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‎NSFnugget.html‎

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<li><a href="products/pdfgetx3.html">PDFgetX3</a></li>
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<li><a href="products/pdfgui.html">PDFgui</a></li>
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<li><a href="products/pythonpackages.html">Python Packages</a></li>
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<li><a href="products/SrMise.html">SrMise</a></li>
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</ul>
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‎_images/srmise_screenshot.png‎

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‎_sources/index.txt‎

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products/SrMise

‎_sources/products/SrMise.txt‎

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##########
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SrMise
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##########
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SrMise is the DiffPy tool for peak extraction and peak fitting from atomic
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pair distribution functions (PDFs). It implements a powerful
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information-theoretic multimodeling approach based on the Akaike information
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criterion (AIC) to generate and rank physically plausible sets of peaks even in
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the absence of a constraining structural model. This approach to peak
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extraction is premised upon PDFs reporting accurate experimentally-determined
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uncertainties, and when these are unavailable results are contingent on a
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user-specified *ad hoc* uncertainty.
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The software aids rapid analysis of crystalline and nanostructured
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materials. Reasonable values for nearly all program parameters can be
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estimated directly from the data, although the PDF baseline of non-crystalline
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materials requires user judgment. Crystalline (linear) and spherical
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nanoparticles baselines are included, but SrMise also supports arbitrary
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polynomial and interpolated baselines. Other key features include peak
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functions incorporating termination effects, standard uncertainty reporting, and
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a framework enabling a flexible AIC-driven multimodeling analysis. A
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command-line tool exposes basic peak extraction functionality, with full
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functionality available through Python scripting.
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.. figure:: ../images/srmise_screenshot.png
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:align: center
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This is an alpha release of SrMise, and the capabilities and documentation of
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the project will evolve. In particular, the multimodeling API is expected to
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change significantly in a future version. The DiffPy team encourages
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investigators to use the software even at this early stage, and invites
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feedback and suggestions.
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Getting Started
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------------------------------------------------------------------------
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The diffpy.srfit package requires Python 2.6 or 2.7 and the following software:
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* ``setuptools`` - software distribution tools for Python
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* ``NumPy`` - numerical mathematics and fast array operations for Python
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* ``SciPy`` - scientific libraries for Python
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* ``matplotlib`` - python plotting library
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On Ubuntu Linux, the required software can easily be installed using
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the system package manager::
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sudo apt-get install \
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python-setuptools python-numpy python-scipy python-matplotlib
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For Mac OS X systems with the MacPorts package manager, the required
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software can be installed with ::
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sudo port install \
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python27 py27-setuptools py27-numpy py27-scipy py27-matplotlib
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When installing for MacPorts, make sure the MacPorts bin directory is the first
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in the system PATH and that python27 is selected as the default Python version
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in MacPorts::
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sudo port select --set python python27
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For Windows systems, the easiest way to obtain ``setuptools`` if not already
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installed is downloading the ``pip`` setup script `get-pip.py
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<https://bootstrap.pypa.io/get-pip.py>`_ and running ::
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python get-pip.py
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It is recommended to install all other dependencies using prebuilt binaries.
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Visit http://www.scipy.org and http://www.matplotlib.org for instructions.
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Alternately, install a full Python distribution such as Python(x,y) or
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Enthought Canopy which already includes the required components.
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Installation
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------------------------------------------------------------------------
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The simplest way to obtain diffpy.srmise on Unix, Linux, and Mac systems (see the :doc:`license <SrMiselicense>` for terms and conditions of use) is
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using ``pip`` to download and install the latest release from the
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`Python Package Index <https://pypi.python.org>`_ (PyPI). ::
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sudo pip install diffpy.srmise
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If you prefer to install from sources, download them from the
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`GitHub <https://github.com/diffpy/diffpy.srmise/releases>`_ or
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`PyPI <https://pypi.python.org/pypi/diffpy.srmise>`_ pages for SrMise. Then
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run ::
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sudo python setup.py install
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This installs diffpy.srmise for all users in the default system location. If
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administrator (root) access is not available, see the usage info from
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``python setup.py install --help`` for options to install to user-writable
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directories.
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To install on Windows run either of the commands above omitting ``sudo``.
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What next?
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==========
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Explore the `SrMise examples <http://diffpy.github.io/diffpy.srmise/examples.html>`_!
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.. toctree::
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:hidden:
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SrMiselicense
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‎_sources/products/SrMiselicense.txt‎

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.. this page only contains the LICENSE text for SrMise
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.. include:: SrMise_LICENSE.txt
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:literal:

‎_sources/publications.txt‎

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* |citeJuhasAca15|
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* |citeGranlundAca15|
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* |citeJuhasJac13|
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* |citeFarrowJpcm07|

‎acknowledgements.html‎

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<li><a href="products/pdfgetx3.html">PDFgetX3</a></li>
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<li><a href="products/pdfgui.html">PDFgui</a></li>
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<li><a href="products/pythonpackages.html">Python Packages</a></li>
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<li><a href="products/SrMise.html">SrMise</a></li>
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</ul>
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</li>
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‎community.html‎

