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_templates/menu01.html

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<li><a href="{{pathto('products/SrMise')}}">SrMise</a></li>
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<li><a href="{{pathto('products/mPDF')}}">mPDF</a></li>
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<li><a href="{{pathto('products/xinterpdf')}}">xINTERPDF</a></li>
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<li><a href="{{pathto('products/pythonpackages')}}">Python Packages</a></li>
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<li><a href="{{pathto('products/pdfmorph')}}">PDFmorph</a></li>
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<li><a href="{{pathto('products/pythonpackages')}}">Python Packages</a></li>
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</ul>
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</li>

products/pdfmorph.rst

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========
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.. note::
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The PDFmorph application has a Command Line Interface. If you
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are unfamiliar with the terminal or windows command prompt, it
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is recommended that you consult online resources and become
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somewhat familiar before using PDFmorph.
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PDFmorph is a Python software package designed to increase the insight
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researchers can obtain from measured atomic pair distribution functions
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(PDFs) in a model-independent way. The program was designed to help a
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researcher answer the question: Has my material undergone a phase
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transition between these two measurements?
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PDFmorph makes use of several data manipulation techniques to correct
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for benign effects such as thermal expansion and increased thermal
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motion before computing and plotting a difference curve between two PDFs.
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One PDF is identified as the "target" PDF and the second is "morphed"
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by "stretching", "smearing", and "scaling". PDFmorph will vary amplitude
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of morphing transformations to obtain the best fit between morphed and
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target PDFs, then plot them along with the difference curve plotted
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below.
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PDFmorph is currently run from the command line, which requires
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opening and typing into a terminal window or Windows command
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prompt. It is recommended that you consult online resources and
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become somewhat familiar before using PDFmorph.
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PDFmorph is a Python software package designed to increase the insight
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researchers can obtain from measured atomic pair distribution functions
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(PDFs) in a model-independent way. The program was designed to help a
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researcher answer the question: "Has my material undergone a phase
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transition between these two measurements?"
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PDFmorph makes use of several data manipulation techniques to correct
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for benign effects such as thermal expansion (peak shift) and increased
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thermal motion (peak broadening) or a cahnge in scale due to differences
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in incident flux, for example. PDFmorph will do its best to correct
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for these benign effects before computing and plotting a difference
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curve.
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One PDF (typically that collected at higher temperature) is identified
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as the "target" PDF and the second is "morphed" by "stretching" (changing
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the r-axis to simulate a uniform lattice expansion), "smearing"
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(broadening peaks through a uniform convolution to simulate increased
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thermal motion), and "scaling" (self-explanatory). PDFmorph will vary
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amplitude of morphing transformations to obtain the best fit between
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morphed and target PDFs, then plot them along with the difference curve
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plotted below.
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There are also a few other morphing transformations in the program.
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Finally, we note that PDFmorph should work on other spectra that are
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Finally, we note that PDFmorph should work on other spectra that are
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not PDFs, though it has not been extensively tested beyond the PDF.
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.. 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.
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.. figure:: ../images/pdfmorph_nacl_ex.png
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:align: center
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Transformation techniques (scale, smear, and stretch, respectively)
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Transformation techniques (scale, smear, and stretch, respectively)
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utilized by PDFmorph applied sequentially on an NaCl sample
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Installation
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============
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By downloading and using this software, you are agreeing to the conditions
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By downloading and using this software, you are agreeing to the conditions
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specified in the :doc:`software license <pdfmorph_license>`.
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PDFmorph is distributed using conda. To install software using conda
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you will first have to download and install ``Anaconda`` or ``mini-conda``
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In order to take automatically take care of software dependency
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downloads, we recomment you install PDFmorph using conda. To do that,
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you will first have to download and install *Anaconda* or *mini-conda*
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from `continuum <https://www.continuum.io>`__.
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PDFmorph is available for all operating systems supported by Anaconda,
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PDFmorph is available for all operating systems supported by Anaconda,
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namely for 32 and 64-bit Linux, Mac OS X, and 32 and 64-bit Windows.
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.. note::
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We recommend that you run PDFmorph in a Python 3 conda virtual
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environment. With Anaconda or mini-conda installed on your system,
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environment. With Anaconda or mini-conda installed on your system,
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first create the virtual environment by typing ::
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conda create --name=py3 python=3
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conda create --name=<env_name> python=3
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You can give the environment any name you like but it should
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have some Python version 3 installed. You only need to create
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the environment once, but every time you want to use PDFmorph
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you will have to activate the environment in which it is installed
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by typing ::
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You can give the environment any name you like but it should
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have some Python version 3 installed (though PDFmorph also works
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on Python 2.7). You only need to create the environment once,
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but every time you want to use PDFmorph you will have to
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reactivate the environment in which it is installed by typing ::
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source activate py3
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on Mac/Linux, or ::
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activate py3
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source activate <env_name>
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on Windows.
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on Mac/Linux, or ``activate <env_name>`` on Windows.
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PDFmorph is available from the "conda-forge" channel of Anaconda packages.
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Open a *Terminal* window or *Anaconda Command Prompt* on Windows and
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install PDFmorph using the :program:`conda` command ::
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Once you're in your desired conda environment, you can install PDFmorph
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from either the ``diffpy`` or ``conda-forge`` channels of Anaconda packages
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by running opening a *Terminal* window or *Anaconda Command Prompt*
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on Windows and using the :program:`conda` command ::
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conda config --add channels conda-forge
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conda install diffpy.pdfmorph
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And it should be installed! To make sure that installation has completed
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correctly, run the following command from your relevant conda environment ::
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If you prefer to install from the diffpy channel, simply replace
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``conda-forge`` with ``diffpy`` in the commands above.
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By then it should be installed! To make sure that installation has
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completed correctly, run the following command from your PDFmorph-equipped
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conda environment ::
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pdfmorph --version
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This command should return PDFmorph's current version number.
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This command should return the version of PDFmorph you have on your
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machine.
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PDFmorph Updates
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================
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The Anaconda package system makes it easy to prepare and distribute
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software packages and bugfixes. To update the latest version of PDFmorph,
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The Anaconda package system makes it easy to prepare and distribute
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software packages and bugfixes. To update the latest version of PDFmorph,
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use ::
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conda update diffpy.pdfmorph
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With other Python distributions, the program can be updated to the
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With other Python distributions, the program can be updated to the
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latest version with ::
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easy_install --upgrade diffpy.pdfmorph
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Documentation/Help
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==================
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0.0.1 - latest
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0.1.0 - latest
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----------------------
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* User manual (available in HTML and PDF)
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* Installation instructions
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* `Sample PDF files <https://github.com/diffpy/diffpy.pdfmorph/tree/master/tests/testdata>`__
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* Tutorial
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* Please, join the :doc:`community forum <../community>` for tips,
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* Please, join the :doc:`community forum <../community>` for tips,
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tricks, and feedback.
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.. References// # update upon paper resease
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.. toctree::
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:hidden:
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pdfmorph_license

