diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index c243e7d..baaeb7a 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -24,6 +24,7 @@ add_library(fabm_models_ersem OBJECT carbonate.F90 oxygen.F90 nitrification.F90 + nitrous_oxide.F90 benthic_column.F90 benthic_column_dissolved_matter.F90 benthic_column_particulate_matter.F90 diff --git a/src/bacteria_docdyn.F90 b/src/bacteria_docdyn.F90 index 0e4cea6..fe27692 100644 --- a/src/bacteria_docdyn.F90 +++ b/src/bacteria_docdyn.F90 @@ -14,15 +14,17 @@ module ersem_bacteria_docdyn type,extends(type_ersem_pelagic_base),public :: type_ersem_bacteria_docdyn ! Variables - type (type_state_variable_id) :: id_O3c, id_O2o, id_TA + type (type_state_variable_id) :: id_O3c, id_O2o, id_TA, id_N3n type (type_state_variable_id) :: id_R1c, id_R2c, id_R3c type (type_state_variable_id) :: id_R1p type (type_state_variable_id) :: id_R1n - type (type_state_variable_id) :: id_N1p,id_N4n,id_N7f + type (type_state_variable_id) :: id_N1p,id_N4n,id_N7f,id_N6 type (type_dependency_id) :: id_ETW,id_eO2mO2 type (type_state_variable_id),allocatable,dimension(:) :: id_RPc,id_RPp,id_RPn,id_RPf type (type_model_id), allocatable,dimension(:) :: id_RP - type (type_diagnostic_variable_id) :: id_fB1O3c, id_fB1NIn, id_fB1N1p, id_bgeff + + type (type_diagnostic_variable_id) :: id_fB1O3c, id_fB1NIn, id_fB1N1p,id_bgeff,id_fdenit,id_fanox,id_freox + type (type_diagnostic_variable_id) :: id_fR1B1c, id_fR2B1c, id_fR3B1c,id_fRPB1c,id_fB1R1c, id_fB1R2c, id_fB1R3c type (type_diagnostic_variable_id) :: id_fR1B1n,id_fB1R1n,id_fR1B1p,id_fB1R1p,id_fRPB1n,id_fRPB1p type (type_diagnostic_variable_id) :: id_minn,id_minp @@ -39,6 +41,8 @@ module ersem_bacteria_docdyn real(rk) :: rR2B1X,rR3B1X real(rk),allocatable :: sRPR1(:) real(rk) :: frB1R3 + real(rk) :: DeniX,reoX,omroX,omonX,chN3oX + integer :: denit ! Remineralization real(rk) :: sR1N1X,sR1N4X @@ -84,6 +88,22 @@ subroutine initialize(self,configunit) call self%get_parameter(self%qpB1cX, 'qpc', 'mmol P/mg C','maximum phosphorus to carbon ratio') call self%get_parameter(self%qnB1cX, 'qnc', 'mmol N/mg C','maximum nitrogen to carbon ratio') call self%get_parameter(self%urB1_O2X,'ur_O2', 'mmol O_2/mg C','oxygen consumed per carbon respired') + call self%get_parameter(self%denit, 'denit', '-', 'denitrification switch (0: off, 1: on)',default=0) + + if (self%denit == 1) then + call self%get_parameter(self%DeniX, 'DeniX', '1/d', 'specific denitrification rate') + call self%get_parameter(self%reoX, 'reoX', '1/d', 'specific reoxidation rate of reduction equivalents') + call self%get_parameter(self%omroX, 'omroX', 'mmol HS mmol O2-1', 'stoichiometric coefficient') + call self%get_parameter(self%omonX, 'omonX', 'mmol O2 mmol N-1', 'stoichiometric coefficient for denitrification reaction') + call self%get_parameter(self%chN3oX, 'chN3o', '(mmol O_2/m^3)^3', 'Michaelis-Menten constant for cubic oxygen dependence of nitrification') + + call self%register_state_dependency(self%id_N3n,'N3n','mmol N/m^3','nitrate') + call self%register_state_dependency(self%id_N6,'N6','mmol HS-/m^3','reduction equivalent') + + call self%register_diagnostic_variable(self%id_fdenit,'fdenit','mmol N/m^3/d','denitrification', missing_value=0._rk) + call self%register_diagnostic_variable(self%id_fanox,'fanox', '-', 'fanox', missing_value=0._rk) + call self%register_diagnostic_variable(self%id_freox,'freox', '-', 'freox', missing_value=0._rk) + end if ! Remineralization