yu-mcal 0.2.1__tar.gz → 0.3.1__tar.gz

{yu_mcal-0.2.1 → yu_mcal-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: yu-mcal
-Version: 0.2.1
+Version: 0.3.1
 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>
@@ -167,16 +167,6 @@ Plot mobility tensor as a 2D polar plot on specified crystallographic plane.
   - `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`
-Calculate diffusion coefficient tensor using kinetic Monte Carlo method.
-- **Example**: `mcal xxx.cif p --mc`
-
-#### `--ode`
-Calculate diffusion coefficient tensor using Ordinary Differential Equation method.
-- **Example**: `mcal xxx.cif p --ode`
-
 ## Practical Usage Examples
 
 ### Basic Calculations
@@ -215,12 +205,6 @@ mcal xxx.cif p --resume
 mcal xxx.cif p -p
 ```
 
-### Comparing Diffusion Coefficients
-```bash
-# Compare with normal calculation + kinetic Monte Carlo + ODE methods
-mcal xxx.cif p --mc --ode
-```
-
 ## Output
 
 ### Standard Output

{yu_mcal-0.2.1 → yu_mcal-0.3.1}/README.md

@@ -119,16 +119,6 @@ Plot mobility tensor as a 2D polar plot on specified crystallographic plane.
   - `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`
-Calculate diffusion coefficient tensor using kinetic Monte Carlo method.
-- **Example**: `mcal xxx.cif p --mc`
-
-#### `--ode`
-Calculate diffusion coefficient tensor using Ordinary Differential Equation method.
-- **Example**: `mcal xxx.cif p --ode`
-
 ## Practical Usage Examples
 
 ### Basic Calculations
@@ -167,12 +157,6 @@ mcal xxx.cif p --resume
 mcal xxx.cif p -p
 ```
 
-### Comparing Diffusion Coefficients
-```bash
-# Compare with normal calculation + kinetic Monte Carlo + ODE methods
-mcal xxx.cif p --mc --ode
-```
-
 ## Output
 
 ### Standard Output

{yu_mcal-0.2.1 → yu_mcal-0.3.1}/README_ja.md

@@ -120,16 +120,6 @@ 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
   - `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`
-モンテカルロ法を使用して拡散係数テンソルを計算します。(テスト用)
-- **例**: `mcal xxx.cif p --mc`
-
-#### `--ode`
-常微分方程式法を使用して拡散係数テンソルを計算します。(テスト用)
-- **例**: `mcal xxx.cif p --ode`
-
 ## 使用例
 
 ### 基本的な計算
@@ -168,12 +158,6 @@ mcal xxx.cif p --resume
 mcal xxx.cif p -p
 ```
 
-### 拡散係数の比較
-```bash
-# 通常計算 + モンテカルロ法 + ODEで比較
-mcal xxx.cif p --mc --ode
-```
-
 ## 出力
 
 ### 標準出力

{yu_mcal-0.2.1 → yu_mcal-0.3.1}/docs/_modules/mcal/calculations/hopping_mobility_model.html

@@ -233,7 +233,7 @@
         </div>
         <article role="main" id="furo-main-content">
           <h1>Source code for mcal.calculations.hopping_mobility_model</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;hopping_mobility_model.py (2025/10/06)&quot;&quot;&quot;</span>
+<span></span><span class="sd">&quot;&quot;&quot;hopping_mobility_model.py (2026/01/29)&quot;&quot;&quot;</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">math</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">random</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">List</span><span class="p">,</span> <span class="n">Tuple</span>
@@ -259,11 +259,11 @@
     <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">D</span><span class="p">:</span>
         <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
     <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Diffusion coefficient tensor (ODE):&quot;</span><span class="p">)</span>
-    <span class="n">D_ode</span> <span class="o">=</span> <span class="n">diffusion_coefficient_tensor_ODE</span><span class="p">(</span><span class="n">lattice</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
+    <span class="n">D_ode</span> <span class="o">=</span> <span class="n">_diffusion_coefficient_tensor_ODE</span><span class="p">(</span><span class="n">lattice</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
     <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">D_ode</span><span class="p">:</span>
         <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
     <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Diffusion coefficient tensor (MC):&quot;</span><span class="p">)</span>
-    <span class="n">D_mc</span> <span class="o">=</span> <span class="n">diffusion_coefficient_tensor_MC</span><span class="p">(</span><span class="n">lattice</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
+    <span class="n">D_mc</span> <span class="o">=</span> <span class="n">_diffusion_coefficient_tensor_MC</span><span class="p">(</span><span class="n">lattice</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
     <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">D_mc</span><span class="p">:</span>
         <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
 
@@ -280,11 +280,11 @@
     <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">D</span><span class="p">:</span>
         <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
     <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Diffusion coefficient tensor (ODE):&quot;</span><span class="p">)</span>
