C++ calculators of PDF, bond valence sum and other pair quantities
libdiffpy is a C++ library for calculating atomic pair distribution function (PDF), bond valence sums, atom overlaps for a hard-sphere model, bond distances and directions up to a specified maximum distance. The atomic structure models are represented by classes for non-periodic, periodic or structures with space group symmetries. libdiffpy supports Crystal and Molecule classes from the ObjCryst crystallographic library. 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. libdiffpy supports object serialization and parallel computations using parallel map function. PDF calculations can be performed 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 calculator objects in libdiffpy share a common procedure for iteration over atom pairs and only specialize the processing of pair contributions. New calculator classes can thus be readily defined for any quantity that is obtained by iteration over atom pairs.
For more information see user manual at http://www.diffpy.org/doc/libdiffpy.
libdiffpy library requires C++ compiler and the following software:
scons- software constructions tool (1.0 or later)
libboost-dev- Boost C++ libraries development files (1.43 or later)
GSL- GNU Scientific Library for C
libobjcryst- C++ library of free objects for crystallography, https://github.com/diffpy/libobjcryst
cxxtest- CxxTest Unit Testing Framework, http://cxxtest.com
The required software is commonly available in the system package manager. For example, on Ubuntu Linux the required software can be installed using
sudo apt-get install \ build-essential scons libboost-dev libgsl0-dev
libdiffpy is also available as a pre-compiled package for Anaconda Python. A Python interface to libdiffpy is provided by Anaconda package diffpy.srreal.
Installation from sources
Use sources from the git repository or extract the latest source bundle from https://github.com/diffpy/libdiffpy/releases/latest.
tar xzf libdiffpy-VERSION.tar.gz cd libdiffpy-VERSION
To build and install the libdiffpy library use
sudo scons -j4 install
This installs libdiffpy for all users under the
If administrator (root) access is not available, see the output from
scons --help for options to install to a user-writable location.
To verify libdiffpy installation, compile and run the included test code examples/testlib.cpp
cd examples c++ testlib.cpp -ldiffpy ./a.out
If compilation fails because of missing header files or missing libdiffpy
library, adjust the
LIBRARY_PATH environment variables or
-L compiler options. If the shared library libdiffpy
is unavailable at runtime, add a
-Wl,-rpath,SomePath option to the
c++ command or adjust the
LD_LIBRARY_PATH environment variable.
Installation for Anaconda Python
The libdiffpy library can be installed from the "diffpy" channel of Anaconda packages
conda config --add channels diffpy conda install libdiffpy
libdiffpy is also included in the "diffpy-cmi" collection of packages for structure analysis
conda install diffpy-cmi
When compiling with the Anaconda version of libdiffpy it is essential to specify header path, library path and runtime path of the active Anaconda environment
# resolve prefix directory P of the active Anaconda environment P="$(conda info --json | grep default_prefix | cut -d\" -f4)" cd examples c++ testlib.cpp -I$P/include -L$P/lib -Wl,-rpath,$P/lib -ldiffpy ./a.out
On Mac OS X the libdiffpy package is built for OS X version
10.7 which may be incompatible with codes emitted on newer OS.
To fix this add
-mmacosx-version-min=10.7 option to the
c++ compiler or set it with an environment variable as
libdiffpy is an open-source software developed as a part of the DiffPy-CMI complex modeling initiative at the Brookhaven National Laboratory. The libdiffpy sources are hosted at https://github.com/diffpy/libdiffpy.
Feel free to fork the project and contribute. When developing it is
preferable to compile with
build=develop option, which compiles the
library with debug information and C-assertions checks:
scons -j4 build=develop
The build script checks for a presence of
sconsvars.py file, which
can be used to permanently set the
build variable. The SCons
construction environment can be further customized in a
script. The library integrity can be verified by executing unit tests with
scons -j4 test (requires the CxxTest framework).
For more information about libdiffpy please visit the project web-page
or email Prof. Simon Billinge at email@example.com.