parameters call self%get_parameter(self%sR1N1X, 'sR1N1', '1/d', 'mineralisation rate of labile dissolved organic phosphorus') @@ -189,7 +209,7 @@ subroutine do(self,_ARGUMENTS_DO_) real(rk) :: ETW,eO2mO2 real(rk) :: B1c,B1n,B1p real(rk) :: B1cP,B1nP,B1pP - real(rk) :: N1pP,N4nP,R1c,R1cP,R1pP,R1nP,R2c + real(rk) :: N1pP,N4nP,R1c,R1cP,R1pP,R1nP,R2c,N3n,N6,O2o real(rk) :: qpB1c,qnB1c real(rk) :: etB1,eO2B1 real(rk) :: sB1RD,sutB1,rumB1,sugB1,rugB1,rraB1,fB1O3c @@ -201,6 +221,7 @@ subroutine do(self,_ARGUMENTS_DO_) real(rk) :: fB1R1c real(rk) :: totsubst real(rk) :: CORROX + real(rk) :: fdenit,denitpot,deniteff,o2state,freox,fanox integer :: iRP real(rk),dimension(self%nRP) :: RPc,RPcP,RPnP,RPpP real(rk),dimension(self%nRP) :: fRPB1c,fRPB1p,fRPB1n @@ -239,6 +260,15 @@ subroutine do(self,_ARGUMENTS_DO_) qpB1c = B1p/B1c qnB1c = B1n/B1c + + if (self%denit == 1) then + _GET_(self%id_N3n,N3n) + _GET_(self%id_O2o,O2o) + O2o = max(0.0_rk,O2o) + o2state = O2o**3/(O2o**3 + self%chN3oX) + _GET_(self%id_N6,N6) + end if + !..Temperature effect on pelagic bacteria: etB1 = max(0.0_rk,self%q10B1X**((ETW-10._rk)/10._rk) - self%q10B1X**((ETW-32._rk)/3._rk)) @@ -294,6 +324,25 @@ subroutine do(self,_ARGUMENTS_DO_) fB1R3c=self%frB1R3*rraB1 fB1RDc = fB1R1c + fB1R2c + fB1R3c +! Denitrification implemented as in Sankar et al. (2008), doi.org/10.1016/j.ecolmodel.2018.01.016 + if (self%denit == 1) then + denitpot = self%DeniX * N3n !eq.6 + deniteff = max(0._rk, self%urB1_O2X * (1._rk-o2state) * fB1O3c / self%omonX) !eq.7 + fdenit = min(denitpot, deniteff) !eq.5 + + _SET_DIAGNOSTIC_(self%id_fdenit,fdenit) + _SET_ODE_(self%id_N3n, -fdenit) + +! Reduced sulfur formation corresponds to eq.9 in Sankar et al. (2008) + fanox = self%omrox * (self%urB1_O2X * (1._rk-o2state) * fB1O3c - self%omonX * fdenit) + freox = self%reoX * etB1 * o2state * N6 + + _SET_DIAGNOSTIC_(self%id_fanox,freox) + _SET_DIAGNOSTIC_(self%id_freox,fanox) + + _SET_ODE_(self%id_N6, fanox - freox) + end if + !..net bacterial production netb1 = rugB1 - fB1o3c - fB1RDc diff --git a/src/ersem_model_library.F90 b/src/ersem_model_library.F90 index d1e3e8c..912abcc 100644 --- a/src/ersem_model_library.F90 +++ b/src/ersem_model_library.F90 @@ -14,6 +14,7 @@ module ersem_model_library use ersem_bacteria use ersem_bacteria_docdyn use ersem_nitrification + use ersem_nitrous_oxide use ersem_light use ersem_light_iop use ersem_light_iop_ady @@ -65,6 +66,7 @@ subroutine create(self,name,model) case ('bacteria'); allocate(type_ersem_bacteria::model) case ('bacteria_docdyn'); allocate(type_ersem_bacteria_docdyn::model) case ('nitrification'); allocate(type_ersem_nitrification::model) + case ('nitrous_oxide'); allocate(type_ersem_nitrous_oxide::model) case ('light'); allocate(type_ersem_light::model) case ('light_iop'); allocate(type_ersem_light_iop::model) case ('light_iop_ady'); allocate(type_ersem_light_iop_ady::model) diff --git a/src/nitrification.F90 b/src/nitrification.F90 index 4c89d23..33be55d 100644 --- a/src/nitrification.F90 +++ b/src/nitrification.F90 @@ -15,14 +15,15 @@ module ersem_nitrification type,extends(type_ersem_pelagic_base),public :: type_ersem_nitrification ! Variables type (type_state_variable_id) :: id_O2o,id_TA - type (type_state_variable_id) :: id_N3n,id_N4n + type (type_state_variable_id) :: id_N3n,id_N4n,id_O5n type (type_dependency_id) :: id_ETW,id_phx - type (type_diagnostic_variable_id) :: id_nitrification + type (type_diagnostic_variable_id) :: id_nitrification, id_fN4O5n, id_fN4N3n ! Parameters real(rk) :: q10 - real(rk) :: sN4N3X,chN3oX,chN4nX + real(rk) :: sN4N3X,chN3oX,chN4nX, N4O5minX integer :: ISWphx + logical :: ISWn2o contains ! Model procedures procedure :: initialize @@ -50,15 +51,20 @@ subroutine initialize(self,configunit) call self%get_parameter(self%ISWphx,'ISWph','', 'pH impact on nitrification (0: off, 1: on)') call self%get_parameter(self%sN4N3X,'sN4N3','1/d', 'specific nitrification rate') call self%get_parameter(self%chN3oX,'chN3o','(mmol O_2/m^3)^3','Michaelis-Menten constant for cubic oxygen dependence of nitrification') + call self%get_parameter(self%ISWn2o,'ISWn2o','', 'activate n2o production', default = .false.) + if (self%ISWn2o) call self%get_parameter(self%N4O5minX,'N4O5minX','-','minimal fraction of N2O production') call self%get_parameter(self%chN4nX,'chN4n','(mmol N/m^3)^3','Michaelis-Menten constant for cubic ammonium dependence of nitrification', default=0.0_rk) ! Register diagnostic variables call self%register_diagnostic_variable(self%id_nitrification,"rate","mmol/m3/d","rate") + call self%register_diagnostic_variable(self%id_fN4N3n,'fN4N3n','mmol N/m^3/d','nitrification',output=output_time_step_averaged) + if (self%ISWn2o) call self%register_diagnostic_variable(self%id_fN4O5n,'fN4O5n','mmol N/m^3/d','N2O production',output=output_time_step_averaged) ! Register links to nutrient and oxygen pools. call self%register_state_dependency(self%id_N3n,'N3n','mmol N/m^3', 'nitrate') call self%register_state_dependency(self%id_N4n,'N4n','mmol N/m^3', 'ammonium') call self%register_state_dependency(self%id_O2o,'O2o','mmol O_2/m^3','oxygen') + if (self%ISWn2o) call self%register_state_dependency(self%id_O5n,'O5n','mmol N/m^3','nitrous oxide') call self%register_state_dependency(self%id_TA,standard_variables%alkalinity_expressed_as_mole_equivalent) ! Register environmental dependencies (temperature, pH) @@ -73,7 +79,7 @@ subroutine do(self,_ARGUMENTS_DO_) _DECLARE_ARGUMENTS_DO_ real(rk) :: ETW,phx,O2o,N4n,N4nP - real(rk) :: etB1,o2state,n4state,Fph,fN4N3n + real(rk) :: etB1,o2state,n4state,Fph,fN4N3n,fN4O5n ! Leave spatial loops (if any) _LOOP_BEGIN_ @@ -101,6 +107,22 @@ subroutine do(self,_ARGUMENTS_DO_) Fph = min(2._rk,max(0._rk,0.6111_rk*phx-3.8889_rk)) fN4N3n = fN4N3n * Fph end if + ! N2O production + ! A fixed quota of N is assumed to go to N2O during nitrification + ! Depending on O2 limitation this quota may increase up to 20 time + ! (Cadispoti, 2010). Note that N2O is given as mmol of N m-3 (i.e. 1/2 + ! mmole N2O m-2)! (Luca, July 2016) + + if (self%ISWn2o) then + fN4O5n=self%N4O5minX*fN4N3n*min(20._rk,(1._rk/o2state)) + _SET_ODE_(self%id_O5n,fN4O5n) + _SET_ODE_(self%id_N3n, -fN4O5n) + _SET_DIAGNOSTIC_(self%id_fN4O5n,fN4O5n) + end if + + _SET_DIAGNOSTIC_(self%id_fN4N3n,fN4N3n) + + _SET_ODE_(self%id_N3n, + fN4N3n) _SET_ODE_(self%id_N4n, - fN4N3n) diff --git a/src/nitrous_oxide.F90 b/src/nitrous_oxide.F90 new file mode 100644 index 0000000..3167ae4 --- /dev/null +++ b/src/nitrous_oxide.F90 @@ -0,0 +1,144 @@ +#include "fabm_driver.h" + +!------------------------------------------------------------------------ +! This module calculates saturation concentrations and air-sea +! exchange of nitrous oxide. Production of nitrous oxide is implemented +! in nitrification module (nitrification.F90). +! For implementation and validation of nitrous oxide on the North-West +! European Shelf see Lessin et al. (2020): doi.org/10.1029/2019JG005613 +!