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<!DOCTYPE html>
<html>
<!--- HEAD --->
<head>
<meta charset="UTF-8">
<link href="style/main.css" rel="stylesheet">
<link href="style/umanual.css" rel="stylesheet">
<link href="icons/easydiffraction.ico" rel="shortcut icon" type="image/x-icon">
<title>easyDiffraction User Manual</title>
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gtag('config', 'UA-153564910-1');
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<body>
<!--- header with navigation --->
<header>
<section>
<nav>
<ul>
<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>
<li><a href="contact.html"><img src="icons/envelope.svg">Contact</a></li>
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</section>
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<!--- header with navigation --->
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<div class="main row">
<section>
<!--- toc area --->
<div class="toc-area">
<article>
<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 class="current">
<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>
<!--- toc area --->
<!--- doc area --->
<div class="doc-area">
<!--- chapter --->
<div class="doc-chapter" id="3.-how-to-use">
<article>
<h1>3. How to Use</h1>
<p>In this chapter we'll look at how to work with <a href="index.html">easyDiffraction</a>.</p>
</article>
<!--- section --->
<div class="doc-section" id="3.1.-easydiffraction-user-interface">
<article>
<h2>3.1. easyDiffraction user interface</h2>
<p>Here you can see what the program looks like. The application window is divided into parts that
provide you with quick and easy access to everything you'll need. The parts are <b>Toolbar</b>,
<b>Main Window</b> and <b>Sidebar</b> described in the following sections.</p>
<figure>
<a href="#img-3_1" class="screenshot"><img src="images/ed_how-to-use_analysis.png"></a>
<a href="#_" class="overlay" id="img-3_1"><img src="images/ed_how-to-use_analysis.png"></a>
</figure>
</article>
<!-- sub-section -->
<div class="doc-subsection" id="3.1.1.-toolbar">
<article>
<h3>3.1.1. Toolbar</h3>
<p>The toolbar at the top of the application window contains three groups of buttons, indicated on the
screenshot below.</p>
<figure>
<a href="#img-3_1_1a" class="screenshot"><img src="images/ed_how-to-use_toolbar_overview.png"></a>
<a href="#_" class="overlay" id="img-3_1_1a"><img src="images/ed_how-to-use_toolbar_overview.png"></a>
</figure>
<p>On the left side in <b>group A</b> the following buttons are available: </p>
<ol>
<li><code>Application preferences</code> Opens dialog where application settings can be changed. </li>
<li><code>Save current project state</code> Saves the current state of project to a .zip file. </li>
</ol>
<p>The buttons in <b>group C</b> are undo and redo buttons that can be used if a mistake is made.</p>
<p>The central group of buttons, <b>group B</b>, represents the data analysis workflow. When you create a new project,
all toolbar workflow buttons except <code>Home</code> are disabled. When each step in the workflow is completed,
the toolbar workflow button which corresponds to the next step becomes enabled.</p>
<figure>
<a href="#img-3_1_1b" class="screenshot"><img src="images/ed_how-to-use_toolbar.png"></a>
<a href="#_" class="overlay" id="img-3_1_1b"><img src="images/ed_how-to-use_toolbar.png"></a>
</figure>
<p>The following workflow buttons (workflow steps) are present in the <a href="index.html">easyDiffraction</a> toolbar:</p>
<ol>
<li><code>Home</code> introduction page, links to about, help and contact. </li>
<li><code>Project</code> to manage your project (create new, open existing, etc.) </li>
<li><code>Sample</code> to describe sample phases.</li>
<li><code>Experiment</code> to load experimentally measured data files.</li>
<li><code>Analysis</code> to perform refinement of structural parameters.</li>
<li><code>Summary</code> to view and export summary report.</li>
</ol>
<!--<p>You can switch between the available tabs at any time by clicking on their names.</p>-->
</article>
</div>
<!-- sub-section -->
<!-- sub-section -->
<div class="doc-subsection" id="3.1.2.-main-window">
<article>
<h3>3.1.2. Main window</h3>
<p>The <b>Main Window</b> of the program is located below the <b>Toolbar</b> and it can contain
several tabs depending on the current step in the data analysis workflow. An example of the <b>Main Window</b> for
the analysis step is shown in the figure below. You can switch between the <code>Fitting</code> and
<code>Text View</code> at any time clicking on the required tab.
