Merge pull request #733 from JGCRI/dev

Hector V3.2.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hector
 Title: The Hector Simple Climate Model
-Version: 3.1.1
+Version: 3.2.0
 Authors@R: c(person("Kalyn", "Dorheim", 
 	        email = "[email protected]",
 	        role = c("aut", "cre"),

NEWS.md

@@ -1,3 +1,8 @@
+# hector 3.2.0 
+
+* Correct aerosol forcing coefficients based on Zelinka et al. (2023)
+* Enable permafrost module and recalibrate model's default parameterization
+
 # hector 3.1.1 
 
 Return global mean surface temperature as a Hector output.

R/biome.R

@@ -83,7 +83,7 @@ split_biome <- function(core,
         sum(fnpp_flux0) == 1, all(fnpp_flux0 > 0)
     )
 
-    # If user supplied values in ... for warmingfactor, etc., use thos
+    # If user supplied values in ... for warmingfactor, etc., use those
     # Otherwise use the old biome's values
     cv <- get_biome_inits(core, old_biome) # current values
     dots <- list(...)
@@ -142,7 +142,8 @@ get_biome_inits <- function(core, biome) {
         sendmessage(core, GETDATA(), VEG_C(biome), 0, NA, ""),
         sendmessage(core, GETDATA(), DETRITUS_C(biome), 0, NA, ""),
         sendmessage(core, GETDATA(), SOIL_C(biome), 0, NA, ""),
-        sendmessage(core, GETDATA(), PERMAFROST_C(biome), 0, NA, "")
+        sendmessage(core, GETDATA(), PERMAFROST_C(biome), 0, NA, ""),
+        sendmessage(core, GETDATA(), THAWEDP_C(biome), 0, NA, "")
     )
     current_data_2 <- fetchvars(core, NA, c(
         NPP_FLUX0(biome),

README.Rmd

@@ -56,7 +56,7 @@ hector_tas_results$scenario <- ifelse(hector_tas_results$scenario == "ssp534-ove
 hector_tas_results$scenario <- ifelse(hector_tas_results$year <= 2016, "historical",
                                       hector_tas_results$scenario)
 ggplot(hector_tas_results) +
-    geom_line(aes(year, value, color = scenario), size = 1) +
+    geom_line(aes(year, value, color = scenario), linewidth = 1) +
     theme_bw(base_size = 15) +
     labs(color = NULL, x = NULL, y = expression("Temperature Anomaly ("~degree~"C)")) +
     scale_color_manual(values = SSP_COLORS)

data-raw/generate-comp-data.R

@@ -20,7 +20,7 @@ hector_commit <- system("git rev-parse --short HEAD", intern = TRUE)
 
 
 vars_to_save <- c(CONCENTRATIONS_CO2(), GLOBAL_TAS(), RF_TOTAL(), RF_CO2(), HEAT_FLUX(),
-                  OCEAN_C(), PH_HL(), ATMOSPHERIC_CO2(), SST())
+                  OCEAN_C(), PH_HL(), ATMOSPHERIC_CO2(), SST(), PERMAFROST_C())
 dates_to_save <- 1745:2300
 
