diffpy · sbillinge · Jan 21, 2022 · Dec 24, 2021
diff --git a/NSFnugget.html b/NSFnugget.html
@@ -4,8 +4,7 @@
 <html>
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
-
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Enabling new science in nanoscale structure characterization of complex materials &#8212; DiffPy  documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/bootstrap-sphinx.css" />
@@ -93,7 +92,7 @@
   <div class="row">
     <div class="body col-md-12 content" role="main">
 
-  <section id="enabling-new-science-in-nanoscale-structure-characterization-of-complex-materials">
+  <div class="section" id="enabling-new-science-in-nanoscale-structure-characterization-of-complex-materials">
 <h1>Enabling new science in nanoscale structure characterization of complex materials<a class="headerlink" href="#enabling-new-science-in-nanoscale-structure-characterization-of-complex-materials" title="Permalink to this headline">¶</a></h1>
 <p><em>C. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch,
 and S. J. L. Billinge (Michigan State University)</em></p>
@@ -106,12 +105,10 @@ <h1>Enabling new science in nanoscale structure characterization of complex mate
 sub-group of the DANSE project recently released a new software tool that
 will have a large impact in nanostructure characterization using x-ray and
 neutron diffraction.</p>
-<figure class="align-center" id="id3">
+<div class="figure align-center" id="id3">
 <a class="reference internal image-reference" href="_images/PDFgui_screenshot_707.png"><img alt="_images/PDFgui_screenshot_707.png" src="_images/PDFgui_screenshot_707.png" style="width: 399.5px; height: 294.5px;" /></a>
-<figcaption>
-<p><span class="caption-text">Screen-shot of PDFgui during a refinement of multiple data-sets</span><a class="headerlink" href="#id3" title="Permalink to this image">¶</a></p>
-</figcaption>
-</figure>
+<p class="caption"><span class="caption-text">Screen-shot of PDFgui during a refinement of multiple data-sets</span><a class="headerlink" href="#id3" title="Permalink to this image">¶</a></p>
+</div>
 <p>The diffraction data are Fourier transformed to obtain the atomic pair distribution
 function (PDF) and analyzed by quantitatively fitting nanostructure models to the
 data. PDFgui allows rapid setup of individual and multiple
@@ -133,7 +130,7 @@ <h1>Enabling new science in nanoscale structure characterization of complex mate
 <a class="reference external" href="doc/pdfgui/Farrow-jpcm-2007.pdf"><img alt="downloadFarrowJpcm07" src="_images/pdficon_small.png" /></a></p>
 </dd>
 </dl>
-</section>
+</div>
 
 
     </div>

diff --git a/acknowledgements.html b/acknowledgements.html
@@ -4,8 +4,7 @@
 <html>
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
-
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Acknowledgements &#8212; DiffPy  documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/bootstrap-sphinx.css" />
@@ -93,16 +92,16 @@
   <div class="row">
     <div class="body col-md-12 content" role="main">
 
-  <section id="acknowledgements">
+  <div class="section" id="acknowledgements">
 <h1>Acknowledgements<a class="headerlink" href="#acknowledgements" title="Permalink to this headline">¶</a></h1>
-<section id="developers">
+<div class="section" id="developers">
 <h2>Developers<a class="headerlink" href="#developers" title="Permalink to this headline">¶</a></h2>
 <p>The active DiffPy development team is Pavol Juhas, Kevin Knox, Xiaohao
 Yang, Michael McKerns, Chris Farrow, and Simon J. L. Billinge. Former
 members of the project are Emil Bozin, Wenduo Zhou, Peng Tian, Timur
 Davis, Jiwu Liu, and Dmitriy Bryndin.</p>
-</section>
-<section id="funding">
+</div>
+<div class="section" id="funding">
 <h2>Funding<a class="headerlink" href="#funding" title="Permalink to this headline">¶</a></h2>
 <p>The DiffPy project is currently supported by Laboratory Directed
 Research and Development (LDRD) Program 12-007 (Complex Modeling) at
@@ -118,14 +117,14 @@ <h2>Funding<a class="headerlink" href="#funding" title="Permalink to this headli
 recommendations expressed in this material are those of the author(s)
 and do not necessarily reflect the views of the respective funding
 bodies.</p>
-</section>
-<section id="additional-contributions">
+</div>
+<div class="section" id="additional-contributions">
 <h2>Additional Contributions<a class="headerlink" href="#additional-contributions" title="Permalink to this headline">¶</a></h2>
 <p>The DiffPy team would like to thank multiple users for their help and
 comments during the development of this release: Dragica Podgorski,
 Valentina Felsen, and Kirsten M. Ø. Jensen.</p>
-</section>
-</section>
+</div>
+</div>
 
