cleanup use of logarithms

[rrsettgast]

• remove non-log(c) option
• create aliases for log/exp
• use aliases everywhere in the code
• correct derivatives wrt log by multiplying by ln(10) when using base10, and 1 when using base_e

[azibitsker]

Should it be?
dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, i ) = logmath::dWrtLogConst() * speciesConcentration_i;

[azibitsker]

I went went through the changes and based on my current understanding of the framework, I think there is only one type of correction that I see in the derivative of aggregate wrt to log(C^primary) that should have a ln(10) factor in front of C_i.

[azibitsker]

Similarly, should it be?
dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, i ) = logmath::dWrtLogConst() * speciesConcentration_i;
dMobileAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, i ) = logmath::dWrtLogConst() * speciesConcentration_i;

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (97a1fb1) to head (0f6cc11).

Additional details and impacted files

@@            Coverage Diff            @@
##              main       #19   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           25        26    +1     
  Lines          830       743   -87     
=========================================
- Hits           830       743   -87     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[frankfeifan]

There are a few places missing logmath::dWrtLogConst< RealType >() but multiplied back somewhere else, so the unit tests don't complain. I've left my comments in some places and will check all other places.

[frankfeifan]

Suggested change

	data.reactionRatesDerivatives( r, i ) = data.reactionRatesDerivatives( r, i ) * logmath::exp( -data.speciesConcentration[i] );
	data.reactionRatesDerivatives( r, i ) = data.reactionRatesDerivatives( r, i ) * logmath::exp( -data.speciesConcentration[i] ) / logmath::dWrtLogConst< double >();

[frankfeifan]

I think it is better to account for logmath::dWrtLogConst< REAL_TYPE >() when we calculate reactionRatesDerivatives in kineticReactions::computeReactionRates instead of here.