adding HO array and LJ testsystem

wiederm commented 8 months ago

Description

This PR will add additional test systems (HO array and LJ fluids), functionality, and tests for combined sampling with LangevinIntegrator and MC moves as well as PBC

Todos

[x] HO array test system
[x] LJ test system

Status

[x] Ready to go

chrisiacovella commented 8 months ago

I changed around a bit of the code structure, causing the test_potential tests to fail. Will fix that in a bit.

chrisiacovella commented 8 months ago

Summary of additions so far:

updated the pairlist calculation (fixing some bugs causing the LJ test to fail) and making it use jax functions to enable compatibility with jax.grad
Added in the neighborlist; require small refactoring to the base potential class (namely passing an instance of the neighborlist).
Tests have been added for the neighborlist and additional tests to the state (including fixing a typing issue that seemed to be causing some issues for returning values with units dropped: explicit tests were added for this).

To do still:

Additional tests for the LJ potential to ensure we are getting the correct energy and force for a 2 particle system.
Refactor the langevin integrator to know about the neighborlist, as during a set of moves we will need to check and rebuild as necessary. These functions will also be jitted.
implement lj fluid test system.

wiederm commented 8 months ago

I think this looks good as it is. After review, we can merge IMHO.

codecov-commenter commented 8 months ago

Codecov Report

Merging #4 (6be72aa) into main (98dd17d) will increase coverage by 7.66%. The diff coverage is 90.77%.

Additional details and impacted files

choderalab / chiron