<!--When new files are opened the only first tab is
visible. Every next tab appear when the main action on the previous tab is done.-->
<figure>
<a href="#img-3_1_2" class="screenshot"><img src="images/ed_how-to-use_main-window.png"></a>
<a href="#_" class="overlay" id="img-3_1_2"><img src="images/ed_how-to-use_main-window.png"></a>
</figure>
<!--<p>The following tabs are available and described in the sections below.</p>
<ol>
<li><code>Input Text</code> tab contains the text viewer to show the content of the opened data files.</li>
<li><code>Extracted Tables</code> tab contains the table viewer to show the data extracted from the opened text files.</li>
<li><code>Visualized Plots</code> tab contains the graphical viewer to show the plots based on the extracted data.</li>
<li><code>Output Table</code> tab contains the table viewer with all the calculated parameters for each peak.</li>
</ol>-->
</article>
</div>
<!-- sub-section -->
<!-- sub-section -->
<div class="doc-subsection" id="3.1.3.-sidebar">
<article>
<h3>3.1.3. Sidebar</h3>
<p>The <b>Sidebar</b> is located at the right side of the application window, below the <b>Toolbar</b>. It has 2 tabs:
<code>Basic controls</code> and <code>Advanced controls</code>. Their contents depend on the selected tab in the
<b>Toolbar</b> and the respective tab in the <b>Main Window</b>. You can switch between them at any time clicking
on the required tab.</p>
<figure>
<a href="#img-3_1_3" class="screenshot"><img src="images/ed_how-to-use_sidebar.png"></a>
<a href="#_" class="overlay" id="img-3_1_3"><img src="images/ed_how-to-use_sidebar.png"></a>
</figure>
<ol>
<li><code>Basic controls</code> tab provides an access to essential actions and information fields.</li>
<li><code>Advanced controls</code> tab describes additional actions recommended for advanced users.</li>
</ol>
<p>The content of the <code>Basic controls</code> and <code>Advanced controls</code> tabs for every workflow step are described
in the sections below.</p>
</article>
</div>
<!-- sub-section -->
<!-- sub-section -->
<div class="doc-subsection" id="3.1.4.-settings">
<article>
<h3>3.1.4. Settings</h3>
<p>The <b>Application preferences</b> can be opened from the gear icon in the <b>Toolbar</b>.</p>
<figure>
<a href="#img-3_1_4" class="screenshot"><img src="images/ed_how-to-use_settings.png"></a>
<a href="#_" class="overlay" id="img-3_1_4"><img src="images/ed_how-to-use_settings.png"></a>
</figure>
Currently only the two first settings are enabled:
<ol>
<li><code>Show Animated Intro</code> Enables or disables an animation when starting the program.</li>
<li><code>Show User Guides</code> Shows the built-in step-by-step user guides.</li>
</ol>
</article>
</div>
<!-- sub-section -->
</div>
<!--- section --->
<!--- section --->
<div class="doc-section" id="3.2.-project-files">
<article>
<h2>3.2. easyDiffraction project files</h2>
<p>Input/output files are in simple and human-readable data format STAR/CIF
with the specifications of International Union of Crystallography, where possible.
Click <a href="umanual_intro.html#1.2.-cif-based-format">here</a> for more details.</p>
<p>The project consists of the following files:</p>
<ol>
<li><code>project.cif</code> with project description.</li>
<li><code>samples.cif</code> describes sample phases.</li>
<li><code>experiments.cif</code> contains instrumental parameters and experimentally measured data.</li>
<li><code>calculations.cif</code> is the output file with the calculation results.</li>
</ol>
</article>
<!-- sub-section -->
<div class="doc-subsection" id="3.2.1.-unpolarized-diffraction">
<article>
<h3>3.2.1. Unpolarized diffraction</h3>
<p>Example of <b>.cif</b> files for 1D <b>unpolarized</b> neutron powder diffraction data are given below:</p>
<h4><a>project.cif</a></h4>
<p><code class=code-block>
<font color=#2380b5>_name</font> PbSO4 <br />
<font color=#2380b5>_keywords</font> 'unpolarised neutron powder diffraction, D1A at ILL' <br />
<font color=#2380b5>_samples</font> samples.cif <br />
<font color=#2380b5>_experiments</font> experiments.cif <br />
<font color=#2380b5>_calculations</font> calculations.cif
</code></p>
<h4><a>samples.cif</a></h4>
<p><code class=code-block>
<font color=#b95e39>data_PbSO4</font><br /><br />
<font color=#2380b5>_space_group_name_H-M_ref</font> 'P n m a'<br />
<font color=#2380b5>_space_group_IT_coordinate_system_code</font> abc<br /><br />
<font color=#2380b5>_cell_length_a</font> 8.477425(36)<br />
<font color=#2380b5>_cell_length_b</font> 5.395977(24)<br />
<font color=#2380b5>_cell_length_c</font> 6.957024(33)<br />
<font color=#2380b5>_cell_angle_alpha</font> 90.0<br />
