msd_output_file_writer

A module containing the classes for writing related to an MSD analysis to a file.

Summary

Classes:

`MSDDataWriter`	Class for writing the data of an `MSD` analysis to a file.
`MSDLogWriter`	Class for writing the log (setup parameters) of an `MSD` analysis to a file.

Reference

class MSDDataWriter(filename: str)[source]

Bases: BaseWriter

Class for writing the data of an MSD analysis to a file.

The output file is written in the legacy Diffcalc format: one row per lag index with the columns lag index, MSD in x, MSD in y and MSD in z (all in Angstrom^2).

Parameters:: filename (str) – the filename to write to

write( data: tuple[Np1DNumberArray, Np1DNumberArray, Np1DNumberArray, Np1DNumberArray, Np1DNumberArray], )[source]

Writes the data to the file.

Parameters:: data (Tuple[Np1DNumberArray, Np1DNumberArray,) – Np1DNumberArray, Np1DNumberArray, Np1DNumberArray] the data output from the MSD.run() method

class MSDLogWriter(filename: str | None)[source]

Bases: BaseWriter

Class for writing the log (setup parameters) of an MSD analysis to a file.

Parameters:: filename (str | None) – the filename to write to if None, the output is printed to stdout

write_after_run( msd: MSD, )[source]

Writes the log after the MSD run() method is called.

This includes the elapsed time of the MSD run() method and, if a time step was given, the diffusion coefficients obtained from the linear fit of the MSD tail.

Parameters:: msd (MSD) – the MSD analysis object

write_before_run( msd: MSD, )[source]

Writes the log before the MSD run() method is called.

This includes the general header of PQAnalysis and the most important setup parameters of the MSD analysis.

Parameters:: msd (MSD) – the MSD analysis object