------------------------------------------------------------------------ + +module ersem_nitrous_oxide + + use fabm_types + use fabm_particle + + use ersem_shared + use ersem_pelagic_base + + implicit none + + private + + type,extends(type_ersem_pelagic_base),public :: type_ersem_nitrous_oxide + ! Variables + type (type_dependency_id) :: id_ETW,id_X1X + type (type_horizontal_dependency_id) :: id_wnd,id_pN2Oa + type (type_horizontal_diagnostic_variable_id) :: id_airsea + type (type_diagnostic_variable_id) :: id_satp + + integer :: iswN2O + + contains +! Model procedures + procedure :: initialize + procedure :: do_surface + procedure :: do + end type + +contains + + subroutine initialize(self,configunit) +! +! !DESCRIPTION: +! +! !INPUT PARAMETERS: + class (type_ersem_nitrous_oxide),intent(inout),target :: self + integer, intent(in) :: configunit +! +!EOP +!----------------------------------------------------------------------- +!BOC + call self%initialize_ersem_base(sedimentation=.false.) + + call self%add_constituent('n',0.0_rk) + + call self%register_dependency(self%id_ETW,standard_variables%temperature) + call self%register_dependency(self%id_X1X,standard_variables%practical_salinity) + call self%register_dependency(self%id_wnd,standard_variables%wind_speed) + call self%register_dependency(self%id_pN2Oa,partial_pressure_of_n2o) + call self%register_diagnostic_variable(self%id_satp,'satp','%','nitrous oxide % saturation') + call self%register_diagnostic_variable(self%id_airsea,'airsea','mmol N2O/m^2/d','airsea flux of N2O',source=source_do_surface) + call self%get_parameter(self%iswN2O,'iswN2O','','air-sea flux switch (0: off, 1: on)',default=1) + + end subroutine initialize + + subroutine do(self,_ARGUMENTS_DO_) + class (type_ersem_nitrous_oxide), intent(in) :: self + _DECLARE_ARGUMENTS_DO_ + + real(rk) :: O5n,ETW,X1X + real(rk) :: koN2O,pN2Oa + + _LOOP_BEGIN_ + _GET_(self%id_n,O5n) + _GET_(self%id_ETW,ETW) + _GET_(self%id_X1X,X1X) + _GET_HORIZONTAL_(self%id_pN2Oa,pN2Oa) + + koN2O = n2o_transfer_coefficient(self,ETW,X1X) + + _SET_DIAGNOSTIC_(self%id_satp,(100._rk*O5n*0.5_rk/(KoN2O*pN2Oa*1.e-9*1.e6))) + _LOOP_END_ + end subroutine + + subroutine do_surface(self,_ARGUMENTS_DO_SURFACE_) + class (type_ersem_nitrous_oxide), intent(in) :: self + _DECLARE_ARGUMENTS_DO_SURFACE_ + + real(rk) :: O5n,ETW,X1X,wnd, fwind + real(rk) :: koN2O,sc,n2oflux,pN2Oa + + _HORIZONTAL_LOOP_BEGIN_ + _GET_(self%id_n,O5n) + _GET_(self%id_ETW,ETW) + _GET_(self%id_X1X,X1X) + _GET_HORIZONTAL_(self%id_wnd,wnd) + _GET_HORIZONTAL_(self%id_pN2Oa,pN2Oa) + +! Schmidt number for N2O (Wanninkhof, 1992) + + sc=2301._rk-151._rk*ETW+4.74_rk*ETW**2._rk-0.06_rk*ETW**3 + fwind = 0.39_rk * wnd**2 *(sc/660._rk)**(-0.5_rk) + fwind=fwind*24._rk/100._rk ! convert to m/day + + koN2O = n2o_transfer_coefficient(self,ETW,X1X) + +! PNOatm is given in natm, so it is here converted to atm by means of a 1.-9 factor. As KoNO is +! given in mol L-1 atm -1 (Weiss and Price, 1980), a conversion factor of +! 