 
     </div>

diff --git a/community.html b/community.html
@@ -4,8 +4,7 @@
 <html>
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
-
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Community &#8212; DiffPy  documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/bootstrap-sphinx.css" />
@@ -93,7 +92,7 @@
   <div class="row">
     <div class="body col-md-12 content" role="main">
 
-  <section id="community">
+  <div class="section" id="community">
 <h1>Community<a class="headerlink" href="#community" title="Permalink to this headline">¶</a></h1>
 <p>To ensure a bright future for the DiffPy project it is essential to build a strong community
 of users and contributing developers. There are several Google groups for support and
@@ -122,7 +121,7 @@ <h1>Community<a class="headerlink" href="#community" title="Permalink to this he
 <a class="reference external" href="mailto:sb2896&#37;&#52;&#48;columbia&#46;edu">Simon J<span>&#46;</span> L<span>&#46;</span> Billinge</a>.</p>
 <p>To report or browse bugs, please visit <a class="reference external" href="https://github.com/diffpy">https://github.com/diffpy</a>
 and continue to the relevant project and its Issues.</p>
-</section>
+</div>
 
 
     </div>

diff --git a/doc/pdfgetx/2.1.2/PDFgetXNS3_manual.pdf b/doc/pdfgetx/2.1.2/PDFgetXNS3_manual.pdf
diff --git a/doc/pdfgetx/2.1.2/_images/nickelfqgr.png b/doc/pdfgetx/2.1.2/_images/nickelfqgr.png
diff --git a/doc/pdfgetx/2.1.2/_images/nickelfqgrnoisy.png b/doc/pdfgetx/2.1.2/_images/nickelfqgrnoisy.png
diff --git a/doc/pdfgetx/2.1.2/_images/tunenickelfqgr.png b/doc/pdfgetx/2.1.2/_images/tunenickelfqgr.png
diff --git a/doc/pdfgetx/2.1.2/_images/tunenickelt4gr.png b/doc/pdfgetx/2.1.2/_images/tunenickelt4gr.png
diff --git a/doc/pdfgetx/2.1.2/_images/twothetazerofit.svgz b/doc/pdfgetx/2.1.2/_images/twothetazerofit.svgz
diff --git a/doc/pdfgetx/2.1.2/_sources/files.rst.txt b/doc/pdfgetx/2.1.2/_sources/files.rst.txt
@@ -0,0 +1,102 @@
+Files used in PDF extraction
+========================================================================
+
+.. include:: abbreviations.txt
+.. _my-configfile:
+.. program:: pdfgetx3
+
+Configuration file
+------------------------------------------------------------------------
+
+Configuration files may define the PDF processing parameters.
+By default, the :program:`pdfgetx3` program attempts to read
+:file:`.pdfgetx3.cfg` file from the user HOME directory,
+then :file:`.pdfgetx3.cfg` and :file:`pdfgetx3.cfg` files
+from the current working directory.
+If configuration file has a different name, it needs to be specified
+with the :option:`-c, --config <-c>` option.
+The :program:`pdfgetn3` program works in the same way,
+except it checks for configuration files
+:file:`~/.pdfgetn3.cfg`, :file:`.pdfgetn3.cfg` and :file:`pdfgetn3.cfg`.
+
+The easiest way of creating a configuration file is to generate
+a template content using the :option:`--createconfig` option as ::
+
+   pdfgetx3 --createconfig=test.cfg
+
+and then change the generated test.cfg file in your favorite text
+editor.  The configuration file follows a simple "varname=value" syntax,
+any lines starting with "#" are ignored as comments.
+
+The configuration file has several sections marked as ``[SECTIONNAME]``.
+The ``[DEFAULT]`` section is mandatory and it contains the default
+global settings.  Any other sections are optional and they are applied
+only when selected with the :option:`-s, --section <-s>` option on the
+command line.  Thus ::
+
+   pdfgetx3 --config=test.cfg --section=nacl
+
+would read the parameters from the ``[nacl]`` section after reading the
+defaults.  Having several sections in the configuration
+file is useful when there are multiple measurements that share most of
+the parameters, but differ in a few of them, for example in chemical
+composition.  The configuration file can then contain sections per each
