Add xinterpdf

_templates/menu01.html

@@ -13,6 +13,7 @@
       <li><a href="{{pathto('products/pdfgui')}}">PDFgui</a></li>
       <li><a href="{{pathto('products/SrMise')}}">SrMise</a></li>
       <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>
   </ul>
 </li>

abbreviations.txt

@@ -1,5 +1,11 @@
 .. vim: set ft=rst:
 
+.. Named web links -----------------------------------------------------
+
+.. _diffpy-users: https://groups.google.com/d/forum/diffpy-users
+
+.. Citations -----------------------------------------------------------
+
 .. |citeJuhasJac13| replace::
    P. Juhás and T. Davis, C. L. Farrow, S. J. L. Billinge, `PDFgetX3:
    A rapid and highly automatable program for processing powder
@@ -238,3 +244,10 @@
 .. |JensenNc16title| replace::
    Polymorphism in magic-sized Au\ :sub:`144`\ (SR)\ :sub:`60` clusters
 .. _JensenNc16title: http://dx.doi.org/10.1038/ncomms11859
+
+
+.. |citeShiJac18| replace::
+   C. Shi,
+   xINTERPDF: a GUI program for analyzing intermolecular pair
+   distribution functions of organic compounds from X-ray total
+   scattering data, under review, *J. Appl. Crystallogr.*, (2018).

index.rst

@@ -83,3 +83,4 @@ centered at Columbia University and, before that, Michigan State University.
    products/pythonpackages
    products/SrMise
    products/mPDF
+   products/xinterpdf

products/xinterpdf.rst

@@ -0,0 +1,99 @@
+#########
+xINTERPDF
+#########
+
+xINTERPDF is a Python GUI program for analyzing X-ray pair distribution
+function (PDF) data of organic compounds collected at synchrotron and/or
+laboratory X-ray sources. It uses DiffPy-CMI as a backend for simulation
+of PDFs.
+
+Currently it supports:
+
+* The study of intermolecular interaction (e.g. hydrogen bonds) by
+  subtracting out the scattering signal(s) of single molecule(s) in real
+  space.
+* The PDF model fit of the crystalline organic compound using the method
+  proposed by Prill *et al*. (`J. Appl. Crystallogr., 48, 171-178, 2015
+  <http://scripts.iucr.org/cgi-bin/paper?S1600576714026454>`__).
+* The phase quantification of physical mixtures of organics.
+* Generate Score/Scree plots based on Principle Component Analysis (PCA).
+
+A video demo about installation and usage is available at
+https://www.youtube.com/watch?v=lAFZ5VYEH1g. The code for xINTERPDF
+is hosted on `GitHub <https://github.com/curieshicy/xINTERPDF>`__.
+
+.. figure:: ../images/xinterpdf.png
+   :align: center
+
+This is a first release of the program (v.0.1.0). Comments and
+suggestions are welcome. Please send an email to Chenyang Shi at
+cs3000@columbia.edu or post your questions to `diffpy-users`_
+Google Group.
+
+Getting Started
+===============
+
+The xINTERPDF package requires Python 2.7 and the following dependency packages:
+
+* ``NumPy`` - Numerical mathematics and fast array operations for Python
+* ``SciPy`` - Scientific libraries for Python
+* ``matplotlib`` - Python plotting library
+* ``Scikit-Learn`` - Python machine learning library; its PCA module is called.
+* ``diffpy-cmi`` - Versatile Python packages for simulation of atomic pair distribution functions
+* ``Tkinter`` - Python default library for creation of graphical user interface
+
+See the :doc:`xINTERPDF license <xinterpdflicense>` for terms and conditions of use.
+
+Installation
+------------
+
+xINTERPDF can be installed on Linux and Mac OS machines. The recommended
+way to install this package is through conda. Please visit
+https://www.continuum.io/downloads, and select Python 2.7 version
+to download and install. Once conda is installed, you can follow the
+steps below to install xINTERPDF.
+
+*Step 1: Add the diffpy conda channel to your conda configuration.* ::
+
+    conda config --add channels diffpy
+
+*Step 2: Create a virtural environment and install the program there.* ::
+
+    conda create –c curieshicy –n xinterpdf xinterpdf
+
+This command first adds a *curieshicy* channel, then creates a virtual
+environment *xinterpdf*, before finally install the *xinterpdf* program.
+Note that you can name the environment anything you choose by passing it
+a different name after the *-n* flag in the command.
+
+*Step 3: Activate the virtual environment and start the program.* ::
+
+    source activate xinterpdf
+    xinterpdf
+
+The first command starts the virtual environment and the second invokes
+the main GUI window of the xINTERPDF program.
+
+User Guide
+----------
+
+Please see `user manual <../doc/xinterpdf/xINTERPDF_User_Guide_20180615.pdf>`__
+for more details.
+
+References
+----------
+
+If you use this software in a research work which leads to publication,
+we ask you to acknowledge the use of xINTERPDF by citing the following
+papers:
+
+* |citeShiJac18|
+* |citeJuhasAca15|
+
+
+.. include:: ../abbreviations.txt
+
+.. toctree::
+   :hidden:
+
+   xinterpdflicense

