| |
|
| | <!DOCTYPE html> |
| |
|
| |
|
| | <html lang="en" data-content_root="./" > |
| |
|
| | <head> |
| | <meta charset="utf-8" /> |
| | <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" /> |
| |
|
| | <title>Results Files Documentation — PyXplore Book</title> |
| | |
| | |
| | |
| | <script data-cfasync="false"> |
| | document.documentElement.dataset.mode = localStorage.getItem("mode") || ""; |
| | document.documentElement.dataset.theme = localStorage.getItem("theme") || ""; |
| | </script> |
| | |
| | |
| | <link href="_static/styles/theme.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" /> |
| | <link href="_static/styles/bootstrap.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" /> |
| | <link href="_static/styles/pydata-sphinx-theme.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" /> |
| |
|
| | |
| | <link href="_static/vendor/fontawesome/6.5.2/css/all.min.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" /> |
| | <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-solid-900.woff2" /> |
| | <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-brands-400.woff2" /> |
| | <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" /> |
| |
|
| | <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b76e3c8a" /> |
| | <link rel="stylesheet" type="text/css" href="_static/styles/sphinx-book-theme.css?v=eba8b062" /> |
| | <link rel="stylesheet" type="text/css" href="_static/togglebutton.css?v=13237357" /> |
| | <link rel="stylesheet" type="text/css" href="_static/copybutton.css?v=76b2166b" /> |
| | <link rel="stylesheet" type="text/css" href="_static/mystnb.8ecb98da25f57f5357bf6f572d296f466b2cfe2517ffebfabe82451661e28f02.css" /> |
| | <link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css?v=4fa983c6" /> |
| | <link rel="stylesheet" type="text/css" href="_static/sphinx-design.min.css?v=95c83b7e" /> |
| | |
| | |
| | <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b" /> |
| | <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" /> |
| | <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script> |
| |
|
| | <script src="_static/documentation_options.js?v=9eb32ce0"></script> |
| | <script src="_static/doctools.js?v=888ff710"></script> |
| | <script src="_static/sphinx_highlight.js?v=dc90522c"></script> |
| | <script src="_static/clipboard.min.js?v=a7894cd8"></script> |
| | <script src="_static/copybutton.js?v=f281be69"></script> |
| | <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script> |
| | <script>let toggleHintShow = 'Click to show';</script> |
| | <script>let toggleHintHide = 'Click to hide';</script> |
| | <script>let toggleOpenOnPrint = 'true';</script> |
| | <script src="_static/togglebutton.js?v=4a39c7ea"></script> |
| | <script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script> |
| | <script src="_static/design-tabs.js?v=f930bc37"></script> |
| | <script>const THEBE_JS_URL = "https://unpkg.com/thebe@0.8.2/lib/index.js"; const thebe_selector = ".thebe,.cell"; const thebe_selector_input = "pre"; const thebe_selector_output = ".output, .cell_output"</script> |
| | <script async="async" src="_static/sphinx-thebe.js?v=c100c467"></script> |
| | <script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script> |
| | <script>const THEBE_JS_URL = "https://unpkg.com/thebe@0.8.2/lib/index.js"; const thebe_selector = ".thebe,.cell"; const thebe_selector_input = "pre"; const thebe_selector_output = ".output, .cell_output"</script> |
| | <script>DOCUMENTATION_OPTIONS.pagename = 'resultsFiles';</script> |
| | <link rel="index" title="Index" href="genindex.html" /> |
| | <link rel="search" title="Search" href="search.html" /> |
