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 classes 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 package requires Python 3.7, 3.6, 3.5 or 2.7, C++ compiler and the following software:
- setuptools - tools for installing Python packages
- NumPy - library for scientific computing with Python
- python-dev - header files for interfacing Python with C
- libboost-all-dev - Boost C++ libraries and 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
- scons - software construction tool (optional)
- 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.
We recommend to use Anaconda Python as it allows to install all software dependencies together with diffpy.srreal. For other Python distributions 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-numpy scons \ build-essential python-dev libboost-all-dev
To install the remaining packages see the installation instructions at their respective web pages.
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.srreal
diffpy.srreal is also included in the “diffpy-cmi” collection of packages for structure analysis
conda install diffpy-cmi
If you prefer to install from sources, make sure all required software packages are in place and then run
python setup.py install
You may need to use sudo with system Python so the process is allowed to copy files to the system directories. If administrator (root) access is not available, see the output from python setup.py install --help for options to install to a user-writable location. The installation integrity can be verified by executing the included tests with
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 C++ files in several parallel jobs (-j4)
sudo scons -j4 install
See scons -h for decription of build targets and options.
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]
When developing with Anaconda Python it is essential to specify header path, library path and runtime library path for the active Anaconda environment. This can be achieved by setting the CPATH, LIBRARY_PATH and LDFLAGS environment variables as follows:
# resolve the prefix directory P of the active Anaconda environment P="$(conda info --json | grep default_prefix | cut -d\" -f4)" export CPATH=$P/include export LIBRARY_PATH=$P/lib export LDFLAGS=-Wl,-rpath,$P/lib # compile and re-install diffpy.srreal scons -j4 build=debug develop
On Mac OS X the distributed Anaconda packages are built for operating system version 10.7, which may be incompatible with codes compiled on a newer OS. To avoid this problem set the environment variable MACOSX_DEPLOYMENT_TARGET=10.7. This allows to build diffpy.srreal against the Anaconda package for the libdiffpy library.
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