PDFfit2 - 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.
For more information about the diffpy.pdffit2 library, please consult our online documentation.
If you use diffpy.pdffit2 in a scientific publication, we would like you to cite the following paper:
C. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch, Th. Proffen and S. J. L. Billinge, PDFfit2 and PDFgui: computer programs for studying nanostructure in crystals (https://stacks.iop.org/0953-8984/19/335219), J. Phys.: Condens. Matter, 19, 335219 (2007)
diffpy.pdffit2 requires Python 3.10 or later and the following external software:
setuptools- software distribution tools for Pythonpython-dev- header files for interfacing Python with CGSL- GNU Scientific Library for Cg++- GNU C++ compilerdiffpy.structure- simple storage and manipulation of atomic structures, https://github.com/diffpy/diffpy.structure
The preferred method is to use Miniconda Python and install from the "conda-forge" channel of Conda packages.
To add "conda-forge" to the conda channels, run the following in a terminal.
conda config --add channels conda-forge
We want to install our packages in a suitable conda environment.
The following creates and activates a new environment named diffpy.pdffit2_env
conda create -n diffpy.pdffit2_env python=3 conda activate diffpy.pdffit2_env
Then, to fully install diffpy.pdffit2 in our active environment, run
conda install diffpy.pdffit2
The less preferred approach is the install using pip to download and install the latest release from Python Package Index. In this case you currently have to build the codes on your computer from the sources and you will have to have a C++ installer available.
To install the C++ compiler and required dependencies in your diffpy.pdffit2_env environment, type
conda install \ --file requirements/run.txt \ --file requirements/build.txt
And then type
pip install diffpy.pdffit2
If you prefer to install from sources, use the above conda install \ .. instruction to install the dependencies in run.txt and build.txt in diffpy.pdffit2_env , obtain the source archive from
GitHub. Once installed, cd into your diffpy.pdffit2 directory
and run the following
pip install .
To confirm that the installation was successful, run the following in a terminal
python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)"
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.
Diffpy user group is the discussion forum for general questions and discussions about the use of diffpy.pdffit2. Please join the diffpy.pdffit2 users community by joining the Google group. The diffpy.pdffit2 project welcomes your expertise and enthusiasm!
If you see a bug or want to request a feature, please report it as an issue and/or submit a fix as a PR. You can also post it to the Diffpy user group.
Feel free to fork the project and contribute. To install diffpy.pdffit2 in a development mode, with its sources being directly used by Python rather than copied to a package directory, use the following in the root directory
pip install -e .
To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit hooks.
- Install pre-commit in your working environment by running
conda install pre-commit. - Initialize pre-commit (one time only)
pre-commit install.
Thereafter your code will be linted by black and isort and checked against flake8 before you can commit. If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should pass after they are modified). If the flake8 test fails please see the error messages and fix them manually before trying to commit again.
Improvements and fixes are always appreciated.
Before contributing, please read our Code of Conduct.
For more information on diffpy.pdffit2 please visit the project web-page or email Prof. Simon Billinge at sb2896@columbia.edu.