| | <link rel="next" title="Tutorial Overview" href="tutorials/index.html" /> |
| | <link rel="prev" title="Parameters and Functions Documentation" href="parameter.html" /> |
| | <meta name="viewport" content="width=device-width, initial-scale=1"/> |
| | <meta name="docsearch:language" content="en"/> |
| | </head> |
| | |
| | |
| | <body data-bs-spy="scroll" data-bs-target=".bd-toc-nav" data-offset="180" data-bs-root-margin="0px 0px -60%" data-default-mode=""> |
| |
|
| | |
| | |
| | <div id="pst-skip-link" class="skip-link d-print-none"><a href="#main-content">Skip to main content</a></div> |
| | |
| | <div id="pst-scroll-pixel-helper"></div> |
| | |
| | <button type="button" class="btn rounded-pill" id="pst-back-to-top"> |
| | <i class="fa-solid fa-arrow-up"></i>Back to top</button> |
| |
|
| | |
| | <input type="checkbox" |
| | class="sidebar-toggle" |
| | id="pst-primary-sidebar-checkbox"/> |
| | <label class="overlay overlay-primary" for="pst-primary-sidebar-checkbox"></label> |
| | |
| | <input type="checkbox" |
| | class="sidebar-toggle" |
| | id="pst-secondary-sidebar-checkbox"/> |
| | <label class="overlay overlay-secondary" for="pst-secondary-sidebar-checkbox"></label> |
| | |
| | <div class="search-button__wrapper"> |
| | <div class="search-button__overlay"></div> |
| | <div class="search-button__search-container"> |
| | <form class="bd-search d-flex align-items-center" |
| | action="search.html" |
| | method="get"> |
| | <i class="fa-solid fa-magnifying-glass"></i> |
| | <input type="search" |
| | class="form-control" |
| | name="q" |
| | id="search-input" |
| | placeholder="Search this book..." |
| | aria-label="Search this book..." |
| | autocomplete="off" |
| | autocorrect="off" |
| | autocapitalize="off" |
| | spellcheck="false"/> |
| | <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span> |
| | </form></div> |
| | </div> |
| |
|
| | <div class="pst-async-banner-revealer d-none"> |
| | <aside id="bd-header-version-warning" class="d-none d-print-none" aria-label="Version warning"></aside> |
| | </div> |
| |
|
| | |
| | <header class="bd-header navbar navbar-expand-lg bd-navbar d-print-none"> |
| | </header> |
| | |
| |
|
| | <div class="bd-container"> |
| | <div class="bd-container__inner bd-page-width"> |
| | |
| | |
| | |
| | <div class="bd-sidebar-primary bd-sidebar"> |
| | |
| |
|
| | |
| | <div class="sidebar-header-items sidebar-primary__section"> |
| | |
| | |
| | |
| | |
| | </div> |
| | |
| | <div class="sidebar-primary-items__start sidebar-primary__section"> |
| | <div class="sidebar-primary-item"> |
| |
|
| | |
| | |
| | |
| |
|
| | <a class="navbar-brand logo" href="intro.html"> |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | <img src="_static/logo.png" class="logo__image only-light" alt="PyXplore Book - Home"/> |
| | <script>document.write(`<img src="_static/logo.png" class="logo__image only-dark" alt="PyXplore Book - Home"/>`);</script> |
| | |
| | |
| | </a></div> |
| | <div class="sidebar-primary-item"> |
| |
|
| | <script> |
| | document.write(` |
| | <button class="btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip"> |
| | <i class="fa-solid fa-magnifying-glass"></i> |
| | <span class="search-button__default-text">Search</span> |
| | <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span> |
| | </button> |
| | `); |
| | </script></div> |
| | <div class="sidebar-primary-item"><nav class="bd-links bd-docs-nav" aria-label="Main"> |
| | <div class="bd-toc-item navbar-nav active"> |
| | |
| | <ul class="nav bd-sidenav bd-sidenav__home-link"> |
| | <li class="toctree-l1"> |
| | <a class="reference internal" href="intro.html"> |
