From 5a9fa94cb57ce4e2e24e0c0ae03c474b8ffcac2a Mon Sep 17 00:00:00 2001
From: kdorheim <kalyn.dorheim@pnnl.gov>
Date: Thu, 12 Mar 2026 14:03:05 -0400
Subject: [PATCH 1/2] increase the size of the earth c pool to work with
 idealized runs

---
 src/simpleNbox.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/simpleNbox.cpp b/src/simpleNbox.cpp
index 91b9481b8..96c039fbf 100644
--- a/src/simpleNbox.cpp
+++ b/src/simpleNbox.cpp
@@ -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

From 8a7d19670b37a0f293b9cdbb5a928117b4a66fb8 Mon Sep 17 00:00:00 2001
From: kdorheim <kalyn.dorheim@pnnl.gov>
Date: Fri, 13 Mar 2026 11:19:56 -0400
Subject: [PATCH 2/2] remove atmos C pool

---
 data-raw/input_params.csv          |   1 -
 data/inputstable.rda               | Bin 4078 -> 4072 bytes
 inst/input/hector_picontrol.ini    |   1 -
 inst/input/hector_ssp119.ini       |   3 +--
 inst/input/hector_ssp126.ini       |   3 +--
 inst/input/hector_ssp245.ini       |   3 +--
 inst/input/hector_ssp370.ini       |   3 +--
 inst/input/hector_ssp434.ini       |   3 +--
 inst/input/hector_ssp460.ini       |   3 +--
 inst/input/hector_ssp534-over.ini  |   3 +--
 inst/input/hector_ssp585.ini       |   3 +--
 src/simpleNbox.cpp                 |  12 +-----------
 tests/testthat/input/luc_pulse.ini |   1 -
 13 files changed, 9 insertions(+), 30 deletions(-)

diff --git a/data-raw/input_params.csv b/data-raw/input_params.csv
index 26bfd6354..c32367e32 100644
--- a/data-raw/input_params.csv
+++ b/data-raw/input_params.csv
@@ -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
diff --git a/data/inputstable.rda b/data/inputstable.rda
index c7df81fca22f8aea1166cccfd156f1c4c690e680..454460acaab7a45a8d8eea77613e2120eb25c63b 100644
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diff --git a/inst/input/hector_picontrol.ini b/inst/input/hector_picontrol.ini
index f43df54d6..11dd564cb 100644
--- a/inst/input/hector_picontrol.ini
+++ b/inst/input/hector_picontrol.ini
@@ -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
 
diff --git a/inst/input/hector_ssp119.ini b/inst/input/hector_ssp119.ini
index 38124d6c5..b5db9cad3 100644
--- a/inst/input/hector_ssp119.ini
+++ b/inst/input/hector_ssp119.ini
@@ -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
@@ -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
diff --git a/inst/input/hector_ssp126.ini b/inst/input/hector_ssp126.ini
index 417a3a6d2..2ded73eb6 100644
--- a/inst/input/hector_ssp126.ini
+++ b/inst/input/hector_ssp126.ini
@@ -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
@@ -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
diff --git a/inst/input/hector_ssp245.ini b/inst/input/hector_ssp245.ini
index 2bd7259af..2f170eb22 100644
--- a/inst/input/hector_ssp245.ini
+++ b/inst/input/hector_ssp245.ini
@@ -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
@@ -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
diff --git a/inst/input/hector_ssp370.ini b/inst/input/hector_ssp370.ini
index 2a0782ba3..8df3619ee 100644
--- a/inst/input/hector_ssp370.ini
+++ b/inst/input/hector_ssp370.ini
@@ -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
@@ -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
diff --git a/inst/input/hector_ssp434.ini b/inst/input/hector_ssp434.ini
index f4fecdf68..dcb3c17a6 100644
--- a/inst/input/hector_ssp434.ini
+++ b/inst/input/hector_ssp434.ini
@@ -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
@@ -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
diff --git a/inst/input/hector_ssp460.ini b/inst/input/hector_ssp460.ini
index ff0e1ff53..8ffc4ff48 100644
--- a/inst/input/hector_ssp460.ini
+++ b/inst/input/hector_ssp460.ini
@@ -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
@@ -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
diff --git a/inst/input/hector_ssp534-over.ini b/inst/input/hector_ssp534-over.ini
index a969ad43e..674b1362d 100644
--- a/inst/input/hector_ssp534-over.ini
+++ b/inst/input/hector_ssp534-over.ini
@@ -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
@@ -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
diff --git a/inst/input/hector_ssp585.ini b/inst/input/hector_ssp585.ini
index 75a27fc14..289113367 100644
--- a/inst/input/hector_ssp585.ini
+++ b/inst/input/hector_ssp585.ini
@@ -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
@@ -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
diff --git a/src/simpleNbox.cpp b/src/simpleNbox.cpp
index 96c039fbf..399b75429 100644
--- a/src/simpleNbox.cpp
+++ b/src/simpleNbox.cpp
@@ -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");
diff --git a/tests/testthat/input/luc_pulse.ini b/tests/testthat/input/luc_pulse.ini
index 901ef82d0..e0aea8d30 100644
--- a/tests/testthat/input/luc_pulse.ini
+++ b/tests/testthat/input/luc_pulse.ini
@@ -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