address response to pr 758

R/RcppExports.R

@@ -4,7 +4,7 @@
 #' @describeIn emissions Emissions hydrogen gas (\code{"Tg H2"})
 NULL
 
-#' @describeIn oh coefficent for the h2 emissions
+#' @describeIn oh coefficient for the h2 emissions
 NULL
 
 #' @describeIn msgtype Message type for retrieving data from a component

inst/include/component_data.hpp

@@ -277,11 +277,11 @@
 // oh component
 #define D_LIFETIME_OH "TAU_OH"
 #define D_INITIAL_LIFETIME_OH "TOH0"
-#define D_COEFFICENT_NOX "CNOX"
-#define D_COEFFICENT_CH4 "CCH4"
-#define D_COEFFICENT_NMVOC "CNMVOC"
-#define D_COEFFICENT_CO "CCO"
-#define D_COEFFICENT_H2 "CH2"
+#define D_COEFFICIENT_NOX "CNOX"
+#define D_COEFFICIENT_CH4 "CCH4"
+#define D_COEFFICIENT_NMVOC "CNMVOC"
+#define D_COEFFICIENT_CO "CCO"
+#define D_COEFFICIENT_H2 "CH2"
 #define D_EMISSIONS_H2 "H2_emissions"
 
 

inst/include/oh_component.hpp

@@ -67,11 +67,11 @@ class OHComponent : public IModelComponent {
   unitval M0;   // initial CH4 concentration
   unitval TOH0; // preindustrial OH lifetime
 
-  double CCO;    // coefficent for CO
-  double CNMVOC; // coefficent for NMVOC
-  double CNOX;   // coefficent for NOX
-  double CCH4;   // coefficent for CH4
-  unitval CH2;   // coefficent for CH4
+  double CCO;    // coefficient for CO
+  double CNMVOC; // coefficient for NMVOC
+  double CNOX;   // coefficient for NOX
+  double CCH4;   // coefficient for CH4
+  unitval CH2;   // coefficient for CH4
 
 
   // logger

inst/input/hector_ssp119.ini

@@ -134,11 +134,11 @@ H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time se
 
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 ;------------------------------------------------------------------------
 [ozone]

inst/input/hector_ssp126.ini

@@ -133,11 +133,11 @@ NMVOC_emissions=csv:tables/ssp126_emiss-constraints_rf.csv   ; emissions time se
 H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time series
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------

inst/input/hector_ssp245.ini

@@ -134,11 +134,11 @@ H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time se
 
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------

inst/input/hector_ssp370.ini

@@ -134,11 +134,11 @@ H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time se
 
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------

inst/input/hector_ssp434.ini

@@ -37,7 +37,7 @@ preind_interdeep_c=37100	; intermediate and deep ocean C, IPCC AR6 Figure 5.12
 atmos_co2=590.33	; initial atmospheric carbon pool Pg C of CO2 size used in spin up, consistent with C0
 C0=277.15			; preindustrial CO2 from table 7.SM.1 IPCC AR6; CO2 radiative forcing is calibrated to this value
 npp_flux0=56.2		; preindustrial net primary production, Pg C/yr from Ito et al. 2011
-;pf.npp_flux0=5.6	; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978 
+;pf.npp_flux0=5.6	; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978
 ;nonpf.npp_flux0=50.6
 
 veg_c=550			; initial vegetation pool, Pg C
@@ -73,7 +73,7 @@ f_litterd=0.98		; Fraction of litter flux to detritus (balance to soil)
 ;nonpf.f_litterd=0.98
 
 ; Anthropogenic contributions: emissions, direct air carbon capture and storage, and land use change, Pg C/yr
-ffi_emissions=csv:tables/ssp434_emiss-constraints_rf.csv	
+ffi_emissions=csv:tables/ssp434_emiss-constraints_rf.csv
 daccs_uptake=csv:tables/ssp434_emiss-constraints_rf.csv
 luc_emissions=csv:tables/ssp434_emiss-constraints_rf.csv
 luc_uptake=csv:tables/ssp434_emiss-constraints_rf.csv
@@ -134,11 +134,11 @@ H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time se
 
