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diffpy / diffpy.pdffit2

real space structure refinement to atomic PDF
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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 <http://ipython.org>__ 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 <https://diffpy.github.io/diffpy.pdffit2>_.

Citation

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)

Installation

diffpy.pdffit2 requires Python 3.10 or later and the following external software:

The preferred method is to use Miniconda Python <https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>_ 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 <https://pypi.python.org>_. 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 <https://github.com/diffpy/diffpy.pdffit2/>_. 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__)"

Support and Contribute

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 <https://groups.google.com/g/diffpy-users>_ 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 <https://github.com/diffpy/diffpy.pdffit2/issues> and/or submit a fix as a PR <https://github.com/diffpy/diffpy.pdffit2/pulls>. You can also post it to the Diffpy user group <https://groups.google.com/g/diffpy-users>_.

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.

  1. Install pre-commit in your working environment by running conda install pre-commit.

  2. 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 <https://github.com/diffpy/diffpy.pdffit2/blob/main/CODE_OF_CONDUCT.rst>_.

Contact

For more information on diffpy.pdffit2 please visit the project web-page <https://diffpy.github.io/>_ or email Prof. Simon Billinge at sb2896@columbia.edu.