<font color=#2380b5>_cell_angle_beta</font> 90.0<br />
<font color=#2380b5>_cell_angle_gamma</font> 90.0<br /><br />
<font color=#888>loop_</font><br />
<font color=#669431>_atom_site_label</font><br />
<font color=#669431>_atom_site_type_symbol</font><br />
<font color=#669431>_atom_site_fract_x</font><br />
<font color=#669431>_atom_site_fract_y</font><br />
<font color=#669431>_atom_site_fract_z</font><br />
<font color=#669431>_atom_site_occupancy</font><br />
<font color=#669431>_atom_site_adp_type</font><br />
<font color=#669431>_atom_site_u_iso_or_equiv</font><br />Pb Pb 0.188 0.25 0.166 1.0 Uiso 0.01692<br />S S 0.065
0.25 0.685 1.0 Uiso 0.00258<br />O1 O 0.908 0.25 0.595 1.0 Uiso 0.02469<br />O2 O 0.194
0.25 0.543 1.0 Uiso 0.01803<br />O3 O 0.081 0.027 0.808 1.0 Uiso 0.01655
</code></p>
<h4><a>experiments.cif</a></h4>
<p><code class=code-block>
<font color=#b95e39>data_NPD</font><br /><br />
<font color=#2380b5>_setup_wavelength</font> 1.912<br />
<font color=#2380b5>_setup_offset_2theta</font> 0.0()<br /><br />
<font color=#2380b5>_pd_instr_resolution_u</font> 0.14207<br />
<font color=#2380b5>_pd_instr_resolution_v</font> -0.4181<br />
<font color=#2380b5>_pd_instr_resolution_w</font> 0.38629<br />
<font color=#2380b5>_pd_instr_resolution_x</font> 0.0<br />
<font color=#2380b5>_pd_instr_resolution_y</font> 0.09038<br /><br />
<font color=#888>loop_</font><br />
<font color=#669431>_phase_label</font><br />
<font color=#669431>_phase_scale</font><br />
<font color=#669431>_phase_igsize</font><br />PbSO4 1.0() 0.0<br /><br />
<font color=#888>loop_</font><br />
<font color=#669431>_pd_background_2theta</font><br />
<font color=#669431>_pd_background_intensity</font><br /> 11.0 205.6<br /> 50.0 208.0<br />153.0 230.3<br /><br />
<font color=#888>loop_</font><br />
<font color=#669431>_pd_meas_2theta</font><br />
<font color=#669431>_pd_meas_intensity</font><br />
<font color=#669431>_pd_meas_intensity_sigma</font><br />10.05 214.0 15.0<br />10.10 219.0 15.0<br />10.15 224.0 15.0<br />10.20 198.0 14.0<br />10.25 229.0 15.0<br />
...
</code></p>
<h4><a>experiments.dat/experiments.xye</a> (if experiments.cif is not available)</h4>
<p><code class=code-block>
10.05 214.0 15.0<br>
10.10 219.0 15.0<br>
10.15 224.0 15.0<br>
10.20 198.0 14.0<br>
10.25 229.0 15.0<br>
...
</code></p>
</article>
</div>
<!-- sub-section -->
<!-- sub-section -->
<div class="doc-subsection" id="3.2.2.-polarized-diffraction">
<article>
<h3>3.2.2. Polarized diffraction</h3>
<p>Example of <b>.cif</b> files for 1D <b>polarized</b> neutron powder diffraction data are given below:</p>
<h4><a>project.cif</a></h4>
<p><code class=code-block>
<font color=#2380b5>_name</font> Fe3O4 <br />
<font color=#2380b5>_keywords</font> 'polarised neutron powder diffraction, B = 5T, 6T2 at LLB' <br />
<font color=#2380b5>_samples</font> samples.cif <br />
<font color=#2380b5>_experiments</font> experiments.cif <br />
<font color=#2380b5>_calculations</font> calculations.cif
</code></p>
<h4><a>samples.cif</a></h4>
<p><code class=code-block>
<font color=#b95e39>data_Fe3O4</font><br /><br />
<font color=#2380b5>_space_group_name_H-M_ref</font> 'F d -3 m'<br />
<font color=#2380b5>_space_group_IT_coordinate_system_code</font> 2<br /><br />
<font color=#2380b5>_cell_length_a</font> 8.57()<br />
<font color=#2380b5>_cell_length_b</font> 8.57<br />
<font color=#2380b5>_cell_length_c</font> 8.57<br />
<font color=#2380b5>_cell_angle_alpha</font> 90.0<br />
<font color=#2380b5>_cell_angle_beta</font> 90.0<br />
<font color=#2380b5>_cell_angle_gamma</font> 90.0<br /><br />
<font color=#888>loop_</font><br />
<font color=#669431>_atom_site_label</font><br />
<font color=#669431>_atom_site_type_symbol</font><br />
<font color=#669431>_atom_site_fract_x</font><br />
<font color=#669431>_atom_site_fract_y</font><br />
<font color=#669431>_atom_site_fract_z</font><br />
<font color=#669431>_atom_site_occupancy</font><br />
<font color=#669431>_atom_site_adp_type</font><br />
<font color=#669431>_atom_site_u_iso_or_equiv</font><br />Fe3A Fe3+ 0.125 0.125 0.125 1.0 Uiso 0.0<br />Fe3B Fe3+ 0.5 0.5 0.5 1.0 Uiso
0.0<br />O O2- 0.255 0.255 0.255 1.0 Uiso 0.0<br /><br />
<font color=#888>loop_</font><br />
<font color=#669431>_atom_site_susceptibility_label</font><br />
<font color=#669431>_atom_site_susceptibility_chi_type</font><br />
<font color=#669431>_atom_site_susceptibility_chi_11</font><br />
<font color=#669431>_atom_site_susceptibility_chi_22</font><br />
<font color=#669431>_atom_site_susceptibility_chi_33</font><br />
<font color=#669431>_atom_site_susceptibility_chi_12</font><br />
<font color=#669431>_atom_site_susceptibility_chi_13</font><br />
