Toolkit 0.11 support

[Yoshanuikabundi]

Description

Update QCSubmit to work with the OpenFF Toolkit 0.11+

Todos

• [x] Pin Toolkit >= 0.11 in environments

Test failures (running locally on my machine):

• [x] Many test failures due to moving from OpenMM units to OpenFF units in locally executed code that were fixed with simple find+replace
• [x] Several test failures due to https://github.com/openforcefield/openff-toolkit/issues/1416 that are fixed in https://github.com/openforcefield/openff-toolkit/pull/1417
• [x] A usage of pytest.approx that needed updating with the new units package
• [x] Manual unit handling in combine_openff_molecules around np.vstack() that is no longer necessary with OpenFF units
• [x] A number of tests that seem to come from the same root cause (see below)

Remaining failing tests

The remaining failing tests seem to all stem from the same cause. I think what's happening is that we're passing conformers to geomeTRIC as OpenFF units, when it expects OpenMM units, but I can't find the place in code where this happens. I think the fix will be as simple as inserting an .to_openmm() in the right spot, but I don't know where that spot is. Here's the relevant Tornado output:

INFO     tornado.application:managers.py:622 Processed 1 tasks: 0 succeeded / 1 failed).
INFO     tornado.application:managers.py:623 Task ids, submission status, calculation status below
INFO     tornado.application:managers.py:625     Task 5 : sent / failed: unknown
INFO     tornado.application:managers.py:627 The following tasks failed with the errors:
INFO     tornado.application:managers.py:629 Error message for task id 5
INFO     tornado.application:managers.py:630     Error type: unknown
INFO     tornado.application:managers.py:631     Backtrace: 
geomeTRIC run_json error:
Traceback (most recent call last):
  File "/home/joshmitchell/Documents/openff/qcsubmit/nogit/env/lib/python3.9/site-packages/geometric/run_json.py", line 225, in geometric_run_json
    geometric.optimize.Optimize(coords, M, IC, engine, None, params)
  File "/home/joshmitchell/Documents/openff/qcsubmit/nogit/env/lib/python3.9/site-packages/geometric/optimize.py", line 1331, in Optimize
    return optimizer.optimizeGeometry()
  File "/home/joshmitchell/Documents/openff/qcsubmit/nogit/env/lib/python3.9/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
    self.calcEnergyForce()
  File "/home/joshmitchell/Documents/openff/qcsubmit/nogit/env/lib/python3.9/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
    spcalc = self.engine.calc(self.X, self.dirname)
  File "/home/joshmitchell/Documents/openff/qcsubmit/nogit/env/lib/python3.9/site-packages/geometric/engine.py", line 873, in calc
    return self.calc_new(coords, dirname)
  File "/home/joshmitchell/Documents/openff/qcsubmit/nogit/env/lib/python3.9/site-packages/geometric/engine.py", line 865, in calc_new
    raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
  File "/home/joshmitchell/Documents/openff/qcsubmit/nogit/env/lib/python3.9/site-packages/qcengine/util.py", line 114, in compute_wrapper
    yield metadata
  File "/home/joshmitchell/Documents/openff/qcsubmit/nogit/env/lib/python3.9/site-packages/qcengine/compute.py", line 105, in compute
    output_data = executor.compute(input_data, config)
  File "/home/joshmitchell/Documents/openff/qcsubmit/nogit/env/lib/python3.9/site-packages/qcengine/programs/openmm.py", line 300, in compute
    context.setPositions(off_mol.conformers[0])
  File "/home/joshmitchell/Documents/openff/qcsubmit/nogit/env/lib/python3.9/site-packages/openmm/openmm.py", line 12108, in setPositions
    return _openmm.Context_setPositions(self, positions)
ValueError: in method Context_setPositions, argument 2 could not be converted to type std::vector< Vec3,std::allocator< Vec3 > > const &

Questions

• [x] Could use some help with the last tests!

Status

• [ ] Requires https://github.com/MolSSI/QCEngine/pull/378 in a release on conda forge
• [ ] Requires https://github.com/openforcefield/openff-toolkit/pull/1417 in a release on conda forge
• [ ] Ready to go

[jthorton]

Hi @Yoshanuikabundi, thanks for taking this on!

The issue with the tests is due to this line in qcengine which assumes that the conformer is already in openmm units should be an easy fix I think!

[Yoshanuikabundi]

Oh I didn't realise QCEngine used OpenFF Molecules internally! Thanks for pointing that out @jthorton!

[Yoshanuikabundi]

OK this PR now passes tests locally when used together with https://github.com/MolSSI/QCEngine/pull/378 and https://github.com/openforcefield/openff-toolkit/pull/1417

This is probably best released as 0.4.0 - I've made no attempt to preserve compatibility with earlier versions of the toolkit, so if bug patch releases for the old toolkit is required it'll be helpful to have the v0.3 series available.

[Yoshanuikabundi]

I've had to move CI from Python 3.7 to 3.8 as it is required by v0.11.

[Yoshanuikabundi]

Superseded by #204