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Manual installation instructions
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‎doc/manual/acknowledgements.texinfo‎

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‎doc/manual/disclaimer.texinfo‎

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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎doc/manual/pdfmorph.texinfo‎

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\input texinfo @c -*-texinfo-*-
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@documentencoding UTF-8
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@ifnottex
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@macro smallskip{}
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@vskip 6pt
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@end macro
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@macro medskip{}
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@vskip 12pt
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@end macro
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@macro bigskip{}
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@vskip 24pt
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@end macro
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@end ifnottex
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@macro EquationMark{}
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@html
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<!-- EquationMark -->
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@end html
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@end macro
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@macro ScreenShot{f}
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@center @image{\f\, 5in}
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@end macro
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@macro ReleaseDate{}
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June 2024
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@end macro
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@exampleindent 2
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@c start of header
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@setfilename pdfmorph
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@settitle PDFmorph, release 1.0, @ReleaseDate{}
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@c end of header
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@c Part 1: copying
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@copying
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Copyright 2009-2024, Board of Trustees of Columbia University in the city of New York.
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@end copying
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@c Part 2: title
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@titlepage
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@title PDFmorph user guide
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@subtitle 1.0 release
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@subtitle @ReleaseDate{}
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@author C. L. Farrow, C. J. Wright, P. Juhás, C.-H. Liu, T. Davis,
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@author S. M. Román, A. Yang, and S. J. L. Billinge
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@page
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@vskip 0pt plus 1filll
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@c @insertcopying
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@ifhtml
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@node acknowledgments
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@end ifhtml
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@heading Acknowledgments
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@cindex acknowledgments
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@include acknowledgements.texinfo
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@page
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@vskip 0pt plus 1filll
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@majorheading Preface
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@heading Redistribution
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@include redistribution.texinfo
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@heading Disclaimer
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@include disclaimer.texinfo
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@end titlepage
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@c Part 3: content
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@contents
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@c Make menu if html
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@ifhtml
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@node Top
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@top
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@menu
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* Introduction::
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* Installation::
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* Quick start tutorial::
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* Available morphs::
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* PDFmorph options::
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* Index::
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@end menu
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@end ifhtml
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@page
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@vskip 0pt plus 1filll
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@node Introduction, Installation, Top, Top
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@chapter Introduction
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@cindex introduction
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PDFmorph is a Python package that increases the insight researchers can
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obtain from measured atomic pair distribution functions (PDFs) in a
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model-independent way. It was originally designed to help a researcher
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answer a question: "Has my material undergone a phase transition between
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these two measurements?"
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@page
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@vskip 0pt plus 1filll
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@node Installation, Quick start tutorial, Introduction, Top
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@chapter Installation
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@cindex installation
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@menu
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* Availability::
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* Requirements::
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* Installation instructions::
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@end menu
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@node Availability, Requirements, Installation, Installation
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@section Availability
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@cindex availability
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PDFmorph is open source and distributed under the BSD license.
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It runs on Windows, Mac OS, Linux, and all major Unix systems.
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The source code is freely available at @url{https://github.com/diffpy/diffpy.pdfmorph}.
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@node Requirements, Installation instructions, Availability, Installation
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@section Requirements
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@cindex requirements
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PDFmorph is currently run from the command line, so it is recommended that users
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first familiarize themselves with their operating system's command line interface.
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PDFmorph currently requires Python 3.10 or higher to run. It also makes use of
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the following third party libraries:
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@itemize @bullet
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@item @url{https://numpy.org/, NumPy} - Python's fast scientific computing library
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@item @url{https://matplotlib.org/, Matplotlib} - Python plotting library
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@item @url{https://scipy.org/, SciPy} - Python's technical computing library
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@item @url{https://www.diffpy.org/diffpy.utils/, diffpy.utils}
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- @url{https://www.diffpy.org/, DiffPy} general utility functions
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@end itemize
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These dependencies will be installed automatically if you use the conda installation
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procedure described in the following section (@ref{Installation instructions}).
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@node Installation instructions, Quick start tutorial, Requirements, Installation
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@section Installation instructions
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@cindex installationinstrunctions
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We recommend installing the package and its dependencies using conda.
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Miniconda, a minimal installer for conda, can be downloaded
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@url{https://docs.anaconda.com/free/miniconda/, here}.
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Miniconda makes it easy to manage dependencies in isolated environments.
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Once Miniconda is installed, run @code{conda} on the command line
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to test that it has been installed properly.
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To create and activate a conda environment to use PDFmorph, run the following command.
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@example
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conda create -n pdfmorph_env python=3 --yes
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conda activate pdfmorph_env
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@end example
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A conda environment must be active to use the packages within.
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In future sessions, make sure to run @code{conda activate pdfmorph_env} to activate the
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environment before interacting with the PDFmorph program.
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Once active, you can install PDFmorph into your environment from the
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@url{https://conda-forge.org/, conda-forge} channel of Anaconda packages by running
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@example
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conda config --add channels conda-forge
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conda install diffpy.pdfmorph
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@end example
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This installation only needs to be done once. The next time you activate the environment,
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these packages will already be installed.
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When you are finished with the session, exit the environment by running
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@example
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conda deactivate pdfmorph_env
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@end example
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If you do not wish to use conda to install, PDFmorph is also available on the
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@url{https://pypi.org/, Python Package Index} or can be installed from source
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at @url{https://github.com/diffpy/diffpy.pdfmorph}. Note that these installation
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methods will require you to first install the dependencies listed in the previous section
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(@ref{Requirements}).
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@page
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@vskip 0pt plus 1filll
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@node Quick start tutorial, Available morphs, Installation, Top
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@chapter Quick start tutorial
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@cindex quickstarttutorial
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Download packaged tutorial files
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@page
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@vskip 0pt plus 1filll
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@node Available morphs, PDFmorph options, Quick start tutorial, Top
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@chapter Available morphs
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@cindex availablemorphs
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In this section, we detail a few use-cases for morphs
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@page
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@vskip 0pt plus 1filll
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@node PDFmorph options, Index, Available morphs, Top
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@chapter PDFmorph options
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@cindex pdfmorphoptions
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Explaination of options
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@c End TexInfo file
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@node Index, Top
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@unnumbered Index
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@printindex cp
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@bye

‎doc/manual/redistribution.texinfo‎

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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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@bigskip{}
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Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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@bigskip{}
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Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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@bigskip{}
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Neither the names of COLUMBIA UNIVERSITY, MICHIGAN STATE UNIVERSITY nor the
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names of their contributors may be used to endorse or promote products
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derived from this software without specific prior written permission.

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