-    <span class="n">D_ode</span> <span class="o">=</span> <span class="n">diffusion_coefficient_tensor_ODE</span><span class="p">(</span><span class="n">lattice</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
+    <span class="n">D_ode</span> <span class="o">=</span> <span class="n">_diffusion_coefficient_tensor_ODE</span><span class="p">(</span><span class="n">lattice</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
     <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">D_ode</span><span class="p">:</span>
         <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
     <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Diffusion coefficient tensor (MC):&quot;</span><span class="p">)</span>
-    <span class="n">D_mc</span> <span class="o">=</span> <span class="n">diffusion_coefficient_tensor_MC</span><span class="p">(</span><span class="n">lattice</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
+    <span class="n">D_mc</span> <span class="o">=</span> <span class="n">_diffusion_coefficient_tensor_MC</span><span class="p">(</span><span class="n">lattice</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
     <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">D_mc</span><span class="p">:</span>
         <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
 
@@ -307,11 +307,11 @@
     <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">D</span><span class="p">:</span>
         <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
     <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Diffusion coefficient tensor (ODE):&quot;</span><span class="p">)</span>
-    <span class="n">D_ode</span> <span class="o">=</span> <span class="n">diffusion_coefficient_tensor_ODE</span><span class="p">(</span><span class="n">lattice</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
+    <span class="n">D_ode</span> <span class="o">=</span> <span class="n">_diffusion_coefficient_tensor_ODE</span><span class="p">(</span><span class="n">lattice</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
     <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">D_ode</span><span class="p">:</span>
         <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
     <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Diffusion coefficient tensor (MC):&quot;</span><span class="p">)</span>
-    <span class="n">D_mc</span> <span class="o">=</span> <span class="n">diffusion_coefficient_tensor_MC</span><span class="p">(</span><span class="n">lattice</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
+    <span class="n">D_mc</span> <span class="o">=</span> <span class="n">_diffusion_coefficient_tensor_MC</span><span class="p">(</span><span class="n">lattice</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
     <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">D_mc</span><span class="p">:</span>
         <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">d</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="si">:</span><span class="s2">9.6f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span></div>
 
@@ -470,12 +470,10 @@
 
 
 
-<div class="viewcode-block" id="diffusion_coefficient_tensor_ODE">
-<a class="viewcode-back" href="../../../mcal.calculations.html#mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_ODE">[docs]</a>
-<span class="k">def</span><span class="w"> </span><span class="nf">diffusion_coefficient_tensor_ODE</span><span class="p">(</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">_diffusion_coefficient_tensor_ODE</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">hop</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">Tuple</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">]],</span>
-    <span class="n">max_steps</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">200</span><span class="p">,</span>
+    <span class="n">max_steps</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">10000</span><span class="p">,</span>
     <span class="n">size</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">40</span><span class="p">,</span>
     <span class="n">max_rate</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.05</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>
@@ -529,16 +527,13 @@
         <span class="n">avg_outer_product</span> <span class="o">+=</span> <span class="n">prob</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">l</span><span class="p">]</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">outer</span><span class="p">(</span><span class="n">vec</span><span class="p">,</span> <span class="n">vec</span><span class="p">)</span>
 
     <span class="n">D</span> <span class="o">=</span> <span class="n">avg_outer_product</span> <span class="o">/</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">max_steps</span> <span class="o">*</span> <span class="n">dt</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">D</span></div>
-
+    <span class="k">return</span> <span class="n">D</span>
 
 