<font color=#669431>_atom_site_susceptibility_chi_23</font><br />Fe3A Cani -0.0860() -0.0860 -0.0860 0.0 0.0 0.0<br />Fe3B Cani 0.0784() 0.0784 0.0784 0.0 0.0 0.0<br /><br />
<font color=#888>loop_</font><br />
<font color=#669431>_atom_site_scat_label</font><br />
<font color=#669431>_atom_site_scat_lande</font><br />
<font color=#669431>_atom_site_scat_kappa</font><br />Fe3A 2.0 1.0<br />Fe3B 2.0 1.0
</code></p>
<h4><a>experiments.cif</a></h4>
<p><code class=code-block>
<font color=#b95e39>data_PolNPD5T</font><br /><br />
<font color=#2380b5>_setup_wavelength</font> 2.4<br />
<font color=#2380b5>_setup_field</font> 5.0<br />
<font color=#2380b5>_setup_offset_2theta</font> -0.36<br /><br />
<font color=#2380b5>_pd_instr_resolution_u</font> 11.34<br />
<font color=#2380b5>_pd_instr_resolution_v</font> -2.983<br />
<font color=#2380b5>_pd_instr_resolution_w</font> 1.141<br />
<font color=#2380b5>_pd_instr_resolution_x</font> 0.0<br />
<font color=#2380b5>_pd_instr_resolution_y</font> 0.404<br /><br />
<font color=#2380b5>_diffrn_radiation_polarization</font> 0.6243<br />
<font color=#2380b5>_diffrn_radiation_efficiency</font> 1.0<br /><br />
<font color=#2380b5>_chi2_sum</font> True<br />
<font color=#2380b5>_chi2_diff</font> True<br />
<font color=#2380b5>_chi2_up</font> False<br />
<font color=#2380b5>_chi2_down</font> False<br /><br />
<font color=#888>loop_</font><br />
<font color=#669431>_phase_label</font><br />
<font color=#669431>_phase_scale</font><br />
<font color=#669431>_phase_igsize</font><br />Fe3O4 0.162() 0.0<br /><br />
<font color=#888>loop_</font><br />
<font color=#669431>_pd_background_2theta</font><br />
<font color=#669431>_pd_background_intensity</font><br />10.0 183.0<br />40.0 258.1<br />72.0 361.0<br /><br />
<font color=#888>loop_</font><br />
<font color=#669431>_pd_meas_2theta</font><br />
<font color=#669431>_pd_meas_intensity_up</font><br />
<font color=#669431>_pd_meas_intensity_up_sigma</font><br />
<font color=#669431>_pd_meas_intensity_down</font><br />
<font color=#669431>_pd_meas_intensity_down_sigma</font><br />10.0 180.31 28.49 184.69 28.47<br />10.2 182.67 26.88 176.10 26.86<br />10.4 192.40 26.33 160.49 26.28<br />10.6 186.10 25.81
179.53 25.84<br />10.8 202.31 24.48 197.54 24.41<br />11.0 194.79 24.02 180.75 23.98<br />
...
</code>
</p>
<h4><a>experiments.dat/experiments.xye</a> (if experiments.cif is not available)</h4>
<p><code class=code-block>
10.0 180.31 28.49 184.69 28.47<br />10.2 182.67 26.88 176.10 26.86<br />10.4 192.40 26.33 160.49 26.28<br />10.6 186.10 25.81
179.53 25.84<br />10.8 202.31 24.48 197.54 24.41<br />11.0 194.79 24.02 180.75 23.98<br />
...
</code></p>
</article>
</div>
<!-- sub-section -->
</div>
<!-- section -->
<!--- section --->
<div class="doc-section" id="3.3.-data-analysis-workflow">
<article>
<h2>3.3. Data analysis workflow</h2>
<p>This section describes all the steps in the data processing with
<a href="index.html">easyDiffraction</a>, starting from the loading of input data files
and ending with saving the calculated parameters.</p>
</article>
<!-- sub-section -->
<div class="doc-subsection" id="3.3.1.-home-page">
<article>
<h3>3.3.1. Home page</h3>
<p>Choose to read about the project, get help or start data analysis with <a href="index.html">easyDiffraction</a>,
see the screenshot below:</p>
<figure>
<a href="#img-3_2_1" class="screenshot"><img src="images/ed_how-to-use_home.png"></a>
<a href="#_" class="overlay" id="img-3_2_1"><img src="images/ed_how-to-use_home.png"></a>
</figure>
</article>
</div>
<!-- sub-section -->
<!-- sub-section -->
<div class="doc-subsection" id="3.3.2.-project">
<article>
<h3>3.3.2. Create/Open project</h3>
<p>All manipulations of the project can be performed on the <code>Project</code> tab.</p>
<p>To start using <a href="index.html">easyDiffraction</a>, please click the <code>Create a new project</code>
button to start a new project, or click the <code>Open an existing project</code> button and select zipped
project saved earlier or <b>main.cif</b> file from the existing project folder. Alternatively, you can
load one of the provided examples by clicking <code>Open</code> button in the Examples table.</p>
<figure>
<a href="#img-3_2_2" class="screenshot"><img src="images/ed_how-to-use_project.png"></a>
<a href="#_" class="overlay" id="img-3_2_2"><img src="images/ed_how-to-use_project.png"></a>
</figure>
</article>
</div>
<!-- sub-section -->
<!--- sub-sub-section
<div class="doc-subsubsection">
<h4>Supported file formats</h4>
<p>Currently, <a href="index.html">easyDiffraction</a> works best with the STAR/CIF data format.
