Create RestCapableHybridTopologyFactory

[zhang-ivy]

Description

A subclass of HybridTopologyFactory that handles:
- alchemical modification of atoms
- REST scaling
- 4th dimension softcore
with custom forces. Supports one alchemical region and one REST region.

See docstring of RestCapablePMEHybridTopologyFactory for more details.

Motivation and context

Resolves #???

How has this been tested?

Change log

[codecov]

Codecov Report

Merging #848 (7cae422) into main (d3649d1) will increase coverage by 2.59%.
The diff coverage is 83.48%.

[ijpulidos]

CC #873 and port back to this when it works

[ijpulidos]

@jchodera Your feedback is welcomed here! :)

[mikemhenry]

https://docs.python.org/3/library/functions.html?#hasattr

[zhang-ivy]

As discussed, to fix the tests with current OpenMM versions. We could support current/previous versions of Openmm by checking the addComputedValue attribute and use it if available. We can use hasattr(CustomNonbondedForce, "addComputedValue") for this purpose.

Done!

The tests are now failing because pytest is not defined? @mikemhenry @ijpulidos

==================================== ERRORS ====================================
________________ ERROR collecting perses/tests/test_relative.py ________________
perses/tests/test_relative.py:1041: in <module>
    @pytest.mark.gpu_needed
E   NameError: name 'pytest' is not defined
________________ ERROR collecting perses/tests/test_relative.py ________________
perses/tests/test_relative.py:1041: in <module>
    @pytest.mark.gpu_needed
E   NameError: name 'pytest' is not defined

[mikemhenry]

As discussed, to fix the tests with current OpenMM versions. We could support current/previous versions of Openmm by checking the addComputedValue attribute and use it if available. We can use hasattr(CustomNonbondedForce, "addComputedValue") for this purpose.

Done!

The tests are now failing because pytest is not defined? @mikemhenry @ijpulidos

==================================== ERRORS ====================================
________________ ERROR collecting perses/tests/test_relative.py ________________
perses/tests/test_relative.py:1041: in <module>
    @pytest.mark.gpu_needed
E   NameError: name 'pytest' is not defined
________________ ERROR collecting perses/tests/test_relative.py ________________
perses/tests/test_relative.py:1041: in <module>
    @pytest.mark.gpu_needed
E   NameError: name 'pytest' is not defined

I think I fixed this! I actually introduced this error when I marked the test to run on the GPU, sorry!

[zhang-ivy]

@mikemhenry : No worries, thanks!

[zhang-ivy]

@mikemhenry : I think the only thing this PR is missing is addressing #899

[mikemhenry]

@zhang-ivy So sorry! I didn't realize you were still working on this!! Sorry about that merge commit, I hope I did it right!

[zhang-ivy]

@mikemhenry : No worries! I just realized I forgot something, which is why I just committed, but this PR is done, except I think we are waiting on you to add the API point: #899 !

[mikemhenry]

I just sat down to work on adding that and saw that I needed a merge 😆

[ijpulidos]

Looks good, great work!! Just a few changes that should be very easy to make.

[ijpulidos]

Looks great!

We just have to keep in mind the cost of having the LongRangeCorrection setting.