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<div id="jb-print-docs-body" class="onlyprint">
    <h1>Results Files Documentation</h1>
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                <h2> Contents </h2>
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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#general-information">General Information</a><ul class="nav section-nav flex-column">
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#file-naming-conventions">File Naming Conventions</a></li>
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<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#background-fitting">1. <strong>Background Fitting</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#xrd-refinement">2. <strong>XRD Refinement</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#amorphous-fitting">3. <strong>Amorphous Fitting</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#cif-parsing">4. <strong>CIF Parsing</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#solid-solution-modeling">5. <strong>Solid Solution Modeling</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#xrd-simulation">6. <strong>XRD Simulation</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#cif-preprocessing">7. <strong>CIF Preprocessing</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#substitutional-search">8. <strong>Substitutional Search</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#xps-analysis">9. <strong>XPS Analysis</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#exafs-analysis">10. <strong>EXAFS Analysis</strong></a></li>
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  <section class="tex2jax_ignore mathjax_ignore" id="results-files-documentation">
<h1>Results Files Documentation<a class="headerlink" href="#results-files-documentation" title="Link to this heading">#</a></h1>
<p>This page provides an overview of the output files generated by the <strong>WPEM</strong> software for diffraction refinement, background fitting, amorphous component analysis, solid solution modeling, and simulation tasks.</p>
<hr class="docutils" />
<section id="general-information">
<h2>General Information<a class="headerlink" href="#general-information" title="Link to this heading">#</a></h2>
<p>All results are saved in the <strong>working directory</strong> (<code class="docutils literal notranslate"><span class="pre">work_dir</span></code>), which can be specified by the user during execution. If not specified, outputs default to the current directory.</p>
<section id="file-naming-conventions">
<h3>File Naming Conventions<a class="headerlink" href="#file-naming-conventions" title="Link to this heading">#</a></h3>
<ul class="simple">
<li><p><strong>Prefix</strong>: Indicates the task type (e.g., <code class="docutils literal notranslate"><span class="pre">XRD</span></code>, <code class="docutils literal notranslate"><span class="pre">Background</span></code>, <code class="docutils literal notranslate"><span class="pre">Amorphous</span></code>, etc.).</p></li>
<li><p><strong>Suffix</strong>: Usually includes a timestamp to prevent file overwriting.</p></li>
</ul>
</section>
</section>
<hr class="docutils" />
<section id="output-files-by-function">
<h2>Output Files by Function<a class="headerlink" href="#output-files-by-function" title="Link to this heading">#</a></h2>
<section id="background-fitting">
<h3>1. <strong>Background Fitting</strong><a class="headerlink" href="#background-fitting" title="Link to this heading">#</a></h3>
<p><strong>Folder</strong>: <code class="docutils literal notranslate"><span class="pre">ConvertedDocuments</span></code></p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">bac.csv</span></code>: Fitted background intensities.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">no_bac_intensity.csv</span></code>: Diffraction signals after background removal.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">bac_points.csv</span></code>: Selected background points.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">intensity_fft.csv</span></code>: Diffraction signals processed by Fast Fourier Transform.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">de_backgroundfittingcurve.png</span></code>: Plot of the original data, fitted background, and background-subtracted signals.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">backgroundfittingcurve.png</span></code>: Visualization showing the raw data, selected background points, and the fitted background curve.</p></li>
</ul>
</section>
<hr class="docutils" />
<section id="xrd-refinement">
<h3>2. <strong>XRD Refinement</strong><a class="headerlink" href="#xrd-refinement" title="Link to this heading">#</a></h3>
<p><strong>Folder</strong>: <code class="docutils literal notranslate"><span class="pre">WPEMFittingResults</span></code></p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">CrystalSystem0_WPEMout_&lt;time&gt;.csv</span></code>: Refined crystal information, including:</p>
<ul>
<li><p><code class="docutils literal notranslate"><span class="pre">code</span></code>: Indicates Kα1 or Kα2 origin.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">H</span></code>, <code class="docutils literal notranslate"><span class="pre">K</span></code>, <code class="docutils literal notranslate"><span class="pre">L</span></code>: Miller indices.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">wi</span></code>, <code class="docutils literal notranslate"><span class="pre">Ai</span></code>, <code class="docutils literal notranslate"><span class="pre">L_gamma_i</span></code>, <code class="docutils literal notranslate"><span class="pre">G_sigma2_i</span></code>: Peak shape parameters (refer to the WPEM paper for details).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">mu_i</span></code>: Peak positions.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">intensity</span></code>: Peak intensities.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">system0</span></code>, <code class="docutils literal notranslate"><span class="pre">system1</span></code>, etc.: Refers to different phases.</p></li>
</ul>
</li>
<li><p><code class="docutils literal notranslate"><span class="pre">hkl0_&lt;time&gt;.csv</span></code>: Diffraction indices for each peak in phase 0.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">WPEMfittingProfile_&lt;time&gt;.csv</span></code>: WPEM-generated fitting profile.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">WPEMPeakParas_&lt;time&gt;.csv</span></code>: Peak location and shape parameters, with profile fitting quality metrics.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">ResidualWPEM_fittingresult_&lt;time&gt;.png</span></code>: Plot comparing fitted results with experimental data.</p></li>
</ul>
</section>
<hr class="docutils" />
<section id="amorphous-fitting">
<h3>3. <strong>Amorphous Fitting</strong><a class="headerlink" href="#amorphous-fitting" title="Link to this heading">#</a></h3>