-<div class="viewcode-block" id="diffusion_coefficient_tensor_MC">
-<a class="viewcode-back" href="../../../mcal.calculations.html#mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_MC">[docs]</a>
-<span class="k">def</span><span class="w"> </span><span class="nf">diffusion_coefficient_tensor_MC</span><span class="p">(</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">_diffusion_coefficient_tensor_MC</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">hop</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">Tuple</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">]],</span>
-    <span class="n">steps</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">100</span><span class="p">,</span>
+    <span class="n">steps</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">10000</span><span class="p">,</span>
     <span class="n">particles</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">10000</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>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Calculate diffusion coefficient tensor from Monte Carlo simulation using Gillespie algorithm.</span>
@@ -593,8 +588,7 @@
 
     <span class="c1"># Calculate diffusion coefficient</span>
     <span class="n">D</span> <span class="o">=</span> <span class="n">sum_outer_product</span> <span class="o">/</span> <span class="p">(</span><span class="n">particles</span> <span class="o">*</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">max_time</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">D</span></div>
-
+    <span class="k">return</span> <span class="n">D</span>
 
 
 <div class="viewcode-block" id="print_tensor">

{yu_mcal-0.2.1 → yu_mcal-0.3.1}/docs/_modules/mcal/mcal.html

@@ -253,8 +253,8 @@
 <span class="kn">from</span><span class="w"> </span><span class="nn">mcal.utils.gjf_maker</span><span class="w"> </span><span class="kn">import</span> <span class="n">GjfMaker</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">mcal.calculations.hopping_mobility_model</span><span class="w"> </span><span class="kn">import</span> <span class="p">(</span>
     <span class="n">diffusion_coefficient_tensor</span><span class="p">,</span>
-    <span class="n">diffusion_coefficient_tensor_MC</span><span class="p">,</span>
-    <span class="n">diffusion_coefficient_tensor_ODE</span><span class="p">,</span>
+    <span class="n">_diffusion_coefficient_tensor_MC</span><span class="p">,</span>
+    <span class="n">_diffusion_coefficient_tensor_ODE</span><span class="p">,</span>
     <span class="n">marcus_rate</span><span class="p">,</span>
     <span class="n">mobility_tensor</span>
 <span class="p">)</span>
@@ -308,10 +308,6 @@
 <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>
-<span class="sd">        $ python hop_mcal.py xxx.cif p --mc --ode</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="c1"># Error range for skipping calculation of transfer integrals using moment of inertia and distance between centers of weight.</span>
     <span class="n">CENTER_OF_WEIGHT_ERROR</span> <span class="o">=</span> <span class="mf">1.0e-7</span>
@@ -354,10 +350,10 @@
         <span class="n">help</span><span class="o">=</span><span class="s1">&#39;do not process for speeding up using moment of inertia and distance between centers of weight&#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;--mc&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;use Monte Carlo 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="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--mc&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="n">argparse</span><span class="o">.</span><span class="n">SUPPRESS</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="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
         <span class="s1">&#39;--ode&#39;</span><span class="p">,</span>
-        <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">help</span><span class="o">=</span><span class="n">argparse</span><span class="o">.</span><span class="n">SUPPRESS</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>
@@ -388,7 +384,7 @@
     <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 0.2.1 (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; mcal 0.3.1 (2026/02/05) 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>
@@ -568,7 +564,7 @@
 
     <span class="c1">##### Simulate mobility tensor calculation using Monte Carlo method #####</span>
     <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">mc</span><span class="p">:</span>
-        <span class="n">D_MC</span> <span class="o">=</span> <span class="n">diffusion_coefficient_tensor_MC</span><span class="p">(</span><span class="n">cif_reader</span><span class="o">.</span><span class="n">lattice</span> <span class="o">*</span> <span class="mf">1e-8</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