Click <a href="umanual_intro.html#1.2.-cif-based-format">here</a> to learn more about that.
It is however also possible to load experimental data as plain text in <b>.dat</b> or <b>.xye</b> formats.
Three columns are interpreted as <b>2theta</b>, <b>Intensity</b> and <b>Error</b> from an unpolarized neutron
diffraction experiment, while five columns are interpreted as polarized data with <b>2theta</b>,
<b>Spin up intensity</b>, its <b>Error</b> followed by <b>Spin down intensity</b> and its <b>Error</b>.</p>
</div>
sub-sub-section --->
<!--- sub-sub-section --->
<div class="doc-subsubsection">
<article>
<h4>Application main window</h4>
<p>The application's main window shows:
</p>
<ul>
<li>Project name.</li>
<li>Project related information (Keywords, Phases labels, etc.).</li>
<li>Figures of the crystal structure and refinement curves.</li>
</ul>
</article>
</div>
<!--- sub-sub-section --->
<!--- sub-sub-section --->
<div class="doc-subsubsection">
<article>
<h4>Application sidebar</h4>
<p>The application's sidebar contains the following groups:
</p>
<ul>
<li><b>Get Started</b> group contains buttons to create, open, clone (currently disabled) or save the project.</li>
<li><b>Examples</b> group contains a few selected examples.</li>
</ul>
<p>The very bottom of the sidebar contains the following buttons:
</p>
<ul>
<li><code>Sample</code> to go to the next step in the data processing.</li>
<li><code>Get Online Help</code> for the current tab.</li>
<li><code>Report a bug or issue</code> online.</li>
</ul>
</article>
</div>
<!--- sub-sub-section --->
<!-- sub-section -->
<div class="doc-subsection" id="3.3.3.-sample-model">
<article>
<h3>3.3.3. Define sample model</h3>
<p>All manipulations with sample phases can be performed on the <code>Sample</code> tab.</p>
<figure>
<a href="#img-3_2_3" class="screenshot"><img src="images/ed_how-to-use_phases.png"></a>
<a href="#_" class="overlay" id="img-3_2_3"><img src="images/ed_how-to-use_phases.png"></a>
</figure>
<!--- sub-sub-section
<div class="doc-subsubsection">
<h4>Supported file formats</h4>
<p>Currently, the structural model is taken from the <b>phases.cif</b> file, where
it is described in the same way as in pure <a href="https://www.iucr.org/resources/cif">CIF</a>.
An example is shown below. Explanations about the full syntax can be found
<a href="https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax">elsewhere</a>.</p>
<p>An example of a <b>.cif</b> file for 1D <b>unpolarized</b> neutron powder diffraction data is given below:
<code class=code-block>
data_PbSO4<br>
<br>
_space_group_name_H-M_alt 'P n m a'<br>
_space_group_IT_coordinate_system_code abc<br>
<br>
_cell_length_a 8.477425(36)<br>
_cell_length_b 5.395977(24)<br>
_cell_length_c 6.957025(33)<br>
_cell_angle_alpha 90.0<br>
_cell_angle_beta 90.0<br>
_cell_angle_gamma 90.0<br>
<br>
loop_<br>
_atom_site_label<br>
_atom_site_type_symbol<br>
_atom_site_fract_x<br>
_atom_site_fract_y<br>
_atom_site_fract_z<br>
_atom_site_occupancy<br>
_atom_site_adp_type<br>
_atom_site_u_iso_or_equiv<br>
Pb Pb 0.18800 0.25 0.166807 1.0 Uiso 0.01692<br>
S S 0.06500 0.25 0.685000 1.0 Uiso 0.00258<br>
O1 O 0.90800 0.25 0.595000 1.0 Uiso 0.02469<br>
O2 O 0.19357 0.25 0.543237 1.0 Uiso 0.01803<br>
O3 O 0.08148 0.027453 0.808367 1.0 Uiso 0.01655<br>
</code></p>
<p>Here is an example of a <b>.cif</b> file for 1D <b>polarized</b> neutron powder diffraction data.
