diff --git a/_templates/menu01.html b/_templates/menu01.html index 82ad0bc7..a9ee97ab 100644 --- a/_templates/menu01.html +++ b/_templates/menu01.html @@ -13,6 +13,7 @@
  • PDFgui
  • SrMise
  • mPDF
  • +
  • xINTERPDF
  • Python Packages
  • diff --git a/abbreviations.txt b/abbreviations.txt index 167bfc08..ec41b1fd 100644 --- a/abbreviations.txt +++ b/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). diff --git a/images/xinterpdf.png b/images/xinterpdf.png new file mode 100644 index 00000000..f415044d Binary files /dev/null and b/images/xinterpdf.png differ diff --git a/index.rst b/index.rst index 12a55407..ec3275eb 100644 --- a/index.rst +++ b/index.rst @@ -83,3 +83,4 @@ centered at Columbia University and, before that, Michigan State University. products/pythonpackages products/SrMise products/mPDF + products/xinterpdf diff --git a/products/xinterpdf.rst b/products/xinterpdf.rst new file mode 100644 index 00000000..f14c70b2 --- /dev/null +++ b/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 + `__). +* 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 `__. + +.. 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 ` 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 diff --git a/products/xinterpdflicense.rst b/products/xinterpdflicense.rst new file mode 100644 index 00000000..a87b07c5 --- /dev/null +++ b/products/xinterpdflicense.rst @@ -0,0 +1,6 @@ +.. this page only contains the LICENSE text for xINTERPDF + +.. title:: xINTERPDF License + +.. literalinclude:: xinterpdflicense.txt + :language: text diff --git a/products/xinterpdflicense.txt b/products/xinterpdflicense.txt new file mode 100644 index 00000000..3a27e1df --- /dev/null +++ b/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. diff --git a/static_root/doc/xinterpdf/xINTERPDF_User_Guide_20180615.pdf b/static_root/doc/xinterpdf/xINTERPDF_User_Guide_20180615.pdf new file mode 100644 index 00000000..1c418924 Binary files /dev/null and b/static_root/doc/xinterpdf/xINTERPDF_User_Guide_20180615.pdf differ