dynasor – Correlations for everyone

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 also possible to directly predict experimental spectra.

Specifically dynasor can be used to calculate the following quantities

• Partial van Hove functions

• Partial intermediate scattering functions

• Partial dynamic structure factors, including the incoherent (or self) part

• Longitudinal and transversal partial current correlations

• Spectral energy densities

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. The following snippet illustrates how one can calculate dynamic structure factors from such a trajectory

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_npz('test.npz')

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.

Main

• 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
  • Relation to scattering experiments
  • Spectral energy density method
  • Damped harmonic oscillator model
• Workflow
  • Internal units
  • The trajectory
  • Atomic types
  • q-space sampling parameters
  • Time sampling parameters
  • Incoherent intermediate scattering function
  • Post-processing
  • Limitations
• Performance
  • Parallelization
  • Typical use cases
  • Trajectory reading
• Credits

Tutorials and examples

• Tutorials
  • Dynamic properties of liquid Al
    • Set up the trajectory for reading
    • Select q-points to sample
    • Run calculation of correlation functions
    • Spherical average over q-points
    • Visualize dynamic structure factor
    • Slices in |q|-space
  • Dynamic properties of FCC-Al
    • Set up the Trajectory
    • Set up path through Brillouin zone
    • Run calculation of correlation functions
    • Visualize dynamic structure factor
    • Visualize current correlations
  • Static structure factor in halide perovskite (CsPbI3)
    • Structure and potential files
    • MD simulations
    • S(q) for ideal structures
    • S(q) from MD simulations
    • Observing the phase transition in S(q)
  • Time convergence
  • Auto correlation functions and FFTs
    • Damped harmonic oscillator
    • Signal in time
    • Autocorrelation function
    • Fourier transforms and spectral
  • Peak fitting using damped harmonic oscillator model
    • Damped harmonic oscillator
    • Al FCC
    • Cubic BaZrO3
  • Spectral energy density
    • Setup and visualization of structures
    • Phonopy calculations
    • Molecular dynamics simulations
• Examples
  • Liquid and Solid Aluminium
    • Liquid
    • Crystalline
  • Molten Sodium Chloride
    • Structure factors: F(q,t)
    • Current correlations: C(q,w)

Function reference

• Python interface
  • Trajectory handling
    • Trajectory
  • Correlation functions
    • compute_dynamic_structure_factors()
    • compute_static_structure_factors()
    • compute_spectral_energy_density()
  • Sample
    • read_sample_from_npz()
    • DynamicSample
    • StaticSample
  • q-points
    • get_spherical_qpoints()
    • get_supercell_qpoints_along_path()
  • Post processing
    • NeutronScatteringLengths
    • Weights
    • fourier_cos_filon()
    • get_sample_averaged_over_independent_runs()
    • get_spherically_averaged_sample_binned()
    • get_spherically_averaged_sample_smearing()
    • get_weighted_sample()
  • Tools
    • compute_acf()
    • fermi_dirac()
    • gaussian_decay()
    • smoothing_function()
    • acf_position_dho()
    • acf_velocity_dho()
    • psd_position_dho()
    • psd_velocity_dho()
  • Unit conversion
  • Logging
    • set_logging_level()
• Command line interface
  • Trajectory options
  • q-point sampling options
  • Time sampling options
  • Output options
  • Incoherent intermediate scattering function and current correlations

Backmatter

• References
• Index
• Glossary