<code class=code-block>
data_Fe3O4<br>
<br>
_space_group_name_H-M_ref 'F d -3 m'<br>
_space_group_IT_coordinate_system_code 2<br>
<br>
_cell_length_a 8.57()<br>
_cell_length_b 8.57<br>
_cell_length_c 8.57<br>
_cell_angle_alpha 90.0<br>
_cell_angle_beta 90.0<br>
_cell_angle_gamma 90.0<br>
<br>
loop_<br>
_atom_site_label<br>
_atom_site_type_symbol<br>
_atom_site_fract_x<br>
_atom_site_fract_y<br>
_atom_site_fract_z<br>
_atom_site_occupancy<br>
_atom_site_adp_type<br>
_atom_site_u_iso_or_equiv<br>
Fe3A Fe3+ 0.125 0.125 0.125 1.0 Uiso 0.0<br>
Fe3B Fe3+ 0.5 0.5 0.5 1.0 Uiso 0.0<br>
O O2- 0.25521 0.25521 0.25521 1.0 Uiso 0.0<br>
<br>
loop_<br>
_atom_site_susceptibility_label<br>
_atom_site_susceptibility_chi_type<br>
_atom_site_susceptibility_chi_11<br>
_atom_site_susceptibility_chi_22<br>
_atom_site_susceptibility_chi_33<br>
_atom_site_susceptibility_chi_12<br>
_atom_site_susceptibility_chi_13<br>
_atom_site_susceptibility_chi_23<br>
Fe3A Cani -0.08601() -0.08601 -0.08601 0.0 0.0 0.0<br>
Fe3B Cani 0.07840() 0.07840 0.07840 0.0 0.0 0.0<br>
<br>
loop_<br>
_atom_site_scat_label<br>
_atom_site_scat_lande<br>
_atom_site_scat_kappa<br>
Fe3A 2.0 1.0<br>
Fe3B 2.0 1.0<br>
</code></p>
</div>
sub-sub-section --->
</article>
</div>
<!-- sub-section -->
<!--- sub-sub-section --->
<div class="doc-subsubsection">
<article>
<h4>Application main window</h4>
<p>The application's main window contains the following tabs:
</p>
<ol>
<li><code>Structure View</code> shows a 3D crystal structure model.</li>
<li><code>Text View</code> displays the structure model in the
<a href="https://www.iucr.org/resources/cif">CIF</a> format.</li>
</ol>
<p>An interaction with the plot is performed as follows:
</p>
<ul>
<li><b>Rotate structure</b>: Drag with right mouse button pressed.</li>
<li><b>Zoom in/out</b>: Scroll using mouse wheel.</li>
<li><b>Reset zoom and rotation</b>: Click left mouse button.</li>
</ul>
</article>
</div>
<!--- sub-sub-section --->
<!--- sub-sub-section --->
<div class="doc-subsubsection">
<article>
<h4>Application sidebar</h4>
<p>The application's sidebar contains the following groups:
</p>
<ul>
<li><b>Structural phases</b> group shows the table of crystalline phases present
in the sample. The parameters of the selected phase are given in the groups below.</li>
<li><b>Symmetry and cell parameters</b> group contains information about space group
<a href="https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_crystal_system.html">crystal system,</a>
<a href="https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_IT_number.html">number,</a>
<a href="https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_name_H-M_alt.html">name</a>
and setting, as well as unit cell <a href="https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html">lengths</a>
and <a href="https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html">angles</a>.</li>
<li><b>Atoms, atomic coordinates and occupations</b> group contains details about the atom sites, such as
<a href="https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_label.html">label</a>,
color in the structure plot, <a href="https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html">coordinates</a>
and <a href="https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_occupancy.html">occupancy</a>.</li>
<li><b>Atomic displacement parameters</b>, also known as atomic vibration parameters or thermal parameters, are
presented here.</li>
<li><b>Magnetic susceptibility parameters</b>, or atomic site susceptibility tensor within local susceptibility
approach, are given here.</li>
</ul>
<p>The very bottom of the sidebar contains the following buttons (it may be necessary to close some groups to view these):
</p>
<ul>
<li><code>Project</code> to go to the previous step in the data processing.</li>
<li><code>Experiment</code> to go to the next step in the data processing.</li>
<li><code>Get Online Help</code> for the current tab.</li>
<li><code>Report a bug or issue</code> online.</li>
</ul>
</article>
</div>
<!--- sub-sub-section --->
<!-- sub-section -->
<div class="doc-subsection" id="3.3.4.-experimental-data">
<article>
<h3>3.3.4. Load experimental data</h3>
<p>All manipulations with experimentally measured data can be performed on the
<code>Experiment</code> tab.</p>
<figure>
<a href="#img-3_2_4" class="screenshot"><img src="images/ed_how-to-use_experiments.png"></a>
<a href="#_" class="overlay" id="img-3_2_4"><img src="images/ed_how-to-use_experiments.png"></a>
</figure>
<!--- sub-sub-section
<div class="doc-subsubsection">
<h4>Supported file formats</h4>
<p>The measured data are taken from an <b>experiments.cif</b> (including instrumental parameters).
It is also possible to load experimental data as plain text in <b>.dat</b> or <b>.xye</b> formats.
