calculators for PDF, bond valence sum, and other quantities based on atom pair interaction.
Calculators for PDF, bond valence sum and other pair quantities
The diffpy.srreal package provides calculators for atomic pair distribution function (PDF), bond valence sums (BVS), atom overlaps for a hard-sphere model, bond distances and directions up to specified maximum distance. The atomic structure models are represented with internal classes as non-periodic, periodic or structures with space group symmetries. The package provides implicit adapters from diffpy.Structure class or from Crystal or Molecule objects from pyobjcryst. Adapters can be easily defined for any other structure representations in Python allowing their direct use with the calculators. Calculators support two evaluation models - BASIC, which performs a full pair-summation every time, and OPTIMIZED, which updates only pair contributions that have changed since the last evaluation. Calculations can be split among parallel jobs using Python multiprocessing package or any other library that provides parallel map function. PDF calculations can be done in two modes - either as a real-space summation of peak profiles (PDFCalculator) or as a reciprocal-space Debye summation and Fourier transform of the total scattering structure function (DebyePDFCalculator).
The diffpy.srreal package is a Python binding to the C++ library libdiffpy (https://github.com/diffpy/libdiffpy). Calculators are created as objects of a given calculator type and so multiple instances of the same calculator type can exist with different configurations. Calculators are composed of other objects that perform lower-level tasks, such as calculating peak profile or looking up atom scattering factors. These objects can be re-assigned at runtime allowing to easily customize the calculation procedure. New classes can be defined using object inheritance either in Python or in C++ and used with the existing calculators; as an example, this allows to calculate PDF with a user-defined profile function. A new calculator class can be also defined for any quantity that is obtained by iteration over atom pairs, by defining only the function that processes atom-pair contributions.
For more information about the diffpy.srreal library, see users manual at http://diffpy.github.io/diffpy.srreal.
The diffpy.srreal requires Python 2.6 or 2.7 and the following software:
- setuptools - tools for installing Python packages
- NumPy - library for scientific computing with Python
- scons - software constructions tool (1.0 or later)
- python-dev - header files for interfacing Python with C
- libboost-dev - Boost C++ libraries development files (1.43 or later)
- libdiffpy - C++ library for PDF, bond valence sum and other pair quantity calculators https://github.com/diffpy/libdiffpy
- diffpy.Structure - simple storage and manipulation of atomic structures https://github.com/diffpy/diffpy.Structure
- periodictable - periodic table of elements in Python http://www.reflectometry.org/danse/elements.html
- pyobjcryst - Python bindings to ObjCryst++, the Object Oriented Crystallographic library for C++, https://github.com/diffpy/pyobjcryst.
Some of the required software may be available in the system package manager, for example, on Ubuntu Linux the dependencies can be installed as:
sudo apt-get install \ python-setuptools python-numpy scons \ build-essential python-dev libboost-dev
For Mac OS X machine with the MacPorts package manager one could do
sudo port install \ python27 py27-setuptools py27-numpy scons boost
When installing with MacPorts, make sure the MacPorts bin directory is the first in the system PATH and that python27 is selected as the default Python version in MacPorts:
sudo port select --set python python27
For other required packages see their respective web pages for installation instructions.
The easiest option is to use the latest DiffPy-CMI release bundle from http://www.diffpy.org, which comes with diffpy.srreal and all other dependencies included.
If you prefer to install from sources, make sure all required software packages are in place and then run
sudo python setup.py install
This installs diffpy.srreal for all users in the default system location. If administrator (root) access is not available, see the usage info from python setup.py install --help for options to install to a user-writable location. The installation integrity can be verified by changing to the HOME directory and running
python -m diffpy.srreal.tests.run
An alternative way of installing diffpy.srreal is to use the SCons tool, which can speed up the process by compiling the C++ files in parallel (-j4):
sudo scons -j4 install
See scons -h for build parameters and options to install to a user-writable directory.
diffpy.srreal is an open-source software developed as a part of the DiffPy-CMI complex modeling initiative at the Brookhaven National Laboratory. The diffpy.srreal sources are hosted at https://github.com/diffpy/diffpy.srreal.
Feel free to fork the project and contribute. To install diffpy.srreal 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
To rebuild the C++ extension module and then optionally test the code integrity, use
scons -j4 build=debug develop [test]