+        <span class="n">D_MC</span> <span class="o">=</span> <span class="n">_diffusion_coefficient_tensor_MC</span><span class="p">(</span><span class="n">cif_reader</span><span class="o">.</span><span class="n">lattice</span> <span class="o">*</span> <span class="mf">1e-8</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
         <span class="n">print_tensor</span><span class="p">(</span><span class="n">D_MC</span><span class="p">,</span> <span class="n">msg</span><span class="o">=</span><span class="s2">&quot;Diffusion coefficient tensor (cm^2/s) (MC)&quot;</span><span class="p">)</span>
         <span class="n">mu_MC</span> <span class="o">=</span> <span class="n">mobility_tensor</span><span class="p">(</span><span class="n">D_MC</span><span class="p">)</span>
         <span class="n">print_tensor</span><span class="p">(</span><span class="n">mu_MC</span><span class="p">,</span> <span class="n">msg</span><span class="o">=</span><span class="s2">&quot;Mobility tensor (cm^2/Vs) (MC)&quot;</span><span class="p">)</span>
@@ -577,7 +573,7 @@
 
     <span class="c1">##### Simulate mobility tensor calculation using Ordinary Differential Equation method #####</span>
     <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">ode</span><span class="p">:</span>
-        <span class="n">D_ODE</span> <span class="o">=</span> <span class="n">diffusion_coefficient_tensor_ODE</span><span class="p">(</span><span class="n">cif_reader</span><span class="o">.</span><span class="n">lattice</span> <span class="o">*</span> <span class="mf">1e-8</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
+        <span class="n">D_ODE</span> <span class="o">=</span> <span class="n">_diffusion_coefficient_tensor_ODE</span><span class="p">(</span><span class="n">cif_reader</span><span class="o">.</span><span class="n">lattice</span> <span class="o">*</span> <span class="mf">1e-8</span><span class="p">,</span> <span class="n">hop</span><span class="p">)</span>
         <span class="n">print_tensor</span><span class="p">(</span><span class="n">D_ODE</span><span class="p">,</span> <span class="n">msg</span><span class="o">=</span><span class="s2">&quot;Diffusion coefficient tensor (cm^2/s) (ODE)&quot;</span><span class="p">)</span>
         <span class="n">mu_ODE</span> <span class="o">=</span> <span class="n">mobility_tensor</span><span class="p">(</span><span class="n">D_ODE</span><span class="p">)</span>
         <span class="n">print_tensor</span><span class="p">(</span><span class="n">mu_ODE</span><span class="p">,</span> <span class="n">msg</span><span class="o">=</span><span class="s2">&quot;Mobility tensor (cm^2/Vs) (ODE)&quot;</span><span class="p">)</span>

{yu_mcal-0.2.1 → yu_mcal-0.3.1}/docs/_modules/mcal/utils/cif_reader.html

@@ -233,7 +233,7 @@
         </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 (2026/01/29)&quot;&quot;&quot;</span>
+<span></span><span class="sd">&quot;&quot;&quot;CifReader beta (2026/02/05)&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>
@@ -457,9 +457,9 @@
         <span class="k">for</span> <span class="n">atom_idx</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">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">c</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">calc_cen_of_weight</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">atom_idx</span><span class="p">])):</span>
                 <span class="k">if</span> <span class="mi">1</span> <span class="o">&lt;=</span> <span class="n">c</span><span class="p">:</span>
-                    <span class="n">change</span> <span class="o">=</span> <span class="o">-</span><span class="nb">int</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+                    <span class="n">change</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">floor</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
                 <span class="k">elif</span> <span class="n">c</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">:</span>
-                    <span class="n">change</span> <span class="o">=</span> <span class="nb">abs</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">c</span><span class="p">))</span> <span class="o">+</span> <span class="mi">1</span>
+                    <span class="n">change</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">ceil</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">c</span><span class="p">))</span>
                 <span class="k">else</span><span class="p">:</span>
                     <span class="n">change</span> <span class="o">=</span> <span class="mi">0</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">sym_coords</span><span class="p">[</span><span class="n">atom_idx</span><span class="p">,</span> <span class="n">i</span><span class="p">]</span> <span class="o">+=</span> <span class="n">change</span>

{yu_mcal-0.2.1 → yu_mcal-0.3.1}/docs/_sources/index.rst.txt

@@ -190,23 +190,6 @@ Plot mobility tensor as a 2D polar plot on specified crystallographic plane.