Three columns are interpreted as <b>2theta</b>, <b>Intensity</b> and <b>Error</b> from an unpolarized neutron
diffraction experiment, while five columns are interpreted as polarized data with <b>2theta</b>,
<b>Spin up intensity</b>, its <b>Error</b> followed by <b>Spin down intensity</b> and its <b>Error</b>.</p>
<p>An example of a <b>.cif</b> file for 1D <b>unpolarized</b> neutron powder diffraction data is given below:
<code class=code-block>
data_NPD<br>
<br>
_setup_wavelength 1.912<br>
_setup_offset_2theta 0.0000()<br>
<br>
_pd_instr_resolution_u 0.14207<br>
_pd_instr_resolution_v -0.41810<br>
_pd_instr_resolution_w 0.38629<br>
_pd_instr_resolution_x 0.0<br>
_pd_instr_resolution_y 0.09038<br>
<br>
loop_<br>
_phase_label<br>
_phase_scale<br>
_phase_igsize<br>
PbSO4 1.0000() 0.0<br>
<br>
loop_<br>
_pd_background_2theta<br>
_pd_background_intensity<br>
11.0 205.6<br>
50.0 208.0<br>
153.0 230.3<br>
<br>
loop_<br>
_pd_meas_2theta<br>
_pd_meas_intensity<br>
_pd_meas_intensity_sigma<br>
10.05 214.0 15.0<br>
10.1 219.0 15.0<br>
10.15 224.0 15.0<br>
10.2 198.0 14.0<br>
10.25 229.0 15.0<br>
...
</code></p>
<ul>
<li><b>_pd_meas_2theta</b>: Angular position of the Bragg peak.</li>
<li><b>_pd_meas_intensity</b>: Intensity of scattered beam of neutrons.</li>
<li><b>_pd_meas_intensity_sigma</b>: Standard deviation of intensity.</li>
</ul>
<p>Here an example of an <b>.xye</b>/<b>.dat</b> file is shown:
<code class=code-block>
10.05 214.0 15.0<br>
10.1 219.0 15.0<br>
10.15 224.0 15.0<br>
10.2 198.0 14.0<br>
10.25 229.0 15.0<br>
...
</code></p>
<p>Here is an example of a <b>.cif</b> file for 1D <b>polarized</b> neutron powder diffraction data,
a <b>.xye</b>/<b>.dat</b> file with five columns in the same order can be used as well.
<code class=code-block>
data_PolNPD5T<br>
<br>
_setup_wavelength 2.4<br>
_setup_field 5.0<br>
_setup_offset_2theta -0.360<br>
<br>
_pd_instr_resolution_u 11.34<br>
_pd_instr_resolution_v -2.983<br>
_pd_instr_resolution_w 1.141<br>
_pd_instr_resolution_x 0.000<br>
_pd_instr_resolution_y 0.404<br>
<br>
_diffrn_radiation_polarization 0.6243<br>
_diffrn_radiation_efficiency 1.0<br>
<br>
_chi2_sum True<br>
_chi2_diff True<br>
_chi2_up False<br>
_chi2_down False<br>
<br>
loop_<br>
_phase_label<br>
_phase_scale<br>
_phase_igsize<br>
Fe3O4 0.162() 0.0<br>
<br>
loop_<br>
_pd_background_2theta<br>
_pd_background_intensity<br>
10.0 183.0<br>
35.0 253.0<br>
72.0 361.0<br>
<br>
loop_<br>
_pd_meas_2theta<br>
_pd_meas_intensity_up<br>
_pd_meas_intensity_up_sigma<br>
_pd_meas_intensity_down<br>
_pd_meas_intensity_down_sigma<br>
10.0 180.31984 28.49124 184.6922 28.47456<br>
10.2 182.67721 26.8855 176.10072 26.8625<br>
10.4 192.40581 26.33115 160.49695 26.28884<br>
10.6 186.10276 25.81657 179.5374 25.84404<br>
...
</code>
<ul>
<li><b>_pd_meas_2theta</b>: Angular position of the Bragg peak.</li>
<li><b>_pd_meas_intensity_up</b>: Intensity of scattered beam of neutrons polarized with spin "UP".</li>
<li><b>_pd_meas_intensity_up_sigma</b>: Standard deviation of intensity "UP".</li>
<li><b>_pd_meas_intensity_down</b>: Intensity of scattered beam of neutrons polarized with spin "DOWN".</li>
<li><b>_pd_meas_intensity_down_sigma</b>: Standard deviation of intensity "DOWN".</li>
</ul>
</p>
</div>
sub-sub-section --->
</article>
</div>
<!--- sub-sub-section --->
<!--- sub-sub-section --->
<div class="doc-subsubsection">
<article>
<h4>Application main window</h4>
<p>The application's main window contains the following tabs:
</p>
<ol>
<li><code>Plot View</code> shows the experimental data plots.</li>
<li><code>Table View</code> contains a table with the extracted data.</li>
<li><code>Text View</code> displays the content of the data file.</li>
</ol>
<p>An interaction with the plot is performed as follows:
</p>
<ul>
<li><b>Show coordinates</b>: Hover mouse pointer over the data point.</li>
<li><b>Zoom in</b>: Drag with left mouse button pressed.</li>
<li><b>Reset zoom</b>: Click right mouse button.</li>
</ul>
</article>
</div>
<!--- sub-sub-section --->
<!--- sub-sub-section --->
<div class="doc-subsubsection">
<article>
<h4>Application sidebar</h4>
<p>The application's sidebar contains the following groups:
</p>
<ul>
<li><b>Data explorer</b> shows experimental data file and contains button for loading data.</li>
<li><b>Instrument and experiment type</b> contains information about the neutron scattering instrument.</li>
<li><b>Diffraction radiation</b> contains polarization and polarising efficiency for polarized neutron data.</li>
<li><b>Setup parameters</b> contains experimental zero shift, wavelength and magnetic field.</li>
<li><b>Peak profile</b> contains information about the peak profile.</li>
<li><b>Peak profile</b> contains background points.</li>
