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<!DOCTYPE html>
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<head>
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  <title>easyDiffraction User Manual</title>
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          <li><a href="index.html"><img src="icons/easydiffraction.svg">easyDiffraction</a></li>
          <li><a class="active" href="documentation.html"><img src="icons/book-reader.svg">Documentation</a></li>
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        <article class="current">
          <h2> <a href="umanual_intro.html">1. Introduction</a> </h2>
          <h4> <a href="umanual_intro.html#1.1.-what-is-easydiffraction-for?">1.1. What is easyDiffraction for?</a> </h4>
          <h4> <a href="umanual_intro.html#1.2.-easydiffraction-features">1.2. easyDiffraction features</a> </h4>
        </article>
        <article>
          <h2> <a href="umanual_start.html">2. Getting Started</a> </h2>
          <h4> <a href="umanual_start.html#2.1.-installing-easydiffraction">2.1. Installing easyDiffraction</a> </h4>
          <h4> <a href="umanual_start.html#2.2.-launching-easydiffraction">2.2. Launching easyDiffraction</a> </h4>
          <h4> <a href="umanual_start.html#2.3.-uninstalling-easydiffraction">2.3. Uninstalling easyDiffraction</a> </h4>
        </article>
        <article>
          <h2> <a href="umanual_use.html">3. How to Use</a> </h2>
          <h4> <a href="umanual_use.html#3.1.-easydiffraction-user-interface">3.1. easyDiffraction user interface</a> </h4>
          <h6> <a href="umanual_use.html#3.1.1.-toolbar">3.1.1. Toolbar</a> </h6>
          <h6> <a href="umanual_use.html#3.1.2.-main-window">3.1.2. Main window</a> </h6>
          <h6> <a href="umanual_use.html#3.1.3.-sidebar">3.1.3. Sidebar</a> </h6>
          <h6> <a href="umanual_use.html#3.1.4.-settings">3.1.4. Settings</a> </h6>
          <h4> <a href="umanual_use.html#3.2.-project-files">3.2. easyDiffraction project files</a> </h4>
          <h6> <a href="umanual_use.html#3.2.1.-unpolarized-diffraction">3.2.1. Unpolarized diffraction</a> </h6>
          <h6> <a href="umanual_use.html#3.2.2.-polarized-diffraction">3.2.2. Polarized diffraction</a> </h6>
          <h4> <a href="umanual_use.html#3.3.-data-analysis-workflow">3.3. Data analysis workflow</a> </h4>
          <h6> <a href="umanual_use.html#3.3.1.-home-page">3.3.1. Home page</a> </h6>
          <h6> <a href="umanual_use.html#3.3.2.-project">3.3.2. Create/Open project</a> </h6>
          <h6> <a href="umanual_use.html#3.3.3.-sample-model">3.3.3. Define sample model</a> </h6>
          <h6> <a href="umanual_use.html#3.3.4.-experimental-data">3.3.4. Load experimental data</a> </h6>
          <h6> <a href="umanual_use.html#3.3.5.-analysis">3.3.5. Perform data analysis</a> </h6>
          <h6> <a href="umanual_use.html#3.3.6.-summary">3.3.6. Generate summary report</a> </h6>
        </article>
      </div>
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      <div class="doc-area">

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        <div class="doc-chapter" id="1.-introduction">
          <h1>1. Introduction</h1>
          <!--- article --->
          <article>
            <p>
              <a href="index.html">easyDiffraction</a> is a scientific software for modelling and analysis
              of neutron diffraction data. We have just started to work on this project, so
              <a href="index.html">easyDiffraction</a> is available as a prototype, covering classical
              1D polarized and unpolarized neutron powder diffraction data collected at a constant wavelength.
