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‎.buildinfo

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# Sphinx build info version 1
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# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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config: f9c3b408a5ee6fd42eee6a4792c56501
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config: a4b1e149a39399211ea604929ec830e4
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tags: 645f666f9bcd5a90fca523b33c5a78b7

‎_downloads/032062351bf34c8fe361e08dc302b237/Ni data.zip

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‎_downloads/0ef3e2edfca13d573862b655df0a2b60/Doping data series.zip

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‎_downloads/152427a3fb2089faa71c17d4774bb0e8/Ni-xray.gr

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‎_downloads/2c50488e54890de4446320c8083064d0/tui_mno_bond_lengths.py

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#!/usr/bin/env python
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"""Extract the shortest Mn-O bond lengths from all fits in PDFgui project.
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This script loops through all refined phases in PDFgui project and calculates
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their shortest Mn-O bond lengths using diffpy.pdffit2 library. The results
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are plotted versus temperature and saved to "mno-bond-lengths.dat" file.
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"""
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import pylab
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from diffpy.pdffit2 import PdfFit
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# Import tui (Text User Interface) functions from diffpy.pdfgui
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from diffpy.pdfgui import tui
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# PDFgui project file
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project_file = "lmo-template.ddp3"
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output_file = "mno-bond-lengths.dat"
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# load project file
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prj = tui.LoadProject(project_file)
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# Define a function for calculating shortest MnO bond length
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# using diffpy.pdffit2
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# Create a PDF calculator object that will be used in that function.
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pf = PdfFit()
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def shortestBond_MnO(stru):
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"""extract the shortest MnO bond length in a structure.
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stru -- initial or refined phase from a PDFgui project
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Return the shortest bond length.
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"""
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pf.reset()
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pf.add_structure(stru)
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bnds = pf.bond_length_types("Mn", "O", 0.01, 3)
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return bnds["dij"][0]
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# Extract temperatures from PDFgui project to Python list.
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# Temperature needs to be defined per each dataset in the project.
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temperatures = prj.getTemperatures()
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# Build a list of shortest Mn-O bonds from all refined phases.
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MnO_bond_lengths = []
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for phase in prj.getPhases():
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if phase.refined is None:
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print("Cannot find phase refinement results in", project_file)
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print("Open the file in PDFgui, run refinement, save and try again.")
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# terminate the script by raising error condition
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raise RuntimeError("Missing refinement results.")
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MnO_bond_lengths.append(shortestBond_MnO(phase.refined))
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# Save bond lengths to a file
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outfile = open(output_file, "w")
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print("# Shortest Mn-O bond length extracted from {}".format(project_file), file=outfile)
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print("# temperature(K) bond_length(A)", file=outfile)
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for t, b in zip(temperatures, MnO_bond_lengths):
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print("{}, {}".format(t, b), file=outfile)
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outfile.close()
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dashline = 78 * "-"
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print(dashline)
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print("Mn-O bond lengths saved to {}".format(output_file))
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print(dashline)
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# Plot results using matplotlib; pylab is a part of matplotlib that
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# provides MATLAB-like plotting functions.
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pylab.plot(temperatures, MnO_bond_lengths, "o--")
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pylab.title("Data from refined phases in PDFgui project %s" % project_file)
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pylab.xlabel("temperature (K)")
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pylab.ylabel("shortest Mn-O bond (A)")
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# Show the plot window. This must be the last command in the script.
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pylab.show()

‎_downloads/5c534d55babfa2f2f0098cfa8fe20fea/Ni.stru

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‎_downloads/74679939e242a632e3c46d39852bd6c9/Nanoparticle structure.zip

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‎_downloads/96f93e59ce2c84278c696ef7f0b09a4e/Temperature data series.zip

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‎_modules/diffpy/pdfgui/applications/pdfgui.html

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<head>
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<meta charset="utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>diffpy.pdfgui.applications.pdfgui &mdash; diffpy.pdfgui 3.1.0rc4 documentation</title>
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<title>diffpy.pdfgui.applications.pdfgui &mdash; diffpy.pdfgui 3.1.0rc5 documentation</title>
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<link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=fa44fd50" />
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<script src="../../../../_static/jquery.js?v=5d32c60e"></script>
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<script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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<script src="../../../../_static/documentation_options.js?v=6a5857df"></script>
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<script src="../../../../_static/documentation_options.js?v=c31823b9"></script>
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<script src="../../../../_static/doctools.js?v=9a2dae69"></script>
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<script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
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<script src="../../../../_static/js/theme.js"></script>
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diffpy.pdfgui
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</a>
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<div class="version">
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3.1.0rc4
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3.1.0rc5
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</div>
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<div role="search">
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<form id="rtd-search-form" class="wy-form" action="../../../../search.html" method="get">
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../../license.html">License</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../../release.html">Release Notes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../../manual.html">Manual</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../../api/diffpy.pdfgui.html">Package API</a></li>
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</ul>
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‎_modules/diffpy/pdfgui/control/calculation.html