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------
@@ -236,7 +236,7 @@ delta_HFC32=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0					; grams
 HFC32_emissions=csv:tables/ssp434_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon]				
+[HFC4310_halocarbon]
 ; This is equivalent to HFC-43-10mee
 tau=17.0					; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357				; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)

inst/input/hector_ssp460.ini

@@ -37,7 +37,7 @@ preind_interdeep_c=37100	; intermediate and deep ocean C, IPCC AR6 Figure 5.12
 atmos_co2=590.33	; initial atmospheric carbon pool Pg C of CO2 size used in spin up, consistent with C0
 C0=277.15			; preindustrial CO2 from table 7.SM.1 IPCC AR6; CO2 radiative forcing is calibrated to this value
 npp_flux0=56.2		; preindustrial net primary production, Pg C/yr from Ito et al. 2011
-;pf.npp_flux0=5.6	; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978 
+;pf.npp_flux0=5.6	; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978
 ;nonpf.npp_flux0=50.6
 
 veg_c=550			; initial vegetation pool, Pg C
@@ -73,7 +73,7 @@ f_litterd=0.98		; Fraction of litter flux to detritus (balance to soil)
 ;nonpf.f_litterd=0.98
 
 ; Anthropogenic contributions: emissions, direct air carbon capture and storage, and land use change, Pg C/yr
-ffi_emissions=csv:tables/ssp460_emiss-constraints_rf.csv	
+ffi_emissions=csv:tables/ssp460_emiss-constraints_rf.csv
 daccs_uptake=csv:tables/ssp460_emiss-constraints_rf.csv
 luc_emissions=csv:tables/ssp460_emiss-constraints_rf.csv
 luc_uptake=csv:tables/ssp460_emiss-constraints_rf.csv
@@ -134,11 +134,11 @@ H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time se
 
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------
@@ -236,7 +236,7 @@ delta_HFC32=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0					; grams
 HFC32_emissions=csv:tables/ssp460_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon]				
+[HFC4310_halocarbon]
 ; This is equivalent to HFC-43-10mee
 tau=17.0					; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357				; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)

inst/input/hector_ssp534-over.ini

@@ -134,11 +134,11 @@ H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv           ; emissions ti
 
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------

inst/input/hector_ssp585.ini

@@ -133,11 +133,11 @@ NMVOC_emissions=csv:tables/ssp585_emiss-constraints_rf.csv   ; emissions time se
 H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time series
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------

src/oh_component.cpp

@@ -57,14 +57,14 @@ void OHComponent::init(Core *coreptr) {
 
   // Inform core what data we can provide
   core->registerCapability(D_LIFETIME_OH, getComponentName());
-  core->registerCapability(D_COEFFICENT_H2, getComponentName());
+  core->registerCapability(D_COEFFICIENT_H2, getComponentName());
   // Register inputs accepted.  Note that more than one component
   // can accept an input
   core->registerInput(D_EMISSIONS_CO, getComponentName());
   core->registerInput(D_EMISSIONS_NMVOC, getComponentName());
   core->registerInput(D_EMISSIONS_NOX, getComponentName());
   core->registerInput(D_EMISSIONS_H2, getComponentName());
-  core->registerInput(D_COEFFICENT_H2, getComponentName());
+  core->registerInput(D_COEFFICIENT_H2, getComponentName());
 
