add missing files, removed files that are too big

.gitignore

@@ -166,4 +166,9 @@ cython_debug/
 .DS_Store
 
 # Backup
-backup
+<<<<<<< HEAD
+backup
+=======
+backup
+examples/sweep/*.csv
+>>>>>>> 2cb53ab (add missed files)

docs/_build/html/genindex.html

@@ -101,13 +101,15 @@ <h2 id="C">C</h2>
 </li>
       <li><a href="decomnano.html#decomnano.sweep.SweepDecomNano.calc_sweep">calc_sweep() (decomnano.sweep.SweepDecomNano method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="decomnano.html#decomnano.sweep.SweepDecomNano.calc_sweep_const_2param">calc_sweep_const_2param() (decomnano.sweep.SweepDecomNano method)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="decomnano.html#decomnano.decomnano.DecomNano.check_duplicate_input">check_duplicate_input() (decomnano.decomnano.DecomNano method)</a>
 </li>
-      <li><a href="decomnano.html#decomnano.decomnano.DecomNano.column">column (decomnano.decomnano.DecomNano attribute)</a>
+      <li><a href="decomnano.html#decomnano.decomnano.DecomNano.column">column (decomnano.decomnano.DecomNano attribute)</a>, <a href="decomnano.html#id0">[1]</a>
+</li>
+      <li><a href="decomnano.html#decomnano.decomnano.DecomNano.column_hollow">column_hollow (decomnano.decomnano.DecomNano attribute)</a>
 </li>
       <li><a href="decomnano.html#decomnano.decomnano.DecomNano.convert_dict">convert_dict() (decomnano.decomnano.DecomNano method)</a>
 </li>
@@ -150,6 +152,8 @@ <h2 id="D">D</h2>
 </li>
       </ul></li>
       <li><a href="decomnano.html#decomnano.decomnano.DecomNano.decomnano_equation">decomnano_equation (decomnano.decomnano.DecomNano attribute)</a>
+</li>
+      <li><a href="decomnano.html#decomnano.decomnano.DecomNano.decomnano_equation_hollow">decomnano_equation_hollow (decomnano.decomnano.DecomNano attribute)</a>
 </li>
       <li><a href="decomnano.html#decomnano.decomnano.DecomNano.dict_regex">dict_regex (decomnano.decomnano.DecomNano attribute)</a>
 </li>
@@ -228,6 +232,8 @@ <h2 id="P">P</h2>
 <h2 id="R">R</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="decomnano.html#decomnano.decomnano.DecomNano.respawn_kernel">respawn_kernel() (decomnano.decomnano.DecomNano method)</a>
+</li>
       <li><a href="decomnano.html#decomnano.decomnano.DecomNano.results">results (decomnano.decomnano.DecomNano attribute)</a>
 </li>
   </ul></td>

docs/_build/html/modules.html

@@ -104,12 +104,16 @@ <h1>decomnano<a class="headerlink" href="#decomnano" title="Permalink to this he
 <li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.dict_regex"><code class="docutils literal notranslate"><span class="pre">DecomNano.dict_regex</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.calc_decomnano"><code class="docutils literal notranslate"><span class="pre">DecomNano.calc_decomnano()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.check_duplicate_input"><code class="docutils literal notranslate"><span class="pre">DecomNano.check_duplicate_input()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="decomnano.html#id0"><code class="docutils literal notranslate"><span class="pre">DecomNano.column</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.column_hollow"><code class="docutils literal notranslate"><span class="pre">DecomNano.column_hollow</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.convert_dict"><code class="docutils literal notranslate"><span class="pre">DecomNano.convert_dict()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.decomnano_equation"><code class="docutils literal notranslate"><span class="pre">DecomNano.decomnano_equation</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.decomnano_equation_hollow"><code class="docutils literal notranslate"><span class="pre">DecomNano.decomnano_equation_hollow</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.init_input"><code class="docutils literal notranslate"><span class="pre">DecomNano.init_input()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.load_results"><code class="docutils literal notranslate"><span class="pre">DecomNano.load_results()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.print_input"><code class="docutils literal notranslate"><span class="pre">DecomNano.print_input()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.print_results"><code class="docutils literal notranslate"><span class="pre">DecomNano.print_results()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.respawn_kernel"><code class="docutils literal notranslate"><span class="pre">DecomNano.respawn_kernel()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.save_results"><code class="docutils literal notranslate"><span class="pre">DecomNano.save_results()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.solve_decomnano"><code class="docutils literal notranslate"><span class="pre">DecomNano.solve_decomnano()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="decomnano.html#decomnano.decomnano.DecomNano.terminate"><code class="docutils literal notranslate"><span class="pre">DecomNano.terminate()</span></code></a></li>

docs/_build/html/readme.html

@@ -98,7 +98,7 @@
 <h1>DecomNano<a class="headerlink" href="#decomnano" title="Permalink to this heading"></a></h1>
 <a class="reference external image-reference" href="https://pypi.python.org/pypi/decomnano"><img alt="https://img.shields.io/pypi/v/decomnano.svg" src="https://img.shields.io/pypi/v/decomnano.svg" /></a>
 <a class="reference external image-reference" href="https://travis-ci.com/Ameyanagi/decomnano"><img alt="https://img.shields.io/travis/Ameyanagi/decomnano.svg" src="https://img.shields.io/travis/Ameyanagi/decomnano.svg" /></a>
-<a class="reference external image-reference" href="https://github.com/Ameyanagi/DecomNano/actions/workflows/documentation.yaml/badge.svg"><img alt="Documentation Status" src="https://ameyanagi.github.io/DecomNano/index.html" /></a>
+<a class="reference external image-reference" href="https://ameyanagi.github.io/DecomNano/index.html"><img alt="Documentation Status" src="https://github.com/Ameyanagi/DecomNano/actions/workflows/documentation.yaml/badge.svg" /></a>
 <p>DecomNano is a heterogeneity analysis of bimetallic nanoparticles using coordination numbers obtained from XAS analysis.</p>
 <ul class="simple">
 <li><p>Free software: MIT license</p></li>
@@ -117,6 +117,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <p>Detailed instructions for installation are available in the <a class="reference external" href="https://ameyanagi.github.io/DecomNano/installation.html">installation documentation</a>.</p>
 <section id="installation-from-pypi">
 <h3>Installation from PyPI<a class="headerlink" href="#installation-from-pypi" title="Permalink to this heading"></a></h3>
+<p>(This method is not available yet. It will be available after the submission.)</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>decomnano
 </pre></div>
 </div>