 # Second run.

data-raw/input_params.csv

@@ -1,57 +1,67 @@
 section,parameter,biome-specific,time-variant,required,default,units,description
-core,run_name,n,n,y,,(unitless),
-core,startDate,n,n,y,1745,year,
-core,endDate,n,n,y,2300,year,
-core,trackingDate,n,n,y,9999,year,year to start tracking (only carbon currently)
-core,do_spinup,n,n,y,1,(unitless),"if 1, spin up model before running (default=1)"
-core,max_spinup,n,n,y,2000,(unitless),maximum steps allowed for spinup (default=2000)
-ocean,enabled,n,n,y,1,(unitless),putting 'enabled=0' will disable any component
-ocean,spinup_chem,n,n,y,0,(unitless),run surface chemistry during spinup phase?
-ocean,tt,n,n,y,7.20E+07,m3 s-1,thermohaline circulation
-ocean,tu,n,n,y,4.90E+07,m3 s-1,high latitude overturning
-ocean,twi,n,n,y,1.25E+07,m3 s-1,warm-intermediate exchange
-ocean,tid,n,n,y,2.00E+08,m3 s-1,intermediate-deep exchange
-ocean,preind_surface_c,n,n,n,900,Pg C,surface ocean carbon
-ocean,preind_interdeep_c,n,n,n,37100,Pg C,intermediate + deep ocean carbon
-simpleNbox,atmos_co2,n,n,y,588.071,Pg C,
-simpleNbox,C0,n,n,y,277.15,Pg C,preindustrial CO2 from table 7.SM.1 IPCC AR6
-simpleNbox,boreal.veg_c,y,n,y,100,Pg C,
-simpleNbox,tropical.veg_c,y,n,y,450,Pg C,
-simpleNbox,veg_c,n,n,y,550,Pg C,vegetation
-simpleNbox,boreal.detritus_c,y,n,y,15,Pg C,
-simpleNbox,tropical.detritus_c,y,n,y,45,Pg C,
-simpleNbox,detritus_c,n,n,y,55,Pg C,detritus
-simpleNbox,boreal.soil_c,y,n,y,1200,Pg C,
-simpleNbox,tropical.soil_c,y,n,y,578,Pg C,
-simpleNbox,soil_c,n,n,y,1782,Pg C,soil
-simpleNbox,boreal.permafrost_c,y,n,n,865,Pg C,permafrost
-simpleNbox,tropical.permafrost_c,y,n,n,0,Pg C,permafrost
-simpleNbox,permafrost_c,n,n,n,0,Pg C,permafrost
-simpleNbox,boreal.npp_flux0,y,n,y,5,Pg C yr-1,
-simpleNbox,tropical.npp_flux0,y,n,y,45,Pg C yr-1,
-simpleNbox,npp_flux0,n,n,y,56.2,Pg C yr-1,net primary production
+core,run_name,n,n,y,,(unitless),Name of model run
+core,startDate,n,n,y,1745,year,Start date of model run
+core,endDate,n,n,y,2300,year,End date of model run
+core,trackingDate,n,n,y,9999,year,Year to start tracking carbon
+core,do_spinup,n,n,y,1,(unitless),"If 1, spin up model before running (default=1)"
+core,max_spinup,n,n,y,2000,(unitless),Maximum steps allowed for spinup (default=2000)
+ocean,enabled,n,n,y,1,(unitless),Putting 'enabled=0' will disable any component
+ocean,spinup_chem,n,n,y,0,(unitless),Run ocean surface chemistry during spinup phase?
+ocean,tt,n,n,y,7.20E+07,m3 s-1,Ocean thermohaline circulation
+ocean,tu,n,n,y,4.90E+07,m3 s-1,Ocean high latitude overturning
+ocean,twi,n,n,y,1.25E+07,m3 s-1,Ocean warm-intermediate exchange
+ocean,tid,n,n,y,2.00E+08,m3 s-1,Ocean intermediate-deep exchange
