Remove reaction specializations

[ischoegl]

Changes proposed in this pull request

• Deprecate ThreeBodyReaction in C++ and Python
• Deprecate FalloffReaction in C++ and Python
• Remove ReactionFactory and deprecate newReaction constructors
• Update Python Reaction.__repr__ output
• Implement ThirdBody object in Python and deprecate efficiencies argument in constructor

Incorporates #1332

If applicable, fill in the issue number this pull request is fixing

Closes #1220; partially addresses Cantera/enhancements#142

If applicable, provide an example illustrating new features this pull request is introducing

In [1]: import cantera as ct

In [2]: ct.Reaction(equation="2 O + O2 <=> 2 O2", rate=ct.ArrheniusRate())
Out[2]: 2 O + O2 <=> O2 + O2    <three-body-Arrhenius>

In [3]: ct.Reaction(equation="2 O (+M) <=> O2 (+M)", rate=ct.TroeRate())
Out[3]: 2 O (+M) <=> O2 (+M)    <falloff-Troe>

In [4]: ct.Reaction("O:2", "O2:1", rate=ct.ArrheniusRate(), third_body=ct.ThirdBody())
Out[4]: 2 O + M <=> O2 + M    <three-body-Arrhenius>

In [5]: ct.Reaction("O:2", "O2:1", rate=ct.ArrheniusRate(), third_body=ct.ThirdBody("O2"))
Out[5]: 2 O + O2 <=> O2 + O2    <three-body-Arrhenius>

In [6]: ct.Reaction(equation="2 O + M <=> O2 + M", rate=ct.BlowersMaselRate())
Out[6]: 2 O + M <=> O2 + M    <three-body-Blowers-Masel>

Comments

• three-body type entry is now optional in YAML input
• Third body is supported for Blowers-Masel rates

Checklist

• The pull request includes a clear description of this code change
• Commit messages have short titles and reference relevant issues
• Build passes (scons build & scons test) and unit tests address code coverage
• Style & formatting of contributed code follows contributing guidelines
• The pull request is ready for review

[ischoegl]

Rebased and updated to incorporate changes to yaml2ck. This should be good for a review now (with the caveat that the first couple of commits are repeated from #1332)

[ischoegl]

@speth … thanks for the quick review on #1332! After the merge, I rebased this again so now it’s just what goes beyond CustomReaction

[speth]

Thanks, @ischoegl, I think this is an exciting step forward in simplifying the handling of different reaction rate parameterizations.

One thing that you only barely touched on is that by handling third bodies in the common Reaction class, these can in principle be used for any rate parameterization. However, there are a couple of quirks here that I think are worth ironing out. One is that there are a few places that single out the TwoTempPlasmaRate class as not being able to handle third bodies, but I don't understand why that would be the case now. Shouldn't any reaction type be able to handle third bodies now, with the exception that we explicitly remove them from Plog and Chebyshev reactions in acknowledgment that the third-body pressure dependence is already embedded in those rate constants?

The second is that there are a few situations where the automatic detection of specific third body colliders prevents instantiation of reactions as non-third-body reactions, even though I don't think these should be seen as problematic. For instance, the following reaction definitions raise exceptions, but were (I think correctly) permitted in Cantera 2.6:

R1 = ct.Reaction(
    equation="HO2 + O2 <=> OH + O + O2",
    rate={"type": "pressure-dependent-Arrhenius",
          "rate-constants": [
               {"P": 1013.25, "A": 1.2124e+16, "b": -0.5779, "Ea": 45491376.8},
               {"P": 101325., "A": 4.9108e+31, "b": -4.8507, "Ea": 103649395.2}
          ],
    }
)

R2 = ct.Reaction(
    equation="H + OH + 2 O2 = H2O + 2 O2",
    rate={"A": 1.234e5, "b": 0, "Ea": 4321.0}
)

[ischoegl]

@speth ... thanks for the feedback. I ended up being a lot more permissive/selective with the detection of third bodies, which I believe does make sense.

Regarding the two reactions you mentioned, they now produce the following:

In [2]: ct.Reaction(
   ...:     equation="HO2 + O2 <=> OH + O + O2",
   ...:     rate={
   ...:         "type": "pressure-dependent-Arrhenius",
   ...:         "rate-constants": [
   ...:             {"P": 1013.25, "A": 1.2124e16, "b": -0.5779, "Ea": 45491376.8},
   ...:             {"P": 101325.0, "A": 4.9108e31, "b": -4.8507, "Ea": 103649395.2},
   ...:         ],
   ...:     },
   ...: )
Out[2]: HO2 + O2 <=> O + OH + O2    <three-body-pressure-dependent-Arrhenius>

In [3]: ct.Reaction(
   ...:     equation="H + OH + 2 O2 = H2O + 2 O2", rate={"A": 1.234e5, "b": 0, "Ea": 4321.0}
   ...: )
Out[3]: H + 2 O2 + OH <=> H2O + 2 O2    <Arrhenius>

[ischoegl]

@speth ... I agree that there should be some updates to the Science section, but I think the rest is done! Thank you for the suggestions ... this should complete the work left over on refactoring of Reaction and ReactionRate outside of the website.

[ischoegl]

@speth ... I opened Cantera/cantera-website#216 to track the remaining documentation work.

[speth]

Thanks, @ischoegl - I think this is good to go.