name = "yu-mcal"
-version = "0.1.4"
+version = "0.1.6"
 source = { editable = "." }
 dependencies = [
     { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },