yu-mcal 0.1.6__tar.gz → 0.2.1__tar.gz

{yu_mcal-0.1.6 → yu_mcal-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: yu-mcal
-Version: 0.1.6
+Version: 0.2.1
 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>
@@ -40,6 +40,7 @@ Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: >=3.9
+Requires-Dist: matplotlib>=3.9.4
 Requires-Dist: numpy>=2.0.2
 Requires-Dist: pandas>=2.3.3
 Requires-Dist: yu-tcal==3.1.0
@@ -57,6 +58,7 @@ Description-Content-Type: text/markdown
 * Python 3.9 or newer
 * NumPy
 * Pandas
+* Matplotlib
 * yu-tcal==3.1.0
 * Gaussian 09 or 16
 
@@ -157,6 +159,14 @@ Specify the number of unit cells to expand in each direction around the central
 Save calculation results to a pickle file.
 - **Example**: `mcal xxx.cif p -p`
 
+#### `--plot-plane <plane>`
+Plot mobility tensor as a 2D polar plot on specified crystallographic plane.
+- **Available planes**: `ab`, `ac`, `ba`, `bc`, `ca`, `cb`
+- **Default**: None (no plot generated)
+- **Examples**: 
+  - `mcal xxx.cif p --plot-plane ab` (plot on ab-plane)
+  - `mcal xxx.cif p --plot-plane bc` (plot on bc-plane)
+
 ### Diffusion Coefficient Calculation Methods
 
 #### `--mc`

{yu_mcal-0.1.6 → yu_mcal-0.2.1}/README.md

@@ -10,6 +10,7 @@
 * Python 3.9 or newer
 * NumPy
 * Pandas
+* Matplotlib
 * yu-tcal==3.1.0
 * Gaussian 09 or 16
 
@@ -110,6 +111,14 @@ Specify the number of unit cells to expand in each direction around the central
 Save calculation results to a pickle file.
 - **Example**: `mcal xxx.cif p -p`
 
+#### `--plot-plane <plane>`
+Plot mobility tensor as a 2D polar plot on specified crystallographic plane.
+- **Available planes**: `ab`, `ac`, `ba`, `bc`, `ca`, `cb`
+- **Default**: None (no plot generated)
+- **Examples**: 
+  - `mcal xxx.cif p --plot-plane ab` (plot on ab-plane)
+  - `mcal xxx.cif p --plot-plane bc` (plot on bc-plane)
+
 ### Diffusion Coefficient Calculation Methods
 
 #### `--mc`

{yu_mcal-0.1.6 → yu_mcal-0.2.1}/README_ja.md

@@ -11,6 +11,7 @@
 * Python 3.9以降
 * NumPy
 * Pandas
+* Matplotlib
 * yu-tcal==3.1.0
 * Gaussian 09または16
 
@@ -111,6 +112,14 @@ Gaussianを実行せずに既存のlogファイルから結果を読み取りま
 計算結果をpickleファイルに保存します。
 - **例**: `mcal xxx.cif p -p`
 
+#### `--plot-plane <plane>`
+指定した結晶学的面上で移動度テンソルを2D極座標プロットで描画します。
+- **利用可能な面**: `ab`, `ac`, `ba`, `bc`, `ca`, `cb`
+- **デフォルト**: None（プロットは生成されません）
+- **例**: 
+  - `mcal xxx.cif p --plot-plane ab`（ab面にプロット）
+  - `mcal xxx.cif p --plot-plane bc`（bc面にプロット）
+
 ### 拡散係数計算手法
 
 #### `--mc`

{yu_mcal-0.1.6 → yu_mcal-0.2.1}/docs/_modules/mcal/mcal.html

@@ -241,6 +241,9 @@
 <span class="kn">from</span><span class="w"> </span><span class="nn">time</span><span class="w"> </span><span class="kn">import</span> <span class="n">time</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">Optional</span><span class="p">,</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">Union</span>
 
