dynasor 2.0

Dynamical structure factors and correlation

dynasor is a tool for calculating total and partial dynamic structure factors as well as related correlation functions from molecular dynamics (MD) simulations. Analysis of these functions enables one to access the dynamics of a system without resorting to perturbative approaches. By combining in particular the structure factor with the cross sections (or form factors) of, e.g., neutrons, X-rays or electrons, it is even possible to directly predict experimental spectra.

The main input consists of a trajectory from a MD simulation, i.e., a file containing snapshots of the particle coordinates, and optionally velocities that correspond to consecutively and equally spaced points in (simulation) time. dynasor provides both python and a command line interface. The following snippet illustrates how one can calculate dynamic structure factors using the former:

.. code-block:: python

traj = Trajectory(‘dump.xyz’, trajectory_format=’extxyz’) q_points = generate_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_npy(‘test.npy’)

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 paper:

Dynasor – A tool for extracting dynamical structure factors and current correlation functions from molecular dynamics simulations

Erik Fransson, Mattias Slabanja, Paul Erhart, and Göran Wahnström

Advanced Theory and Simulations 4, 2000240 (2021); DOI:10.1002/adts.202000240