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‎_sources/NSFnugget.txt‎

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@@ -3,40 +3,39 @@ Enabling new science in nanoscale structure characterization of complex material
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.. include:: abbreviations.txt
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6-
*C. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch,
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*C. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch,
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and S. J. L. Billinge (Michigan State University)*
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9-
To understand and control the properties of materials it is necessary to have
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a detailed knowledge of their atomic structure. Increasingly, we are interested
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in exploiting materials with complex structures on the nanoscale, which presents
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special experimental challenges as crystallography, the standard approach to
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structure determination, loses its power on these length-scales. Alternative
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methods sensitive to nanoscale order are under development. The diffraction
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sub-group of the DANSE project recently released a new software tool that
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will have a large impact in nanostructure characterization using x-ray and
9+
To understand and control the properties of materials it is necessary to have
10+
a detailed knowledge of their atomic structure. Increasingly, we are interested
11+
in exploiting materials with complex structures on the nanoscale, which presents
12+
special experimental challenges as crystallography, the standard approach to
13+
structure determination, loses its power on these length-scales. Alternative
14+
methods sensitive to nanoscale order are under development. The diffraction
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sub-group of the DANSE project recently released a new software tool that
16+
will have a large impact in nanostructure characterization using x-ray and
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neutron diffraction.
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2020

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.. figure:: images/PDFgui_screenshot_707.png
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:align: center
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:scale: 50 %
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:scale: 50 %
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Screen-shot of PDFgui during a refinement of multiple data-sets
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The diffraction data are Fourier transformed to obtain the atomic pair distribution
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function (PDF) and analyzed by quantitatively fitting nanostructure models to the
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data. PDFgui allows rapid setup of individual and multiple
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refinements. This program will be implemented at the
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POWGEN3 and NOMAD diffractometers at SNS with macros to allow real-time parametric
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refinements similar to those shown, allowing researchers to make scientific
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discoveries during data collection, at the beam-time, and not a-posteriori after
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the beamtime is over. PDFgui has numerous extensions
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that are described in more detail in [#]_. The beta version of PDFgui
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is now in public release, available for Windows, Linux and Mac OSX platforms,
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and in the first month has been downloaded 220 times. More information can be
28+
The diffraction data are Fourier transformed to obtain the atomic pair distribution
29+
function (PDF) and analyzed by quantitatively fitting nanostructure models to the
30+
data. PDFgui allows rapid setup of individual and multiple
31+
refinements. This program will be implemented at the
32+
POWGEN3 and NOMAD diffractometers at SNS with macros to allow real-time parametric
33+
refinements similar to those shown, allowing researchers to make scientific
34+
discoveries during data collection, at the beam-time, and not a-posteriori after
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the beamtime is over. PDFgui has numerous extensions
36+
that are described in more detail in [#]_. The beta version of PDFgui
37+
is now in public release, available for Windows, Linux and Mac OSX platforms,
38+
and in the first month has been downloaded 220 times. More information can be
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found at http://www.diffpy.org.
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.. [#] |citeFarrowJpcm07|
42-

‎_sources/acknowledgements.txt‎

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@@ -1,4 +1,4 @@
1-
Acknowledgements
1+
Acknowledgements
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================
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@@ -34,4 +34,4 @@ Additional Contributions
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The DiffPy team would like to thank multiple users for their help and
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comments during the development of this release: Dragica Podgorski,
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Valentina Felsen, and Kirsten M. Ø. Jensen.
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Valentina Felsen, and Kirsten M. Ø. Jensen.