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<li><a href="products/pdfgetx3.html">PDFgetX3</a></li>
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<li><a href="products/pdfgui.html">PDFgui</a></li>
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<li><a href="products/pythonpackages.html">Python Packages</a></li>
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<li><a href="products/SrMise.html">SrMise</a></li>
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</ul>
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</li>
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‎index.html‎

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<li><a href="products/pdfgetx3.html">PDFgetX3</a></li>
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<li><a href="products/pdfgui.html">PDFgui</a></li>
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<li><a href="products/pythonpackages.html">Python Packages</a></li>
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<li><a href="products/SrMise.html">SrMise</a></li>
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</ul>
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</li>
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‎products/SrMise.html‎

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<!DOCTYPE html>
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<html xmlns="http://www.w3.org/1999/xhtml">
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<head>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title>SrMise &mdash; DiffPy documentation</title>
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<link rel="stylesheet" href="../_static/basic.css" type="text/css" />
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<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
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<link rel="stylesheet" href="../_static/bootswatch-3.1.0/cerulean/bootstrap.min.css" type="text/css" />
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<link rel="stylesheet" href="../_static/bootstrap-sphinx.css" type="text/css" />
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<link rel="stylesheet" href="../_static/diffpy-styles.css" type="text/css" />
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<script type="text/javascript">
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var DOCUMENTATION_OPTIONS = {
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URL_ROOT: '../',
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VERSION: '',
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COLLAPSE_INDEX: false,
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FILE_SUFFIX: '.html',
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HAS_SOURCE: true
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};
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</script>
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<script type="text/javascript" src="../_static/jquery.js"></script>
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<script type="text/javascript" src="../_static/underscore.js"></script>
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<script type="text/javascript" src="../_static/doctools.js"></script>
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<script type="text/javascript" src="../_static/js/jquery-1.11.0.min.js"></script>
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<script type="text/javascript" src="../_static/js/jquery-fix.js"></script>
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<script type="text/javascript" src="../_static/bootstrap-3.1.0/js/bootstrap.min.js"></script>
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<script type="text/javascript" src="../_static/bootstrap-sphinx.js"></script>
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<link rel="shortcut icon" href="../_static/diffpy_logo_header.ico"/>
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<link rel="top" title="DiffPy documentation" href="../index.html" />
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<link rel="next" title="&lt;no title&gt;" href="SrMiselicense.html" />
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<link rel="prev" title="Python Packages" href="pythonpackages.html" />
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<meta charset='utf-8'>
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<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
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<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
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<meta name="apple-mobile-web-app-capable" content="yes">
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</head>
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<body role="document">
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<div id="navbar" class="navbar navbar-inverse navbar-default navbar-fixed-top">
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<div class="container">
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<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse">
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</button>
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<a class="navbar-brand" href="../index.html"><img src="../_static/diffpy_logo_header.png">
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DiffPy</a>
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<span class="navbar-text navbar-version pull-left"><b></b></span>
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</div>
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<div class="collapse navbar-collapse nav-collapse">
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<ul class="nav navbar-nav">
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<li class="divider-vertical"></li>
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<li><a href="../community.html">Community</a></li>
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<li><a href="../publications.html">Publications</a></li>
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<li class="dropdown menu01-container">
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<a role="button"
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id="dLabelMenu01"
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data-toggle="dropdown"
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data-target="#"
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href="../index.html">Products <b class="caret"></b></a>
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<ul class="dropdown-menu menu01"
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role="menu"
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aria-labelledby="dLabelMenu01">
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<li><a href="diffpycmi/index.html">DiffPy-CMI</a></li>
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<li><a href="xPDFsuite.html">xPDFsuite</a></li>
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<li><a href="pdfgetx3.html">PDFgetX3</a></li>
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<li><a href="pdfgui.html">PDFgui</a></li>
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<li><a href="pythonpackages.html">Python Packages</a></li>
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<li><a href="#">SrMise</a></li>
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</ul>
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</li>
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</ul>
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<form class="navbar-form navbar-right" action="../search.html" method="get">
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<div class="form-group">
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<input type="text" name="q" class="form-control" placeholder="Search" />
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</div>
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<input type="hidden" name="check_keywords" value="yes" />
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<input type="hidden" name="area" value="default" />
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</form>
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</div>
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</div>
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</div>
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<div class="container">
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<div class="row">
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<div class="col-md-12">
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<div class="section" id="srmise">
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<h1>SrMise<a class="headerlink" href="#srmise" title="Permalink to this headline"></a></h1>
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<p>SrMise is the DiffPy tool for peak extraction and peak fitting from atomic
112+
pair distribution functions (PDFs). It implements a powerful
113+
information-theoretic multimodeling approach based on the Akaike information
114+
criterion (AIC) to generate and rank physically plausible sets of peaks even in
115+
the absence of a constraining structural model. This approach to peak
116+
extraction is premised upon PDFs reporting accurate experimentally-determined