+ocean,preind_surface_c,n,n,n,900,Pg C,Initial surface ocean carbon
+ocean,preind_interdeep_c,n,n,n,37100,Pg C,Initial intermediate + deep ocean carbon
+simpleNbox,atmos_co2,n,n,y,588.071,Pg C,Initial atmospheric CO2
+simpleNbox,C0,n,n,y,277.15,Pg C,Initial atmospheric C pool
+simpleNbox,pf.veg_c,y,n,n,55,Pg C,Initial vegetation C pool
+simpleNbox,nonpf.veg_c,y,n,n,495,Pg C,Initial vegetation C pool
+simpleNbox,veg_c,n,n,y,550,Pg C,Initial vegetation C pool
+simpleNbox,pf.detritus_c,y,n,n,5,Pg C,Initial detritus C pool
+simpleNbox,nonpf.detritus_c,y,n,n,50,Pg C,Initial detritus C pool
+simpleNbox,detritus_c,n,n,y,55,Pg C,Initial detritus C pool
+simpleNbox,pf.soil_c,y,n,n,308,Pg C,Initial soil C pool
+simpleNbox,nonpf.soil_c,y,n,n,609,Pg C,Initial soil C pool
+simpleNbox,soil_c,n,n,y,917,Pg C,Initial soil C pool
+simpleNbox,pf.permafrost_c,y,n,n,865,Pg C,Initial permafrost C pool
+simpleNbox,nonpf.permafrost_c,y,n,n,0,Pg C,Initial permafrost C pool
+simpleNbox,permafrost_c,n,n,y,865,Pg C,Initial permafrost C pool
+simpleNbox,pf.npp_flux0,y,n,n,5.6,Pg C yr-1,Preindustrial net primary production
+simpleNbox,nonpf.npp_flux0,y,n,n,50.6,Pg C yr-1,Preindustrial net primary production
+simpleNbox,npp_flux0,n,n,y,56.2,Pg C yr-1,Preindustrial net primary production
+simpleNbox,pf.f_nppv,n,n,y,0.35,(unitless),Fraction of NPP to vegetation
+simpleNbox,nonpf.f_nppv,n,n,y,0.35,(unitless),Fraction of NPP to vegetation
 simpleNbox,f_nppv,n,n,y,0.35,(unitless),Fraction of NPP to vegetation
+simpleNbox,pf.f_nppd,n,n,y,0.35,(unitless),Fraction of NPP to vegetation
+simpleNbox,nonpf.f_nppd,n,n,y,0.35,(unitless),Fraction of NPP to vegetation
 simpleNbox,f_nppd,n,n,y,0.6,(unitless),Fraction of NPP to detritus (balance to soil)
+simpleNbox,pf.f_litterd,n,n,n,0.35,(unitless),Fraction of NPP to vegetation
+simpleNbox,nonpf.f_litterd,n,n,n,0.35,(unitless),Fraction of NPP to vegetation
 simpleNbox,f_litterd,n,n,y,0.98,(unitless),Fraction of litter flux to detritus (balance to soil)
 simpleNbox,ffi_emissions,n,y,y,"""(csv)""",Pg C yr-1,Anthropogenic contributions: emissions
 simpleNbox,daccs_uptake,n,y,y,"""(csv)""",Pg C yr-1,Anthropogenic contributions: direct air carbon capture and storage
 simpleNbox,luc_emissions,n,y,y,"""(csv)""",Pg C yr-1,Anthropogenic contributions: land use change
 simpleNbox,luc_uptake,n,y,y,"""(csv)""",Pg C yr-2,Anthropogenic contributions: land use change
-simpleNbox,CO2_constrain,n,y,n,"""(csv)""",ppmv,atmospheric CO2 constraint
-simpleNbox,NBP_constrain,n,y,n,"""(csv)""",Pg C yr-1,net biome production (land-atmosphere C flux) constaint
-simpleNbox,beta,n,n,y,0.36,(unitless),