 
 }
@@ -108,19 +108,19 @@ void OHComponent::setData(const string &varName, const message_data &data) {
     } else if (varName == D_INITIAL_LIFETIME_OH) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       TOH0 = data.getUnitval(U_YRS);
-    } else if (varName == D_COEFFICENT_CH4) {
+    } else if (varName == D_COEFFICIENT_CH4) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       CCH4 = data.getUnitval(U_UNDEFINED);
-    } else if (varName == D_COEFFICENT_CO) {
+    } else if (varName == D_COEFFICIENT_CO) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       CCO = data.getUnitval(U_UNDEFINED);
-    } else if (varName == D_COEFFICENT_NMVOC) {
+    } else if (varName == D_COEFFICIENT_NMVOC) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       CNMVOC = data.getUnitval(U_UNDEFINED);
-    } else if (varName == D_COEFFICENT_NOX) {
+    } else if (varName == D_COEFFICIENT_NOX) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       CNOX = data.getUnitval(U_UNDEFINED);
-    } else if (varName == D_COEFFICENT_H2) {
+    } else if (varName == D_COEFFICIENT_H2) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       CH2 = data.getUnitval(U_UNDEFINED);
     } else {
@@ -162,28 +162,28 @@ void OHComponent::run(const double runToDate) {
   const double previous_ch4 =
       core->sendMessage(M_GETDATA, D_CH4_CONC, oldDate).value(U_PPBV_CH4);
 
+  // toh is a sum of coefficients in an exponential representation of OH lifetime
   double toh = 0.0;
   if (previous_ch4 != M0) // if we are not at the first time
   {
-    const double a =
+    const double toh_ch4 =
         CCH4 * ((1.0 * log(previous_ch4)) - log(M0.value(U_PPBV_CH4)));
-    const double b =
+    const double toh_nox =
         CNOX * ((1.0 * current_nox) -
                 NOX_emissions.get(NOX_emissions.firstdate()).value(U_TG_N));
-    const double c =
+    const double toh_co =
         CCO * ((1.0 * +current_co) -
                CO_emissions.get(CO_emissions.firstdate()).value(U_TG_CO));
-    const double d =
+    const double toh_nmvoc =
         CNMVOC *
         ((1.0 * +current_nmvoc) -
          NMVOC_emissions.get(NMVOC_emissions.firstdate()).value(U_TG_NMVOC));
-    const double f =
+    const double toh_h2 =
          CH2 *
           ((1.0 * +current_h2) -
            H2_emissions.get(H2_emissions.firstdate()).value(U_TG_H2));
 
-
-    toh = a + b + c + d + f;
+    toh = toh_ch4 + toh_nox + toh_co + toh_nmvoc + toh_h2;
     H_LOG(logger, Logger::DEBUG)
         << "Year " << runToDate << " toh = " << toh << std::endl;
   }
@@ -215,7 +215,7 @@ unitval OHComponent::getData(const std::string &varName, const double date) {
     H_ASSERT(date != Core::undefinedIndex(),
              "Date required for NMVOC emissions");
     returnval = NMVOC_emissions.get(date);
-  } else if (varName == D_COEFFICENT_H2) {
+  } else if (varName == D_COEFFICIENT_H2) {
     H_ASSERT(date == Core::undefinedIndex(), "Date not allowed for H2 coefficent");
     returnval = CH2 ;
   } else if (varName == D_EMISSIONS_H2) {

src/rcpp_constants.cpp

@@ -1505,7 +1505,7 @@ String FLUX_INTERIOR() { return D_FLUX_INTERIOR; }
 String HEAT_FLUX() { return D_HEAT_FLUX; }
 
 
-//' @describeIn oh coefficent for the h2 emissions
+//' @describeIn oh coefficient for the h2 emissions
  //' @export
  // [[Rcpp::export]]
- String COEFF_H2() { return D_COEFFICENT_H2; }
+ String COEFF_H2() { return D_COEFFICIENT_H2; }

tests/testthat/input/luc_pulse.ini

@@ -112,10 +112,10 @@ CO_emissions=csv:luc_pulse_tables.csv      ; emissions time series
 NMVOC_emissions=csv:luc_pulse_tables.csv   ; emissions time series
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105			; coefficent for CO
-CNMVOC=-0.000315		; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105			; coefficient for CO
+CNMVOC=-0.000315		; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
 
 ;------------------------------------------------------------------------
 [ozone]