misc changes for the mip work

NAMESPACE

@@ -135,7 +135,6 @@ export(LL_WARNING)
 export(LO_WARMING_RATIO)
 export(LUC_EMISSIONS)
 export(MLD_OCEAN_CARBON)
-export(MLD_THERMAL)
 export(N2O_CONSTRAIN)
 export(NATURAL_CH4)
 export(NAT_EMISSIONS_N2O)

R/RcppExports.R

@@ -1491,18 +1491,12 @@ HEAT_FLUX <- function() {
     .Call('_hector_HEAT_FLUX', PACKAGE = 'hector')
 }
 
-#' @describeIn special Ocean carbon mixed layer depth
+#' @describeIn ocean define the depth of the mixed layer in the ocean carbon cycle, default is 100m.
 #' @export
 MLD_OCEAN_CARBON <- function() {
     .Call('_hector_MLD_OCEAN_CARBON', PACKAGE = 'hector')
 }
 
-#' @describeIn special Thermal ocean mixed layer depth
-#' @export
-MLD_THERMAL <- function() {
-    .Call('_hector_MLD_THERMAL', PACKAGE = 'hector')
-}
-
 newcore_impl <- function(inifile, loglevel, suppresslogging, name) {
     .Call('_hector_newcore_impl', PACKAGE = 'hector', inifile, loglevel, suppresslogging, name)
 }

inst/include/component_data.hpp

@@ -387,7 +387,6 @@
 #define D_FLUX_MIXED            "flux_mixed"
 #define D_FLUX_INTERIOR         "flux_interior"
 #define D_HEAT_FLUX             "heatflux"
-#define D_THERMAL_MLD            "thermal_mld"
 
 
 // ------------------- messages being passed between components -------------------------

inst/include/forcing_component.hpp

@@ -80,17 +80,17 @@ class ForcingComponent : public IModelComponent {
 
 
     // CO2 parameters
-    const double a1 = -2.4785e-7;        // (W m–2 ppm–2) IPCC AR6 parameter for CH4 SARF Table 7.SM.1
-    const double b1 =  7.5906e-4;        // (W m–2 ppm–1) IPCC AR6 parameter for CH4 SARF Table 7.SM.1
-    const double c1 = -2.1492e-3;        // (W m–2 ppb–1/2) IPCC AR6 parameter for CH4 SARF Table 7.SM.1
-    const double d1 =  5.2488;           // (W m–2) IPCC AR6 parameter for CH4 SARF Table 7.SM.1
+    const double a1 = -2.4785e-7;        // (W m–2 ppm–2) IPCC AR6 parameter for CO2 SARF Table 7.SM.1
+    const double b1 =  7.5906e-4;        // (W m–2 ppm–1) IPCC AR6 parameter for CO2 SARF Table 7.SM.1
+    const double c1 = -2.1492e-3;        // (W m–2 ppb–1/2) IPCC AR6 parameter for CO2 SARF Table 7.SM.1
+    const double d1 =  5.2488;           // (W m–2) IPCC AR6 parameter for CO2 SARF Table 7.SM.1
     unitval delta_co2;                  // forcing tropospheric adjustment for CO2 see 7.3.2.1 of IPCC AR6
 
     // N2O parameters
-    const double a2 = -3.4197e-4;       // (W m–2 ppm–1) IPCC AR6 parameter for CH4 SARF Table 7.SM.1
-    const double b2 = 2.5455e-4;        // (W m–2 ppb–1) IPCC AR6 parameter for CH4 SARF Table 7.SM.1
-    const double c2 = -2.4357e-4;       // (W m–2 ppb–1) IPCC AR6 parameter for CH4 SARF Table 7.SM.1
-    const double d2 = 0.12173;          // (W m-2 ppb–1/2) IPCC AR6 parameter for CH4 SARF Table 7.SM.1
+    const double a2 = -3.4197e-4;       // (W m–2 ppm–1) IPCC AR6 parameter for N2O SARF Table 7.SM.1
+    const double b2 = 2.5455e-4;        // (W m–2 ppb–1) IPCC AR6 parameter for N2O SARF Table 7.SM.1
+    const double c2 = -2.4357e-4;       // (W m–2 ppb–1) IPCC AR6 parameter for N2O SARF Table 7.SM.1
+    const double d2 = 0.12173;          // (W m-2 ppb–1/2) IPCC AR6 parameter for N2O SARF Table 7.SM.1
     unitval delta_n2o;                  // forcing tropospheric adjustment for N2O see 7.3.2.3 of IPCC AR6
 