-simpleNbox,q10_rh,n,n,y,2,(unitless),respiration response Q10
-simpleNbox,boreal.warmingfactor,y,n,n,1.2,(unitless),biome-specific warming factors
-simpleNbox,RF_albedo,n,n,y,"""(csv)""",W m-2,albedo effect
+simpleNbox,CO2_constrain,n,y,n,"""(csv)""",ppmv,Atmospheric CO2 constraint
+simpleNbox,NBP_constrain,n,y,n,"""(csv)""",Pg C yr-1,Net biome production (land-atmosphere C flux) constaint
+simpleNbox,pf.beta,n,n,n,0.36,(unitless),CO2 fertilization factor
+simpleNbox,nonpf.beta,n,n,n,0.36,(unitless),CO2 fertilization factor
+simpleNbox,beta,n,n,y,0.36,(unitless),CO2 fertilization factor
+simpleNbox,pf.q10_rh,n,n,n,2,(unitless),Respiration temperature response (Q10)
+simpleNbox,nonpf.q10_rh,n,n,n,2,(unitless),Respiration temperature response (Q10)
+simpleNbox,q10_rh,n,n,y,2,(unitless),Respiration temperature response (Q10)
+simpleNbox,pf.warmingfactor,y,n,n,2,(unitless),biome-specific warming factors
+simpleNbox,RF_albedo,n,n,y,"""(csv)""",W m-2,Albedo radiative forcing effect
 simpleNbox,permafrost_c,y,n,y,0,Pg C,Preindustrial permafrost carbon pool
-simpleNbox,fpf_static,y,n,n,0.74,(unitless),fraction of permafrost that is static (non-labile)
-simpleNbox,rh_ch4_frac,y,n,n,0.023,(unitless),fraction of thawed permafrost decomposed as CH4
-simpleNbox,pf_mu,y,n,n,1.67,(unitless),permafrost thaw parameter; see Woodard et al. 2021
-simpleNbox,pf_sigma,y,n,n,0.986,(unitless),permafrost thaw parameter; see Woodard et al. 2021
-carbon-cycle-solver,eps_abs,n,n,y,1.00E-06,(unitless),solution tolerance
-carbon-cycle-solver,eps_rel,n,n,y,1.00E-06,(unitless),solution tolerance
-carbon-cycle-solver,dt,n,n,y,0.25,(unitless),default time step
-carbon-cycle-solver,eps_spinup,n,n,y,0.001,Pg C,"spinup tolerance (drift), Pg C"
+simpleNbox,fpf_static,y,n,n,0.74,(unitless),Fraction of permafrost that is static (non-labile)
+simpleNbox,rh_ch4_frac,y,n,n,0.023,(unitless),Fraction of thawed permafrost decomposed as CH4
+simpleNbox,pf_mu,y,n,n,1.67,(unitless),Permafrost thaw parameter; see Woodard et al. 2021
+simpleNbox,pf_sigma,y,n,n,0.986,(unitless),Permafrost thaw parameter; see Woodard et al. 2021
+carbon-cycle-solver,eps_abs,n,n,y,1.00E-06,(unitless),Solver solution tolerance
+carbon-cycle-solver,eps_rel,n,n,y,1.00E-06,(unitless),Solver solution tolerance
+carbon-cycle-solver,dt,n,n,y,0.25,(unitless),Solver default time step
+carbon-cycle-solver,eps_spinup,n,n,y,0.001,Pg C,"Model spinup tolerance (drift), Pg C"
 so2,SO2_emissions,n,y,y,"""(csv)""",,emissions time series
 so2,SV,n,y,y,"""(csv)""",,volcanic radiative forcing time series
 CH4,M0,n,n,y,731.41,ppb,"preindustrial methane IPCC AR6 Table 7.SM.1, the CH4 forcing equations is calibrated to a M0 of 731.41 ppb"

