Pdfmorph web-page

_templates/menu01.html

@@ -15,5 +15,6 @@
       <li><a href="{{pathto('products/mPDF')}}">mPDF</a></li>
       <li><a href="{{pathto('products/xinterpdf')}}">xINTERPDF</a></li>
       <li><a href="{{pathto('products/pythonpackages')}}">Python Packages</a></li>
+      <li><a href="{{pathto('products/pdfmorph')}}">PDFmorph</a></li>
   </ul>
 </li>

index.rst

@@ -86,3 +86,4 @@ centered at Columbia University and, before that, Michigan State University.
    products/SrMise
    products/mPDF
    products/xinterpdf
+   products/pdfmorph

products/pdfmorph.rst

@@ -0,0 +1,119 @@
+.. include:: ../abbreviations.txt
+
+########
+PDFmorph
+########
+
+Overview
+========
+
+.. note::
+	The PDFmorph application has a Command Line Interface. If you are 
+	unfamiliar with the terminal or windows command prompt, it is recommended 
+	that you consult online resources and become somewhat familiar before 
+	using PDFmorph.
+
+PDFmorph is a Python software package designed to increase the insight researchers
+can obtain from measured atomic pair distribution functions (PDFs) in a model 
+independent way. The program was designed to help a researcher answer the question: 
+"has my material undergone a phase transition between these two measurements?"
+
+PDFmorph makes use of several data manipulation techniques to correct for benign
+effects such as thermal expansion and increased thermal motion before computing and
+plotting a difference curve between two PDFs. One PDF is identified as the "target" 
+PDF and the second is "morphed" by "stretching", "smearing", and "scaling". PDFmorph
+will vary amplitude of morphing transformations to obtain the best fit between
+morphed and target PDFs, then plot them along with the difference curve plotted
+below.
+
+There are also a few other morphing transformations in the program.
+
+Finally, we note that PDFmorph should work on other spectra that are not PDFs, 
+though it has not been extensively tested beyond the PDF.
+
+.. PDFmorph will soon be included in :doc:`xPDFsuite <xPDFsuite>`, a powerful end-to-end software for X-ray PDF analysis. xPDFsuite is designed for flexible, high throughput PDF analyses and contains many features for interrogating, comparing, and modeling data as well as simply doing data reduction.
+
+.. figure:: ../images/pdfmorph_nacl_ex.png
+	:align: center
+
+	Transformation techniques (scale, smear, and stretch, respectively) 
+	utilized by PDFmorph applied sequentially on an NaCl sample
+
+
+Installation
+============
+
+By downloading and using this software, you are agreeing to the conditions 
+specified in the :doc:`software license <pdfmorph_license>`.
+
+PDFmorph is distributed as a software package for `Anaconda Python <https://www.continuum.io>`__.
+PDFmorph is available for all operating systems supported by Anaconda, namely for
+32 and 64-bit Linux, Mac OS X, and 32 and 64-bit Windows.
+
+As a prerequisite for PDFmorph installation, download and install Anaconda
+from |anaconda-download|.
+
+.. note::
+	PDFmorph is a software which operates on any version of Python 3. Anaconda
+	should install the latest version of Python by default, but in case you 
+	already use Anaconda for a prior release of Python, create a separate
+	Anaconda environment *py3x* which will provide your preferred version of 
+	Python 3 (substitute x for your preferred release) instead of Python 2.7 
+	or earlier. ::
+
+		conda create --name=py3x python=3.x 
+		conda activate py3x
+
+	On Windows use just ``activate py3x``. Make sure that *py3x* environment is
+	activated in your shell prior to running the "install" or "update" commands
+	below.
+
+PDFmorph is available from the "conda-forge" channel of Anaconda packages. Open a 
+*Terminal* window or *Anaconda Command Prompt* on Windows and install PDFmorph
+using the :program:`conda` command ::
+
+	conda config --add channels conda-forge
+	conda install diffpy.pdfmorph
+
+And it should be installed! To make sure that installation has completed correctly, 
+run the following command from your relevant conda environment :: 
+
+	pdfmorph --version
+
+If installed correctly, this command should return PDFmorph's current version number.
+
+
+PDFmorph Updates
+================
+
+The Anaconda package sustem makes it easy to prepare and distribute software
+packages and bugfixes. To update the lates version of PDFmorph use ::
+
+	conda update diffpy.pdfmorph
+
+With other Python distributions, the program can be updated to the latest version
+as follows ::
+
+	easy_install --upgrade diffpy.pdfmorph
+
+To use a development version, visit the project source repository at
+https://github.com/diffpy/diffpy.pdfmorph and consult its README file.
+
+
+Documentation/Help
+==================
+
+0.0.1 - latest
+----------------------
+
+* User manual (available in HTML and PDF) to be made available soon
+* Installation instructions to come
+* Tutorial files will be made available soon
+* Please, join the :doc:`community forum <../community>` for tips, 
+  tricks, and feedback.
+
+
+References
+==========
+
+Paper on PDfmorph will be released soon.

products/pdfmorph_license.rst

@@ -0,0 +1,6 @@
+.. This page only contains the LICENSE text for PDFmorph
+
+.. title:: PDFmorph License
+
+.. literalinclude:: pdfmorph_license.txt
+   :language: text

products/pdfmorph_license.txt

@@ -0,0 +1,33 @@
+This program is part of the DiffPy open-source projects at Columbia
+University and is available subject to the conditions and terms laid out below.
+
+Copyright © 2009-2019, Trustees of Columbia University in the City of New York,
+all rights reserved.
+
+For more information please visit the diffpy web-page at http://diffpy.org or
+email Prof. Simon Billinge at [email protected].
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+  * Redistributions of source code must retain the above copyright notice, this
+    list of conditions and the following disclaimer.
+
+  * Redistributions in binary form must reproduce the above copyright notice,
+    this list of conditions and the following disclaimer in the documentation
+    and/or other materials provided with the distribution.
+
+  * Neither the names of COLUMBIA UNIVERSITY, MICHIGAN STATE UNIVERSITY nor the
+    names of their contributors may be used to endorse or promote products
+    derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.