   * ``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``
-^^^^^^^^
-
-Calculate diffusion coefficient tensor using kinetic Monte Carlo method.
-
-* **Example**: ``mcal xxx.cif p --mc``
-
-``--ode``
-^^^^^^^^^
-
-Calculate diffusion coefficient tensor using Ordinary Differential Equation method.
-
-* **Example**: ``mcal xxx.cif p --ode``
-
 Practical Usage Examples
 -------------------------
 
@@ -252,14 +235,6 @@ Reusing Results
    # Save results to pickle file
    mcal xxx.cif p -p
 
-Comparing Diffusion Coefficients
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. code-block:: bash
-
-   # Compare with normal calculation + kinetic Monte Carlo + ODE methods
-   mcal xxx.cif p --mc --ode
-
 Output
 ------
 

{yu_mcal-0.2.1 → yu_mcal-0.3.1}/docs/genindex.html

@@ -319,14 +319,10 @@
   <table style="width: 100%" class="indextable genindextable"><tr>
     <td style="width: 33%; vertical-align: top;"><ul>
         <li><a href="mcal.calculations.html#mcal.calculations.hopping_mobility_model.demo">demo() (in module mcal.calculations.hopping_mobility_model)</a>
-</li>
-        <li><a href="mcal.calculations.html#mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor">diffusion_coefficient_tensor() (in module mcal.calculations.hopping_mobility_model)</a>
 </li>
     </ul></td>
     <td style="width: 33%; vertical-align: top;"><ul>
-        <li><a href="mcal.calculations.html#mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_MC">diffusion_coefficient_tensor_MC() (in module mcal.calculations.hopping_mobility_model)</a>
-</li>
-        <li><a href="mcal.calculations.html#mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_ODE">diffusion_coefficient_tensor_ODE() (in module mcal.calculations.hopping_mobility_model)</a>
+        <li><a href="mcal.calculations.html#mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor">diffusion_coefficient_tensor() (in module mcal.calculations.hopping_mobility_model)</a>
 </li>
     </ul></td>
   </tr></table>

{yu_mcal-0.2.1 → yu_mcal-0.3.1}/docs/index.html

@@ -426,23 +426,6 @@ for transfer integral calculations.</p>
 </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>
-<section id="mc">
-<h5><code class="docutils literal notranslate"><span class="pre">--mc</span></code><a class="headerlink" href="#mc" title="Link to this heading">¶</a></h5>
-<p>Calculate diffusion coefficient tensor using kinetic Monte Carlo method.</p>
-<ul class="simple">
-<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">--mc</span></code></p></li>
-</ul>
-</section>
-<section id="ode">
-<h5><code class="docutils literal notranslate"><span class="pre">--ode</span></code><a class="headerlink" href="#ode" title="Link to this heading">¶</a></h5>
-<p>Calculate diffusion coefficient tensor using Ordinary Differential Equation method.</p>
-<ul class="simple">
-<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">--ode</span></code></p></li>
-</ul>
-</section>
-</section>
 </section>
 <section id="practical-usage-examples">
 <h3>Practical Usage Examples<a class="headerlink" href="#practical-usage-examples" title="Link to this heading">¶</a></h3>
@@ -485,13 +468,6 @@ mcal<span class="w"> </span>xxx.cif<span class="w"> </span>p<span class="w"> </s
 </pre></div>
 </div>
 </section>
-<section id="comparing-diffusion-coefficients">
-<h4>Comparing Diffusion Coefficients<a class="headerlink" href="#comparing-diffusion-coefficients" title="Link to this heading">¶</a></h4>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Compare with normal calculation + kinetic Monte Carlo + ODE methods</span>
-mcal<span class="w"> </span>xxx.cif<span class="w"> </span>p<span class="w"> </span>--mc<span class="w"> </span>--ode
-</pre></div>
-</div>
-</section>
 </section>
 <section id="output">
 <h3>Output<a class="headerlink" href="#output" title="Link to this heading">¶</a></h3>
@@ -671,18 +647,12 @@ mcal<span class="w"> </span>xxx.cif<span class="w"> </span>p<span class="w"> </s
 <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>
-<li><a class="reference internal" href="#mc"><code class="docutils literal notranslate"><span class="pre">--mc</span></code></a></li>
-<li><a class="reference internal" href="#ode"><code class="docutils literal notranslate"><span class="pre">--ode</span></code></a></li>
-</ul>
-</li>
 </ul>
 </li>
 <li><a class="reference internal" href="#practical-usage-examples">Practical Usage Examples</a><ul>
