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Merged
jahn merged 2 commits into from
Dec 2, 2025
Merged

Add macromolecular growth parameterization #9

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9d73a02
Add macromolecular growth parameterization
shlomitsharoni Jul 28, 2025
a55a498
Merge branch 'darwin' into macromol_ssh
jahn Dec 1, 2025
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40 changes: 40 additions & 0 deletions pkg/darwin/DARWIN_DIAGS.h
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,15 @@ C Contains indices into diagnostics array
integer ifnut
integer ifIph
integer ifTph
# ifdef DARWIN_MACROMOLECULAR_GROWTH
integer iPChl, iVN, iVP
integer iCChl, iNChl, iNPho, iNSyn, iNPrn, iNRNA
integer iNDNA, iNSTO, iNEXC
integer iPRNA, iPDNA, iPTHY, iPCON, iPSTO, iPEXC
integer iFPHO, iFSTO, iFEXC, iY_RQ
integer iMODE, iFe_C, iexQc
integer ilimC, ilimL
# endif
#endif
#ifdef DARWIN_ALLOW_CSTORE
integer iEX
Expand Down Expand Up @@ -133,7 +142,38 @@ C Contains indices into diagnostics array
PARAMETER(ifnut=ilimS+nplank)
PARAMETER(ifIph=ifnut+nplank)
PARAMETER(ifTph=ifIph+nplank)
# ifdef DARWIN_MACROMOLECULAR_GROWTH
PARAMETER(iPChl=ifTph+nplank)
PARAMETER(iVN= iPChl+nPhoto)
PARAMETER(iVP= iVN +nPhoto)
PARAMETER(iMODE=iVP +nPhoto)
PARAMETER(iFe_C=iMODE+nPhoto)
PARAMETER(iexQc=iFe_C+nPhoto)
PARAMETER(iCChl=iexQc+nPhoto)
PARAMETER(iNChl=iCChl+nPhoto)
PARAMETER(iNPho=iNChl+nPhoto)
PARAMETER(iNSyn=iNPho+nPhoto)
PARAMETER(iNPrn=iNSyn+nPhoto)
PARAMETER(iNRNA=iNPrn+nPhoto)
PARAMETER(iNDNA=iNRNA+nPhoto)
PARAMETER(iNSTO=iNDNA+nPhoto)
PARAMETER(iNEXC=iNSTO+nPhoto)
PARAMETER(iPRNA=iNEXC+nPhoto)
PARAMETER(iPDNA=iPRNA+nPhoto)
PARAMETER(iPTHY=iPDNA+nPhoto)
PARAMETER(iPCON=iPTHY+nPhoto)
PARAMETER(iPSTO=iPCON+nPhoto)
PARAMETER(iPEXC=iPSTO+nPhoto)
PARAMETER(iFPHO=iPEXC+nPhoto)
PARAMETER(iFSTO=iFPHO+nPhoto)
PARAMETER(iFEXC=iFSTO+nPhoto)
PARAMETER(iY_RQ=iFEXC+nPhoto)
PARAMETER(ilimC=iY_RQ+nPhoto)
PARAMETER(ilimL=ilimC+nPhoto)
PARAMETER(darwin_nDiag=ilimL+nPhoto-1)
# else
PARAMETER(darwin_nDiag=ifTph+nplank-1)
# endif
#else
PARAMETER(iPCplank=iPPplank)
PARAMETER(iGRplank=iPPplank)
Expand Down
13 changes: 8 additions & 5 deletions pkg/darwin/DARWIN_OPTIONS.h
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Expand Up @@ -51,11 +51,8 @@ C but will use solvesaphe dissociation coefficient options.
C this needs to be defined for coupling to atmospheric model:
#undef DARWIN_USE_PLOAD

C enable RADI sediment metamodel v1
#undef DARWIN_ALLOW_RADIv1

C enable RADI sediment metamodel v2
#undef DARWIN_ALLOW_RADIv2
C enable macromolecular growth code; requires N, P and Fe quotas
#undef DARWIN_MACROMOLECULAR_GROWTH


