dynasor – Correlations for everyone

dynasor is a tool for calculating total and partial dynamic structure factors from molecular dynamics (MD) simulations. 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 has been developed at Chalmers University of Technology in Gothenburg, Sweden, in the Condensed Matter and Materials Theory division at the Department of Physics. Please consult the credits page for information on how to cite dynasor.

For questions and help please use the dynasor discussion forum on matsci.org. dynasor and its development are hosted on gitlab. Bugs and feature requests are ideally submitted via the gitlab issue tracker.

Main

• Introduction
• Installation
  • Installation via pip or conda
  • Installation via setup.py
  • Requirements
  • numba and icc_rt
• Theoretical background
  • Dynamic structure factor
  • Velocity correlation functions
  • Multi component systems and liquids
  • Relation to scattering experiments
  • Damped harmonic oscillator model
• Input parameters
  • The trajectory
  • Atomic types and the index file
  • q-space sampling parameters
  • Time sampling parameters
  • Self-part of the intermediate scattering function
• Trajectory formats
  • Units
  • Lammps dump
  • Extended xyz
• Implementation details
  • Overview
  • Internal units
  • Limitations
  • External libraries
• Performance
  • Parallelization
  • Typical use cases
  • Trajectory reading
• Credits

Tutorials and examples

• Tutorials
  • Time convergence
• Examples
  • Liquid and Solid Aluminium
    • Liquid
    • Crystalline
  • Molten Sodium Chloride
    • Structure factors: F(q,t)
    • Current correlations: C(q,w)

Function reference

• Python interface
  • compute_correlation_functions_dynamic_qiso()
  • compute_correlation_functions_dynamic_qline()
  • compute_correlation_functions_static_qiso()
  • compute_correlation_functions_static_qline()
  • compute_spectral_energy_density()
  • Trajectory handling
    • get_itraj()
    • iwindow
  • Fourier transformations
    • cos_integral()
    • fourier_cos()
    • sin_integral()
• Command line interface
  • q-point sampling options
  • Time sampling options
  • Output options
  • Self-part of the intermediate scattering function

Backmatter

• References
• Index