     // CH4 parameters

inst/include/ocean_component.hpp

@@ -88,7 +88,7 @@ class OceanComponent : public CarbonCycleModel {
     // The warm low-latitude surface box makes up the rest.
      double part_high = 0.15;
      double part_low = 1-part_high;
-    
+
     /*****************************************************************
      * State variables for the component
      * All of these will need to be recorded at the end of a timestep,
@@ -120,6 +120,8 @@ class OceanComponent : public CarbonCycleModel {
     unitval tu;          //!< m3/s high latitude overturning
     unitval twi;         //!< m3/s warm-intermediate exchange
     unitval tid;         //!< m3/s intermediate-deep exchange
+    unitval ocean_carbon_mld;         //!< m3/s intermediate-deep exchange
+
 
     /*****************************************************************
      * Input data
@@ -174,7 +176,7 @@ class OceanComponent : public CarbonCycleModel {
     tseries<unitval> temp_LL_ts;
     tseries<unitval> co3_HL_ts;
     tseries<unitval> co3_LL_ts;
-  
+
     // timestep control
     tseries<double> max_timestep_ts;
     tseries<int> reduced_timestep_timeout_ts;

src/RcppExports.cpp

@@ -2500,16 +2500,6 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// MLD_THERMAL
-String MLD_THERMAL();
-RcppExport SEXP _hector_MLD_THERMAL() {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    rcpp_result_gen = Rcpp::wrap(MLD_THERMAL());
-    return rcpp_result_gen;
-END_RCPP
-}
 // newcore_impl
 Environment newcore_impl(String inifile, int loglevel, bool suppresslogging, String name);
 RcppExport SEXP _hector_newcore_impl(SEXP inifileSEXP, SEXP loglevelSEXP, SEXP suppressloggingSEXP, SEXP nameSEXP) {
@@ -2906,7 +2896,6 @@ static const R_CallMethodDef CallEntries[] = {
     {"_hector_FLUX_INTERIOR", (DL_FUNC) &_hector_FLUX_INTERIOR, 0},
     {"_hector_HEAT_FLUX", (DL_FUNC) &_hector_HEAT_FLUX, 0},
     {"_hector_MLD_OCEAN_CARBON", (DL_FUNC) &_hector_MLD_OCEAN_CARBON, 0},
-    {"_hector_MLD_THERMAL", (DL_FUNC) &_hector_MLD_THERMAL, 0},
     {"_hector_newcore_impl", (DL_FUNC) &_hector_newcore_impl, 4},
     {"_hector_shutdown", (DL_FUNC) &_hector_shutdown, 1},
     {"_hector_reset", (DL_FUNC) &_hector_reset, 2},

src/ocean_component.cpp

@@ -81,6 +81,7 @@ void OceanComponent::init( Core* coreptr ) {
     oceanflux_constrain.name = "atm_ocean_constrain";
 
     SST.set( 0.0, U_DEGC );
+    ocean_carbon_mld.set( 100, U_UNITLESS);
 
 	lastflux_annualized.set( 0.0, U_PGC );
 
@@ -112,13 +113,16 @@ void OceanComponent::init( Core* coreptr ) {
     core->registerCapability( D_CO3_HL, getComponentName() );
     core->registerCapability( D_CO3_LL, getComponentName() );
     core->registerCapability( D_CO3, getComponentName() );
+    core->registerCapability( D_OC_MLD, getComponentName() );
 
