[Python 3.9] Reimplement Clar Optimization with Scipy MILP

[JacksonBurns]

This PR replaces #2623 as discussed in this comment: #2687 (comment)

[xiaoruiDong]

@xiaoruiDong Mark this PR.

[JacksonBurns]

@xiaoruiDong here are the remaining test failures which we should address in this PR.

FAILED test/rmgpy/data/solvationTest.py::TestSoluteDatabase::test_saturation_density - AssertionError: assert 1.93 == 0
 +  where 1.93 = round(1.9298279226322848, 2)
 +    where 1.9298279226322848 = abs((6385.1498279226325 - 6383.22))
 +      where 6385.1498279226325 = get_liquid_saturation_density('Hexane', 400)
FAILED test/rmgpy/data/thermoTest.py::TestCyclicThermo::test_add_poly_ring_correction_thermo_data_from_heuristic_using_pyrene - AssertionError: assert 'Benzene' in []
FAILED test/rmgpy/data/thermoTest.py::TestMolecularManipulationInvolvedInThermoEstimation::test_bicyclic_decomposition_for_polyring_using_pyrene - assert [0, 0, 0, 0, 0] == [0, 6, 6, 6, 6]
  At index 1 diff: 0 != 6
  Full diff:
  - [0, 6, 6, 6, 6]
  + [0, 0, 0, 0, 0]
FAILED test/rmgpy/data/kinetics/familyTest.py::TestTreeGeneration::test_f_rules - ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (7, 6) + inhomogeneous part.
FAILED test/rmgpy/data/kinetics/familyTest.py::TestTreeGeneration::test_d_regularization_dims - Exception: Unable to calculate free energy for species 'C6H6-5': no thermo or statmech data available.
FAILED test/rmgpy/molecule/moleculeTest.py::TestMolecule::test_count_aromatic_rings - assert [2, 0] == [2, 1, 0]
  At index 1 diff: 0 != 1
  Right contains one more item: 0
  Full diff:
  - [2, 1, 0]
  ?     ---
  + [2, 0]
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_naphthyl - assert 2 == 4
 +  where 2 = len([Molecule(smiles="[c]1cccc2ccccc12"), Molecule(smiles="[C]1=C2C=CC=CC2=CC=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_napthalene - assert 2 == 4
 +  where 2 = len([Molecule(smiles="Cc1cccc2ccccc12"), Molecule(smiles="CC1=CC=CC2=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_phenanthrene - assert 2 == 3
 +  where 2 = len([Molecule(smiles="Cc1cccc2c1ccc1ccccc12"), Molecule(smiles="CC1=CC=CC2=C1C=CC1=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_phenanthrene_radical - assert 2 == 9
 +  where 2 = len([Molecule(smiles="[CH2]c1cccc2c1ccc1ccccc12"), Molecule(smiles="[CH2]C1=CC=CC2=C1C=CC1=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_c13h11_rad - assert 2 == 6
 +  where 2 = len([Molecule(smiles="Cc1ccc([CH]c2ccccc2)cc1"), Molecule(smiles="CC1=CC=C([CH]C2=CC=CC=C2)C=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_aryne_3_rings - assert 4 == 5
 +  where 4 = len([Molecule(smiles="C1#Cc2c(ccc3ccccc23)C=C1"), Molecule(smiles="C1=C=C2C(=CC=1)C=Cc1ccccc12"), Molecule(smiles="C1#CC2=C(C=C1)C=Cc1ccccc12"), Molecule(smiles="C1#CC2=C(C=C1)C=CC1=C2C=CC=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_polycyclic_aromatic_with_non_aromatic_ring2 - assert 2 == 4
 +  where 2 = len([Molecule(smiles="C=C1C=Cc2cc3c(ccc4cc5ccccc5cc43)cc2C1=C"), Molecule(smiles="C=C1C=CC2=CC3=C(C=CC4=CC5=CC=CC=C5C=C43)C=C2C1=C")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_false_negative_polycyclic_aromaticity_perception - assert 2 == 6
 +  where 2 = len([Molecule(smiles="[CH2]c1cccc2ccccc12"), Molecule(smiles="C=C1C=CC=C2C=C[CH]C=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_false_negative_polycylic_aromaticity_perception2 - assert 6 == 7
 +  where 6 = len([Molecule(smiles="[CH2]C=C1C=CC(=C)c2ccccc21"), Molecule(smiles="[CH2]c1ccc(C=C)c2ccccc12"), Molecule(smiles="C=C[C]1C=CC(=C)c2ccccc21"), Molecule(smiles="C=CC1=C[CH]C(=C)c2ccccc21"), Molecule(smiles="[CH2]C1=CC=C(C=C)c2ccccc21"), Molecule(smiles="[CH2]C=C1C=CC(=C)C2=C1C=CC=C2")])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_clar_optimization - ValueError: not enough values to unpack (expected 4, got 2)
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_phenanthrene - assert 0 == 1
 +  where 0 = len([])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_phenalene - assert 0 == 2
 +  where 0 = len([])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_corannulene - assert 0 == 5
 +  where 0 = len([])
FAILED test/rmgpy/statmech/ndTorsionsTest.py::TestHinderedRotorClassicalND::test_hindered_rotor_nd - assert 4e-05 == 0
 +  where 4e-05 = round((2.8993250143510827 - 2.899287634962152), 5)
 +    where 2.8993250143510827 = abs(2.8993250143510827)
 +      where 2.8993250143510827 = <bound method HinderedRotorClassicalND.calc_partition_function of Mode(quantum=False)>(300.0)
 +        where <bound method HinderedRotorClassicalND.calc_partition_function of Mode(quantum=False)> = Mode(quantum=False).calc_partition_function

There are a couple test failures which look like actual failures to run (test/rmgpy/data/kinetics/familyTest.py::TestTreeGeneration::test_f_rules and test/rmgpy/data/kinetics/familyTest.py::TestTreeGeneration::test_d_regularization_dims) - the remained run, but produce 'incorrect' results. Some of these might not actually be incorrect, and the tests need updating. Others are likely issues with the reimplemented CLAR optimization. Please let me know how I can help get these running again!

[JacksonBurns]

Hi @xiaoruiDong will you be able to work on this PR, or should we re-assign?

[xiaoruiDong]

Hi @xiaoruiDong will you be able to work on this PR, or should we re-assign?

I will work on this but don't have time in a week or two... If this is something urgent, I am ok with re-assignment and can talk to the people who will work on this.

[JacksonBurns]

It's not especially urgent - I am going to try and fix some of the failures, but we can continue to chat about it once you have the time!

[JacksonBurns]

These are the commits that are specific to the CLAR re-implementation in this PR: https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2694/files/756439fd5096859f3e67002571c0a9e1c19258ff