<li><b>Structural phases</b> contains name and scale of the associated phase.</li>
<li><b>Refinement</b> contains type of refinement for polarized neutron data.</li>
</ul>
<p>The very bottom of the sidebar contains the following buttons:
</p>
<ul>
<li><code>Sample</code> to go to the previous step in the data processing.</li>
<li><code>Analysis</code> to go to the next step in the data processing.</li>
<li><code>Get Online Help</code> for the current tab.</li>
<li><code>Report a bug or issue</code> online.</li>
</ul>
</article>
</div>
<!--- sub-sub-section --->
<!-- sub-section -->
<div class="doc-subsection" id="3.3.5.-analysis">
<article>
<h3>3.3.5. Perform data analysis</h3>
<p>Data analysis (structure refinement) is performed in the <code>Analysis</code> tab.</p>
<figure>
<a href="#img-3_2_5" class="screenshot"><img src="images/ed_how-to-use_analysis.png"></a>
<a href="#_" class="overlay" id="img-3_2_5"><img src="images/ed_how-to-use_analysis.png"></a>
</figure>
</article>
</div>
<!--- sub-section --->
<!--- sub-sub-section --->
<div class="doc-subsubsection">
<article>
<h4>Application main window</h4>
<p>The application's main window contains the following tabs:
</p>
<ol>
<li><code>Fitting</code> shows plot of the data and model using current parameters.</li>
<li><code>Text View</code> displays the results of structure refinement in the START/CIF format.</li>
</ol>
<p>An interaction with the plot shown in the <code>Fitting</code> tab is performed as follows:
</p>
<ul>
<li><b>View data point</b>: Hover mouse over data point.</li>
<li><b>Zoom in</b>: Hold left click and drag a box over desired area.</li>
<li><b>Reset view</b>: Right mouse button.</li>
</ul>
</article>
</div>
<!--- sub-sub-section --->
<!--- sub-sub-section --->
<div class="doc-subsubsection">
<article>
<h4>Application sidebar</h4>
<p>Each of the tabs of the main window have independent sidebar options.</p>
<p>The <code>Fitting</code> sidebar contains the following elements:
</p>
<ul>
<li><b>Parameters</b> group shows the table of parameters. Starting values are shown, along with
units, standard deviation and a checkbox for selecting the variable for fitting.</li>
<li><b>Start/Stop fitting</b> button that initiates and stops fitting.</li>
</ul>
<p>The <code>Text View</code> sidebar contains the following elements:
</p>
<ul>
<li><b>Find</b> Search in the CIF file (currently disabled).</li>
</ul>
<p>The very bottom of the sidebar contains the following buttons of each tab:
</p>
<ul>
<li><code>Experiment</code> to go to the previous step in the data processing.</li>
<li><code>Summary</code> to go to the next step in the data processing.</li>
<li><code>Get Online Help</code> for the current tab.</li>
<li><code>Report a bug or issue</code> online.</li>
</ul>
</article>
</div>
<!--- sub-sub-section --->
<!-- sub-section -->
<div class="doc-subsection" id="3.3.6.-summary">
<article>
<h3>3.3.6. Generate summary report</h3>
<p>Here you can view and export the summary report as a pdf file.</p>
<figure>
<a href="#img-3_2_6" class="screenshot"><img src="images/ed_how-to-use_summary.png"></a>
<a href="#_" class="overlay" id="img-3_2_6"><img src="images/ed_how-to-use_summary.png"></a>
</figure>
</article>
</div>
<!-- sub-section -->
<!--- sub-sub-section --->
<div class="doc-subsubsection">
<article>
<h4>Application main window</h4>
<p>The application's main window contains the following tabs:
</p>
<ol>
<li><code>Report</code> shows the report for the performed data analysis.</li>
</ol>
<p>The report contains the following:
</p>
<ul>
<li><b>Project</b> related information.</li>
<li><b>Parameters</b> displays table with all parameters.</li>
<li><b>Fitting</b> shows plot of data and model with current parameters.</li>
<li><b>Structure</b> contains 3D view of structure.</li>
</ul>
</article>
</div>
<!--- sub-sub-section --->
<!--- sub-sub-section --->
<div class="doc-subsubsection">
<article>
<h4>Application sidebar</h4>
<p>The application's sidebar contains the following elements:
</p>
<ul>
<li><b>Export as...</b> contains export button, field for custom report name and drop down menu for file format.</li>
<li><b>Export elements</b> has checkboxes for each element in the report to select those that should be exported (currently disabled).</li>
</ul>
<p>The very bottom of the sidebar contains the following buttons of each tab:
</p>
<ul>
<li><code>Analysis</code> to go to the previous step in the data processing.</li>
<li><code>Get Online Help</code> for the current tab.</li>
<li><code>Report a bug or issue</code> online.</li>
</ul>
</article>
</div>
<!--- sub-sub-section --->
</div>
<!--- sub-section --->
</div>
<!--- chapter --->
</div>
<!--- doc area --->
</section>
</div>
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