+<span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib</span>
+<span class="n">matplotlib</span><span class="o">.</span><span class="n">use</span><span class="p">(</span><span class="s1">&#39;Agg&#39;</span><span class="p">)</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">plt</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">from</span><span class="w"> </span><span class="nn">numpy.typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">NDArray</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">tcal</span><span class="w"> </span><span class="kn">import</span> <span class="n">Tcal</span>
@@ -270,40 +273,41 @@
 <span class="sd">    --------</span>
 <span class="sd">    Basic usage:</span>
 <span class="sd">        - Calculate p-type mobility for xxx crystal\n</span>
-<span class="sd">        $ python hop_mcal.py xxx.cif p</span>
+<span class="sd">        $ mcal xxx.cif p</span>
 
 <span class="sd">        - Calculate n-type mobility for xxx crystal\n</span>
-<span class="sd">        $ python hop_mcal.py xxx.cif n</span>
+<span class="sd">        $ mcal xxx.cif n</span>
 
 <span class="sd">    With resource options:</span>
 <span class="sd">        - Use 8 CPUs and 16GB memory\n</span>
-<span class="sd">        $ python hop_mcal.py xxx.cif p -c 8 -m 16</span>
+<span class="sd">        $ mcal xxx.cif p -c 8 -m 16</span>
 
 <span class="sd">        - Use different calculation method (default is B3LYP/6-31G(d,p))\n</span>
-<span class="sd">        $ python hop_mcal.py xxx.cif p -M &quot;B3LYP/6-311G(d,p)&quot;</span>
+<span class="sd">        $ mcal xxx.cif p -M &quot;B3LYP/6-311G(d,p)&quot;</span>
 
 <span class="sd">    High-precision calculation:</span>
 <span class="sd">        - Calculate all transfer integrals without speedup using moment of inertia and distance between centers of weight\n</span>
-<span class="sd">        $ python hop_mcal.py xxx.cif p --fullcal</span>
-
-<span class="sd">        - Expand calculation range to 3x3x3 supercell\n</span>
-<span class="sd">        $ python hop_mcal.py xxx.cif p --cellsize 1</span>
+<span class="sd">        $ mcal xxx.cif p --fullcal</span>
 
 <span class="sd">        - Expand calculation range to 5x5x5 supercell to widen transfer integral calculation range\n</span>
-<span class="sd">        $ python hop_mcal.py xxx.cif p --cellsize 2</span>
+<span class="sd">        $ mcal xxx.cif p --cellsize 2</span>
 
 <span class="sd">    Resume and save results:</span>
 <span class="sd">        - Resume from existing calculations\n</span>
-<span class="sd">        $ python hop_mcal.py xxx.cif p --resume</span>
+<span class="sd">        $ mcal xxx.cif p --resume</span>
 
 <span class="sd">        - Save results to pickle file\n</span>
-<span class="sd">        $ python hop_mcal.py xxx.cif p --pickle</span>
+<span class="sd">        $ mcal xxx.cif p --pickle</span>
 
 <span class="sd">        - Read results from existing pickle file\n</span>
-<span class="sd">        $ python hop_mcal.py xxx_result.pkl p -rp</span>
+<span class="sd">        $ mcal xxx_result.pkl p -rp</span>
 
 <span class="sd">        - Read results from existing log files without running Gaussian\n</span>
-<span class="sd">        $ python hop_mcal.py xxx.cif p -r</span>
+<span class="sd">        $ mcal xxx.cif p -r</span>
+
+<span class="sd">    Plot mobility tensor in 2D plane:</span>
+<span class="sd">        - Plot mobility tensor in 2D plane (Examples: ab, ac, ba, bc, ca, cb (default is ab))\n</span>
+<span class="sd">        $ python hop_mcal.py xxx.cif p --plot-plane ab</span>
 
 <span class="sd">    Compare calculation methods:</span>
 <span class="sd">        - Compare results using kinetic Monte Carlo and ODE methods\n</span>
@@ -356,6 +360,13 @@
         <span class="n">help</span><span class="o">=</span><span class="s1">&#39;use Ordinary Differential Equation method to calculate diffusion coefficient&#39;</span><span class="p">,</span>
         <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">,</span>
     <span class="p">)</span>
+    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+        <span class="s1">&#39;--plot-plane&#39;</span><span class="p">,</span>
+        <span class="n">help</span><span class="o">=</span><span class="s1">&#39;plot mobility tensor in 2D plane (Examples: ab, ac, ba, bc, ca, cb (default is ab))&#39;</span><span class="p">,</span>
+        <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+        <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+        <span class="n">choices</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;ab&#39;</span><span class="p">,</span> <span class="s1">&#39;ac&#39;</span><span class="p">,</span> <span class="s1">&#39;ba&#39;</span><span class="p">,</span> <span class="s1">&#39;bc&#39;</span><span class="p">,</span> <span class="s1">&#39;ca&#39;</span><span class="p">,</span> <span class="s1">&#39;cb&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
         <span class="s1">&#39;--resume&#39;</span><span class="p">,</span>
         <span class="n">help</span><span class="o">=</span><span class="s1">&#39;resume calculation&#39;</span><span class="p">,</span>
@@ -377,11 +388,11 @@
     <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 0.1.6 (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; mcal 0.2.1 (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>
-        <span class="n">read_pickle</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">file</span><span class="p">)</span>
+        <span class="n">read_pickle</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">file</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">plot_plane</span><span class="p">)</span>
         <span class="n">exit</span><span class="p">()</span>
 
     <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">Calculate as </span><span class="si">{</span><span class="n">args</span><span class="o">.</span><span class="n">osc_type</span><span class="si">}</span><span class="s1">-type organic semiconductor.&#39;</span><span class="p">)</span>
@@ -589,6 +600,14 @@
                 <span class="s1">&#39;mobility_vector&#39;</span><span class="p">:</span> <span class="n">vector</span>
             <span class="p">},</span> <span class="n">f</span><span class="p">)</span>
 
+    <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">plot_plane</span><span class="p">:</span>
+        <span class="n">plot_mobility_2d</span><span class="p">(</span>
+            <span class="n">Path</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">cif_path_without_ext</span><span class="si">}</span><span class="s1">_result.pkl&#39;</span><span class="p">),</span>
+            <span class="n">mu</span><span class="p">,</span>
+            <span class="n">cif_reader</span><span class="o">.</span><span class="n">lattice</span><span class="p">,</span>
+            <span class="n">args</span><span class="o">.</span><span class="n">plot_plane</span>
+        <span class="p">)</span>
+
     <span class="n">Tcal</span><span class="o">.</span><span class="n">print_timestamp</span><span class="p">()</span>
     <span class="n">end_time</span> <span class="o">=</span> <span class="n">time</span><span class="p">()</span>
     <span class="n">elapsed_time</span> <span class="o">=</span> <span class="n">end_time</span> <span class="o">-</span> <span class="n">start_time</span>
@@ -988,6 +1007,85 @@
 
 
 
+<div class="viewcode-block" id="plot_mobility_2d">
+<a class="viewcode-back" href="../../mcal.html#mcal.mcal.plot_mobility_2d">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">plot_mobility_2d</span><span class="p">(</span>
+    <span class="n">save_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span>
+    <span class="n">mobility_tensor</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="n">lattice</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="n">plane</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;ab&#39;</span><span class="p">,</span> <span class="s1">&#39;ac&#39;</span><span class="p">,</span> <span class="s1">&#39;ba&#39;</span><span class="p">,</span> <span class="s1">&#39;bc&#39;</span><span class="p">,</span> <span class="s1">&#39;ca&#39;</span><span class="p">,</span> <span class="s1">&#39;cb&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;ab&#39;</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Plot mobility tensor in 2D plane.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    save_path : Path</span>
+<span class="sd">        Path to save the plot</span>
+<span class="sd">    mobility_tensor : NDArray[np.float64]</span>
+<span class="sd">        Mobility tensor</span>
+<span class="sd">    lattice : NDArray[np.float64]</span>
+<span class="sd">        Lattice vectors [Å]</span>
+<span class="sd">    plane : Literal[&#39;ab&#39;, &#39;ac&#39;, &#39;ba&#39;, &#39;bc&#39;, &#39;ca&#39;, &#39;cb&#39;]</span>
+<span class="sd">        Plane to plot, by default &#39;ab&#39;</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Plot mobility in </span><span class="si">{</span><span class="n">plane</span><span class="si">}</span><span class="s2"> plane.&quot;</span><span class="p">)</span>
+    <span class="n">angle_list</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">360</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+    <span class="n">mobility_values</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="n">a_vec</span> <span class="o">=</span> <span class="n">lattice</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+    <span class="n">b_vec</span> <span class="o">=</span> <span class="n">lattice</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+    <span class="n">c_vec</span> <span class="o">=</span> <span class="n">lattice</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+    <span class="k">if</span> <span class="n">plane</span> <span class="o">==</span> <span class="s1">&#39;ab&#39;</span><span class="p">:</span>
+        <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">,</span> <span class="o">=</span> <span class="n">a_vec</span><span class="p">,</span> <span class="n">b_vec</span>
+    <span class="k">elif</span> <span class="n">plane</span> <span class="o">==</span> <span class="s1">&#39;ba&#39;</span><span class="p">:</span>
+        <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">,</span> <span class="o">=</span> <span class="n">b_vec</span><span class="p">,</span> <span class="n">a_vec</span>
+    <span class="k">elif</span> <span class="n">plane</span> <span class="o">==</span> <span class="s1">&#39;bc&#39;</span><span class="p">:</span>
+        <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">,</span> <span class="o">=</span> <span class="n">b_vec</span><span class="p">,</span> <span class="n">c_vec</span>
+    <span class="k">elif</span> <span class="n">plane</span> <span class="o">==</span> <span class="s1">&#39;cb&#39;</span><span class="p">:</span>
+        <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">,</span> <span class="o">=</span> <span class="n">c_vec</span><span class="p">,</span> <span class="n">b_vec</span>
+    <span class="k">elif</span> <span class="n">plane</span> <span class="o">==</span> <span class="s1">&#39;ac&#39;</span><span class="p">:</span>
+        <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">,</span> <span class="o">=</span> <span class="n">a_vec</span><span class="p">,</span> <span class="n">c_vec</span>
+    <span class="k">elif</span> <span class="n">plane</span> <span class="o">==</span> <span class="s1">&#39;ca&#39;</span><span class="p">:</span>
+        <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span> <span class="o">=</span> <span class="n">c_vec</span><span class="p">,</span> <span class="n">a_vec</span>
+
+    <span class="c1"># Angle between the two specified crystal axes</span>
+    <span class="n">second_axis_angle</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">rad2deg</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">arccos</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</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">v1</span><span class="p">)</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">v2</span><span class="p">))))</span>
+    <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Crystal axis directions in the plotted plane:&#39;</span><span class="p">)</span>
+    <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">plane</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s1">-axis: 0.0 deg&#39;</span><span class="p">)</span>
+    <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">plane</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s1">-axis: </span><span class="si">{</span><span class="n">second_axis_angle</span><span class="si">:</span><span class="s1">.1f</span><span class="si">}</span><span class="s1"> deg&#39;</span><span class="p">)</span>
+    <span class="nb">print</span><span class="p">()</span>
+
+    <span class="c1"># Gram–Schmidt orthonormalization</span>
+    <span class="n">e1</span> <span class="o">=</span> <span class="n">v1</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">v1</span><span class="p">)</span>
+    <span class="n">e2</span> <span class="o">=</span> <span class="n">v2</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">v2</span><span class="p">,</span> <span class="n">e1</span><span class="p">)</span> <span class="o">*</span> <span class="n">e1</span>
+    <span class="n">e2</span> <span class="o">=</span> <span class="n">e2</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">e2</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">angle</span> <span class="ow">in</span> <span class="n">angle_list</span><span class="p">:</span>
+        <span class="n">phi</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">deg2rad</span><span class="p">(</span><span class="n">angle</span><span class="p">)</span>
+        <span class="n">direction</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">phi</span><span class="p">)</span> <span class="o">*</span> <span class="n">e1</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">phi</span><span class="p">)</span> <span class="o">*</span> <span class="n">e2</span>
+        <span class="n">mobility_value</span> <span class="o">=</span> <span class="n">direction</span> <span class="o">@</span> <span class="n">mobility_tensor</span> <span class="o">@</span> <span class="n">direction</span>
+        <span class="n">mobility_values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mobility_value</span><span class="p">)</span>
+
+    <span class="n">plt</span><span class="o">.</span><span class="n">rcParams</span><span class="p">[</span><span class="s1">&#39;font.size&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">12</span>
+    <span class="n">width_cm</span><span class="p">,</span> <span class="n">height_cm</span> <span class="o">=</span> <span class="mi">20</span><span class="p">,</span> <span class="mi">8</span>
+    <span class="n">width_inch</span><span class="p">,</span> <span class="n">height_inch</span> <span class="o">=</span> <span class="n">width_cm</span> <span class="o">/</span> <span class="mf">2.54</span><span class="p">,</span> <span class="n">height_cm</span> <span class="o">/</span> <span class="mf">2.54</span>
+
+    <span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="n">subplot_kw</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;projection&#39;</span><span class="p">:</span> <span class="s1">&#39;polar&#39;</span><span class="p">},</span> <span class="n">tight_layout</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="n">width_inch</span><span class="p">,</span> <span class="n">height_inch</span><span class="p">))</span>
+    <span class="n">ax</span><span class="o">.</span><span class="n">set_theta_zero_location</span><span class="p">(</span><span class="s1">&#39;E&#39;</span><span class="p">)</span>
+    <span class="n">ax</span><span class="o">.</span><span class="n">grid</span><span class="p">(</span><span class="kc">True</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s1">&#39;--&#39;</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
+    <span class="n">ax</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">deg2rad</span><span class="p">(</span><span class="n">angle_list</span><span class="p">),</span> <span class="n">mobility_values</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
+
+    <span class="n">ax</span><span class="o">.</span><span class="n">set_rlim</span><span class="p">(</span><span class="n">bottom</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+    <span class="n">ax</span><span class="o">.</span><span class="n">set_xticks</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="o">/</span><span class="mi">6</span><span class="p">))</span>
+    <span class="n">ax</span><span class="o">.</span><span class="n">tick_params</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="s2">&quot;x&quot;</span><span class="p">,</span> <span class="n">pad</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span>
+    <span class="n">ax</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">R</span><span class="s1">&#39;Mobility [$\mathrm</span><span class="si">{cm}</span><span class="s1">^2 \mathrm</span><span class="si">{V}</span><span class="s1">^{-1} \mathrm</span><span class="si">{s}</span><span class="s1">^{-1}$]&#39;</span><span class="p">)</span>
+    <span class="n">ax</span><span class="o">.</span><span class="n">yaxis</span><span class="o">.</span><span class="n">set_label_coords</span><span class="p">(</span><span class="o">-</span><span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">)</span>
+    <span class="n">ax</span><span class="o">.</span><span class="n">set_rlabel_position</span><span class="p">(</span><span class="mi">90</span><span class="p">)</span>
+    <span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="n">save_path</span><span class="o">.</span><span class="n">parent</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">save_path</span><span class="o">.</span><span class="n">stem</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">plane</span><span class="si">}</span><span class="s2">.png&quot;</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">,</span> <span class="n">bbox_inches</span><span class="o">=</span><span class="s1">&#39;tight&#39;</span><span class="p">)</span>
+    <span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div>
+
+
+
 <div class="viewcode-block" id="print_mobility">
 <a class="viewcode-back" href="../../mcal.html#mcal.mcal.print_mobility">[docs]</a>
 <span class="k">def</span><span class="w"> </span><span class="nf">print_mobility</span><span class="p">(</span><span class="n">value</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="n">vector</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="n">sim_type</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;MC&#39;</span><span class="p">,</span> <span class="s1">&#39;ODE&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span><span class="p">):</span>
@@ -1093,14 +1191,24 @@
 
 <div class="viewcode-block" id="read_pickle">
 <a class="viewcode-back" href="../../mcal.html#mcal.mcal.read_pickle">[docs]</a>
-<span class="k">def</span><span class="w"> </span><span class="nf">read_pickle</span><span class="p">(</span><span class="n">file_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">read_pickle</span><span class="p">(</span>
+    <span class="n">file_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">plot_plane</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;ab&#39;</span><span class="p">,</span> <span class="s1">&#39;ac&#39;</span><span class="p">,</span> <span class="s1">&#39;ba&#39;</span><span class="p">,</span> <span class="s1">&#39;bc&#39;</span><span class="p">,</span> <span class="s1">&#39;ca&#39;</span><span class="p">,</span> <span class="s1">&#39;cb&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="kc">None</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Read pickle file and plot mobility tensor in 2D plane.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    file_name : str</span>
+<span class="sd">        Path to the pickle file</span>
+<span class="sd">    plot_plane : Optional[Literal[&#39;ab&#39;, &#39;ac&#39;, &#39;ba&#39;, &#39;bc&#39;, &#39;ca&#39;, &#39;cb&#39;]]</span>
+<span class="sd">        Plane to plot, by default None</span>
+<span class="sd">    &quot;&quot;&quot;</span>
     <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">Input File Name: </span><span class="si">{</span><span class="n">file_name</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
 
     <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_name</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
         <span class="n">results</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
 
-    <span class="c1"># print(results)</span>
-
     <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">Calculate as </span><span class="si">{</span><span class="n">results</span><span class="p">[</span><span class="s2">&quot;osc_type&quot;</span><span class="p">]</span><span class="si">}</span><span class="s1">-type organic semiconductor.&#39;</span><span class="p">)</span>
 
     <span class="n">print_reorg_energy</span><span class="p">(</span><span class="n">results</span><span class="p">[</span><span class="s1">&#39;osc_type&#39;</span><span class="p">],</span> <span class="n">results</span><span class="p">[</span><span class="s1">&#39;reorganization&#39;</span><span class="p">])</span>
@@ -1114,7 +1222,15 @@
 
     <span class="n">print_tensor</span><span class="p">(</span><span class="n">results</span><span class="p">[</span><span class="s1">&#39;mobility_tensor&#39;</span><span class="p">],</span> <span class="n">msg</span><span class="o">=</span><span class="s2">&quot;Mobility tensor (cm^2/Vs)&quot;</span><span class="p">)</span>
 
-    <span class="n">print_mobility</span><span class="p">(</span><span class="n">results</span><span class="p">[</span><span class="s1">&#39;mobility_value&#39;</span><span class="p">],</span> <span class="n">results</span><span class="p">[</span><span class="s1">&#39;mobility_vector&#39;</span><span class="p">])</span></div>
+    <span class="n">print_mobility</span><span class="p">(</span><span class="n">results</span><span class="p">[</span><span class="s1">&#39;mobility_value&#39;</span><span class="p">],</span> <span class="n">results</span><span class="p">[</span><span class="s1">&#39;mobility_vector&#39;</span><span class="p">])</span>
+
+    <span class="k">if</span> <span class="n">plot_plane</span><span class="p">:</span>
+        <span class="n">plot_mobility_2d</span><span class="p">(</span>
+            <span class="n">Path</span><span class="p">(</span><span class="n">file_name</span><span class="p">)</span><span class="o">.</span><span class="n">with_suffix</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">),</span>
+            <span class="n">results</span><span class="p">[</span><span class="s1">&#39;mobility_tensor&#39;</span><span class="p">],</span>
+            <span class="n">results</span><span class="p">[</span><span class="s1">&#39;lattice&#39;</span><span class="p">],</span>
+            <span class="n">plot_plane</span><span class="p">,</span>
+        <span class="p">)</span></div>
 
 
 

{yu_mcal-0.1.6 → yu_mcal-0.2.1}/docs/_sources/index.rst.txt

@@ -32,6 +32,7 @@ Requirements
 * Python 3.9 or newer
 * NumPy
 * Pandas
+* Matplotlib
 * yu-tcal==3.1.0
 * Gaussian 09 or 16
 
@@ -177,6 +178,18 @@ Save calculation results to a pickle file.
 
 * **Example**: ``mcal xxx.cif p -p``
 
+``--plot-plane <plane>``
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Plot mobility tensor as a 2D polar plot on specified crystallographic plane.
+
+* **Available planes**: ``ab``, ``ac``, ``ba``, ``bc``, ``ca``, ``cb``
+* **Default**: None (no plot generated)
+* **Examples**:
+
+  * ``mcal xxx.cif p --plot-plane ab`` (plot on ab-plane)
+  * ``mcal xxx.cif p --plot-plane bc`` (plot on bc-plane)
+
 Diffusion Coefficient Calculation Methods
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