| | Welcome to PyXplore |
| | </a> |
| | </li> |
| | </ul> |
| | <ul class="current nav bd-sidenav"> |
| | <li class="toctree-l1"><a class="reference internal" href="parameter.html">Parameters and Functions Documentation</a></li> |
| | <li class="toctree-l1 current active"><a class="current reference internal" href="#">Results Files Documentation</a></li> |
| | <li class="toctree-l1 has-children"><a class="reference internal" href="tutorials/index.html">Tutorial Overview</a><ul> |
| | <li class="toctree-l2"><a class="reference internal" href="tutorials/basic_opt/1st.html">The tutorial 1st</a></li> |
| | <li class="toctree-l2"><a class="reference internal" href="tutorials/multi_phases/2nd.html">The tutorial 2nd</a></li> |
| | <li class="toctree-l2"><a class="reference internal" href="tutorials/amorphous/3rd.html">The tutorial 3rd</a></li> |
| | <li class="toctree-l2"><a class="reference internal" href="tutorials/simulation/4th.html">The tutorial 4th</a></li> |
| | <li class="toctree-l2"><a class="reference internal" href="tutorials/atomic_dis/5th.html">The tutorial 5th</a></li> |
| | <li class="toctree-l2"><a class="reference internal" href="tutorials/solid_solution/6th.html">The tutorial 6th</a></li> |
| | <li class="toctree-l2"><a class="reference internal" href="tutorials/EXAFS/7th.html">The tutorial 7th</a></li> |
| | <li class="toctree-l2"><a class="reference internal" href="tutorials/XPS/8th.html">The tutorial 8th</a></li> |
| | </ul><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary> |
| | </details></li> |
| | </ul> |
| |
|
| | </div> |
| | </nav></div> |
| | </div> |
| | |
| | |
| | <div class="sidebar-primary-items__end sidebar-primary__section"> |
| | </div> |
| | |
| | <div id="rtd-footer-container"></div> |
| |
|
| |
|
| | </div> |
| | |
| | <main id="main-content" class="bd-main" role="main"> |
| | |
| | |
| |
|
| | <div class="sbt-scroll-pixel-helper"></div> |
| |
|
| | <div class="bd-content"> |
| | <div class="bd-article-container"> |
| | |
| | <div class="bd-header-article d-print-none"> |
| | <div class="header-article-items header-article__inner"> |
| | |
| | <div class="header-article-items__start"> |
| | |
| | <div class="header-article-item"><button class="sidebar-toggle primary-toggle btn btn-sm" title="Toggle primary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip"> |
| | <span class="fa-solid fa-bars"></span> |
| | </button></div> |
| | |
| | </div> |
| | |
| | |
| | <div class="header-article-items__end"> |
| | |
| | <div class="header-article-item"> |
| |
|
| | <div class="article-header-buttons"> |
| |
|
| |
|
| |
|
| |
|
| |
|
| | <div class="dropdown dropdown-source-buttons"> |
| | <button class="btn dropdown-toggle" type="button" data-bs-toggle="dropdown" aria-expanded="false" aria-label="Source repositories"> |
| | <i class="fab fa-github"></i> |
| | </button> |
| | <ul class="dropdown-menu"> |
| | |
| | |
| | |
| | <li><a href="https://github.com/Bin-Cao/PyWPEM" target="_blank" |
| | class="btn btn-sm btn-source-repository-button dropdown-item" |
| | title="Source repository" |
| | data-bs-placement="left" data-bs-toggle="tooltip" |
| | > |
| | |
| |
|
| | <span class="btn__icon-container"> |
| | <i class="fab fa-github"></i> |
| | </span> |
| | <span class="btn__text-container">Repository</span> |
| | </a> |
| | </li> |
| | |
| | |
| | |
| | |
| | <li><a href="https://github.com/Bin-Cao/PyWPEM/issues/new?title=Issue%20on%20page%20%2FresultsFiles.html&body=Your%20issue%20content%20here." target="_blank" |
| | class="btn btn-sm btn-source-issues-button dropdown-item" |
| | title="Open an issue" |
| | data-bs-placement="left" data-bs-toggle="tooltip" |
