rozyczko / diffpy.structure

Crystal structure container and parsers for structure formats.

diffpy.structure

storage and manipulation of crystal structure data

The diffpy.structure package provides objects for storing atomic coordinates, displacement parameters and other crystal structure data. diffpy.structure supports import and export of structure data in several structure formats such as CIF, PDB, and xyz. It provides conversion between fractional and absolute Cartesian coordinates, functions for symmetry expansion of atom sites in the asymmetric unit and generation of symmetry constraints for atom positions and displacement parameters. diffpy.structure includes definitions of all space groups in over 500 symmetry settings.

To learn more about diffpy.structure library see the user manual at http://diffpy.github.io/diffpy.structure.

REQUIREMENTS

The diffpy.structure package requires Python 3.7 or later or 2.7 and the following software:

• setuptools - software distribution tools for Python
• NumPy - numerical mathematics and fast array operations for Python

We recommend to use Anaconda Python as it allows to install all software dependencies together with diffpy.structure. For other Python distributions it is necessary to install the required software separately. As an example on Ubuntu Linux the required software can be installed with

sudo aptitude install python3-setuptools python3-numpy

diffpy.structure also uses the PyCifRW library, which is automatically deployed during the installation process.

INSTALLATION

The preferred method is to use Anaconda Python and install from the "diffpy" channel of Anaconda packages

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

diffpy.structure is also included in the "diffpy-cmi" collection of packages for structure analysis

conda install diffpy-cmi

Another installation option is to use easy_install to download and install the latest release from Python Package Index

easy_install diffpy.structure

If you prefer to install from sources, navigate to the source archive directory and run

python setup.py install

You may need to use sudo with system Python so it is allowed to copy files to system directories. If sudo is not available, check the usage info from python setup.py install --help for options to install to user-writable locations. The installation integrity can be verified by changing to the HOME directory and running

python -m diffpy.structure.tests.run

DEVELOPMENT

diffpy.structure is an open-source software developed as a part of the DiffPy-CMI complex modeling initiative at the Brookhaven National Laboratory. The diffpy.structure sources are hosted at https://github.com/diffpy/diffpy.structure.

Feel free to fork the project and contribute. To install diffpy.structure in a development mode, where the sources are directly used by Python rather than copied to a system directory, use

python setup.py develop --user

ACKNOWLEDGEMENT

Space group codes in spacegroupmod.py and mmlibspacegroups.py originate from the pymmlib project, http://pymmlib.sourceforge.net.

CONTACTS

For more information on diffpy.structure please visit the project web-page

http://www.diffpy.org/

or email Prof. Simon Billinge at [email protected].