‎_sources/community.txt‎

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@@ -1,12 +1,12 @@
11
Community
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=========
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To ensure a bright future for the DiffPy project it is essential to build a strong community
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of users and contributing developers. There are several Google groups for support and
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To ensure a bright future for the DiffPy project it is essential to build a strong community
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of users and contributing developers. There are several Google groups for support and
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development of DiffPy and related applications.
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- `diffpy-users <https://groups.google.com/d/forum/diffpy-users>`_ Help on usage of DiffPy-CMI, PDFgetX3,
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PDFgui, and other DiffPy components. This group is a knowledge base for PDFgui
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- `diffpy-users <https://groups.google.com/d/forum/diffpy-users>`_ Help on usage of DiffPy-CMI, PDFgetX3,
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PDFgui, and other DiffPy components. This group is a knowledge base for PDFgui
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user tips, tricks and troubleshooting. Feel free to search for answers or ask your question here.
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.. raw:: html
@@ -15,9 +15,9 @@ development of DiffPy and related applications.
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<input type="submit" name="sub" value="Subscribe">
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</form>
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- `diffpy-dev <https://groups.google.com/d/forum/diffpy-dev>`_ For bug reports, feature requests, and discussions about development
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and changes of DiffPy-CMI, PDFgetX3,
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PDFgui, and other DiffPy components. Materials scientists, chemists
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- `diffpy-dev <https://groups.google.com/d/forum/diffpy-dev>`_ For bug reports, feature requests, and discussions about development
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and changes of DiffPy-CMI, PDFgetX3,
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PDFgui, and other DiffPy components. Materials scientists, chemists
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physicists, engineers - please contribute by telling us your needs or sharing your suggestions here.
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.. raw:: html
@@ -28,7 +28,7 @@ development of DiffPy and related applications.
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|
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You can also share your comments, suggestions, praise or complaints by sending email to
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You can also share your comments, suggestions, praise or complaints by sending email to
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`Simon J. L. Billinge <sb2896@columbia.edu>`_.
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To report or browse bugs, please use the link at the top of this page.

‎_sources/index.txt‎

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DiffPy - Atomic Structure Analysis in Python
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DiffPy - Atomic Structure Analysis in Python
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============================================
2020
A free and open source software project to provide python software for
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diffraction analysis and the study of the atomic structure of materials.
@@ -29,14 +29,14 @@ diffraction analysis and the study of the atomic structure of materials.
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.. include:: abbreviations.txt
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DiffPy is the home of the |DiffPyCMI|
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Complex Modeling framework, a modular software framework for robust and extensible
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modeling of diffraction data. We welcome contributions to this project from the
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Complex Modeling framework, a modular software framework for robust and extensible
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modeling of diffraction data. We welcome contributions to this project from the
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community.
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The project is currently centered at `Brookhaven National Laboratory`_, a US `Department of
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Energy, Office of Basic Energy Sciences`_ funded laboratory.
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The project is currently centered at `Brookhaven National Laboratory`_, a US `Department of
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Energy, Office of Basic Energy Sciences`_ funded laboratory.
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Many parts of the code were developed under the diffraction part of the DANSE_ project,
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a software construction project funded by the `National Science Foundation`_ to provide
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a software construction project funded by the `National Science Foundation`_ to provide
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data analysis software tools for neutron scattering experiments. This project was previously
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centered at Columbia University and, before that, Michigan State University.
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:height: 10
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.. figure:: logos/BNL_logo.jpg
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:align: left
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:align: left
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:target: `Brookhaven National Laboratory`_
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.. figure:: logos/DOE_logo.png
@@ -80,5 +80,5 @@ centered at Columbia University and, before that, Michigan State University.
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products/xPDFsuite
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products/pdfgui
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products/pdfgetx3
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products/pythonpackages
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products/pythonpackages
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products/SrMise

‎_sources/products/SrMise.txt‎

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@@ -46,7 +46,7 @@ The diffpy.srmise package requires Python 2.6 or 2.7 and the following software:
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* ``matplotlib`` - python plotting library
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See the :doc:`SrMise license <SrMiselicense>` for terms and conditions of use.
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Detailed installation instructions for the :ref:`Windows <windows_install>`,
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Detailed installation instructions for the :ref:`Windows <windows_install>`,
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:ref:`Mac OS X <macosx_install>`, and :ref:`Linux <linux_install>`
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platforms follow.
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The simplest way to obtain diffpy.srmise on Mac OS X systems
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is using ``pip`` to download and install the latest release from
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`PyPI <https://pypi.python.org>`_. ::
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`PyPI <https://pypi.python.org>`_. ::
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sudo pip install diffpy.srmise
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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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This installs diffpy.srmise for all users in the default system location. If
135+
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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.. _linux_install:
@@ -155,7 +155,7 @@ For other Linux distributions consult the appropriate package manager.
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The simplest way to obtain diffpy.srmise on Linux systems
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is using ``pip`` to download and install the latest release from
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`PyPI <https://pypi.python.org>`_. ::
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`PyPI <https://pypi.python.org>`_. ::
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sudo pip install diffpy.srmise
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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
169+
This installs diffpy.srmise for all users in the default system location. If
170+
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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:hidden:
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SrMiselicense
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‎_sources/products/diffpycmi/cmi_exchange.txt‎

