A tool for calculating dynamical structure factors
dynasor is a simple tool for calculating total and partial dynamical structure factors as well as current correlation functions from molecular dynamics (MD) simulations. The main input consists of a trajectory output from a MD simulation, i.e., a file containing snapshots of the particle coordinates and optionally velocities that correspond to consecutive, equally spaced points in (simulation) time.
dynasor can by itself read and parse standard lammpsdump-style trajectories. If libgmx (a library in the gromacs package) is available, dynasor can use it to read gromacs xtc-files. If VMD is available, dynasor can use VMD’s molfileplugin to read other formats (with some limitations) as well.
dynasor is controlled via command line options, provided at command invocation. Output can be written in the form of standard matlab/octave-stype m-files and/or python pickle-files.
A full documentation is provided here.
Python 3.5+, numpy, and a C99-complient C-compiler.