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[WIP] engine_masses feature; use in Gromacs engine#1119

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[WIP] engine_masses feature; use in Gromacs engine#1119
dwhswenson wants to merge 1 commit into
openpathsampling:masterfrom
dwhswenson:external_masses

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@dwhswenson

@dwhswenson dwhswenson commented Aug 9, 2022

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Apparently Gromacs snapshots didn't have masses associated? See #1117. I was pretty sure we've used masses here before, but can't find an example of it.

Note that the better long-term solution for the needs of #1117 will be an engine.randomize_velocities -- we already have the machinery to use this, but haven't actually implemented any examples yet.

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codecov Bot commented Aug 9, 2022 •
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Codecov Report

❌ Patch coverage is 60.00000% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.74%. Comparing base (965d8a2) to head (61d0c3e).
⚠️ Report is 238 commits behind head on master.

Files with missing lines Patch % Lines
openpathsampling/engines/gromacs/engine.py 50.00% 3 Missing ⚠️
openpathsampling/engines/features/engine_masses.py 66.66% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##           master    #1119      +/-   ##
==========================================
- Coverage   81.75%   81.74%   -0.02%     
==========================================
  Files         142      143       +1     
  Lines       15612    15622      +10     
==========================================
+ Hits        12764    12770       +6     
- Misses       2848     2852       +4

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@dwhswenson dwhswenson mentioned this pull request Aug 9, 2022
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@sroet

sroet commented Aug 9, 2022

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Leaving a comment here to keep the issue clean, but about

We'll need to be able to correctly randomize velocities, which requires both creating random velocities and then applying constraints. I don't think we have a way to apply constraints to a Gromacs snapshot yet. These are things that would be good to add, but I probably can't get to this in the very near future.

I am pretty sure that was fixed in PyRETIS by letting gromacs run a 0 step simulation, wouldn't a similar solution work for OPS?

@dwhswenson

dwhswenson commented Aug 9, 2022

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@sroet : Yes, I think that is the approach to take, but implementing and testing it will take a bit of time, and is beyond what I can promise before the end of this month. (Goal for the next two weeks is to get 1.6 released before my ACS talk on Aug 24; I'm just glad to finally be back to working on OPS!)

@sroet

sroet commented Aug 9, 2022

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(Goal for the next two weeks is to get 1.6 released before my ACS talk on Aug 24; I'm just glad to finally be back to working on OPS!)

Good luck with your talk! Just ping me if you want my eyes on something.

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@dwhswenson @sroet