+sample that define only the composition, while all other parameters are
+specified just once in the global DEFAULT section.
+
+
+Input files
+------------------------------------------------------------------------
+
+PDFgetX3 and PDFgetN3 accept input powder diffraction data
+in the form of two-column text file,
+where the first column x is either the scattering angle
+|twotheta| in degrees, momentum transfer *Q* in inverse nanometers or *Q*
+in inverse ångströms.  The second column y contains the corresponding
+scattered intensities normalized per unit solid angle.  The actual type
+of the x-values is identified by the :confval:`dataformat` parameter.
+The input files may contain header with comments or metadata, and the
+actual data are read from the first long section of numerical values.
+
+The input files are usually passed as command-line arguments to
+:program:`pdfgetx3` or :program:`pdfgetn3` programs and must be paths
+accessible from the current working directory.
+
+Input files can be also defined by setting the :confval:`inputfile`
+value in the configuration file.  The :option:`-d, --datapath <-d>`
+option can be then used to provide additional data directories to
+search for these inputs and for the :confval:`backgroundfile`.
+This is to support configuration files located in a different
+directory than the data.
+
+When the :option:`--find <-f>` option is active, the pdfgetx3 arguments
+are understood as filename patterns and the input files are found
+in the current or specified directory.
+
+
+Output files
+------------------------------------------------------------------------
+
+PDFgetX3 and PDFgetN3 can produce up to four different output data files:
+
+* .iq -- |IQ|, the background-corrected
+  intensities sampled on a regular *Q*-space grid in inverse ångströms,
+
+* .sq -- |SQ|, the total scattering structure function,
+  with intensities normalized by average scattering factors and
+  corrected by a polynomial fit,
+
+* .fq -- |FQ|, the reduced structure function equal to *Q*\ (|SQ| - 1),
+
+* .gr -- |Gr|, the resultant PDF, where the first column is the
+  separation *r* in ångströms and the second is the function *G* in
+  Å\ :sup:`-2`.
+
+You can specify what output files should be produced by setting the
+:confval:`outputtypes` parameter in the configuration file or by
+passing the :option:`-t, --outputtypes <-t>` on the command line.
+
+The header of all output files contains the parameter values that were
+used in the calculation and thus it is by itself a valid configuration
+file.  When passed as an argument to the :option:`--config <-c>` option,
+the PDFgetX3 will reproduce the previous calculation.
diff --git a/doc/pdfgetx/2.1.2/_sources/index.rst.txt b/doc/pdfgetx/2.1.2/_sources/index.rst.txt
@@ -0,0 +1,38 @@
+.. PDFgetX3 documentation master file, created by
+   sphinx-quickstart on Tue Sep 21 18:35:11 2010.
+   You can adapt this file completely to your liking,
+   but it should at least contain the root `toctree` directive.
+
+########################################################################
+diffpy.pdfgetx
+########################################################################
+
+User manual for PDFgetX3, PDFgetN3, PDFgetS3 and Python package diffpy.pdfgetx.
+
+| Release |release|
+| |today|
+
+========================================================================
+Table of contents
+========================================================================
+
+
+.. toctree::
+   :maxdepth: 2
+
+   intro
+   install
+   quick-start
+   tutorial
+   files
+   interact
+   options
+   plotdata
+   release
+
+========================================================================
+Indices
+========================================================================
+
+* :ref:`genindex`
+* :ref:`search`