            </p>
          </article>
          <!--- article --->

          <!--- section --->
          <div class="doc-section" id="1.1.-what-is-easydiffraction-for?">
            <h2>1.1. What is easyDiffraction for?</h2>
            <!--- article --->
            <article>
              <div class="instructions">
                <ul>
                  <li><a href="index.html">easyDiffraction</a> allows simulation of diffraction patterns based
                    on a structural model and refinement of its parameters.</li>
                  <li><a href="index.html">easyDiffraction</a> is similar to crystallographic programs like
                    <a href="https://www.ill.eu/sites/fullprof/">FullProf</a>, <a href="http://jana.fzu.cz">Jana</a>,
                    <a href="https://subversion.xray.aps.anl.gov/trac/pyGSAS">GSAS</a>,
                    <a href="http://shelx.uni-goettingen.de/index.php">ShelX</a>, etc.</li>
                  <li>In contrast to the programs mentioned above <a href="index.html">easyDiffraction</a>, is based
                    on external crystallographic libraries, such as <a href="https://github.com/ikibalin/cryspy">CrysPy</a>
                    in order to cover different functionality aspects within a single intuitive and user-friendly graphical
                    interface. In near future we plan to add support for <a href="https://code.ill.fr/scientific-software/crysfml">CrysFML</a>,
                    another crystallographic library.
                  </li>
                </ul>
              </div>
            </article>
            <!--- article --->
          </div>
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          <div class="doc-icon-section" id="1.2.-easydiffraction-features">
            <h2>1.2. easyDiffraction features</h2>
            <!--- article --->
            <article id="1.2.-free-and-open-source">
              <h5>Free and open-source</h5>
              <img src="icons/open-source.svg">
              <div class="paragraph">
                <p>
                  Anyone is free to use <a href="index.html">easyDiffraction</a> and the source code is openly shared on
                  <a href="https://github.com/easyDiffraction/easyDiffraction">GitHub</a> under the
                  <a href="https://github.com/easyDiffraction/easyDiffraction/blob/master/LICENSE">GNU Lesser
                    General Public License v3.0</a>. Be part of the <a href="index.html">easyDiffraction</a> community and
                  help improve the software for everyone.
                </p>
              </div>
            </article>
            <!--- article --->
            <!--- article --->
            <article id="1.2.-cross-platform">
              <h5>Cross-platform</h5>
              <img src="icons/cross-platform.svg">
              <div class="paragraph">
                <p>
                  <a href="index.html">easyDiffraction</a> works across operating systems. You can download
                  precompiled binaries of the <b>Installer</b> for <b>macOS</b>, <b>Windows</b> and
                  <b>Linux (Ubuntu)</b> from the <a href="index.html">main page</a>, or get it from the
                  <a href="https://snapcraft.io/easydiffraction">Snap Store</a> for or all major <b>Linux</b>
                  distributions. Just install <a href="index.html">easyDiffraction</a> on the platform
                  of your choice and forget about Virtual Machines or Emulators.
                </p>
              </div>
            </article>
            <!--- article --->
            <!--- article --->
            <article id="1.2.-easy-to-use">
              <h5>Easy to use</h5>
              <img src="icons/thumbs-up.svg">
              <div class="paragraph">
                <p>
                  Intuitive tabbed interface with built-in step-by-step user guides, and a clear workflow
                  help speed up data modelling and analysis.
                </p>
              </div>
              <div class="video-frame">
                <video autobuffer controls muted>
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                  <source src="videos/ed_features_easy-to-use.mp4" type="video/mp4">
                </video>
              </div>
            </article>
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            <article id="1.2.-everything-is-included">
              <h5>Everything is included</h5>
              <img src="icons/delivery-package.svg">
              <div class="paragraph">
                <p>
                  <a href="index.html">easyDiffraction</a> is distributed as an all-in-one package and everything
                  is already included. There is no need to set environment variables or install additional
                  dependencies anymore. Just run the installer and with just a few clicks you are done.
                </p>
              </div>
              <div class="video-frame">
                <video autobuffer controls muted>
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                  <source src="videos/ed_features_installer.mp4" type="video/mp4">
                </video>
              </div>
            </article>
            <!--- article --->
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            <article id="1.2.-multi-functional">
              <h5>Multi-functional</h5>
              <img src="icons/swiss-pocket-knife.svg">
              <div class="paragraph">
                <p>
                  <a href="index.html">easyDiffraction</a> integrates existing crystallographic libraries, such
                  as <a href="https://github.com/ikibalin/cryspy">CrysPy</a> to cover different functionality. In
                  the near future, we plan to add support for another crystallographic library
                  <a href="https://code.ill.fr/scientific-software/crysfml">CrysFML</a>. More libraries will be
                  added depending on needs and resources available. You are encouraged to contribute additional
                  functionality to <a href="index.html">easyDiffraction</a>.
