GUI for PDF simulation and structure refinement.
Project description
PDFgui
Graphical user interface program for structure refinements to atomic pair distribution function.
PDFgui is a friendly interface to PDFfit2 refinement engine, with many powerful extensions. To get started, please open the manual from the help menu and follow the tutorial instructions. A detailed description is available in the doc/Farrow-jpcm-2007.pdf paper.
REQUIREMENTS
PDFgui requires Python 2.7 and several third-party libraries that are used by PDFgui and its components.
setuptools - tools for installing Python packages
wxpython - graphical user interface toolkit for Python
NumPy - library for scientific computing with Python
matplotlib - Python 2D plotting library
diffpy.pdffit2 - computational engine for PDFgui, https://github.com/diffpy/diffpy.pdffit2
diffpy.Structure - simple storage and manipulation of atomic structures, https://github.com/diffpy/diffpy.Structure
diffpy.utils - shared helper utilities for wx GUI, https://github.com/diffpy/diffpy.utils
We recommend to use Anaconda Python which allows to conveniently install PDFgui and all its software dependencies with a single command. For other Python distributions it is necessary to install the required software separately. As an example, on Ubuntu Linux some of the required software can be installed using
sudo apt-get install \ python-setuptools python-wxtools python-numpy \ python-matplotlib
To install the remaining packages see the installation instructions at their respective web pages.
INSTALLATION
The preferred method is to use Anaconda Python and install from the “diffpy” channel of Anaconda packages
conda config --add channels diffpy conda install diffpy.pdfgui
PDFgui can be then started from a terminal (“Anaconda Prompt” on Windows) by executing the “pdfgui” program. An alternative method on Windows is to start PDFgui through the DiffPy start menu.
If you don’t use Anaconda or prefer to install from sources, make sure the required software is all in place and run
python setup.py install
By default the files are installed to standard system directories, which may require the use of sudo for write privileges. If administrator (root) access is not available, see the output from python setup.py install --help for options to install as a regular user to user-writable locations. Note that installation to non-standard directories may require adjustments to the PATH and PYTHONPATH environment variables. The installation integrity can be verified by changing to the HOME directory and running
python -m diffpy.pdfgui.tests.rundeps
With Anaconda PDFgui can be later upgraded to the latest released version using
conda update diffpy.pdfgui
With other Python distributions the program can be upgraded to the latest version as follows
easy_install --upgrade diffpy.pdfgui
Other software
PDFgui can use an external structure viewer for displaying analyzed structures. We have tested with several structure viewers such as
AtomEye, http://li.mit.edu/A/Graphics/A/
PyMol, http://www.pymol.org
Other viewers should work as well, as long as they understand one of the output structure formats supported by PDFgui.
DEVELOPMENT
PDFgui is an open-source software available in a git repository at https://github.com/diffpy/diffpy.pdfgui.
Feel free to fork the project and contribute. To install PDFgui in a development mode where the source files are used directly rather than copied to a system directory, use
python setup.py develop --user
CONTACTS
For more information on PDFgui please visit the project web-page:
http://www.diffpy.org/products/pdfgui.html
or email Prof. Simon Billinge at sb2896@columbia.edu
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