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<head>
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<meta charset="utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>diffpy.pdfgui.control.calculation &mdash; diffpy.pdfgui 3.1.0rc4 documentation</title>
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<title>diffpy.pdfgui.control.calculation &mdash; diffpy.pdfgui 3.1.0rc5 documentation</title>
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<link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=fa44fd50" />
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<link rel="stylesheet" type="text/css" href="../../../../_static/css/theme.css?v=19f00094" />
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<script src="../../../../_static/jquery.js?v=5d32c60e"></script>
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<script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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<script src="../../../../_static/documentation_options.js?v=6a5857df"></script>
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<script src="../../../../_static/documentation_options.js?v=c31823b9"></script>
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diffpy.pdfgui
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</a>
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<div class="version">
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3.1.0rc4
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3.1.0rc5
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</div>
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<div role="search">
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<form id="rtd-search-form" class="wy-form" action="../../../../search.html" method="get">
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../../license.html">License</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../../release.html">Release Notes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../../manual.html">Manual</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../../api/diffpy.pdfgui.html">Package API</a></li>
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</ul>
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@@ -98,10 +99,11 @@ <h1>Source code for diffpy.pdfgui.control.calculation</h1><div class="highlight"
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<span class="kn">import</span> <span class="nn">copy</span>
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<span class="kn">import</span> <span class="nn">math</span>
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<span class="kn">import</span> <span class="nn">pickle</span>
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<span class="kn">from</span> <span class="nn">diffpy.pdfgui.control.controlerrors</span> <span class="kn">import</span> <span class="n">ControlConfigError</span><span class="p">,</span> <span class="n">ControlKeyError</span><span class="p">,</span> <span class="n">ControlValueError</span>
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<span class="kn">from</span> <span class="nn">diffpy.pdfgui.control.pdfcomponent</span> <span class="kn">import</span> <span class="n">PDFComponent</span>
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<span class="kn">from</span> <span class="nn">diffpy.pdfgui.utils</span> <span class="kn">import</span> <span class="n">pickle_loads</span><span class="p">,</span> <span class="n">safeCPickleDumps</span>
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<span class="kn">from</span> <span class="nn">diffpy.pdfgui.utils</span> <span class="kn">import</span> <span class="n">safeCPickleDumps</span>
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<div class="viewcode-block" id="Calculation">
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<span class="sd"> returns a tree of internal hierachy</span>
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<span class="sd"> &quot;&quot;&quot;</span>
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<span class="n">config</span> <span class="o">=</span> <span class="n">pickle_loads</span><span class="p">(</span><span class="n">z</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">subpath</span> <span class="o">+</span> <span class="s2">&quot;config&quot;</span><span class="p">))</span>
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<span class="n">config</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">z</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">subpath</span> <span class="o">+</span> <span class="s2">&quot;config&quot;</span><span class="p">),</span> <span class="n">encoding</span><span class="o">=</span><span class="s2">&quot;latin1&quot;</span><span class="p">)</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">rmin</span> <span class="o">=</span> <span class="n">config</span><span class="p">[</span><span class="s2">&quot;rmin&quot;</span><span class="p">]</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">rstep</span> <span class="o">=</span> <span class="n">config</span><span class="p">[</span><span class="s2">&quot;rstep&quot;</span><span class="p">]</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">rmax</span> <span class="o">=</span> <span class="n">config</span><span class="p">[</span><span class="s2">&quot;rmax&quot;</span><span class="p">]</span>

‎_modules/diffpy/pdfgui/control/constraint.html

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<head>
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<meta charset="utf-8" />
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<title>diffpy.pdfgui.control.constraint &mdash; diffpy.pdfgui 3.1.0rc4 documentation</title>
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<title>diffpy.pdfgui.control.constraint &mdash; diffpy.pdfgui 3.1.0rc5 documentation</title>
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<script src="../../../../_static/jquery.js?v=5d32c60e"></script>
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<script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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<script src="../../../../_static/documentation_options.js?v=6a5857df"></script>
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<script src="../../../../_static/documentation_options.js?v=c31823b9"></script>
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<script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
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diffpy.pdfgui
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</a>
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<div class="version">
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3.1.0rc5
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</div>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../../license.html">License</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../../release.html">Release Notes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../../manual.html">Manual</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../../api/diffpy.pdfgui.html">Package API</a></li>
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</ul>
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‎_modules/diffpy/pdfgui/control/controlerrors.html

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<title>diffpy.pdfgui.control.controlerrors &mdash; diffpy.pdfgui 3.1.0rc4 documentation</title>
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<title>diffpy.pdfgui.control.controlerrors &mdash; diffpy.pdfgui 3.1.0rc5 documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="../../../../license.html">License</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../../release.html">Release Notes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../../manual.html">Manual</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../../../api/diffpy.pdfgui.html">Package API</a></li>
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</ul>
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