Use openmm.LangevinMiddleIntegrator

[mattwthompson]

Description

Implements #587

Todos

Notable points that this PR has either accomplished or will accomplish.

• openmmtools.integrators.LangevinIntegrator -> openmm.LangevinMiddleIntegrator

Questions

• Arguments actually a drop-in replacement?

Status

• Ready to go

[mattwthompson]

I am quite annoyed that I can't pass named arguments to these SWIG-generated functions:

In [1]: from openmm import LangevinMiddleIntegrator

In [2]: LangevinMiddleIntegrator(1, 1, 1)
Out[2]: <openmm.openmm.LangevinMiddleIntegrator; proxy of <Swig Object of type 'OpenMM::LangevinMiddleIntegrator *' at 0x107e67e40> >

In [3]: LangevinMiddleIntegrator(temperature=1, frictionCoeff=1, stepSize=1)
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[3], line 1
----> 1 LangevinMiddleIntegrator(temperature=1, frictionCoeff=1, stepSize=1)

TypeError: LangevinMiddleIntegrator.__init__() got an unexpected keyword argument 'temperature'

__init__(self, temperature, frictionCoeff, stepSize) → LangevinMiddleIntegrator
__init__(self, other) → LangevinMiddleIntegrator
    Create a LangevinMiddleIntegrator.

    Parameters
    temperature (double) – the temperature of the heat bath (in Kelvin)

    frictionCoeff (double) – the friction coefficient which couples the system to the heat bath (in inverse picoseconds)

    stepSize (double) – the step size with which to integrate the system (in picoseconds)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 87.69%. Comparing base (3637ed9) to head (3a8655f).
Report is 7 commits behind head on main.

Additional details and impacted files

[lilyminium]

Arguments actually a drop-in replacement?

I think they should be -- not only are the units and default argument the same, but the collision_rate is converted to self._gamma in openmmtools, where gamma is typically used to represent the friction coefficient.

[lilyminium]

LGTM -- thanks for the quick fix @mattwthompson!

My only thought -- does this need tests of some kind, e.g. to check the temperature issue? But that might be out of scope and a lot more work for a one-line change, happy to defer to you.

[mattwthompson]

Agree it would be useful but I don't know a quick way to test that right now