Note
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 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?"
PDFmorph makes use of several data manipulation techniques to correct for benign effects such as thermal expansion (peak shift) and increased thermal motion (peak broadening) or a cahnge 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 a difference curve.
One PDF (typically that collected at higher temperature) is identified as the "target" PDF and the second is "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 amplitude of morphing transformations to obtain the best fit between morphed and target PDFs, then plot them along with the difference curve 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.
Transformation techniques (scale, smear, and stretch, respectively) utilized by PDFmorph applied sequentially on an NaCl sample
By downloading and using this software, you are agreeing to the conditions specified in the :doc:`software license <pdfmorph_license>`.
In order to take automatically take care of software dependency downloads, we recomment you install PDFmorph using conda. To do that, you will first have to download and install Anaconda or mini-conda from continuum.
PDFmorph is available for all operating systems supported by Anaconda, namely for 32 and 64-bit Linux, Mac OS X, and 32 and 64-bit Windows.
Note
We recommend that you run PDFmorph in a Python 3 conda virtual environment. With Anaconda or mini-conda installed on your system, first create the virtual environment by typing
conda create --name=<env_name> python=3
You can give the environment any name you like but it should have some Python version 3 installed (though PDFmorph also works on Python 2.7). You only need to create the environment once, but every time you want to use PDFmorph you will have to reactivate the environment in which it is installed by typing
source activate <env_name>
on Mac/Linux, or activate <env_name> on Windows.
Once you're in your desired conda environment, you can install PDFmorph
from either the diffpy or conda-forge channels of Anaconda packages
by running opening a Terminal window or Anaconda Command Prompt
on Windows and using the :program:`conda` command
conda config --add channels conda-forge conda install diffpy.pdfmorph
If you prefer to install from the diffpy channel, simply replace
conda-forge with diffpy in the commands above.
By then it should be installed! To make sure that installation has completed correctly, run the following command from your PDFmorph-equipped conda environment
pdfmorph --version
This command should return the version of PDFmorph you have on your machine.
The Anaconda package system makes it easy to prepare and distribute software packages and bugfixes. To update the latest version of PDFmorph, use
conda update diffpy.pdfmorph
With other Python distributions, the program can be updated to the latest version with
easy_install --upgrade diffpy.pdfmorph
To use a development version, visit the project source repository at https://github.com/diffpy/diffpy.pdfmorph and consult its README file.
- User manual (available in HTML and PDF)
- Installation instructions
- Sample PDF files
- Tutorial
- Please, join the :doc:`community forum <../community>` for tips, tricks, and feedback.
.. toctree::
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pdfmorph_license