products/xinterpdflicense.rst

@@ -0,0 +1,6 @@
+.. this page only contains the LICENSE text for xINTERPDF
+
+.. title:: xINTERPDF License
+
+.. literalinclude:: xinterpdflicense.txt
+   :language: text

products/xinterpdflicense.txt

@@ -0,0 +1,59 @@
+If you use this program to do productive scientific research that
+leads to publication, we ask that you acknowledge use of the
+program by citing the following papers in your publication:
+
+    * Chenyang Shi, "xINTERPDF: a GUI program for analyzing intermolecular
+      pair distribution functions of organic compounds from X-ray total
+      scattering data", under review, J. Appl. Cryst., 2018.
+
+    * Pavol Juhás, Christopher L. Farrow, Xiaohao Yang, Kevin R. Knox,
+      and Simon J. L. Billinge, "Complex modeling: a strategy and software
+      program for combining multiple information sources to solve ill posed
+      structure and nanostructure inverse problems",
+      Acta Crystallogr. A, 71, 562-568, 2015.
+
+Copyright (c) 2009-2011, University of Tennessee
+Copyright (c) 1989, 1991 Free Software Foundation, Inc.
+Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP")
+Copyright (c) 2006-2007, Board of Trustees of Michigan State University
+Copyright (c) 2008-2012, The Trustees of Columbia University in the City
+    of New York
+Copyright (c) 2014-2016, Brookhaven Science Associates, Brookhaven National
+    Laboratory
+Copyright (c) 2014-2018, AbbVie Inc.
+
+For more information please visit the diffpy web-page at
+    http://www.diffpy.org
+or email Chenyang Shi at cs3000@columbia.edu, or Prof. Simon
+Billinge at sb2896@columbia.edu.
+
+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 name of the copyright holder nor the names of its
+    contributors may be used to endorse or promote products derived from
+    this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY COPYRIGHT HOLDER "AS IS". COPYRIGHT
+HOLDER EXPRESSLY DISCLAIMS ANY AND ALL WARRANTIES AND CONDITIONS,
+EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY, TITLE, FITNESS, ADEQUACY OR
+SUITABILITY FOR A PARTICULAR PURPOSE, AND ANY WARRANTIES OF FREEDOM
+FROM INFRINGEMENT OF ANY DOMESTIC OR FOREIGN PATENT, COPYRIGHTS,
+TRADE SECRETS OR OTHER PROPRIETARY RIGHTS OF ANY PARTY. IN NO EVENT
+SHALL COPYRIGHT HOLDER BE LIABLE TO ANY PARTY 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 OR RELATING TO
+THIS AGREEMENT, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.