Add widget for MSD analysis

[PardhavMaradani]

Changes made in this Pull Request:

• Added widget for MSD analysis

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

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Hi @orbeckst, @jeremyleung521, @amruthesht, @HeydenLabASU,

This PR adds a new 'MSD Analysis' widget based on issue #34 raised by @amruthesht that uses MDAnalysis.analysis.msd.EinsteinMSD.

The widget runs every-frame and uses the timestep values from the sliding window buffer to create the plot. In the screenshots shown below, the 'Batch size' / 'Buffer size' is configured as 100 in 'Settings > Universe configuration' and hence the lag time shows up to 2 ps (each step is 0.02 ps in this example simulation).

Here is an example plot with all default values (select='all', msd_type='xyz', fft=False, non_linear=False):

Here is the same plot with a log scale (configurable from the GUI):

Here is the plot with fft=True:

Here is the plot with non_linear=True:

Here are the configurable inputs for this widget:

I added parallel support for this as it seemed to take a bit of time.

Here is a plot with a different selection phrase:

Thanks

[read-the-docs-community]

Documentation build overview

📚 mdadash | 🛠️ Build #33548626 | 📁 Comparing 0d85f72 against latest (a840cf4)

  🔍 Preview build  

14 files changed · + 2 added · ± 12 modified

+ Added

• autosummary/mdadash.backend.analyses.msd.html
• _modules/mdadash/backend/analyses/msd.html

± Modified

• genindex.html
• py-modindex.html
• _modules/index.html
• autosummary/mdadash.backend.analyses.dssp.html
• autosummary/mdadash.backend.analyses.html
• autosummary/mdadash.backend.analyses.rog.html
• autosummary/mdadash.backend.kernel.core.html
• autosummary/mdadash.backend.widgets.base.html
• _modules/mdadash/backend/analyses/dssp.html
• _modules/mdadash/backend/analyses/rog.html
• and 2 more...

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (a1eb59e) to head (0d85f72).

Additional details and impacted files

Components	Coverage Δ
frontend	100.00% <ø> (ø)
backend	100.00% <100.00%> (ø)

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[amruthesht]

@PardhavMaradani, the PR looks like a good start for other lag-time based analyses. There are some issues with the current implementation that I have pointed out. Once resolved, it should be good to go.
Let me know if you need any help or clarification with any points raised or want to discuss possible solutions.

[PardhavMaradani]

Hi @amruthesht , updated the code based on your example in #34 .

I had to make a few minor changes to get this working correctly (verified that the plots were identical to the MDA's MSD ones):

• The indexing was comparing frame 0 with the rest - changed it to compare the most recent one (last in the list) to all the previous ones
• changed msd_dict to use a deque instead of a list to keep this from not growing forever
• had to round the time delta to prevent jagged edges (similar to the non-linear case in MDA's MSD graph above)
• added support for selection phrase and msd_type

Could you please review and let me know if there are any changes needed. Thanks