mdadash.backend.analyses.msd

MSD Analysis

Classes

MSDAnalysis()	MSD Analysis
SlidingWindowMSD(u[, select, dim_type, ...])	Sliding Window MSD

class mdadash.backend.analyses.msd.MSDAnalysis

Bases: WidgetBase

MSD Analysis

This widget calculates the Mean Squared Displacement of a selection.

A custom SlidingWindowMSD is used to calculate MSD of the selection for each new frame against the time-lag buffer / window of past frames.

Important

To correctly compute MSD using this widget, you must supply coordinates in the unwrapped convention, also known as no-jump. That is, when atoms pass the periodic boundary, they must not be wrapped back into the primary simulation cell. You can enable NoJump for the universe in the Universe Configuration section in the Settings page.

Inputs

Run mode

The mode in which the widget is run - serial or parallel

Default: serial

Selection

MDAnalysis selection phrase

Default: all

Dimension type

Desired dimensions to be included in the MSD - xyz, xy, yz, xz, x, y or z

Default: xyz

Show diffusion coefficient

Show self-diffusion coefficient calculated from MSD

Default: False

Show particle MSDs

Show MSDs for individual particles of the selection

Default: False

Caution

Enabling this option for large selections can slow down the analysis and generation of the plot data

Log sale:

Use a log scale for the axes

Default: False

Custom title

Custom title for the plot

Default: ‘’

Output

Here is an example output plot of this widget:

Tip

This widget can run in parallel

apply_parallel_results(values)

apply parallel results handler

description = 'Mean squared displacement analysis'

get_parallel_job()

get parallel job handler

name = 'MSD Analysis'

on_input_change(attribute, _old_value, new_value)

on_input_change handler

on_post_connect()

on_post_connect handler

on_post_create()

on_post_create handler

run_every_frame()

every-frame run handler

class mdadash.backend.analyses.msd.SlidingWindowMSD(u: Universe, select: str = 'all', dim_type: str = 'xyz', show_diffusion_coefficient: bool = False, show_particle_msds: bool = False)

Bases: object

Sliding Window MSD

This class computes the MSD of the selection for each new frame against the time-lag buffer / window of past N frames. The total number of computations for each frame is O(N).

run(parallel: bool = False) → tuple

Run MSD for the current window