| | > |
| | |
| |
|
| | <span class="btn__icon-container"> |
| | <i class="fas fa-lightbulb"></i> |
| | </span> |
| | <span class="btn__text-container">Open issue</span> |
| | </a> |
| | </li> |
| | |
| | </ul> |
| | </div> |
| |
|
| |
|
| |
|
| |
|
| |
|
| |
|
| | <div class="dropdown dropdown-download-buttons"> |
| | <button class="btn dropdown-toggle" type="button" data-bs-toggle="dropdown" aria-expanded="false" aria-label="Download this page"> |
| | <i class="fas fa-download"></i> |
| | </button> |
| | <ul class="dropdown-menu"> |
| | |
| | |
| | |
| | <li><a href="_sources/resultsFiles.md" target="_blank" |
| | class="btn btn-sm btn-download-source-button dropdown-item" |
| | title="Download source file" |
| | data-bs-placement="left" data-bs-toggle="tooltip" |
| | > |
| | |
| |
|
| | <span class="btn__icon-container"> |
| | <i class="fas fa-file"></i> |
| | </span> |
| | <span class="btn__text-container">.md</span> |
| | </a> |
| | </li> |
| | |
| | |
| | |
| | |
| | <li> |
| | <button onclick="window.print()" |
| | class="btn btn-sm btn-download-pdf-button dropdown-item" |
| | title="Print to PDF" |
| | data-bs-placement="left" data-bs-toggle="tooltip" |
| | > |
| | |
| |
|
| | <span class="btn__icon-container"> |
| | <i class="fas fa-file-pdf"></i> |
| | </span> |
| | <span class="btn__text-container">.pdf</span> |
| | </button> |
| | </li> |
| | |
| | </ul> |
| | </div> |
| |
|
| |
|
| |
|
| |
|
| | <button onclick="toggleFullScreen()" |
| | class="btn btn-sm btn-fullscreen-button" |
| | title="Fullscreen mode" |
| | data-bs-placement="bottom" data-bs-toggle="tooltip" |
| | > |
| | |
| |
|
| | <span class="btn__icon-container"> |
| | <i class="fas fa-expand"></i> |
| | </span> |
| |
|
| | </button> |
| |
|
| |
|
| |
|
| | <script> |
| | document.write(` |
| | <button class="btn btn-sm nav-link pst-navbar-icon theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip"> |
| | <i class="theme-switch fa-solid fa-sun fa-lg" data-mode="light"></i> |
| | <i class="theme-switch fa-solid fa-moon fa-lg" data-mode="dark"></i> |
| | <i class="theme-switch fa-solid fa-circle-half-stroke fa-lg" data-mode="auto"></i> |
| | </button> |
| | `); |
| | </script> |
| |
|
| |
|
| | <script> |
| | document.write(` |
| | <button class="btn btn-sm pst-navbar-icon search-button search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip"> |
| | <i class="fa-solid fa-magnifying-glass fa-lg"></i> |
| | </button> |
| | `); |
| | </script> |
| | <button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip"> |
| | <span class="fa-solid fa-list"></span> |
| | </button> |
| | </div></div> |
| | |
| | </div> |
| | |
| | </div> |
| | </div> |
| | |
| | |
| |
|
| | <div id="jb-print-docs-body" class="onlyprint"> |
| | <h1>Results Files Documentation</h1> |
| | |
| | <div id="print-main-content"> |
| | <div id="jb-print-toc"> |
| | |
| | <div> |
| | <h2> Contents </h2> |
| | </div> |
| | <nav aria-label="Page"> |
| | <ul class="visible nav section-nav flex-column"> |
| | <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> |
| | </ul> |
| | </li> |
| | <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#output-files-by-function">Output Files by Function</a><ul class="nav section-nav flex-column"> |
| | <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> |
| | </ul> |
| | </li> |
| | <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#notes">Notes</a></li> |
| | </ul> |
| | </nav> |
| | </div> |
| | </div> |
| | </div> |
| |
|
| | |
| | |
| | <div id="searchbox"></div> |
| | <article class="bd-article"> |
| | |