inst/include/forcing_component.hpp

@@ -120,7 +120,7 @@ class ForcingComponent : public IModelComponent {
 
   // Aerosol parameters for aerosol-cloud interactions (RFaci) see equation
   // Equation 7.SM.1.2 of IPCC AR6
-  double const aci_beta = 2.09841432; // (W m-2) IPCC AR6 7.SM.1.3.1
+  double const aci_beta = 2.279759; // see Dorheim et al. in prep
   double const s_BCOC = 111.05064063; // (Tg C yr-1) IPCC AR6 7.SM.1.3.1
   double const s_SO2 =
       (260.34644166 * 1000) *

inst/include/h_util.hpp

@@ -26,7 +26,7 @@
  * \brief The model version number to be included in logs and outputs.
  * \note  Manually update the git tag to match this.
  */
-#define MODEL_VERSION "3.1.1"
+#define MODEL_VERSION "3.2.0"
 
 #define OUTPUT_DIRECTORY "output/"
 

inst/include/simpleNbox.hpp

@@ -116,15 +116,14 @@ class SimpleNbox : public CarbonCycleModel {
   // Carbon pools -- global
   fluxpool earth_c; //!< earth pool, Pg C; for mass-balance
   fluxpool atmos_c; //!< atmosphere pool, Pg C
-
+  double cumulative_pf_ch4; //!< cumulative release of CH4-C thawed permafrost, Pg C
+
   // Carbon pools -- biome-specific
   fluxpool_stringmap veg_c;      //!< vegetation pools, Pg C
   fluxpool_stringmap detritus_c; //!< detritus pools, Pg C
   fluxpool_stringmap soil_c;     //!< soil pool, Pg C
-  // Permafrost functionality is documented in:
-  // Woodard, D. L., Shiklomanov, A. N., Kravitz, B., Hartin, C., and
-  // Bond-Lamberty, B.: A permafrost implementation in the simple carbon–climate
-  // model Hector v.2.3pf, GMD 14:4751–4767, 2021.
+  // Permafrost functionality is documented in Woodard et al. 2021:
+  // A permafrost implementation in the simple carbon–climate model Hector v.2.3pf,
   // http://dx.doi.org/10.5194/gmd-14-4751-2021
   fluxpool_stringmap permafrost_c; //!< permafrost C pool, Pg C
   // Track thawed peramfrost separately from soil, so that
@@ -146,8 +145,7 @@ class SimpleNbox : public CarbonCycleModel {
   unitval Ca_residual; //!< residual (when constraining [CO2]), Pg C
   double_stringmap tempfertd,
       tempferts; //!< temperature effect on respiration (unitless)
-  double_stringmap f_frozen,
-      new_thaw; //!< relative amounts and changes in permafrost
+  double_stringmap f_frozen; //!< fraction of original permafrost that remains frozen
 
   /*****************************************************************
    * Records of component state
@@ -193,6 +191,7 @@ class SimpleNbox : public CarbonCycleModel {
    *****************************************************************/
 
   double_stringmap co2fert;     //!< CO2 fertilization effect (unitless)
+  double_stringmap f_new_thaw;    //!< New thaw fraction (unitless)
   tseries<double> Tland_record; //!< Record of mean land surface/air temperature
                                 //!< values, for computing soil RH
   bool in_spinup;               //!< flag tracking spinup state

inst/include/temperature_component.hpp

@@ -168,17 +168,12 @@ class TemperatureComponent : public IModelComponent {
 
   // Create a place to store temp time series that are over written when
   // a user provided land ocean warming ratio is being used.
-  unitval lo_tas_land;  //!< place to store land temp when lo is provided by
-                        //!< users, deg C
-  unitval lo_tas_ocean; //!< place to store ocean air temp when lo is provided
-                        //!< by users, deg C
-  unitval lo_seast; //!< place to store sst when lo is provided by users, deg C
-  std::vector<double> lo_temp_landair;  //!< place to store land temp when lo is
-                                        //!< provided by users, deg C
-  std::vector<double> lo_temp_oceanair; //!< place to store land temp when lo is
-                                        //!< provided by users, deg C
-  std::vector<double>
-      lo_sst; //!< place to store land temp when lo is provided by users, deg C
+  unitval lo_tas_land;  //!< land temp when lo is provided by users, deg C
+  unitval lo_tas_ocean; //!< ocean air temp when lo is provided by users, deg C
+  unitval lo_seast; //!< sst when lo is provided by users, deg C
+  std::vector<double> lo_temp_landair;  //!< land temp when lo is provided by users, deg C
+  std::vector<double> lo_temp_oceanair; //!< land temp when lo is provided by users, deg C
+  std::vector<double> lo_sst; //!< land temp when lo is provided by users, deg C
 
   tseries<unitval>
       tas_constrain; //! Temperature change to constrain model to, degC