Synchronized with the source at 501eef3.

Author: benfrandsen

NSFnugget.html

@@ -81,6 +81,7 @@
       <li><a href="products/pdfgetx3.html">PDFgetX3</a></li>
       <li><a href="products/pdfgui.html">PDFgui</a></li>
       <li><a href="products/SrMise.html">SrMise</a></li>
+      <li><a href="products/magPDF.html">magPDF</a></li>
       <li><a href="products/pythonpackages.html">Python Packages</a></li>
   </ul>
 </li>

_images/magpdf_screenshot.png

@@ -82,3 +82,4 @@ centered at Columbia University and, before that, Michigan State University.
    products/pdfgetx3
    products/pythonpackages 
    products/SrMise
+   products/magPDF

_sources/index.txt

@@ -0,0 +1,102 @@
+##########
+magPDF
+##########
+
+The diffpy.magpdf package provides a convenient method for computing the magnetic PDF
+(mPDF) from magnetic structures and performing fits to neutron total scattering
+data. The mPDF is calculated by an mPDFcalculator object, which extracts the spin
+positions and spin vectors from a magStructure object that the mPDFcalculator
+takes as input. The magStructure object in turn can contain multiple magSpecies
+objects, which generate magnetic configurations based on a diffpy.Structure object
+and a set of propagation vectors and basis vectors provided by the user.
+Alternatively, the user can manually define a magnetic unit cell that will be used
+to generate the magnetic structure, or the magnetic structure can be defined simply
+as lists of spin positions and spin vectors provided by the user.
+
+
+
+.. figure:: ../images/magpdf_screenshot.png
+   :align: center
+
+This is an early release of magPDF, and the capabilities and documentation of the
+project will evolve. The DiffPy team encourages investigators to provide feedback,
+suggestions, and feature requests.
+
+
+Getting Started
+=================
+
+The diffpy.magpdf package requires Python 2.6 or 2.7 and the following software:
+
+* ``NumPy`` - numerical mathematics and fast array operations for Python
+* ``SciPy`` - scientific libraries for Python
+* ``matplotlib`` - python plotting library
+* ``diffpy.Structure`` - diffpy package for generating atomic structure
+* ``diffpy.srreal`` - diffpy package for calculating real-space quantities
+
+See the :doc:`magPDF license <magPDFlicense>` for terms and conditions of use.
+
+Installation
+------------
+
+The recommended way to install this package is through conda. For help installing conda,
+please visit `https://www.continuum.io/downloads <https://www.continuum.io/downloads>`__.
+Once conda is installed, you can follow the simple steps below to install diffpy.magpdf.
+You will also install the full diffpy-cmi suite along the way. 
+
+*Step 1: Add the appropriate conda channels to your conda configuration.* ::
+
+    conda config --add channels diffpy
+    conda config --add channels benfrandsen
+
+These commands tell conda to look through these channels on the Anaconda cloud server to
+find the appropriate software.
+
+*Step 2 (recommended): Create and activate a conda environment for diffpy + diffpy.magpdf.* ::
+
+    conda create --name diffpy python=2.7
+    source activate diffpy
+
+Note that you can name the environment anything you choose by passing it a different name
+after the --name flag in the first command.
+    
+*Step 3: Install diffpy.magpdf.* ::
+
+    conda install diffpy.magpdf
+
+Note that this will also install the full diffpy-cmi suite if it has not already been
+installed in this environment.
+    
+*Alternative option: Install from the python package index.*
+
+If you prefer to use the python package index and have pip installed, please install the
+prerequisite software and then use the command ::
+
+    pip install diffpy.magpdf
+
+*Alternative option: Download and install from source.*
+
+If you prefer to install from source, you can also zip and download the entire package
+from `PyPI <https://pypi.python.org/pypi/diffpy.magpdf>`__ or
+`GitHub <https://github.com/benfrandsen/diffpy.magpdf>`__, then unzip the file and
+execute the following command from inside the unzipped directory ::
+
+    python setup.py install
+
+Note that this will only work if all the dependencies are already properly installed.
+
+Documentation
+-------------
+Please see `http://pythonhosted.org/diffpy.magpdf/ <http://pythonhosted.org/diffpy.magpdf/>`__
+for the documentation.
+
+What next?
+============
+
+Explore the magPDF tutorial and examples on the
+`CMI Exchange <https://github.com/diffpy/cmi_exchange>`_!
+
+.. toctree::
+   :hidden:
+
+   magPDFlicense

_sources/products/magPDF.txt

@@ -0,0 +1,4 @@
+.. this page only contains the LICENSE text for magPDF
+
+.. include:: magPDF_LICENSE.txt
+   :literal:

_sources/products/magPDFlicense.txt

@@ -3,8 +3,9 @@ Python Packages
 
 This is a complete list of all Python packages developed by the DiffPy
 team. For more information about a specific package, follow the link to
-the corresponding github page. With the exception of PDFfit2 and SrMise
-all of the packages listed below are bundled in the |DiffPyCMI| release.
+the corresponding github page. With the exception of PDFfit2, SrMise,
+and magPDF, all of the packages listed below are bundled in the |DiffPyCMI|
+release.
 