C optional bits
Expand Down Expand Up @@ -84,6 +81,12 @@ C CDOM is in carbon units and follows POC
C include code for reading nutrient runoff from files
#undef DARWIN_NUTRIENT_RUNOFF

C enable RADI sediment metamodel v1
#undef DARWIN_ALLOW_RADIv1

C enable RADI sediment metamodel v2
#undef DARWIN_ALLOW_RADIv2

C include diel vertical migration code
#undef DARWIN_ALLOW_DVM

Expand Down
9 changes: 6 additions & 3 deletions pkg/darwin/DARWIN_PARAMS.h
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Expand Up @@ -335,6 +335,7 @@ C tempnorm :: [] set temperature function (was 1.0)
C TempAeArr :: [K] slope for pseudo-Arrhenius (TEMP_VERSION 2)
C TemprefArr :: [K] reference temp for pseudo-Arrhenius (TEMP_VERSION 2)
C TempCoeffArr :: [] pre-factor for pseudo-Arrhenius (TEMP_VERSION 2)
C TempAeArrMacromol :: [K] slope for pseudo-Arrhenius for macromolecular (TEMP_VERSION 2)
C reminTempAe :: [1/K] temperature coefficient for remineralization (TEMP_VERSION 4)
C mortTempAe :: [1/K] temperature coefficient for linear mortality (TEMP_VERSION 4)
C mort2TempAe :: [1/K] temperature coefficient for quadr. mortality (TEMP_VERSION 4)
Expand Down Expand Up @@ -377,6 +378,7 @@ C KPON :: [1/s] PON remineralization rate
C KPOP :: [1/s] POP remineralization rate
C KPOFe :: [1/s] POFe remineralization rate
C KPOSi :: [1/s] POSi remineralization rate
C ksatO2remin :: [mmol O2/m3] half-saturation conc. of O2 for remineralization
C
C wC_sink :: [m/s] sinking velocity for POC
C wN_sink :: [m/s] sinking velocity for PON
Expand Down Expand Up @@ -432,7 +434,6 @@ C chl2nmax :: [mg Chl / mmol N] max Chl:N ratio for Chl synthesis
C synthcost :: [mmol C / mmol N] cost of biosynthesis
C inhib_graz :: [(mmol C m-3)-1] inverse decay scale for grazing inhibition
C inhib_graz_exp :: [] exponent for grazing inhibition (0 to turn off inhibition)
C hillnumUptake :: [] exponent for limiting quota uptake in nutrient uptake
C hillnumGraz :: [] exponent for limiting quota uptake in grazing
C hollexp :: [] grazing exponential 1= "Holling 2", 2= "Holling 3"
C phygrazmin :: [mmol C m-3] minimum total prey conc for grazing to occur
Expand Down Expand Up @@ -464,6 +465,7 @@ C depthdenit :: [m] not implemented (depth for denitrific
& TempAeArr,
& TemprefArr,
& TempCoeffArr,
& TempAeArrMacromol,
& reminTempAe,
& mortTempAe,
& mort2TempAe,
Expand Down Expand Up @@ -508,6 +510,7 @@ C depthdenit :: [m] not implemented (depth for denitrific
& KPOP,
& KPOFe,
& KPOSi,
& ksatO2remin,
& wC_sink,
& wN_sink,
& wP_sink,
Expand Down Expand Up @@ -557,7 +560,6 @@ C depthdenit :: [m] not implemented (depth for denitrific
& synthcost,
& inhib_graz,
& inhib_graz_exp,
& hillnumUptake,
