PDFfit2 - real space structure refinement program.
Real space structure refinement to atomic pair distribution function.
The diffpy.pdffit2 package provides functions for calculation and refinement of atomic Pair Distribution Function (PDF) from crystal structure model. It is used as a computational engine by PDFgui. All refinements possible in PDFgui can be done with diffpy.pdffit2, although less conveniently and with a fair knowledge of Python. The package includes an extension for the interactive IPython shell, which tries to mimic the old PDFFIT program. To start IPython with this extension and also with plotting functions enabled, use
ipython --ext=diffpy.pdffit2.ipy_ext --pylab
The IPython extension is suitable for interactive use, however refinement scripts should be preferably written as a standard Python code. This is more reliable and needs only a few extra statements.
To learn more about diffpy.pdffit2 library, see the examples directory included in this distribution or the API documentation at http://www.diffpy.org/doc/pdffit2.
diffpy.pdffit2 requires Python 2.6 or 2.7 and the following external software:
- setuptools - software distribution tools for Python
- python-dev - header files for interfacing Python with C
- GSL - GNU Scientific Library for C
- g++ - GNU C++ compiler
- diffpy.Structure - simple storage and manipulation of atomic structures, https://github.com/diffpy/diffpy.Structure
We recommend to use Anaconda Python as it allows to install all software dependencies together with PDFfit2. 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-dev libgsl0-dev build-essential
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.pdffit2
If you don’t use Anaconda or prefer to install from sources, make sure the required software is in place and run
python setup.py install
By default the files get installed to standard system directories, which may require the use of sudo for write permissions. If administrator (root) access is not available, consult the output from python setup.py install --help for options to install as a regular user to other locations. The installation integrity can be verified by changing to the HOME directory and running
python -m diffpy.pdffit2.tests.rundeps
Anaconda Python allows to later update PDFfit2 using
conda update diffpy.pdffit2
With other Python distributions use the easy_install program to upgraded to the latest version
easy_install --upgrade diffpy.pdffit2
PDFfit2 is not developed anymore and is only maintained due to its status of a sole computational engine for PDFgui. We don’t expect any major developments to the code beyond simple bug fixes and compatibility features. The source code to PDFfit2 is available in a git repository at https://github.com/diffpy/diffpy.pdffit2.
For an actively developed codes for PDF simulations see the DiffPy-CMI framework at http://www.diffpy.org.