| | <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_<time>.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_<time>.csv</span></code>: Diffraction indices for each peak in phase 0.</p></li> |
| | <li><p><code class="docutils literal notranslate"><span class="pre">WPEMfittingProfile_<time>.csv</span></code>: WPEM-generated fitting profile.</p></li> |
| | <li><p><code class="docutils literal notranslate"><span class="pre">WPEMPeakParas_<time>.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_<time>.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_<time>.csv</span></code>: Fitted XPS spectrum data.</p></li> |
| | <li><p><code class="docutils literal notranslate"><span class="pre">XPSPeakParas_<time>.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> |
| |
|
| | <script type="text/x-thebe-config"> |
| | { |
| | requestKernel: true, |
| | binderOptions: { |
| | repo: "binder-examples/jupyter-stacks-datascience", |
| | ref: "master", |
| | }, |
| | codeMirrorConfig: { |
| | theme: "abcdef", |
| | mode: "python" |
| | }, |
| | kernelOptions: { |
| | name: "python3", |
| | path: "./." |
| | }, |
| | predefinedOutput: true |
| | } |
| | </script> |
| | <script>kernelName = 'python3'</script> |
| |
|
| | </article> |
| | |
| |
|
| | |
| | |
| | |
| | |
| | <footer class="prev-next-footer d-print-none"> |
| | |
| | <div class="prev-next-area"> |
| | <a class="left-prev" |
| | href="parameter.html" |
| | title="previous page"> |
| | <i class="fa-solid fa-angle-left"></i> |
| | <div class="prev-next-info"> |
| | <p class="prev-next-subtitle">previous</p> |
| | <p class="prev-next-title">Parameters and Functions Documentation</p> |
| | </div> |
| | </a> |
| | <a class="right-next" |
| | href="tutorials/index.html" |
| | title="next page"> |
| | <div class="prev-next-info"> |
| | <p class="prev-next-subtitle">next</p> |
| | <p class="prev-next-title">Tutorial Overview</p> |
| | </div> |
| | <i class="fa-solid fa-angle-right"></i> |
| | </a> |
| | </div> |
| | </footer> |
| | |
| | </div> |
| | |
| | |
| | |
| | <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner"> |
| |
|
| |
|
| | <div class="sidebar-secondary-item"> |
| | <div class="page-toc tocsection onthispage"> |
| | <i class="fa-solid fa-list"></i> Contents |
| | </div> |
| | <nav class="bd-toc-nav page-toc"> |
| | <ul class="visible nav section-nav flex-column"> |
| | <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> |
| | </ul> |
| | </li> |
| | <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#output-files-by-function">Output Files by Function</a><ul class="nav section-nav flex-column"> |
| | <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> |
| | </ul> |
| | </li> |
| | <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#notes">Notes</a></li> |
| | </ul> |
| | </nav></div> |
| |
|
| | </div></div> |
| | |
| | |
| | </div> |
| | <footer class="bd-footer-content"> |
| | |
| | <div class="bd-footer-content__inner container"> |
| | |
| | <div class="footer-item"> |
| | |
| | <p class="component-author"> |
| | By Bin CAO |
| | </p> |
| |
|
| | </div> |
| | |
| | <div class="footer-item"> |
| | |
| |
|
| | <p class="copyright"> |
| | |
| | © Copyright 2023. |
| | <br/> |
| | |
| | </p> |
| |
|
| | </div> |
| | |
| | <div class="footer-item"> |
| | |
| | </div> |
| | |
| | <div class="footer-item"> |
| | |
| | </div> |
| | |
| | </div> |
| | </footer> |
| | |
| |
|
| | </main> |
| | </div> |
| | </div> |
| | |
| | |
| | <script src="_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b"></script> |
| | <script src="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b"></script> |
| |
|
| | <footer class="bd-footer"> |
| | </footer> |
| | </body> |
| | </html> |