 <li><a class="reference internal" href="#basic-calculations">Basic Calculations</a></li>
 <li><a class="reference internal" href="#high-precision-calculations">High-Precision Calculations</a></li>
 <li><a class="reference internal" href="#reusing-results">Reusing Results</a></li>
-<li><a class="reference internal" href="#comparing-diffusion-coefficients">Comparing Diffusion Coefficients</a></li>
 </ul>
 </li>
 <li><a class="reference internal" href="#output">Output</a><ul>

{yu_mcal-0.2.1 → yu_mcal-0.3.1}/docs/mcal.calculations.html

@@ -246,7 +246,7 @@
 </section>
 <section id="module-mcal.calculations.hopping_mobility_model">
 <span id="mcal-calculations-hopping-mobility-model-module"></span><h2>mcal.calculations.hopping_mobility_model module<a class="headerlink" href="#module-mcal.calculations.hopping_mobility_model" title="Link to this heading">¶</a></h2>
-<p>hopping_mobility_model.py (2025/10/06)</p>
+<p>hopping_mobility_model.py (2026/01/29)</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="mcal.calculations.hopping_mobility_model.cal_pinv">
 <span class="sig-prename descclassname"><span class="pre">mcal.calculations.hopping_mobility_model.</span></span><span class="sig-name descname"><span class="pre">cal_pinv</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">array</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rcond</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.001</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="_modules/mcal/calculations/hopping_mobility_model.html#cal_pinv"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mcal.calculations.hopping_mobility_model.cal_pinv" title="Link to this definition">¶</a></dt>
@@ -298,51 +298,6 @@
 </dl>
 </dd></dl>
 
-<dl class="py function">
-<dt class="sig sig-object py" id="mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_MC">
-<span class="sig-prename descclassname"><span class="pre">mcal.calculations.hopping_mobility_model.</span></span><span class="sig-name descname"><span class="pre">diffusion_coefficient_tensor_MC</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lattice</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hop</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">Tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">steps</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">100</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">particles</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">10000</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="_modules/mcal/calculations/hopping_mobility_model.html#diffusion_coefficient_tensor_MC"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_MC" title="Link to this definition">¶</a></dt>
-<dd><p>Calculate diffusion coefficient tensor from Monte Carlo simulation using Gillespie algorithm.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>lattice</strong> (<em>3x3 numpy.array</em>) – lattice[0,:] is a-axis vector, lattice[1,:] b-axis vector, lattice[2,:] c-axis vector</p></li>
-<li><p><strong>hop</strong> (<em>list</em><em> of </em><em>(</em><em>int</em><em>, </em><em>int</em><em>, </em><em>int</em><em>, </em><em>int</em><em>, </em><em>int</em><em>, </em><em>float</em><em>) </em><em>tuple.</em>) – (s, t, i, j, k, p) means that the hopping rate from s-th molecule in (0, 0, 0) cell to t-th molecule in (i, j, k) cell is p.</p></li>
-<li><p><strong>steps</strong> (<em>int</em>) – Number of steps</p></li>
-<li><p><strong>particles</strong> (<em>int</em>) – Number of particles</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns<span class="colon">:</span></dt>
-<dd class="field-even"><p>Diffusion coefficient tensor</p>
-</dd>
-<dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p>3x3 numpy.array</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py function">
-<dt class="sig sig-object py" id="mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_ODE">