 ======================      ============================================
 Module                      Description
@@ -33,6 +34,9 @@ Module                      Description
 `diffpy.pdffit2`_           Atomic structure refinement and PDF fitting
                             (this is the computational engine used by
                             PDFgui).
+
+`diffpy.magpdf`_            Tools for calculating and refining magnetic
+                            PDFs.
 ======================      ============================================
 
 .. _diffpy.srfit: https://github.com/diffpy/diffpy.srfit
@@ -49,4 +53,6 @@ Module                      Description
 
 .. _diffpy.pdffit2: https://github.com/diffpy/diffpy.pdffit2
 
+.. _diffpy.magpdf: https://github.com/benfrandsen/diffpy.magpdf
+
 .. include:: ../abbreviations.txt

_sources/products/pythonpackages.txt

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

_static/doctools.js

@@ -4,10 +4,8 @@
 .highlight .err { border: 1px solid #FF0000 } /* Error */
 .highlight .k { color: #007020; font-weight: bold } /* Keyword */
 .highlight .o { color: #666666 } /* Operator */
-.highlight .ch { color: #408090; font-style: italic } /* Comment.Hashbang */
 .highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
 .highlight .cp { color: #007020 } /* Comment.Preproc */
-.highlight .cpf { color: #408090; font-style: italic } /* Comment.PreprocFile */
 .highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */
 .highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
 .highlight .gd { color: #A00000 } /* Generic.Deleted */

_static/pygments.css

@@ -4,13 +4,12 @@
  *
  * Sphinx JavaScript utilties for the full-text search.
  *
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 
 
-/* Non-minified version JS is _stemmer.js if file is provided */ 
 /**
  * Porter Stemmer
  */
@@ -374,7 +373,8 @@ var Search = {
     }
 
     // lookup as search terms in fulltext
-    results = results.concat(this.performTermsSearch(searchterms, excluded, terms, titleterms));
+    results = results.concat(this.performTermsSearch(searchterms, excluded, terms, Scorer.term))
+                     .concat(this.performTermsSearch(searchterms, excluded, titleterms, Scorer.title));
 
     // let the scorer override scores with a custom scoring function
     if (Scorer.score) {
@@ -538,47 +538,23 @@ var Search = {
   /**
    * search for full-text terms in the index
    */
-  performTermsSearch : function(searchterms, excluded, terms, titleterms) {
+  performTermsSearch : function(searchterms, excluded, terms, score) {
     var filenames = this._index.filenames;
     var titles = this._index.titles;
 
-    var i, j, file;
+    var i, j, file, files;
     var fileMap = {};
-    var scoreMap = {};
     var results = [];
 
     // perform the search on the required terms
     for (i = 0; i < searchterms.length; i++) {
       var word = searchterms[i];
-      var files = [];
-      var _o = [
-        {files: terms[word], score: Scorer.term},
-        {files: titleterms[word], score: Scorer.title}
-      ];
-
       // no match but word was a required one
-      if ($u.every(_o, function(o){return o.files === undefined;})) {
+      if ((files = terms[word]) === undefined)
         break;
+      if (files.length === undefined) {
+        files = [files];
       }
-      // found search word in contents
-      $u.each(_o, function(o) {
-        var _files = o.files;
-        if (_files === undefined)
-          return
-
-        if (_files.length === undefined)
-          _files = [_files];
-        files = files.concat(_files);
-
-        // set score for the word in each file to Scorer.term
-        for (j = 0; j < _files.length; j++) {
-          file = _files[j];
-          if (!(file in scoreMap))
-            scoreMap[file] = {}
-          scoreMap[file][word] = o.score;
-        }
-      });
-
       // create the mapping
       for (j = 0; j < files.length; j++) {
         file = files[j];
@@ -600,19 +576,14 @@ var Search = {
       // ensure that none of the excluded terms is in the search result
       for (i = 0; i < excluded.length; i++) {
         if (terms[excluded[i]] == file ||
-            titleterms[excluded[i]] == file ||
-            $u.contains(terms[excluded[i]] || [], file) ||
-            $u.contains(titleterms[excluded[i]] || [], file)) {
+          $u.contains(terms[excluded[i]] || [], file)) {
           valid = false;
           break;
         }
       }
 
       // if we have still a valid result we can add it to the result list
       if (valid) {
-        // select one (max) score for the file.
-        // for better ranking, we should calculate ranking by using words statistics like basic tf-idf...
-        var score = $u.max($u.map(fileMap[file], function(w){return scoreMap[file][w]}));
         results.push([filenames[file], titles[file], '', null, score]);
       }
     }