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@@ -33,7 +33,7 @@ You'll notice that there are two directories: ``cmi_plugins`` and
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``cmi_scripts``. The scripts are standalone python scripts that can be
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run directly from the `IPython`_ command line, whereas the plugins are a
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set of functions and `IPython extensions`_
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that provide additional functionality to your IPython session.
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that provide additional functionality to your IPython session.
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Scripts
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^^^^^^^
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activated from the IPython command line by running::
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In [1]: %install_ext name_of_extension.py
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In [2]: %load_ext name_of_extenstion
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In [2]: %load_ext name_of_extenstion
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.. _ipython: http://ipython.org/
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To contribute your own script to the CMI Exchange you must first fork
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the project on github. Once you've added your own code you can issue a
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pull request.
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pull request.
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If you're new to git and don't know what it means to fork a project
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`begin here <https://help.github.com/articles/fork-a-repo>`_.

‎_sources/products/diffpycmi/contents.txt‎

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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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`diffpy.srfit`_ Setup and control of general fitting
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problems.
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`diffpy.srreal`_ Python library for calculation of pair based
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quantities such as the pair distribution
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function (PDF), bond lengths, and bond
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`diffpy.srreal`_ Python library for calculation of pair based
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quantities such as the pair distribution
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function (PDF), bond lengths, and bond
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valence sums.
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`diffpy.Structure`_ Handles storage of crystal structure data.
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`diffpy.utils`_ General purpose shared utilities for the
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`diffpy.Structure`_ Handles storage of crystal structure data.
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`diffpy.utils`_ General purpose shared utilities for the
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diffpy libraries.
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`pyobjcryst`_ Python bindings to the ObjCryst++
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`pyobjcryst`_ Python bindings to the ObjCryst++
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Object-Oriented Crystallographic
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Library.
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`libdiffpy`_ C++ library for calculation of PDF and
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`libdiffpy`_ C++ library for calculation of PDF and
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other real-space quantities.
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====================== ============================================
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.. _libobjcryst: https://github.com/diffpy/libobjcryst
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External libraries
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External libraries
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-------------------
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====================== ============================================
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Module Description
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====================== ============================================
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`periodictable`_ Extensible periodic table of the elements
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with support for mass, density, and
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`periodictable`_ Extensible periodic table of the elements
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with support for mass, density, and
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X-ray/neutron scattering information.
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‎_sources/products/diffpycmi/contributecode.txt‎

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====================== ============================================
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Module Description
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`diffpy.srfit`_ Setup and control of general fitting
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`diffpy.srfit`_ Setup and control of general fitting
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problems.
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`diffpy.srreal`_ Python library for calculation of pair based
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quantities such as the pair distribution
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function (PDF), bond lengths, and bond
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`diffpy.srreal`_ Python library for calculation of pair based
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quantities such as the pair distribution
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function (PDF), bond lengths, and bond
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valence sums.
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`diffpy.Structure`_ Handles storage of crystal structure data.
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`diffpy.utils`_ General purpose shared utilities for the
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`diffpy.Structure`_ Handles storage of crystal structure data.
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`diffpy.utils`_ General purpose shared utilities for the
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diffpy libraries.
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`pyobjcryst`_ Python bindings to the ObjCryst++
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`pyobjcryst`_ Python bindings to the ObjCryst++
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Object-Oriented Crystallographic
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Library.
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`libdiffpy`_ C++ library for calculation of PDF and
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`libdiffpy`_ C++ library for calculation of PDF and
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other real-space quantities.
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`libobjcryst`_ ObjCryst++ re-packaged for installation
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`libobjcryst`_ ObjCryst++ re-packaged for installation
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as a shared library
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====================== ============================================
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.. _libdiffpy: https://github.com/diffpy/libdiffpy
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.. _libobjcryst: https://github.com/diffpy/libobjcryst
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‎_sources/products/diffpycmi/updatesources.txt‎

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For Fedora use ``yum``::
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sudo yum install \
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gsl-devel boost-devel python-devel
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gsl-devel boost-devel python-devel
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python-setuptools numpy scipy \
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python-matplotlib python-lxml \
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python-ipython-notebook scons git zsh \
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To update the codes::
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./install --update[=steps]
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This will perform all or selected software updates from online source repositories.
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Update steps are comma separated integers or ranges such as '1,3,5-6'.
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./install --update[=steps]
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This will perform all or selected software updates from online source repositories.
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Update steps are comma separated integers or ranges such as '1,3,5-6'.
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To rebuild the source code::
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./install --build[=steps]
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./install --build[=steps]
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This will rebuild all or specified packages from sources in the src folder. In both
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cases, you could use option -n to display the build steps.
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