AtomEye is atomistic visualization software fast enough to handle output of molecular dynamics simulations with millions of atoms. It includes parallel and perspective projections with full three-dimensional navigation, customizable bond and coordination number calculation, colour-encoding of arbitrary user-defined quantities, local atomic strain invariant, coloured atom tiling and tracing, up to 16 cutting planes, periodic boundary condition translations, JPEG, PNG, and EPS screenshots, and animation scripting.
Debyer takes a file with atom positions as input and can output X-ray and neutron diffraction patterns, the total scattering structure function, the pair distribution function (PDF), and related functions (RDF, reduced PDF). It can be used for comparison of molecular dynamics simulations or other models of atomistic structure of the material with X-ray and neutron powder diffraction experiments. The parallel version uses the MPI library.
Fityk is nonlinear curve-fitting and data analysis software. It allows data visualization, separation of overlapping peaks, and least squares fitting using standard Levenberg-Marquardt algorithm, a genetic algorithm, or Nelder-Mead simplex method. It knows about many functions (mostly bell-shaped, like Gaussian, Loretzian, Pearson 7, Voigt, Pseudo-Voigt, and Doniach-Sunjic) and user-defined functions can be easily added. It also enables background subtracting, data calibration, and task automation with a simple script language. It is mainly used to analyze powder diffraction patterns, chromatography, photoluminescence, infrared, and Raman spectroscopy, but it can be used to fit analytical functions to any kind of data.
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
xylib is a portable C++ library for reading files that contain x-y data from powder diffraction, spectroscopy, or other experimental methods. Supported formats include plain text (CSV or TSV), Crystallographic Information File for Powder Diffraction (pdCIF), Siemens/Bruker UXD, Siemens/Bruker RAW v1/2/3, Philips UDF, Philips RD (raw scan) V3, Rigaku DAT, Sietronics Sieray CPI, DBWS/DMPLOT data file, Canberra MCA, XFIT/Koalariet XDD, RIET7/LHPM/CSRIET/ILL_D1A5/PSI_DMC DAT, Vamas ISO14976, and Princeton Instruments WinSpec SPE.