Add trajectory reporter to openmm workflow

[orionarcher]

Summary

Include a summary of major changes in bullet points:

• Allows the OpenMM trajectories to report pymatgen trajectories

Additional dependencies introduced (if any)

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[orionarcher]

Would you mind taking a look @janosh?

[janosh]

some variables use camelCase instead of snake_case to match OpenMM's style. i'd advocate for consistency with Python conventions. maybe @utf wants to weigh in what atomate's policy is

2 more suggestions:

• could addi progress tracking for long trajectories
• could add compression options for large trajectories

[janosh]

is there no public openMM API to get these values? seems fragile to rely on _value here which i'm guessing has no backwards compat gurantees?

[orionarcher]

Good catch. I was a bit more clever and fixed it.

[janosh]

what are the implications of using __del__ for file operations? afaik there's no guarantee when it will be called. maybe better to add a explicit save() method instead

[orionarcher]

Good point. I was mirroring an external API and being a bit. I replaced it with a save method to be more robust.

The core problem is that the Reporters usually append to a file at each step but trajectory doesn't easily support that.

[orionarcher]

There are other Reporters that all use the camelCase args. I think OpenMM call's some of the methods internally too, so it's not possible to change them. I'd advocate for sticking with that, even though I agree it's a bit heretical.

EDIT:

To be a little clearer. The Reporter is passed directly to the OpenMM simulation object, which I believe calls the report and describeNextReport methods internally.

[janosh]

looks good! thanks @orionarcher 👍

[codecov]

Codecov Report

Attention: Patch coverage is 0% with 56 lines in your changes missing coverage. Please review.

Project coverage is 4.15%. Comparing base (42bc7b8) to head (c72e87d).
Report is 12 commits behind head on main.

Files with missing lines	Patch %	Lines
src/atomate2/openmm/utils.py	0.00%	45 Missing ⚠️
src/atomate2/openmm/jobs/base.py	0.00%	11 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff            @@
##            main   #1053      +/-   ##
========================================
- Coverage   4.32%   4.15%   -0.18%     
========================================
  Files        178     187       +9     
  Lines      12911   13583     +672     
  Branches    1278    1360      +82     
========================================
+ Hits         559     564       +5     
- Misses     12321   12988     +667     
  Partials      31      31              

Files with missing lines	Coverage Δ
src/atomate2/openmm/jobs/base.py	0.00% <0.00%> (ø)
src/atomate2/openmm/utils.py	0.00% <0.00%> (ø)

... and 2 files with indirect coverage changes

[orionarcher]

This will need one more loop back @janosh