yu-mcal 0.1.5__tar.gz → 0.1.6__tar.gz

{yu_mcal-0.1.5 → yu_mcal-0.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: yu-mcal
-Version: 0.1.5
+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-0.1.5 → yu_mcal-0.1.6}/docs/_modules/mcal/mcal.html

@@ -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 0.1.5 (2026/01/28) 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>

{yu_mcal-0.1.5 → yu_mcal-0.1.6}/docs/_modules/mcal/utils/cif_reader.html

@@ -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 (2026/01/28)&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>
@@ -304,6 +305,8 @@
         <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>
@@ -315,6 +318,14 @@
                 <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>
         <span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">,</span> <span class="n">c</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">cell_lengths</span>
@@ -368,7 +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> \
@@ -376,7 +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>
@@ -599,6 +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-0.1.5 → yu_mcal-0.1.6}/docs/mcal.utils.html

@@ -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 (2026/01/28)</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-0.1.5 → yu_mcal-0.1.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "yu-mcal"
-version = "0.1.5"
+version = "0.1.6"
 description = "Program for the calculation of mobility tensor for organic semiconductor crystals"
 requires-python = ">=3.9"
 dependencies = [

{yu_mcal-0.1.5 → yu_mcal-0.1.6}/src/mcal/mcal.py

@@ -140,7 +140,7 @@ def main():
     cif_path_without_ext = f'{directory}/{filename}'
 
     print('----------------------------------------')
-    print(' mcal 0.1.5 (2026/01/28) by Matsui Lab. ')
+    print(' mcal 0.1.6 (2026/01/29) by Matsui Lab. ')
     print('----------------------------------------')
 
     if args.read_pickle:

{yu_mcal-0.1.5 → yu_mcal-0.1.6}/src/mcal/utils/cif_reader.py

@@ -1,10 +1,11 @@
-"""CifReader beta (2026/01/28)"""
+"""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
@@ -67,6 +68,8 @@ 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()
@@ -78,6 +81,14 @@ class CifReader:
                 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."""
         a, b, c = self.cell_lengths
@@ -131,7 +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]) \
@@ -139,7 +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:
@@ -362,6 +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-0.1.5 → yu_mcal-0.1.6}/uv.lock

@@ -1244,7 +1244,7 @@ wheels = [
 
 [[package]]
 name = "yu-mcal"
-version = "0.1.5"
+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'" },