-<span class="sig-prename descclassname"><span class="pre">mcal.calculations.hopping_mobility_model.</span></span><span class="sig-name descname"><span class="pre">diffusion_coefficient_tensor_ODE</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lattice</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hop</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">Tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_steps</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">200</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">40</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_rate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.05</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="p"><span class="pre">[</span></span><span class="pre">Any</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dtype</span><span class="p"><span class="pre">[</span></span><span class="pre">float64</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="_modules/mcal/calculations/hopping_mobility_model.html#diffusion_coefficient_tensor_ODE"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_ODE" title="Link to this definition">¶</a></dt>
-<dd><p>Calculate diffusion coefficient tensor from numerical solution of Ordinary Differential Equation (ODE)</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>lattice</strong> (<em>3x3 numpy.array</em>) – lattice[0,:] is a-axis vector, lattice[1,:] b-axis vector, lattice[2,:] c-axis vector</p></li>
-<li><p><strong>hop</strong> (<em>list</em><em> of </em><em>(</em><em>int</em><em>, </em><em>int</em><em>, </em><em>int</em><em>, </em><em>int</em><em>, </em><em>int</em><em>, </em><em>float</em><em>) </em><em>tuple.</em>) – (s, t, i, j, k, p) means that the hopping rate from s-th molecule in (0, 0, 0) cell to t-th molecule in (i, j, k) cell is p.</p></li>
-<li><p><strong>max_steps</strong> (<em>int</em>) – Maximum number of steps</p></li>
-<li><p><strong>size</strong> (<em>int</em>) – Size of the simulation box</p></li>
-<li><p><strong>max_rate</strong> (<em>float</em>) – Maximum rate of hopping</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns<span class="colon">:</span></dt>
-<dd class="field-even"><p>Diffusion coefficient tensor</p>
-</dd>
-<dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p>3x3 numpy.array</p>
-</dd>
-</dl>
-</dd></dl>
-
 <dl class="py function">
 <dt class="sig sig-object py" id="mcal.calculations.hopping_mobility_model.marcus_rate">
 <span class="sig-prename descclassname"><span class="pre">mcal.calculations.hopping_mobility_model.</span></span><span class="sig-name descname"><span class="pre">marcus_rate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">transfer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reorganization</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">T</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">300.0</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference internal" href="_modules/mcal/calculations/hopping_mobility_model.html#marcus_rate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mcal.calculations.hopping_mobility_model.marcus_rate" title="Link to this definition">¶</a></dt>
@@ -561,8 +516,6 @@
 <li><a class="reference internal" href="#mcal.calculations.hopping_mobility_model.cal_pinv"><code class="docutils literal notranslate"><span class="pre">cal_pinv()</span></code></a></li>
 <li><a class="reference internal" href="#mcal.calculations.hopping_mobility_model.demo"><code class="docutils literal notranslate"><span class="pre">demo()</span></code></a></li>
 <li><a class="reference internal" href="#mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor"><code class="docutils literal notranslate"><span class="pre">diffusion_coefficient_tensor()</span></code></a></li>
-<li><a class="reference internal" href="#mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_MC"><code class="docutils literal notranslate"><span class="pre">diffusion_coefficient_tensor_MC()</span></code></a></li>
-<li><a class="reference internal" href="#mcal.calculations.hopping_mobility_model.diffusion_coefficient_tensor_ODE"><code class="docutils literal notranslate"><span class="pre">diffusion_coefficient_tensor_ODE()</span></code></a></li>
 <li><a class="reference internal" href="#mcal.calculations.hopping_mobility_model.marcus_rate"><code class="docutils literal notranslate"><span class="pre">marcus_rate()</span></code></a></li>
 <li><a class="reference internal" href="#mcal.calculations.hopping_mobility_model.mobility_tensor"><code class="docutils literal notranslate"><span class="pre">mobility_tensor()</span></code></a></li>
 <li><a class="reference internal" href="#mcal.calculations.hopping_mobility_model.print_tensor"><code class="docutils literal notranslate"><span class="pre">print_tensor()</span></code></a></li>