chloeann95 / diffpy.pdfmorph

PDFmorph

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.

LICENSE

This software is subject to license and copyright restrictions listed here.

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 2.7 and Python 3.5 or higher. We recommend using the Python 3 version. 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

We recommend installing the software using conda. If you have anaconda or mini-conda installed on your computer, you can proceed directly to the instructions below. If not, we recommend that you install mini- conda and test that it is working by opening a terminal and typing conda.

To create and activate a conda environment to use this software, run the following command from the command line

conda create -n pdfmorph_env python=3
source activate pdfmorph_env

If you're using Windows, replace source activate pdfmorph with activate pdfmorph_env.

When you are finished with the session, exit the environment by running

source deactivate pdfmorph_env

or, on Windows, deactivate pdfmorph_env.

For your future sessions with the application: Make sure to run the source activate pdfmorph_env or activate pdfmorph_env commands from your command line beforehand to ensure access to the software.

Once in your desired conda environment, you can install from either the "diffpy" or "conda-forge" channels of Anaconda packages by running either

conda config --add channels diffpy
conda install diffpy.pdfmorph

or

conda config --add channels conda-forge
conda install diffpy.pdfmorph

If you don't use conda or prefer to install from sources, please consult online documentation.

With conda, PDFmorph can be later upgraded to the latest released version using

conda update diffpy.pdfmorph

With other Python distributions the program can be upgraded to the latest version as follows

easy_install --upgrade diffpy.pdfmorph

USING PDFmorph

For detailed instructions and full tutorial, consult online documentation.

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!

DEVELOPMENT

PDFmorph is an open-source software project on Github: https://github.com/diffpy/diffpy.pdfmorph.

Feel free to fork the project and contribute! To install PDFmorph in a development mode where the source files are used directly rather than copied to a system directory, use

python setup.py develop --user

CONTACTS

For more information on PDFmorph, visit the PDFmorph project web-page, or email Professor Simon Billinge at [email protected]