AngularAutoCorrelationsSingleAxis v1#

Summary#

Calculates the angular auto-correlation of molecules in a simulation along a user-defined axis. The axis is defined by the vector connecting the average position of species two and the average position of species one (user input). Timestep must be specified in femtoseconds.

Properties#

Name	Direction	Type	Default	Description
InputFile	Input	string	Mandatory	Input .nc file with an MMTK trajectory
Timestep	Input	string	1.0	Time step between two coordinates in the trajectory, fs
SpeciesOne	Input	string		Specify the first species, e.g. H, He, Li…
SpeciesTwo	Input	string		Specify the second species, e.g. H, He, Li…
OutputWorkspace	Output	Workspace	Mandatory	Output workspace name
OutputWorkspaceFT	Output	Workspace	Mandatory	Fourier Transform output workspace name

Description#

Loads a netcdf file generated by nMoldyn containing MMTK format trajectories. The algorithm calculates angular auto-correlations of molecule in the simulation along a user-defined axis. The trajectory file must therefore contain molecule definitions. The axis vector is drawn from the average position of atoms of type SpeciesOne to the average position of atoms of type SpeciesTwo.

Usage#

output_ws, output_ws_ft = AngularAutoCorrelationsSingleAxis(InputFile = 'trajectory_methyliodide.nc',
                                                                                              Timestep = '10.0',
                                                                                              SpeciesOne = 'C',
                                                                                              SpeciesTwo = 'I')