diffpy.pdfgui 2.0.0

GUI for PDF simulation and structure refinement.

PDFgui

Graphical user interface program for structure refinements to atomic pair distribution function.

PDFgui is a friendly interface to PDFfit2 refinement engine, with many powerful extensions. To get started, please open the manual from the help menu and follow the tutorial instructions. A detailed description is available in the doc/Farrow-jpcm-2007.pdf paper.

REQUIREMENTS

PDFgui requires Python 3.7, 3.8, 3.9, or 2.7 and several third-party libraries that are used by PDFgui and its components.

• setuptools - tools for installing Python packages

• wxpython - graphical user interface toolkit for Python

• numpy - library for scientific computing with Python

• matplotlib - Python 2D plotting library

• diffpy.pdffit2 - computational engine for PDFgui, https://github.com/diffpy/diffpy.pdffit2

• diffpy.structure - simple storage and manipulation of atomic structures, https://github.com/diffpy/diffpy.structure

• diffpy.utils - shared helper utilities for wx GUI, https://github.com/diffpy/diffpy.utils

We recommend to use Anaconda Python which allows to conveniently install PDFgui and all its software dependencies with a single command.

Please note that the Python3 PDFgui will read .ddp3 files. It is also possible for it to read .ddp files that were saved by the Python2 PDFgui but it will sometimes fail to read these. We are working on a solution that will be available in a future version.

INSTALLATION

The preferred method is to use Anaconda Python and install from the “conda-forge” channel of Anaconda packages. pdfgui can be installed with conda

conda install -c conda-forge diffpy.pdfgui

PDFgui can be then started from a terminal (“Anaconda Prompt” on Windows) by executing the “pdfgui” program. An alternative method on Windows is to start PDFgui through the DiffPy start menu.

If you don’t use Anaconda or prefer to install from sources, make sure the required software is all in place

conda install -c conda-forge diffpy.utils diffpy.pdffit2 matplotlib wxpython

Then you are ready to install diffpy.pdfgui from source codes:

python setup.py install

By default the files are installed to standard system directories, which may require the use of sudo for write privileges. If administrator (root) access is not available, see the output from python setup.py install --help for options to install as a regular user to user-writable locations. Note that installation to non-standard directories may require adjustments to the PATH and PYTHONPATH environment variables. The installation integrity can be verified by changing to the HOME directory and running

python -m diffpy.pdfgui.tests.rundeps

To use PDFgui, you can simply type pdfgui, or run the following command

python diffpy.pdfgui/src/diffpy/pdfgui/application/pdfgui.py

If it shows some error like “This program needs access to the screen.”. For Mac, you could install python.app from conda (conda install python.app), then run as follows

python.app diffpy.pdfgui/src/diffpy/pdfgui/application/pdfgui.py

With Anaconda PDFgui can be later upgraded to the latest released version using

conda update -c conda-forge diffpy.pdfgui

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

easy_install --upgrade diffpy.pdfgui

If you would like to use other Python distributions except Anaconda, it is necessary to install the required software separately. As an example, on Ubuntu Linux some of the required software can be installed using

sudo apt-get install \
   python-setuptools python-wxtools python-numpy \
   python-matplotlib

To install the remaining packages see the installation instructions at their respective web pages.

Other software

PDFgui can use an external structure viewer for displaying analyzed structures. We have tested with several structure viewers such as

• AtomEye, http://li.mit.edu/A/Graphics/A/

• PyMol, https://www.pymol.org

• VESTA, http://jp-minerals.org/vesta/en/

Other viewers should work as well, as long as they understand one of the output structure formats supported by PDFgui.

DEVELOPMENT

PDFgui is an open-source software available in a git repository at https://github.com/diffpy/diffpy.pdfgui.

Feel free to fork the project and contribute. To install PDFgui 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 PDFgui please visit the project web-page:

https://www.diffpy.org/products/pdfgui.html

or email Prof. Simon Billinge at [e-mail]