more derivatives

Author: rrsettgast

src/common/logMath.hpp

@@ -35,7 +35,7 @@ struct LogExp
   T dWrtLogConst()
   {
     if constexpr ( Base == LogBase::e ) { return T(1.0); }
-    else                                { return T(ln10()); }
+    else                                { return T(ln10<T>()); }
   }
 
 

src/reactions/massActions/MassActions.hpp

@@ -147,14 +147,14 @@ void calculateAggregatePrimaryConcentrationsWrtLogC( PARAMS_DATA const & params,
   {
     REAL_TYPE const speciesConcentration_i = logmath::exp( logPrimarySpeciesConcentrations[i] );
     aggregatePrimarySpeciesConcentrations[i] = speciesConcentration_i;
-    dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, i ) = speciesConcentration_i;
+    dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, i ) = logmath::dWrtLogConst<REAL_TYPE>() * speciesConcentration_i;
     for( int j = 0; j < numSecondarySpecies; ++j )
     {
       REAL_TYPE const secondarySpeciesConcentrations_j = logmath::exp( logSecondarySpeciesConcentrations[j] );
       aggregatePrimarySpeciesConcentrations[i] += params.stoichiometricMatrix( j, i+numSecondarySpecies ) * secondarySpeciesConcentrations_j;
       for( int k=0; k<numPrimarySpecies; ++k )
       {
-        REAL_TYPE const dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration = logmath::dWrtLogConst() * params.stoichiometricMatrix( j, k+numSecondarySpecies ) * secondarySpeciesConcentrations_j;
+        REAL_TYPE const dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration = logmath::dWrtLogConst<REAL_TYPE>() * params.stoichiometricMatrix( j, k+numSecondarySpecies ) * secondarySpeciesConcentrations_j;
         dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, k ) += params.stoichiometricMatrix( j, i+numSecondarySpecies ) *
                                                                                                       dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration;
       }
@@ -237,8 +237,8 @@ void calculateTotalAndMobileAggregatePrimaryConcentrationsWrtLogC( PARAMS_DATA c
     REAL_TYPE const speciesConcentration_i = logmath::exp( logPrimarySpeciesConcentrations[i] );
     aggregatePrimarySpeciesConcentrations[i] = speciesConcentration_i;
     mobileAggregatePrimarySpeciesConcentrations[i] = speciesConcentration_i;
-    dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, i ) = speciesConcentration_i;
-    dMobileAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, i ) = speciesConcentration_i;
+    dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, i ) = logmath::dWrtLogConst<REAL_TYPE>() * speciesConcentration_i;
+    dMobileAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, i ) = logmath::dWrtLogConst<REAL_TYPE>() * speciesConcentration_i;
 
     for( int j = 0; j < numSecondarySpecies; ++j )
     {
@@ -247,7 +247,7 @@ void calculateTotalAndMobileAggregatePrimaryConcentrationsWrtLogC( PARAMS_DATA c
       mobileAggregatePrimarySpeciesConcentrations[i] += params.stoichiometricMatrix( j, i+numSecondarySpecies ) * secondarySpeciesConcentrations_j * params.mobileSecondarySpeciesFlag( j );
       for( int k=0; k<numPrimarySpecies; ++k )
       {
-        REAL_TYPE const dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration = logmath::dWrtLogConst() * params.stoichiometricMatrix( j, k+numSecondarySpecies ) * secondarySpeciesConcentrations_j;
+        REAL_TYPE const dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration = logmath::dWrtLogConst<REAL_TYPE>() * params.stoichiometricMatrix( j, k+numSecondarySpecies ) * secondarySpeciesConcentrations_j;
         dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, k ) += params.stoichiometricMatrix( j, i+numSecondarySpecies ) *
                                                                                                       dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration;
 

src/reactions/reactionsSystems/MixedEquilibriumKineticReactions_impl.hpp

@@ -78,8 +78,8 @@ MixedEquilibriumKineticReactions< REAL_TYPE,
       REAL_TYPE const speciesConcentration_i = logmath::exp( logPrimarySpeciesConcentrations[i] );
       aggregatePrimarySpeciesConcentrations[i] = speciesConcentration_i;
       mobileAggregatePrimarySpeciesConcentrations[i] = speciesConcentration_i;
-      dAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations( i, i ) = speciesConcentration_i;
-      dMobileAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations( i, i ) = speciesConcentration_i;
+      dAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations( i, i ) = logmath::dWrtLogConst<REAL_TYPE>() * speciesConcentration_i;
+      dMobileAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations( i, i ) = logmath::dWrtLogConst<REAL_TYPE>() * speciesConcentration_i;
     }
   }
 
@@ -168,11 +168,11 @@ MixedEquilibriumKineticReactions< REAL_TYPE,
   {
     for( IntType j = 0; j < numPrimarySpecies; ++j )
     {
-      dReactionRates_dLogPrimarySpeciesConcentrations( i, j ) = reactionRatesDerivatives( i, j + numSecondarySpecies );
+      dReactionRates_dLogPrimarySpeciesConcentrations( i, j ) = logmath::dWrtLogConst<REAL_TYPE>() * reactionRatesDerivatives( i, j + numSecondarySpecies );
 
       for( IntType k = 0; k < numSecondarySpecies; ++k )
       {
-        RealType const dLogSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentrations = params.stoichiometricMatrix( k, j + numSecondarySpecies );
+        RealType const dLogSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentrations = logmath::dWrtLogConst<REAL_TYPE>() * params.stoichiometricMatrix( k, j + numSecondarySpecies );
         dReactionRates_dLogPrimarySpeciesConcentrations( i, j ) += reactionRatesDerivatives( i, k ) * dLogSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentrations;
       }
     }