Dynamics

Scripts that analyze the dynamics of the system.

Scripts 

`extract_renewal_events`	Extract renewal events from a molecular dynamics trajectory.
`msd_layer_parallel`	Calculate the mean displacement (MD) and the mean squared displacement (MSD) of a given compound as function of its initial position.
`msd_layer_serial`	Calculate the mean displacement (MD) and the mean squared displacement (MSD) of a given compound as function of its initial position.

`plot_msd_layer`	Plot the MSD as function of diffusion time for different initial particle positions.
`plot_msd_layer_heatmap`	Plot the MSD as function of the initial particle position and the diffusion time in a heatmap.
`plot_msd_layer_cross_section_at_constant_time`	Plot (one component of) the MSD as function of the initial particle position at a constant diffusion time(s).
`plot_msd_layer_cross_section_xyz_at_constant_time`	Plot the x-, y- and z-component of the MSD as function of the initial particle position at a constant diffusion time.
`plot_msd_layer_cross_section_xyz_at_constant_msd`	Plot the diffusion time at which the x-, y- and z-component of the MSD reach a certain value as function of the initial particle position.