block_averaging

mdtools.check.block_averaging(n_blocks, n_frames, check_CPUs=False, verbose=True)[source]

Check if the number of blocks for block averaging is chosen properly.

The number of blocks must be greater than zero, but less than the number of available frames.

Parameters:

  • n_blocks (int) – Number of blocks for block averaging.

  • n_frames (int) – The number of frames available for analysis, i.e. the number of frames that are/were actually read, not the total number of frames in the trajectory.

  • check_CPUs (bool, optional) – If True, check if the number of available CPUs is a multiple of the number of blocks (or the other way round). If this is not the case, a warning is raised.

  • verbose (bool, optional) – If True (default), any changes to n_blocks are printed to standard output.

Returns:

  • n_blocks (int) – The input or a corrected number of blocks.

  • block_size (int) – The number of frames available for analysis per block.

Warns:

RuntimeWarning – If check_CPUs is True and the number of available CPUs is not an integer multiple of n_blocks (or the other way round).

See also

mdtools.check.frame_slicing()

Check if the input parameters are suitable for slicing MDAnalysis trajectories

mdtools.check.frame_lag()

Check if a frame lag (‘lag time’) is chosen properly

mdtools.check.time_step()

Check whether all frames in a MDAnalysis trajectory have the same time step