uncrustify and clean up

Author: frankfeifan

src/reactions/massActions/MassActions.hpp

@@ -175,13 +175,13 @@ void calculateAggregatePrimaryConcentrationsWrtLogC( PARAMS_DATA const & params,
 
   REAL_TYPE logSecondarySpeciesConcentrations[numSecondarySpecies] = {0};
 
-  calculateAggregatePrimaryConcentrationsWrtLogC< REAL_TYPE, 
-                                                  INT_TYPE, 
-                                                  INDEX_TYPE>( params,
-                                                               logPrimarySpeciesConcentrations,
-                                                               logSecondarySpeciesConcentrations,
-                                                               aggregatePrimarySpeciesConcentrations,
-                                                               dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations );
+  calculateAggregatePrimaryConcentrationsWrtLogC< REAL_TYPE,
+                                                  INT_TYPE,
+                                                  INDEX_TYPE >( params,
+                                                                logPrimarySpeciesConcentrations,
+                                                                logSecondarySpeciesConcentrations,
+                                                                aggregatePrimarySpeciesConcentrations,
+                                                                dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations );
 
 }
 
@@ -241,8 +241,9 @@ void calculateTotalAndMobileAggregatePrimaryConcentrationsWrtLogC( PARAMS_DATA c
                                                                                                       dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration;
 
         dMobileAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, k ) += params.stoichiometricMatrix( j,
-                                                                                                                                        i+numSecondarySpecies ) *
-                                                                                                            dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration * params.mobileSecondarySpeciesFlag( j );
+                                                                                                                                         i+numSecondarySpecies ) *
+                                                                                                            dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration *
+                                                                                                            params.mobileSecondarySpeciesFlag( j );
       }
     }
   }

src/reactions/reactionsSystems/EquilibriumReactionsAggregatePrimaryConcentration_impl.hpp

@@ -128,9 +128,10 @@ EquilibriumReactions< REAL_TYPE,
 
 
   REAL_TYPE residualNorm = 0.0;
- //         0:     1e-20       -0           2 -2.5e+11       1e-20        7           2      1.8           1        5  
-  printf( "iter       X1       R0           X2      R1          X3       R2          X4       R3           S       R4\n");
-  printf( "----   ---------------      ---------------      ---------------      ---------------      ---------------\n");
+  // // Print for MoMaS only
+  // //         0:     1e-20       -0           2 -2.5e+11       1e-20        7           2      1.8           1        5
+  // printf( "iter       X1       R0           X2      R1          X3       R2          X4       R3           S       R4\n" );
+  // printf( "----   ---------------      ---------------      ---------------      ---------------      ---------------\n" );
   for( int k=0; k<150; ++k )
   {
     computeResidualAndJacobianAggregatePrimaryConcentrations( temperature,
@@ -147,18 +148,19 @@ EquilibriumReactions< REAL_TYPE,
     }
     residualNorm = sqrt( residualNorm );
 
-      printf( "%2d:  %8.2g %8.2g    %8.2g %8.2g    %8.2g %8.2g    %8.2g %8.2g    %8.2g %8.2g  \n", 
-              k,
-              exp( logPrimarySpeciesConcentration[0] ),
-              residual[0],
-              exp( logPrimarySpeciesConcentration[1] ),
-              residual[1],
-              exp( logPrimarySpeciesConcentration[2] ),
-              residual[2],
-              exp( logPrimarySpeciesConcentration[3] ),
-              residual[3],
-              exp( logPrimarySpeciesConcentration[4] ),
-              residual[4] );
+    //  // Print for MoMaS only
+    // printf( "%2d:  %8.2g %8.2g    %8.2g %8.2g    %8.2g %8.2g    %8.2g %8.2g    %8.2g %8.2g  \n",
+    //         k,
+    //         exp( logPrimarySpeciesConcentration[0] ),
+    //         residual[0],
+    //         exp( logPrimarySpeciesConcentration[1] ),
+    //         residual[1],
+    //         exp( logPrimarySpeciesConcentration[2] ),
+    //         residual[2],
+    //         exp( logPrimarySpeciesConcentration[3] ),
+    //         residual[3],
+    //         exp( logPrimarySpeciesConcentration[4] ),
+    //         residual[4] );
 
     //printf( "iter, residualNorm = %2d, %16.10g \n", k, residualNorm );
     if( residualNorm < 1.0e-12 )

src/reactions/reactionsSystems/MixedEquilibriumKineticReactions.hpp

@@ -74,7 +74,8 @@ class MixedEquilibriumKineticReactions
    * @param aggregatePrimarySpeciesConcentrations Output aggregate concentrations (per primary)
    * @param mobileAggregatePrimarySpeciesConcentrations Output mobile aggregate concentrations (per primary)
    * @param dAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations Derivatives of aggregate concentrations w.r.t. log
-   * @param dMobileAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations Derivatives of mobile aggregate concentrations w.r.t. log
+   * @param dMobileAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations Derivatives of mobile aggregate concentrations
+   * w.r.t. log
    * primary
    * @param reactionRates Output vector of kinetic reaction rates
    * @param dReactionRates_dLogPrimarySpeciesConcentrations Derivatives of reaction rates w.r.t. log primary species
@@ -227,7 +228,8 @@ class MixedEquilibriumKineticReactions
    * @param aggregatePrimarySpeciesConcentrations Output aggregate concentrations (per primary)
    * @param mobileAggregatePrimarySpeciesConcentrations Output mobile aggregate concentrations (per primary)
    * @param dAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations Derivatives of aggregate concentrations w.r.t. log
-   * @param dMobileAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations Derivatives of mobile aggregate concentrations w.r.t. log
+   * @param dMobileAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations Derivatives of mobile aggregate concentrations
+   * w.r.t. log
    * primary
    * @param reactionRates Output vector of kinetic reaction rates
    * @param dReactionRates_dLogPrimarySpeciesConcentrations Derivatives of reaction rates w.r.t. log primary species