117+
uncertainties, and when these are unavailable results are contingent on a
118+
user-specified <em>ad hoc</em> uncertainty.</p>
119+
<p>The software aids rapid analysis of crystalline and nanostructured
120+
materials. Reasonable values for nearly all program parameters can be
121+
estimated directly from the data, although the PDF baseline of non-crystalline
122+
materials requires user judgment. Crystalline (linear) and spherical
123+
nanoparticles baselines are included, but SrMise also supports arbitrary
124+
polynomial and interpolated baselines. Other key features include peak
125+
functions incorporating termination effects, standard uncertainty reporting, and
126+
a framework enabling a flexible AIC-driven multimodeling analysis. A
127+
command-line tool exposes basic peak extraction functionality, with full
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functionality available through Python scripting.</p>
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<div class="figure align-center">
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<img alt="../_images/srmise_screenshot.png" src="../_images/srmise_screenshot.png" />
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</div>
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<p>This is an alpha release of SrMise, and the capabilities and documentation of
133+
the project will evolve. In particular, the multimodeling API is expected to
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change significantly in a future version. The DiffPy team encourages
135+
investigators to use the software even at this early stage, and invites
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feedback and suggestions.</p>
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<div class="section" id="getting-started">
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<h2>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline"></a></h2>
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<p>The diffpy.srfit package requires Python 2.6 or 2.7 and the following software:</p>
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<ul class="simple">
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<li><code class="docutils literal"><span class="pre">setuptools</span></code> - software distribution tools for Python</li>
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<li><code class="docutils literal"><span class="pre">NumPy</span></code> - numerical mathematics and fast array operations for Python</li>
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<li><code class="docutils literal"><span class="pre">SciPy</span></code> - scientific libraries for Python</li>
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<li><code class="docutils literal"><span class="pre">matplotlib</span></code> - python plotting library</li>
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</ul>
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<p>On Ubuntu Linux, the required software can easily be installed using
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the system package manager:</p>
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<div class="highlight-python"><div class="highlight"><pre>sudo apt-get install \
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python-setuptools python-numpy python-scipy python-matplotlib
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</pre></div>
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</div>
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<p>For Mac OS X systems with the MacPorts package manager, the required
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software can be installed with</p>
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<div class="highlight-python"><div class="highlight"><pre>sudo port install \
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python27 py27-setuptools py27-numpy py27-scipy py27-matplotlib
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</pre></div>
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</div>
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<p>When installing for MacPorts, make sure the MacPorts bin directory is the first
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in the system PATH and that python27 is selected as the default Python version
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in MacPorts:</p>
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<div class="highlight-python"><div class="highlight"><pre>sudo port select --set python python27
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</pre></div>
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</div>
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<p>For Windows systems, the easiest way to obtain <code class="docutils literal"><span class="pre">setuptools</span></code> if not already
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installed is downloading the <code class="docutils literal"><span class="pre">pip</span></code> setup script <a class="reference external" href="https://bootstrap.pypa.io/get-pip.py">get-pip.py</a> and running</p>
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<div class="highlight-python"><div class="highlight"><pre>python get-pip.py
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</pre></div>
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</div>
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<p>It is recommended to install all other dependencies using prebuilt binaries.
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Visit <a class="reference external" href="http://www.scipy.org">http://www.scipy.org</a> and <a class="reference external" href="http://www.matplotlib.org">http://www.matplotlib.org</a> for instructions.
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Alternately, install a full Python distribution such as Python(x,y) or
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Enthought Canopy which already includes the required components.</p>
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</div>
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<div class="section" id="installation">
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<h2>Installation<a class="headerlink" href="#installation" title="Permalink to this headline"></a></h2>
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<p>The simplest way to obtain diffpy.srmise on Unix, Linux, and Mac systems (see the <a class="reference internal" href="SrMiselicense.html"><em>license</em></a> for terms and conditions of use) is
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using <code class="docutils literal"><span class="pre">pip</span></code> to download and install the latest release from the
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<a class="reference external" href="https://pypi.python.org">Python Package Index</a> (PyPI).</p>
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<div class="highlight-python"><div class="highlight"><pre>sudo pip install diffpy.srmise
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</pre></div>
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</div>
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<p>If you prefer to install from sources, download them from the
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<a class="reference external" href="https://github.com/diffpy/diffpy.srmise/releases">GitHub</a> or
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<a class="reference external" href="https://pypi.python.org/pypi/diffpy.srmise">PyPI</a> pages for SrMise. Then
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run</p>
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<div class="highlight-python"><div class="highlight"><pre>sudo python setup.py install
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</pre></div>
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</div>
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<p>This installs diffpy.srmise for all users in the default system location. If
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administrator (root) access is not available, see the usage info from
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<code class="docutils literal"><span class="pre">python</span> <span class="pre">setup.py</span> <span class="pre">install</span> <span class="pre">--help</span></code> for options to install to user-writable
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directories.</p>
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<p>To install on Windows run either of the commands above omitting <code class="docutils literal"><span class="pre">sudo</span></code>.</p>
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<div class="section" id="what-next">
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<h3>What next?<a class="headerlink" href="#what-next" title="Permalink to this headline"></a></h3>
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<p>Explore the <a class="reference external" href="http://diffpy.github.io/diffpy.srmise/examples.html">SrMise examples</a>!</p>
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<div class="toctree-wrapper compound">
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</div>
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