diffpy.pdfmorph 0.1.3

Tools for manipulating and comparing PDF profiles

Tools for manipulating and comparing PDF profiles

PDFmorph is a Python software package designed to increase the insight researchers can obtain from measured atomic pair distribution functions (PDFs) in a model-independent way. The program was designed to help a researcher answer the question: “Has my material undergone a phase transition between these two measurements?”

One approach is to compare the two PDFs in a plot and view the difference curve underneath. However, significant signal can be seen in the difference curve from benign effects such as thermal expansion (peak shifts) and increased thermal motion (peak broadening) or a change in scale due to differences in incident flux, for example. PDFmorph will do its best to correct for these benign effects before computing and plotting the difference curve. One measured PDF (typically that collected at higher temperature) is identified as the target PDF and the second PDF is then morphed by “stretching” (changing the r-axis to simulate a uniform lattice expansion), “smearing” (broadening peaks through a uniform convolution to simulate increased thermal motion), and “scaling” (self-explanatory). PDFmorph will vary the amplitude of the morphing transformations to obtain the best fit between the morphed and the target PDFs, then plot them on top of each other with the difference plotted below.

There are also a few other morphing transformations in the program.

Finally, we note that PDFmorph should work on other spectra that are not PDFs, though it has not been extensively tested beyond the PDF.

For more information about the diffpy.pdfmorph library, please consult our online documentation.

Citation

If you use diffpy.pdfmorph in a scientific publication, we would like you to cite this package as

diffpy.pdfmorph Package, https://github.com/diffpy/diffpy.pdfmorph

REQUIREMENTS

PDFmorph is currently run from the command line, which requires opening and typing into a terminal window or Windows command prompt. It is recommended that you consult online resources and become somewhat familiar before using PDFmorph.

PDFmorph can be run with Python 3.10 or higher. It makes use of several third party libraries that you’ll need to run the app and its components.

• NumPy - library for scientific computing with Python

• matplotlib - Python 2D plotting library

• SciPy - library for highly technical Python computing

• diffpy.utils - shared helper utilities for wx GUI

These dependencies will be installed automatically if you use the conda installation procedure described below.

Installation

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.pdfmorph_env

conda create -n diffpy.pdfmorph_env diffpy.pdfmorph
conda activate diffpy.pdfmorph_env

To confirm that the installation was successful, type:

python -c "import diffpy.pdfmorph; print(diffpy.pdfmorph.__version__)"

The output should print the latest version displayed on the badges above.

If the above does not work, you can use pip to download and install the latest release from Python Package Index. To install using pip into your diffpy.pdfmorph_env environment, we will also have to install dependencies

pip install -r https://raw.githubusercontent.com/diffpy/diffpy.pdfmorph/main/requirements/pip.txt

and then install the package

pip install diffpy.pdfmorph

If you prefer to install from sources, after installing the dependencies, obtain the source archive from GitHub. Once installed, cd into your diffpy.pdfmorph directory and run the following

pip install .

Getting Started

You may consult our online documentation for tutorials and API references.

USING PDFmorph

For detailed instructions and full tutorial, consult the user manual on our website <www.diffpy.org/diffpy.pdfmorph/>.

Once the required software, including PDFmorph is all installed, open up a terminal and check installation has worked properly by running

source activate pdfmorph_env      #if the environment isn't already active
pdfmorph -h                       #get some helpful information
pdfmorph --version

If installed correctly, this last command should return the version of PDFmorph that you have installed on your system. To begin using PDFmorph, run a command like

pdfmorph <target PDF file> <morphed PDF file>

where both PDFs file are text files which contain PDF data, such as .gr or .cgr files that are produced by PDFgetX2, PDFgetX3, or PDFgui. Though some file extensions other than .gr or .cgr, but with the same content structure, have been shown to work with PDFmorph, it is recommended to stick with .gr files.

Enjoy!

Support and Contribute

Diffpy user group is the discussion forum for general questions and discussions about the use of diffpy.pdfmorph. Please join the diffpy.pdfmorph users community by joining the Google group. The diffpy.pdfmorph 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.pdfmorph 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 contribuing, please read our Code of Conduct.

Contact

For more information on diffpy.pdfmorph please visit the project web-page or email Prof. Simon Billinge at [e-mail].