Examples run phases in expected order

[ijpulidos]

Description

Changes the order how phases are run in the examples and templates for benchmarks. Making it to run vacuum, solvent and complex phases in that order.

Motivation and context

Resolves #1121

How has this been tested?

Tested locally

Change log

Examples and benchmarks template input files now run vacuum, solvent and complex phases in order.

[codecov[bot]]

Codecov Report

Merging #1122 (0c2b805) into main (b477551) will not change coverage. The diff coverage is n/a.

[jchodera]

Interestingly, I'm seeing failures here:

=========================== short test summary info ============================
FAILED perses/tests/test_relative_setup.py::test_relative_setup_charge_change - AssertionError: charge diff is -1 but should be zero.
assert False
 +  where False = <function isclose at 0x7f79e2bf2430>(-1, 0)
 +    where <function isclose at 0x7f79e2bf2430> = <module 'numpy' from '/usr/share/miniconda/envs/test/lib/python3.8/site-packages/numpy/__init__.py'>.isclose
====== 1 failed, 97 passed, 21 skipped, 119 warnings in 681.62s (0:11:21) ======

@dominic-rufa @zhang-ivy : Any idea why this test might be failing?

[jchodera]

Oddly enough, the failures are with OpenMM 7.6 and the nightly build, but not OpenMM 7.7.

[mikemhenry]

@jchodera just for the record, we are tracking that error here: https://github.com/choderalab/perses/issues/1113