mmckerns / libdiffpy

DiffPy C++ library for calculation of PDF and other real-space quantities

libdiffpy

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 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 common procedure for iteration over atom pairs and only specialize the processing of pair contributions. New calculator class 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.

REQUIREMENTS

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

Recommended software:

• libobjcryst - C++ library of free objects for crystallography, https://github.com/diffpy/libobjcryst
• cxxtest - CxxTest Unit Testing Framework, http://cxxtest.com

On Ubuntu Linux the required software can be installed using the system package manager:

sudo apt-get install \
    build-essential scons libboost-dev libgsl0-dev

For Mac OS X machine with the MacPorts package manager the installation command is

sudo port install scons boost gsl

For other packages see their project pages for installation instructions.

INSTALLATION

To build and install the libdiffpy library from sources, run

sudo scons -j4 install

This installs libdiffpy for all users under the /usr/local directory. If administrator (root) access is not available, see the usage info 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 CPATH and LIBRARY_PATH environment variables or use the -I or -L compiler options. If the libdiffpy shared library cannot be found at runtime, adjust the LD_LIBRARY_PATH environment variable.

DEVELOPMENT

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 sconscript.local script. The library integrity can be verified by executing unit tests with scons -j4 test (requires the CxxTest framework).

CONTACTS

For more information about libdiffpy please visit the project web-page

http://www.diffpy.org/

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