& hillnumGraz,
& hollexp,
& phygrazmin,
Expand All @@ -584,6 +586,7 @@ C & yono2,
_RL TempAeArr
_RL TemprefArr
_RL TempCoeffArr
_RL TempAeArrMacromol
_RL reminTempAe
_RL mortTempAe
_RL mort2TempAe
Expand Down Expand Up @@ -628,6 +631,7 @@ C & yono2,
_RL KPOP
_RL KPOFe
_RL KPOSi
_RL ksatO2remin
_RL wC_sink
_RL wN_sink
_RL wP_sink
Expand Down Expand Up @@ -677,7 +681,6 @@ C & yono2,
_RL synthcost
_RL inhib_graz
_RL inhib_graz_exp
_RL hillnumUptake
_RL hillnumGraz
_RL hollexp
_RL phygrazmin
Expand Down
68 changes: 68 additions & 0 deletions pkg/darwin/DARWIN_TRAITPARAMS.h
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Expand Up @@ -352,6 +352,36 @@ C
& a_grazTempExp2,
& a_grazTempOptimum,
& a_grazDecayPower,
#ifdef DARWIN_MACROMOLECULAR_GROWTH
& a_Y_CP_Plip,
& a_Y_CN_protein,
& a_Y_NC_chl,
& a_Y_CN_cyano,
& a_Y_PN_nucacid,
& a_Y_CN_DNA,
& a_Y_CN_RNA,
& a_Y_THY_P,
& a_Y_FeN_photo,
& a_ECo2Prod,
& a_maintConsum,
& a_VI_max,
& b_VI_max,
& a_A_I,
& a_QC_other,
& a_QC_pro_other,
& a_QP_other,
& a_QP_RNA_min,
& a_QC_DNA,
& a_QN_sto_max,
& b_QN_sto_max,
& a_Qp_max,
& b_Qp_max,
& a_Qfe_max,
& b_Qfe_max,
& a_A_pho,
& a_A_bio,
& a_AP_RNA,
#endif
#ifdef DARWIN_ALLOW_GEIDER
& a_mQyield,
& a_chl2cmax,
Expand All @@ -365,6 +395,10 @@ C
& a_acclimtimescl_denom,
& a_ksatPON,
& a_ksatDON,
& a_hillnumDIN,
& a_hillnumPO4,
& a_hillnumFeT,
& a_hillnumSiO2,
& a_grazemax,
& a_grazemax_denom,
& b_grazemax,
Expand Down Expand Up @@ -497,6 +531,36 @@ C
_RL a_grazTempExp2(nGroup)
_RL a_grazTempOptimum(nGroup)
_RL a_grazDecayPower(nGroup)
#ifdef DARWIN_MACROMOLECULAR_GROWTH
_RL a_Y_CP_Plip(nGroup)
_RL a_Y_CN_protein(nGroup)
_RL a_Y_NC_chl(nGroup)
_RL a_Y_CN_cyano(nGroup)
_RL a_Y_PN_nucacid(nGroup)
_RL a_Y_CN_DNA(nGroup)
_RL a_Y_CN_RNA(nGroup)
_RL a_Y_THY_P(nGroup)
_RL a_Y_FeN_photo(nGroup)
_RL a_ECo2Prod(nGroup)
_RL a_maintConsum(nGroup)
_RL a_VI_max(nGroup)
_RL b_VI_max(nGroup)
_RL a_A_I(nGroup)
_RL a_QC_other(nGroup)
_RL a_QC_pro_other(nGroup)
_RL a_QP_other(nGroup)
_RL a_QP_RNA_min(nGroup)
_RL a_QC_DNA(nGroup)
_RL a_QN_sto_max(nGroup)
_RL b_QN_sto_max(nGroup)
_RL a_Qp_max(nGroup)
_RL b_Qp_max(nGroup)
_RL a_Qfe_max(nGroup)
_RL b_Qfe_max(nGroup)
_RL a_A_pho(nGroup)
_RL a_A_bio(nGroup)
_RL a_AP_RNA(nGroup)
#endif
#ifdef DARWIN_ALLOW_GEIDER
_RL a_mQyield(nGroup)
_RL a_chl2cmax(nGroup)
Expand All @@ -510,6 +574,10 @@ C
_RL a_acclimtimescl_denom(nGroup)
_RL a_ksatPON(nGroup)
_RL a_ksatDON(nGroup)
_RL a_hillnumDIN(nGroup)
_RL a_hillnumPO4(nGroup)
_RL a_hillnumFeT(nGroup)
_RL a_hillnumSiO2(nGroup)
_RL a_grazemax(nGroup)
_RL a_grazemax_denom(nGroup)
_RL b_grazemax(nGroup)
Expand Down
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