Reliable input file errors

[ischoegl]

Changes proposed in this pull request

• Address InputFileError issues
• Simplify ReactionRate::check
• Avoid NAN as sentinel values for ReactionRate initialization status (see --fast-math enhancement issue)

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

Closes #1281, closes #1283, partially addresses Cantera/enhancements#125

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

Loading the following YAML

phases:
- name: gas
  thermo: ideal-gas
  species: [{h2o2.yaml/species: all}]
  kinetics: gas
  reactions: all
  state: {T: 300.0, P: 1 atm, X: {O2: 0.21, N2: 0.79}}

reactions:
- equation: O + H2 <=> H + OH
  rate-constant: {A: 3.87e+04 cm^6/mol^2/s, b: 2.7, Ea: 6260.0}
- equation: 2 OH (+M) <=> H2O2 (+M)
  type: falloff
- equation: CH3 + OH => CH3O + H
  rate-constant: {A: 1.0, b: 0, Ea: 0}

results in the following error:

CanteraError:
*******************************************************************************
CanteraError thrown by addReactions:

*******************************************************************************
InputFileError thrown by UnitSystem::convert:
Error on line 11 of ./test.yaml:
Incompatible units:
    Units(1.0000000000000002e-06 m^6 / kmol^2 / s) and
    Units(m^3 / kmol / s)
|  Line |
|     6 |   reactions: all
|     7 |   state: {T: 300.0, P: 1 atm, X: {O2: 0.21, N2: 0.79}}
|     8 |
|     9 | reactions:
|    10 | - equation: O + H2 <=> H + OH
>    11 >   rate-constant: {A: 3.87e+04 cm^6/mol^2/s, b: 2.7, Ea: 6260.0}
                               ^
|    12 | - equation: 2 OH (+M) <=> H2O2 (+M)
|    13 |   type: falloff
|    14 | - equation: CH3 + OH => CH3O + H
*******************************************************************************

*******************************************************************************
InputFileError thrown by FalloffRate::validate:
Error on line 12 of ./test.yaml:
Rate object for reaction '2 OH (+M) <=> H2O2 (+M)' is not configured.
|  Line |
|     7 |   state: {T: 300.0, P: 1 atm, X: {O2: 0.21, N2: 0.79}}
|     8 |
|     9 | reactions:
|    10 | - equation: O + H2 <=> H + OH
|    11 |   rate-constant: {A: 3.87e+04 cm^6/mol^2/s, b: 2.7, Ea: 6260.0}
>    12 > - equation: 2 OH (+M) <=> H2O2 (+M)
            ^
|    13 |   type: falloff
|    14 | - equation: CH3 + OH => CH3O + H
|    15 |   rate-constant: {A: 1.0, b: 0, Ea: 0}
*******************************************************************************

*******************************************************************************
InputFileError thrown by Reaction::checkSpecies:
Error on line 14 of ./test.yaml:
Reaction 'CH3 + OH => CH3O + H'
contains undeclared species: 'CH3', 'CH3O'
|  Line |
|     9 | reactions:
|    10 | - equation: O + H2 <=> H + OH
|    11 |   rate-constant: {A: 3.87e+04 cm^6/mol^2/s, b: 2.7, Ea: 6260.0}
|    12 | - equation: 2 OH (+M) <=> H2O2 (+M)
|    13 |   type: falloff
>    14 > - equation: CH3 + OH => CH3O + H
            ^
|    15 |   rate-constant: {A: 1.0, b: 0, Ea: 0}
*******************************************************************************
*******************************************************************************

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

[bryanwweber]

Just a couple small comments I noticed quickly. I haven't gone through everything 😄

[bryanwweber]

@ischoegl This needs a rebase to fix the merge conflict. I'd also like @speth to take a look at this when he has a chance.

[bryanwweber]

A few comments for consideration 😄

[ischoegl]

@bryanwweber / @speth ... rebased and ready for a review.

[speth]

Thanks for this, @ischoegl. Your solution to #1283 was quite a bit cleaner than what I had been expecting to have to do. I just had a couple of minor suggestions.

[ischoegl]

@speth ... thanks for the review! I updated per suggestions.

[ischoegl]

I believe that things are taken care of now.