<p><strong>Folder</strong>: <code class="docutils literal notranslate"><span class="pre">DecomposedComponents</span></code></p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">Amorphous.csv</span></code>: Extracted amorphous signals.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">M_Amorphous_componentsX.csv</span></code>: Identified amorphous peak components (X = index).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">upbackground.csv</span></code>: Updated background after amorphous subtraction.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Decomposed_peaks.png</span></code>: Visualization of decomposed crystalline and amorphous components.</p></li>
</ul>
</section>
<hr class="docutils" />
<section id="cif-parsing">
<h3>4. <strong>CIF Parsing</strong><a class="headerlink" href="#cif-parsing" title="Link to this heading">#</a></h3>
<p><strong>Folder</strong>: <code class="docutils literal notranslate"><span class="pre">output_xrd</span></code></p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">NAMEHKL.csv</span></code>: Calculated diffraction indices, angles, and theoretical intensities.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">NAME_Extinction_peak.csv</span></code>: List of extinction peaks caused by geometrical and systematic extinction.</p></li>
</ul>
</section>
<hr class="docutils" />
<section id="solid-solution-modeling">
<h3>5. <strong>Solid Solution Modeling</strong><a class="headerlink" href="#solid-solution-modeling" title="Link to this heading">#</a></h3>
<p><strong>Folder</strong>: <code class="docutils literal notranslate"><span class="pre">WPEMSitOpt</span></code></p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">substitutional.png</span></code>: Fitting result of the optimized solid solution structure.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">DecompositionPlot.png</span></code>: Overlay of decomposed peaks and experimental data.</p></li>
</ul>
</section>
<hr class="docutils" />
<section id="xrd-simulation">
<h3>6. <strong>XRD Simulation</strong><a class="headerlink" href="#xrd-simulation" title="Link to this heading">#</a></h3>
<p><strong>Function</strong>: <code class="docutils literal notranslate"><span class="pre">XRDSimulation</span></code></p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">Simulated_XRDPattern.csv</span></code>: Simulated XRD pattern based on the provided CIF file.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">SimulatedPeaks.csv</span></code>: Simulated peak positions and intensities.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">SimulationPlot.png</span></code>: Visualization of the simulated XRD pattern.</p></li>
</ul>
</section>
<hr class="docutils" />
<section id="cif-preprocessing">
<h3>7. <strong>CIF Preprocessing</strong><a class="headerlink" href="#cif-preprocessing" title="Link to this heading">#</a></h3>
<p><strong>Function</strong>: <code class="docutils literal notranslate"><span class="pre">CIFpreprocess</span></code></p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">Processed_CIF_LatticeConstants.csv</span></code>: Extracted lattice constants from CIF.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Processed_CIF_Structure.csv</span></code>: Atomic positions and unit cell parameters.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">ProcessedCIFPlot.png</span></code>: Visualization of the crystal structure.</p></li>
</ul>
</section>
<hr class="docutils" />
<section id="substitutional-search">
<h3>8. <strong>Substitutional Search</strong><a class="headerlink" href="#substitutional-search" title="Link to this heading">#</a></h3>
<p><strong>Function</strong>: <code class="docutils literal notranslate"><span class="pre">SubstitutionalSearch</span></code></p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">SubstitutionalSearchResults.csv</span></code>: Possible substitutional configurations and their likelihoods.</p></li>
</ul>
</section>
<hr class="docutils" />
<section id="xps-analysis">
<h3>9. <strong>XPS Analysis</strong><a class="headerlink" href="#xps-analysis" title="Link to this heading">#</a></h3>
<p><strong>Folder</strong>: <code class="docutils literal notranslate"><span class="pre">XPSFittingProfile</span></code></p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">XPSfittingProfile_&lt;time&gt;.csv</span></code>: Fitted XPS spectrum data.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">XPSPeakParas_&lt;time&gt;.csv</span></code>: Peak parameters including binding energies, areas, shapes, and fitting quality.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">WPEM_fittingresult.png</span></code>: Decomposed results of individual photoelectron peaks.</p></li>
</ul>
</section>
<hr class="docutils" />
<section id="exafs-analysis">
<h3>10. <strong>EXAFS Analysis</strong><a class="headerlink" href="#exafs-analysis" title="Link to this heading">#</a></h3>
<p><strong>Folder</strong>: <code class="docutils literal notranslate"><span class="pre">XAFS</span></code> / <code class="docutils literal notranslate"><span class="pre">WXAFS</span></code></p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">FFT_EXAFS_unknown.png</span></code>: Radial distribution function representing local atomic structure.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">interactive_plot.html</span></code>: Interactive 2D wavelet transform visualization.</p></li>
</ul>
</section>
</section>
<hr class="docutils" />
<section id="notes">
<h2>Notes<a class="headerlink" href="#notes" title="Link to this heading">#</a></h2>
<ul class="simple">
<li><p>All files are saved with descriptive names based on their function and timestamp.</p></li>
<li><p>Figures are generated in <code class="docutils literal notranslate"><span class="pre">.png</span></code> format for easy interpretation.</p></li>
<li><p>CSV files are widely compatible with data analysis tools such as Excel, Python, and MATLAB.</p></li>
</ul>
<p>For further reference and source code, please visit the <a class="reference external" href="https://github.com/Bin-Cao/PyWPEM">WPEM GitHub Repository</a>.</p>
</section>
</section>

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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#general-information">General Information</a><ul class="nav section-nav flex-column">
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<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#background-fitting">1. <strong>Background Fitting</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#xrd-refinement">2. <strong>XRD Refinement</strong></a></li>
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<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#cif-parsing">4. <strong>CIF Parsing</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#solid-solution-modeling">5. <strong>Solid Solution Modeling</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#xrd-simulation">6. <strong>XRD Simulation</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#cif-preprocessing">7. <strong>CIF Preprocessing</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#substitutional-search">8. <strong>Substitutional Search</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#xps-analysis">9. <strong>XPS Analysis</strong></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#exafs-analysis">10. <strong>EXAFS Analysis</strong></a></li>
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