                </p>
                <p>
                  Below, you can see a diagram showing a general idea of the <a href="index.html">easyDiffraction</a>
                  project. Currently, we are working on the parts which are colored: Unified API to to communicate
                  with <a href="https://github.com/ikibalin/cryspy">CrysPy</a> and GUI on top of that.
                </p>
                <figure>
                  <a href="#img-1_2_5" class="screenshot"><img src="images/ed_features_diagram.svg"></a>
                  <a href="#_" class="overlay" id="img-1_2_5"><img src="images/ed_features_diagram.svg"></a>
                </figure>
              </div>
            </article>
            <!--- article --->
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            <article id="1.2.-various-techniques">
              <h5>Various techniques</h5>
              <img src="icons/boxes.svg">
              <div class="paragraph">
                <p>
                  We have just started our work on <a href="index.html">easyDiffraction</a>.
                  So, its functionality is still very limited. We support classical 1D polarized and unpolarized
                  neutron powder diffraction data collected at constant wavelength.
                </p>
                <p>
                  In future, we plan to extend <a href="index.html">easyDiffraction</a> to cover the
                  following fields:
                </p>
                <ul>
                  <li>Constant wavelengths and Time-of-Flight data,</li>
                  <li>Single-crystals and powders,</li>
                  <li>Neutrons and X-rays,</li>
                  <li>1D and 2D data,</li>
                  <li>and more...</li>
                </ul>
                <p>
                  Want them to be implemented faster? Need a specific technique not listed above? Become part of
                  the <a href="index.html">easyDiffraction</a> community, contribute additional functionality and
                  help improve the software for everyone.
                </p>
                <figure>
                  <a href="#img-1_2_6" class="screenshot"><img src="images/ed_features_techniques.png"></a>
                  <a href="#_" class="overlay" id="img-1_2_6"><img src="images/ed_features_techniques.png"></a>
                </figure>
              </div>
            </article>
            <!--- article --->
            <!--- article --->
            <article id="1.2.-live-update">
              <h5>Live update of calculations</h5>
              <img src="icons/update-arrows.svg">
              <div class="paragraph">
                <p>
                  In the data analysis process, <a href="index.html">easyDiffraction</a> allows you to modify
                  any refinable parameter manually or with a slider. Both the simulated pattern and the
                  difference between experiment and calculation are automatically recalculated and updated in real time.
                </p>
              </div>
              <div class="video-frame">
                <video autobuffer controls muted>
                  <!--- loop autoplay autobuffer controls muted --->
                  <source src="videos/ed_features_live-update.mp4" type="video/mp4">
                </video>
              </div>
            </article>
            <!--- article --->
            <!--- article --->
            <article id="1.2.-cif-based-format">
              <h5>Human-readable syntax</h5>
              <img src="icons/user.svg">
              <div class="paragraph">
                <p>Input/output files for <a href="index.html">easyDiffraction</a> are written in
                  STAR (Self-Defining Text Archival and Retrieval), a human-readable data format. The STAR syntax
                  provides a way for simple, easy-to-comprehend, flexible and extensible data exchange
                  (see, e.g., <a href="https://doi.org/10.1021/ci00002a020">Hall 1991</a>).
                </p>
                <p>
                  Where possible, we follow the syntax of <a href="https://www.iucr.org/resources/cif">CIF
                    (Crystallographic Information File)</a>, see also
                  <a href="https://doi.org/10.1107/S1600576715021871">Bernstein <em>et al.</em> 2016</a>,
                  which is a restricted derivative of STAR widely used in crystallography and specified
                  by the <a href="https://www.iucr.org">International Union of Crystallography</a>. However, our
                  CIF files also contain additional blocks describing the instrument, etc.
                </p>
                <p>
                  Below you can find comparison between CIF/STAR and other popular data-serialization formats,
                  such as YAML and JSON.
                </p>
              </div>
              <figure>
                <a href="#img-1_2_8" class="screenshot"><img src="images/ed_features_star-cif.svg"></a>
                <a href="#_" class="overlay" id="img-1_2_8"><img src="images/ed_features_star-cif.svg"></a>
              </figure>

            </article>
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