Mean-Square Displacement

class halmd.observables.dynamics.mean_square_displacement(args)

Construct mean-square displacement.

Parameters:

• args – keyword arguments
• args.phase_space – instance of halmd.observables.phase_space

acquire()

Acquire phase space position sample.

Returns:phase space position sample

correlate(first, second)

Correlate two phase space samples.

Parameters:

• first – first phase space sample
• second – second phase space sample

Returns:

mean-square displacement between samples

desc

Module description.

class writer(args)

Construct file writer.

Parameters:

• args (table) – keyword arguments
• args.file – instance of file writer
• args.location (string table) – location within file (optional)

Returns:

file writer as returned by file:writer().

The argument location specifies a path in a structured file format like H5MD given as a table of strings. It defaults to {"dynamics", self.label, "mean_square_displacement"}.