dynasor

dynasor is a tool for calculating total and partial dynamic structure factors as well as related correlation functions from molecular dynamics (MD) simulations. By analyzing these functions one can access the dynamics of a system without resorting to perturbative approaches. Moreover by combining in particular the structure factor with the cross sections (or form factors) of, e.g., neutrons, X-rays or electrons, one can predict experimental spectra. The main input consists of a trajectory from an 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 provides both a Python interface and a command-line interface. The following snippet illustrates how one can calculate dynamic structure factors using the former.

from dynasor import Trajectory, compute_dynamic_structure_factors
from dynasor.qpoints import get_spherical_qpoints

traj = Trajectory('dump.xyz', trajectory_format='extxyz')
q_points = get_spherical_qpoints(traj.cell, q_max=20)
sample = compute_dynamic_structure_factors(traj, q_points=q_points, dt=5, window_size=100)
sample.write_to_npz('test.npz')

dynasor can be installed via pip or conda. Please consult the installation section of the user guide for details.

The full documentation can be found in the user guide. For questions and help please use the dynasor discussion forum on matsci.org. dynasor and its development are hosted on gitlab.

When using dynasor in your research please cite the following papers: