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Merged
kdorheim merged 2 commits into from
Mar 17, 2026
Merged

Initial Carbon Pools #802

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5a9fa94
increase the size of the earth c pool to work with idealized runs
kdorheim Mar 12, 2026
8a7d196
remove atmos C pool
kdorheim Mar 13, 2026
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1 change: 0 additions & 1 deletion data-raw/input_params.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,6 @@ 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
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1 change: 0 additions & 1 deletion inst/input/hector_picontrol.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,6 @@ preind_interdeep_c=37100 ; intermediate and deep ocean C, IPCC AR6 Figure 5.12
; - the nppv, nppd, and litterd partitioning parameters
; - beta and q10_rh

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 question is calibrated to this value
npp_flux0=56.2 ; preindustrial net primary production, Pg C/yr from Ito et al. 2011

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3 changes: 1 addition & 2 deletions inst/input/hector_ssp119.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@ preind_interdeep_c=37100 ; intermediate and deep ocean C, IPCC AR6 Figure 5.12
; - the nppv, nppd, and litterd partitioning parameters
; - beta and q10_rh

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
Expand Down Expand Up @@ -180,7 +179,7 @@ RF_misc[1750]=0
;------------------------------------------------------------------------
[temperature]
S=3.0 ; equilibrium climate sensitivity for 2xCO2 degC (A.4.4 of IPCC AR6)
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
qco2=3.75 ; 2×CO2 RF (7.3.2 of IPCC AR6)

; Optional global temperature constraint
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3 changes: 1 addition & 2 deletions inst/input/hector_ssp126.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@ preind_interdeep_c=37100 ; intermediate and deep ocean C, IPCC AR6 Figure 5.12
; - the nppv, nppd, and litterd partitioning parameters
; - beta and q10_rh

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
Expand Down Expand Up @@ -180,7 +179,7 @@ RF_misc[1750]=0
;------------------------------------------------------------------------
[temperature]
S=3.0 ; equilibrium climate sensitivity for 2xCO2 degC (A.4.4 of IPCC AR6)
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
qco2=3.75 ; 2×CO2 RF (7.3.2 of IPCC AR6)

; Optional global temperature constraint
Expand Down
3 changes: 1 addition & 2 deletions inst/input/hector_ssp245.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@ preind_interdeep_c=37100 ; intermediate and deep ocean C, IPCC AR6 Figure 5.12
; - the nppv, nppd, and litterd partitioning parameters
; - beta and q10_rh

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
Expand Down Expand Up @@ -180,7 +179,7 @@ RF_misc[1750]=0
;------------------------------------------------------------------------
[temperature]
S=3.0 ; equilibrium climate sensitivity for 2xCO2 degC (A.4.4 of IPCC AR6)
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
qco2=3.75 ; 2×CO2 RF (7.3.2 of IPCC AR6)

; Optional global temperature constraint
Expand Down
3 changes: 1 addition & 2 deletions inst/input/hector_ssp370.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@ preind_interdeep_c=37100 ; intermediate and deep ocean C, IPCC AR6 Figure 5.12
; - the nppv, nppd, and litterd partitioning parameters
; - beta and q10_rh

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
Expand Down Expand Up @@ -180,7 +179,7 @@ RF_misc[1750]=0
;------------------------------------------------------------------------
[temperature]
S=3.0 ; equilibrium climate sensitivity for 2xCO2 degC (A.4.4 of IPCC AR6)
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
qco2=3.75 ; 2×CO2 RF (7.3.2 of IPCC AR6)

; Optional global temperature constraint
Expand Down
3 changes: 1 addition & 2 deletions inst/input/hector_ssp434.ini
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@ preind_interdeep_c=37100 ; intermediate and deep ocean C, IPCC AR6 Figure 5.12
; - the nppv, nppd, and litterd partitioning parameters
; - beta and q10_rh

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
Expand Down Expand Up @@ -180,7 +179,7 @@ RF_misc[1750]=0
;------------------------------------------------------------------------
[temperature]
S=3.0 ; equilibrium climate sensitivity for 2xCO2 degC (A.4.4 of IPCC AR6)
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
qco2=3.75 ; 2×CO2 RF (7.3.2 of IPCC AR6)

; Optional global temperature constraint
Expand Down
3 changes: 1 addition & 2 deletions inst/input/hector_ssp460.ini
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@ preind_interdeep_c=37100 ; intermediate and deep ocean C, IPCC AR6 Figure 5.12
; - the nppv, nppd, and litterd partitioning parameters
; - beta and q10_rh

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
Expand Down Expand Up @@ -180,7 +179,7 @@ RF_misc[1750]=0
;------------------------------------------------------------------------
[temperature]
S=3.0 ; equilibrium climate sensitivity for 2xCO2 degC (A.4.4 of IPCC AR6)
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
qco2=3.75 ; 2×CO2 RF (7.3.2 of IPCC AR6)

; Optional global temperature constraint
Expand Down
3 changes: 1 addition & 2 deletions inst/input/hector_ssp534-over.ini
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@ preind_interdeep_c=37100 ; intermediate and deep ocean C, IPCC AR6 Figure 5.12
; - the nppv, nppd, and litterd partitioning parameters
; - beta and q10_rh

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
Expand Down Expand Up @@ -180,7 +179,7 @@ RF_misc[1750]=0
;------------------------------------------------------------------------
[temperature]
S=3.0 ; equilibrium climate sensitivity for 2xCO2 degC (A.4.4 of IPCC AR6)
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
qco2=3.75 ; 2×CO2 RF (7.3.2 of IPCC AR6)

; Optional global temperature constraint
Expand Down
3 changes: 1 addition & 2 deletions inst/input/hector_ssp585.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@ preind_interdeep_c=37100 ; intermediate and deep ocean C, IPCC AR6 Figure 5.12
; - the nppv, nppd, and litterd partitioning parameters
; - beta and q10_rh

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
Expand Down Expand Up @@ -180,7 +179,7 @@ RF_misc[1750]=0
;------------------------------------------------------------------------
[temperature]
S=3.0 ; equilibrium climate sensitivity for 2xCO2 degC (A.4.4 of IPCC AR6)
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
diff=1.042 ; ocean heat diffusivity, cm2/s calibrated to historical observations see PR 789 for details
qco2=3.75 ; 2×CO2 RF (7.3.2 of IPCC AR6)

; Optional global temperature constraint
Expand Down
18 changes: 4 additions & 14 deletions src/simpleNbox.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -69,9 +69,9 @@ SimpleNbox::SimpleNbox() : CarbonCycleModel(8), masstot(0.0) {
// earth_c keeps track of how much fossil C is pulled out
// so that we can do a mass-balance check throughout the run
// 2020-02-05 With the introduction of non-negative 'fluxpool' class
// we can't start earth_c at zero. Value of 5500 is set to avoid
// overdrawing in RCP 8.5
earth_c.set(5500, U_PGC, false, D_EARTHC);
// we can't start earth_c at zero. Value of 6400 is set to avoid
// overdrawing in esm-flat20
earth_c.set(6400, U_PGC, false, D_EARTHC);

// We keep a running total of LUC emissions from (and uptake to) vegetation
// This is used in slowparameval() to calculate npp_luc_adjust
Expand Down Expand Up @@ -246,17 +246,7 @@ void SimpleNbox::setData(const std::string &varName, const message_data &data) {
}
try {
// Initial pools
if (varNameParsed == D_ATMOSPHERIC_CO2) {
// Hector input files specify initial atmospheric CO2 in terms of
// the carbon pool, rather than the CO2 concentration. Since we
// don't have a place to store the initial carbon pool, we convert
// it to initial concentration and store that. It will be converted
// back to carbon content when the state variables are set up in
// prepareToRun.
H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
H_ASSERT(biome == SNBOX_DEFAULT_BIOME, "atmospheric C must be global");
set_c0(data.getUnitval(U_PGC).value(U_PGC) * PGC_TO_PPMVCO2);
} else if (varNameParsed == D_PREINDUSTRIAL_CO2) {
if (varNameParsed == D_PREINDUSTRIAL_CO2) {
H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
H_ASSERT(biome == SNBOX_DEFAULT_BIOME,
"preindustrial CO2 must be global");
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1 change: 0 additions & 1 deletion tests/testthat/input/luc_pulse.ini
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Expand Up @@ -30,7 +30,6 @@ tid=200000000 ; 2.0e8 intermediate-deep exchange, m3/s
; - the nppv, nppd, and litterd partitioning parameters
; - beta and q10_rh

atmos_co2=588.071 ; Pg C in CO2, from Murakami et al. (2010)
C0=277.15 ; preindustrial CO2 from table 7.SM.1 IPCC AR6
;boreal.veg_c=100 ; e.g.
;tropical.veg_c=450
Expand Down
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