| Name | diffpy.pdffit2 JSON |
| Version |
1.5.1
JSON |
| download |
| home_page | None |
| Summary | PDFfit2 - real space structure refinement program. |
| upload_time | 2025-02-07 20:44:29 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | <3.14,>=3.11 |
| license | None |
| keywords |
pdf
structure refinement
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
|Icon| |title|_
===============
.. |title| replace:: diffpy.pdffit2
.. _title: https://diffpy.github.io/diffpy.pdffit2
.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
:target: https://diffpy.github.io/diffpy.pdffit2
:height: 100px
|PyPi| |Forge| |PythonVersion| |PR|
|CI| |Codecov| |Black| |Tracking|
.. |Black| image:: https://img.shields.io/badge/code_style-black-black
:target: https://github.com/psf/black
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:target: https://github.com/diffpy/diffpy.pdffit2/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
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:target: https://codecov.io/gh/diffpy/diffpy.pdffit2
.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.pdffit2
:target: https://anaconda.org/conda-forge/diffpy.pdffit2
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PDFfit2 - real space structure refinement of the atomic pair distribution function
The diffpy.pdffit2 package provides functions for the calculation and
refinement of atomic Pair Distribution Functions (PDF) from crystal
structure models. It is used as a computational engine by PDFgui. All
refinements possible in PDFgui can be done by writing python scripts
directly with diffpy.pdffit2,
although less conveniently and with a fair knowledge of Python.
However, we recommend using `diffpy-cmi
<https://www.diffpy.org/products/diffpycmi/index.html>`_ for carrying
out more advanced, python-scripted refinements of nanostructure.
The PDFfit2 package includes an extension for the interactive `IPython
<http://ipython.org>`_ shell, these days commonly used within
Jupyter notebooks, 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 supports Python 3.11, 3.12, and 3.13.
Windows, macOS (non-Arm64), Linux
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.
Add the "conda-forge" channel by running the following command in a terminal: ::
conda config --add channels conda-forge
Create a new environment named ``diffpy.pdffit2_env`` and install ``diffpy.pdffit2``: ::
conda create -n diffpy.pdffit2_env diffpy.pdffit2
Activate the environment: ::
conda activate diffpy.pdffit2_env
Confirm that the installation was successful: ::
python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)"
macOS (Arm64)
~~~~~~~~~~~~~
Create a new conda environment ``diffpy.pdffit2_env``: ::
conda create -n diffpy.pdffit2_env python=3.13
Activate the environment: ::
conda activate diffpy.pdffit2_env
Install pdffit2 using ``pip`` to download and install the latest version from `Python Package Index <https://pypi.python.org>`_: ::
pip install diffpy.pdffit2
Confirm that the installation was successful: ::
python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)"
Build from source
~~~~~~~~~~~~~~~~~
For advanced users, obtain the source archive, and in the ``diffpy.pdffit2`` directory, run ::
conda create -n diffpy.pdffit2_env python=3.13 \
--file requirements/test.txt \
--file requirements/conda.txt \
--file requirements/build.txt
Activate the environment, build the package, and run unit tests by following commands sequentially: ::
conda activate diffpy.pdffit2_env
pip install . --no-deps
pytest
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.
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It is used as a computational engine by PDFgui. All\nrefinements possible in PDFgui can be done by writing python scripts\ndirectly with diffpy.pdffit2,\nalthough less conveniently and with a fair knowledge of Python.\nHowever, we recommend using `diffpy-cmi\n<https://www.diffpy.org/products/diffpycmi/index.html>`_ for carrying\nout more advanced, python-scripted refinements of nanostructure.\n\nThe PDFfit2 package includes an extension for the interactive `IPython\n<http://ipython.org>`_ shell, these days commonly used within\nJupyter notebooks, which tries to mimic the old PDFFIT\nprogram. To start IPython with this extension and also with plotting\nfunctions enabled, use ::\n\n ipython --ext=diffpy.pdffit2.ipy_ext --pylab\n\nThe IPython extension is suitable for interactive use, however\nrefinement scripts should be preferably written as a standard\nPython code. 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Matter*, 19, 335219 (2007)\n\nInstallation\n------------\n\ndiffpy.pdffit2 supports Python 3.11, 3.12, and 3.13.\n\nWindows, macOS (non-Arm64), Linux\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nThe preferred method is to use `Miniconda Python\n<https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_\nand install from the \"conda-forge\" channel of Conda packages.\n\nAdd the \"conda-forge\" channel by running the following command in a terminal: ::\n\n conda config --add channels conda-forge\n\nCreate a new environment named ``diffpy.pdffit2_env`` and install ``diffpy.pdffit2``: ::\n\n conda create -n diffpy.pdffit2_env diffpy.pdffit2\n\nActivate the environment: ::\n\n conda activate diffpy.pdffit2_env\n\nConfirm that the installation was successful: ::\n\n python -c \"import diffpy.pdffit2; print(diffpy.pdffit2.__version__)\"\n\nmacOS (Arm64)\n~~~~~~~~~~~~~\n\nCreate a new conda environment ``diffpy.pdffit2_env``: ::\n\n conda create -n diffpy.pdffit2_env python=3.13\n\nActivate the environment: ::\n\n conda activate diffpy.pdffit2_env\n\nInstall pdffit2 using ``pip`` to download and install the latest version from `Python Package Index <https://pypi.python.org>`_: ::\n\n pip install diffpy.pdffit2\n\nConfirm that the installation was successful: ::\n\n python -c \"import diffpy.pdffit2; print(diffpy.pdffit2.__version__)\"\n\nBuild from source\n~~~~~~~~~~~~~~~~~\n\nFor advanced users, obtain the source archive, and in the ``diffpy.pdffit2`` directory, run ::\n\n conda create -n diffpy.pdffit2_env python=3.13 \\\n --file requirements/test.txt \\\n --file requirements/conda.txt \\\n --file requirements/build.txt\n\nActivate the environment, build the package, and run unit tests by following commands sequentially: ::\n\n conda activate diffpy.pdffit2_env\n pip install . --no-deps\n pytest\n\nSupport and Contribute\n----------------------\n\nPDFfit2 is not developed anymore and is only maintained due to its\nstatus of a sole computational engine for PDFgui. 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