products/pdfmorph_license.txt

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This program is part of the DiffPy open-source projects at Columbia
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University and is available subject to the conditions and terms laid out below.
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This program is part of the DiffPy open-source project at Columbia
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University and is available subject to the conditions and terms laid
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out below.
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Copyright © 2009-2019, Trustees of Columbia University in the City of New York,
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all rights reserved.
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Copyright © 2009-2019, Trustees of Columbia University in the City of
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New York, all rights reserved.
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For more information please visit the diffpy web-page at http://diffpy.org or
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email Prof. Simon Billinge at [email protected].
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For more information please visit the diffpy web-page at
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http://diffpy.org or email Prof. Simon Billinge at [email protected].
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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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modification, are permitted provided that the following conditions are
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met:
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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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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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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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* Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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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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* The name of COLUMBIA UNIVERSITY nor the names of its contributors
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may be used to endorse or promote products derived from this
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software without specific prior written permission.
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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.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
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IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
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TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
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PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
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TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

products/pythonpackages.rst

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This is a complete list of all Python packages developed by the DiffPy
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team. For more information about a specific package, follow the link to
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the corresponding github page. With the exception of PDFfit2, SrMise,
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and mPDF, all of the packages listed below are bundled in the |DiffPyCMI|
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release.
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mPDF, and PDFmorph, all of the packages listed below are bundled in the
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|DiffPyCMI| release.
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====================== ============================================
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Module Description
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====================== ============================================
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`diffpy.srfit`_ Setup and control of general fitting
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problems.
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`diffpy.mpdf`_ Tools for calculating and refining magnetic
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PDFs.
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`diffpy.pdfmorph`_ Tools for comparing and manipulating two
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PDFs.
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====================== ============================================
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.. _diffpy.srfit: https://github.com/diffpy/diffpy.srfit
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.. _diffpy.mpdf: https://github.com/benfrandsen/diffpy.magpdf
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.. _diffpy.pdfmorph: https://github.com/diffpy/diffpy.pdfmorph
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.. include:: ../abbreviations.txt

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