{yu_mcal-0.1.6 → yu_mcal-0.2.1}/docs/genindex.html

@@ -524,12 +524,14 @@
           <li><a href="mcal.utils.html#mcal.utils.gjf_maker.GjfMaker.parent_dir">(mcal.utils.gjf_maker.GjfMaker attribute)</a>
 </li>
         </ul></li>
-        <li><a href="mcal.html#mcal.mcal.print_mobility">print_mobility() (in module mcal.mcal)</a>
+        <li><a href="mcal.html#mcal.mcal.plot_mobility_2d">plot_mobility_2d() (in module mcal.mcal)</a>
 </li>
-        <li><a href="mcal.html#mcal.mcal.print_reorg_energy">print_reorg_energy() (in module mcal.mcal)</a>
+        <li><a href="mcal.html#mcal.mcal.print_mobility">print_mobility() (in module mcal.mcal)</a>
 </li>
     </ul></td>
     <td style="width: 33%; vertical-align: top;"><ul>
+        <li><a href="mcal.html#mcal.mcal.print_reorg_energy">print_reorg_energy() (in module mcal.mcal)</a>
+</li>
         <li><a href="mcal.calculations.html#mcal.calculations.hopping_mobility_model.print_tensor">print_tensor() (in module mcal.calculations.hopping_mobility_model)</a>
 
         <ul>

{yu_mcal-0.1.6 → yu_mcal-0.2.1}/docs/index.html

@@ -267,6 +267,7 @@ and determines mobility tensors considering anisotropy and path continuity.</p>
 <li><p>Python 3.9 or newer</p></li>
 <li><p>NumPy</p></li>
 <li><p>Pandas</p></li>
+<li><p>Matplotlib</p></li>
 <li><p>yu-tcal==3.1.0</p></li>
 <li><p>Gaussian 09 or 16</p></li>
 </ul>
@@ -410,6 +411,20 @@ for transfer integral calculations.</p>
 <li><p><strong>Example</strong>: <code class="docutils literal notranslate"><span class="pre">mcal</span> <span class="pre">xxx.cif</span> <span class="pre">p</span> <span class="pre">-p</span></code></p></li>
 </ul>
 </section>
+<section id="plot-plane-plane">
+<h5><code class="docutils literal notranslate"><span class="pre">--plot-plane</span> <span class="pre">&lt;plane&gt;</span></code><a class="headerlink" href="#plot-plane-plane" title="Link to this heading">¶</a></h5>
+<p>Plot mobility tensor as a 2D polar plot on specified crystallographic plane.</p>
+<ul class="simple">
+<li><p><strong>Available planes</strong>: <code class="docutils literal notranslate"><span class="pre">ab</span></code>, <code class="docutils literal notranslate"><span class="pre">ac</span></code>, <code class="docutils literal notranslate"><span class="pre">ba</span></code>, <code class="docutils literal notranslate"><span class="pre">bc</span></code>, <code class="docutils literal notranslate"><span class="pre">ca</span></code>, <code class="docutils literal notranslate"><span class="pre">cb</span></code></p></li>
+<li><p><strong>Default</strong>: None (no plot generated)</p></li>
+<li><p><strong>Examples</strong>:</p>
+<ul>
+<li><p><code class="docutils literal notranslate"><span class="pre">mcal</span> <span class="pre">xxx.cif</span> <span class="pre">p</span> <span class="pre">--plot-plane</span> <span class="pre">ab</span></code> (plot on ab-plane)</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">mcal</span> <span class="pre">xxx.cif</span> <span class="pre">p</span> <span class="pre">--plot-plane</span> <span class="pre">bc</span></code> (plot on bc-plane)</p></li>
+</ul>
+</li>
+</ul>
+</section>
 </section>
 <section id="diffusion-coefficient-calculation-methods">
 <h4>Diffusion Coefficient Calculation Methods<a class="headerlink" href="#diffusion-coefficient-calculation-methods" title="Link to this heading">¶</a></h4>
@@ -653,6 +668,7 @@ mcal<span class="w"> </span>xxx.cif<span class="w"> </span>p<span class="w"> </s
 </li>
 <li><a class="reference internal" href="#output-settings">Output Settings</a><ul>
 <li><a class="reference internal" href="#p-pickle"><code class="docutils literal notranslate"><span class="pre">-p,</span> <span class="pre">--pickle</span></code></a></li>
+<li><a class="reference internal" href="#plot-plane-plane"><code class="docutils literal notranslate"><span class="pre">--plot-plane</span> <span class="pre">&lt;plane&gt;</span></code></a></li>
 </ul>
 </li>
 <li><a class="reference internal" href="#diffusion-coefficient-calculation-methods">Diffusion Coefficient Calculation Methods</a><ul>