 
     // Register the inputs we can receive from outside
     core->registerInput(D_TT, getComponentName());
     core->registerInput(D_TU, getComponentName());
     core->registerInput(D_TWI, getComponentName());
     core->registerInput(D_TID, getComponentName());
+    core->registerInput(D_OC_MLD, getComponentName());
+
 }
 
 //------------------------------------------------------------------------------
@@ -167,6 +171,9 @@ void OceanComponent::setData( const string& varName,
         } else if( varName == D_CARBON_LL ) {
             H_ASSERT( data.date == Core::undefinedIndex() , "date not allowed" );
             surfaceLL.set_carbon( data.getUnitval( U_PGC ) );
+        } else if( varName == D_OC_MLD ) {
+            H_ASSERT( data.date == Core::undefinedIndex() , "date not allowed" );
+            ocean_carbon_mld = data.getUnitval(U_UNITLESS);
         } else if( varName == D_CARBON_IO ) {
             H_ASSERT( data.date == Core::undefinedIndex() , "date not allowed" );
             inter.set_carbon( data.getUnitval( U_PGC ) );
@@ -190,6 +197,9 @@ void OceanComponent::setData( const string& varName,
             spinup_chem = (data.getUnitval(U_UNDEFINED) > 0);
         } else if( varName == D_ATM_OCEAN_CONSTRAIN ) {
             H_ASSERT( data.date != Core::undefinedIndex(), "date required" );
+        } else if( varName == D_OC_MLD ) {
+            H_ASSERT( data.date == Core::undefinedIndex() , "date not allowed" );
+            ocean_carbon_mld = data.getUnitval(U_UNDEFINED);
         } else {
             H_THROW( "Unknown variable name while parsing " + getComponentName() + ": "
                     + varName );
@@ -209,8 +219,8 @@ void OceanComponent::prepareToRun() {
     double spy = 60 * 60 * 24 * 365.25;  // seconds per year
 
     // ocean depth
-    double thick_LL = 100;         // (m) Thickness of surface ocean from Knox and McElroy (1984)
-    double thick_HL = 100;         // (m) Thickness of surface ocean from Knox and McElroy (1984)
+    double thick_LL = ocean_carbon_mld;         // (m) Thickness of surface ocean from Knox and McElroy (1984)
+    double thick_HL = ocean_carbon_mld;         // (m) Thickness of surface ocean from Knox and McElroy (1984)
     double thick_inter = 1000-thick_LL;  // (m) Thickness of of intermediate ocean from Knox and McElroy (1984)
     double thick_deep = 3777-thick_inter-thick_LL; // (m) Thickness of deep ocean from Knox and McElroy (1984)
 
@@ -429,6 +439,8 @@ unitval OceanComponent::getData( const std::string& varName,
             returnval = tid;
          } else if( varName == D_TWI ) {
             returnval = twi;
+         } else if( varName == D_OC_MLD ) {
+             returnval = ocean_carbon_mld;
         } else if( varName == D_OMEGACA_HL ) {
             returnval = surfaceHL.mychemistry.OmegaCa;
         } else if( varName == D_OMEGACA_LL ) {

src/rcpp_constants.cpp

@@ -1873,16 +1873,10 @@ return D_HEAT_FLUX;
 }
 
 
-//' @describeIn special Ocean carbon mixed layer depth
+//' @describeIn ocean define the depth of the mixed layer in the ocean carbon cycle, default is 100m.
 //' @export
 // [[Rcpp::export]]
 String MLD_OCEAN_CARBON() {
     return D_OC_MLD;
 }
 
-//' @describeIn special Thermal ocean mixed layer depth
-//' @export
-// [[Rcpp::export]]
-String MLD_THERMAL() {
-    return D_THERMAL_MLD;
-}