docs/conversion_of_PDF_from_particle_average_to_atom_average.md

@@ -0,0 +1,114 @@
+---
+marp:true
+theme: default
+paginate: true
+footer: "Conversion of PDF from particle average to atom average"
+marp: true
+---
+
+# Conversion of PDF from particle average to atom average
+Aug 28, 2023
+
+---
+# Conversion of PDF from particle average to atom average
+
+- Particle size distribution (PDF) measured by TEM is usually a particle average PDF.
+
+- In XAS, The average spectrum is and atom average of all the sites.
+
+- Therefore, the particle size obtained from TEM and particle size obtained from XAS will be different. (*Annu. Rev. Anal. Chem.* **2011**. *4*, 23–39)
+
+- Here, we will discuss how to convert the particle average PDF to atom average PDF.
+
+---
+# Assumptions
+
+- The particle is spherical.
+$$ V(r) = \frac{4}{3}\pi r^3 $$
+$$ V(D) = \frac{1}{6}\pi D^3 $$
+
+- The particle size distribution is normal distribution.
+$$ f(D) = \frac{1}{\sqrt{2\pi}\sigma} \exp\left(-\frac{(D-\mu)^2}{2\sigma^2}\right) $$
+
+---
+# Conversion
+
+When $g(D)$ is the probability density function of particle size distribution scaled by $V(D)$, the conversion of $f(D)$ to $g(D)$ is given by
+$$g(D) = \frac{V(D)f(D)}{\int_{-\infty}^{\infty} V(D)f(D) dD}$$
+
+The expectation and variance of $g(D)$ are given by
+
+$$ \mu = \int_{-\infty}^{\infty} D g(D) dD $$
+$$ \sigma^2 =\int_{-\infty}^{\infty} (D-\mu)^2 g(D) dD $$
+$$= \int_{-\infty}^{\infty} D^2 g(D) dD - \mu^2 $$
+
+
+
+---
+
+# Calculation of normalization factor
+
+The integrals were performed using Wolfram Mathematica 12.3.1. The results are given below.
+$$\int_{-\infty}^{\infty} V(D)f(D) dD = \frac{1}{\sqrt{2\pi}\sigma} \int_{-\infty}^{\infty} \frac{1}{6}\pi D^3 \exp\left(-\frac{(D-\mu)^2}{2\sigma^2}\right) dD$$
+
+$$=\frac{\pi}{6}\mu(\mu^2+3\sigma^2)$$
+
+Mathematica ouput:
+![normalization](./img/normalization.png)
+
+---
+
+# g(D)
+
+$$g(D)  = \frac{x^3}{\mu(\mu^2+3\sigma^2)\sqrt{2\pi}\sigma} \exp\left(-\frac{(D-\mu)^2}{2\sigma^2}\right)$$
+
+---
+# Calculation of expectation
+
+$$ \mu = \int_{-\infty}^{\infty} D g(D) dD $$
+$$ = \frac{\mu^4 + 6\mu^2\sigma^2 + 3\sigma^4}{\mu(\mu^2+3\sigma^2)} $$
+
+Mathematica output:
+![mu](./img/mu.png)
+
+
+---
+# Calculation of variance
+
+$$ \sigma^2 =\int_{-\infty}^{\infty} D^2 g(D) dD - \mu^2 $$
+$$ = \frac{\mu^4 + 10 \mu^2 \sigma^2 +  15 \sigma^4}{\mu^2 + 3\sigma^2} - \mu^2 $$
+
+Mathematica output:
+![variance](./img/variance.png)
+
+---
+
+# Mock example
+
+$\mu = 17 Å$, $\sigma = 6 Å$
+
+
+![width:500px](./img/calculation_of_V_average.png)
+
+---
+# Conclusion
+
+- The conversion of particle average PDF to atom average PDF obtained by 2 assumptions. 
+    - The particle is spherical.
+    - The particle size distribution is normal distribution.
+
+- The converted $\mu$ and $\sigma$ are given by
+$$ \mu = \frac{\mu^4 + 6\mu^2\sigma^2 + 3\sigma^4}{\mu(\mu^2+3\sigma^2)} $$
+$$ \sigma^2 = \frac{\mu^4 + 10 \mu^2 \sigma^2 +  15 \sigma^4}{\mu^2 + 3\sigma^2} - \mu^2 $$
+
+---
+
+# Python code
+
+```python
+def mu_vol(mu, sigma):
+    return (mu**4 + 6*mu**2*sigma**2 + 3*sigma**4)/(mu*(mu**2 + 3*sigma**2))
+
+def sigma_vol(mu, sigma):
+    return np.sqrt((mu**4 + 10 * mu**2 * sigma**2 +  15 * sigma**4)/(mu**2 + 3*sigma**2) - mu_vol(mu, sigma)**2)
+```