1.e6 is used to have the final units of mmol m-3. N0 is given in mmol +! of N so it is multiplied by 0.5 to have mmol of N2O. (Luca, July 2016) + + if (self%iswN2O .eq. 1) then + n2oflux = fwind*(KoN2O*pN2Oa*1.e-9*1.e6-O5n*0.5_rk) + else + n2oflux=0._rk + endif + + _SET_HORIZONTAL_DIAGNOSTIC_(self%id_airsea,n2oflux) + + _SET_SURFACE_EXCHANGE_(self%id_n,n2oflux*2._rk) + + _HORIZONTAL_LOOP_END_ + end subroutine do_surface + + function n2o_transfer_coefficient(self,ETW,X1X) result(koN2O) + class (type_ersem_nitrous_oxide), intent(in) :: self + real(rk), intent(in) :: ETW,X1X + real(rk) :: koN2O + real(rk) :: tk,tk100 + real(rk),parameter :: A1 = -62.7062_rk + real(rk),parameter :: A2 = 97.3066_rk + real(rk),parameter :: A3 = 24.1406_rk + real(rk),parameter :: B1 = -0.05842_rk + real(rk),parameter :: B2 = 0.033193_rk + real(rk),parameter :: B3 = -0.0051_rk + + TK=ETW+273.15_rk + TK100=TK/100._rk + + koN2O = exp(A1+A2/tk100 + A3 * log(tk100) + & + & X1X * (B1 + B2 * tk100 + B3 * tk100 ** 2._rk)) + end function + +end module diff --git a/src/pelagic_base.F90 b/src/pelagic_base.F90 index 407d7f6..446a109 100644 --- a/src/pelagic_base.F90 +++ b/src/pelagic_base.F90 @@ -13,7 +13,7 @@ module ersem_pelagic_base private type,extends(type_particle_model),public :: type_ersem_pelagic_base - type (type_state_variable_id) :: id_c,id_n,id_p,id_f,id_s,id_chl + type (type_state_variable_id) :: id_c,id_n,id_p,id_f,id_s,id_chl,id_h type (type_horizontal_dependency_id) :: id_bedstress,id_wdepth type (type_dependency_id) :: id_dens type (type_horizontal_diagnostic_variable_id) :: id_w_bot @@ -142,6 +142,7 @@ subroutine initialize(self,configunit) call self%register_diagnostic_variable(self%id_kflux_f,'kflux_f','nmolFe/m^3/d','1st order kinetic flux of iron',source=source_do) endif endif + if (index(composition,'h')/=0) call self%add_constituent('h',0.0_rk) end subroutine @@ -207,6 +208,8 @@ subroutine add_constituent(self,name,initial_value,background_value,qn,qp) if (use_iron) call register(self%id_f,'f','umol Fe','iron',standard_variables%total_iron,self%qxf,self%id_fdep,self%id_targetf) case ('chl') call register(self%id_chl,'Chl','mg','chlorophyll a',total_chlorophyll) + case ('h') + call register(self%id_h,'h','mmol','reduction equivalent',total_h) case default call self%fatal_error('add_constituent','Unknown constituent "'//trim(name)//'".') end select diff --git a/src/shared.F90 b/src/shared.F90 index 3faae7f..b468a14 100644 --- a/src/shared.F90 +++ b/src/shared.F90 @@ -26,6 +26,7 @@ module ersem_shared ! Aggregate diagnostics for e.g., carbon budgets. type (type_bulk_standard_variable),parameter :: total_chlorophyll = type_bulk_standard_variable(name='total_chlorophyll',units='mg/m^3',aggregate_variable=.true.) + type (type_bulk_standard_variable),parameter :: total_h = type_bulk_standard_variable(name='total_h',units='mmol/m^3',aggregate_variable=.true.) type (type_bulk_standard_variable),parameter :: total_calcite_in_biota = type_bulk_standard_variable(name='total_calcite_in_biota',units='mg C/m^3',aggregate_variable=.true.) type (type_bulk_standard_variable),parameter :: secchi_depth = type_bulk_standard_variable(name='secchi_depth',units='m') @@ -44,6 +45,7 @@ module ersem_shared type (type_horizontal_standard_variable),parameter :: depth_of_bottom_interface_of_layer_1 = type_horizontal_standard_variable(name='depth_of_bottom_interface_of_layer_1',units='m') type (type_horizontal_standard_variable),parameter :: depth_of_bottom_interface_of_layer_2 = type_horizontal_standard_variable(name='depth_of_bottom_interface_of_layer_2',units='m') type (type_horizontal_standard_variable),parameter :: pelagic_benthic_transfer_constant = type_horizontal_standard_variable(name='pelagic_benthic_transfer_constant',units='d/m') + type (type_horizontal_standard_variable),parameter :: partial_pressure_of_n2o = type_horizontal_standard_variable(name='partial_pressure_of_n2o',units='natm') type (type_horizontal_standard_variable),parameter :: sediment_erosion = type_horizontal_standard_variable(name='sediment_erosion',units='m/d') ! Aggregate absorption and backscatter. diff --git a/testcases/fabm-ersem-15.06-L4-ben-docdyn-iop-denit.yaml b/testcases/fabm-ersem-15.06-L4-ben-docdyn-iop-denit.yaml new file mode 100644 index 0000000..7eeb2f5 --- /dev/null +++ b/testcases/fabm-ersem-15.06-L4-ben-docdyn-iop-denit.yaml @@ -0,0 +1,1188 @@ +check_conservation: false +require_initialization: true +instances: + zenithAngle: + model: ersem/zenith_angle + light: + model: ersem/light_iop + parameters: + a0w: 0.03 # absorption coefficient of clear water (1/m), default = 0.036 + b0w: 0.0015 # backscatter coefficient of clear water (1/m), default = 0.0016 + pEIR_eow: 0.5 # photosynthetically active fraction of shortwave radiation (-), default = 0.5 + N1: + long_name: phosphate + model: ersem/pelagic_base + parameters: + composition: p # elemental composition + c0: 0.001 # background carbon concentration (mg C/m^3), default = 0.0 + initialization: + p: 0.4 # phosphorus (mmol P/m^3) + N3: + long_name: nitrate + model: ersem/pelagic_base + parameters: + composition: n # elemental composition + c0: 0.001 # background carbon concentration (mg C/m^3), default = 0.0 + initialization: + n: 8.0 # nitrogen (mmol N/m^3) + N4: + long_name: ammonium + model: ersem/pelagic_base + parameters: + composition: n # elemental composition + c0: 0.001 # background carbon concentration (mg C/m^3), default = 0.0 + initialization: + n: 0.1 # nitrogen (mmol N/m^3) + N5: + long_name: silicate + model: ersem/pelagic_base + parameters: + composition: s # elemental composition + s0: 0.0003 # background silicon concentration (mmol Si/m^3), default = 0.0 + initialization: + s: 4.5 # silicate (mmol Si/m^3) + N6: + long_name: reduction equivalent + model: ersem/pelagic_base + parameters: + composition: h + c0: 0.000 # background reduction equivalent concentration (mmol S/m^3), default = 0.0 + initialization: + h: 1.e-08 + O2: + long_name: oxygen + model: ersem/oxygen + parameters: + iswO2: 2 # saturation formulation (1: legacy ERSEM, 2: Weiss 1970, 3: Nightingale et al. 2000, 4: Wanninkhof 2014) + initialization: + o: 300.0 # oxygen (mmol O_2/m^3) + O3: + long_name: carbonate + model: ersem/carbonate + parameters: + iswCO2: 1 # carbonate system diagnostics (0: off, 1: on), default = 1 + iswASFLUX: 1 # air-sea CO2 exchange (0: none, 1: Nightingale et al. 2000, 2: Wanninkhof 1992 without chemical enhancement, 3: Wanninkhof 1992 with chemical enhancement, 4: Wanninkhof and McGillis 1999, 5: Wanninkhof 1992 switching to Wanninkhof and McGillis 1999, 6: Wan, default = 6 + iswtalk: 2 # alkalinity formulation (1-4: from salinity and temperature, 5: dynamic alkalinity), default = 5 + pHscale: 1 # pH scale (1: total, 0: SWS, -1: SWS backward compatible), default = 1 + iswbioalk: 1 # use bioalkalinity (0: off, 1: on), default = 1 + initialization: + c: 2130.0 # total dissolved inorganic carbon (mmol C/m^3) + R1: + long_name: labile dissolved organic matter + model: ersem/pelagic_base + parameters: + composition: cnp # elemental composition + c0: 0.0034 # background carbon concentration (mg C/m^3), default = 0.0 + initialization: + c: 10.0 # carbon (mg C/m^3) + n: 0.14 # nitrogen (mmol N/m^3) + p: 0.01 # phosphorus (mmol P/m^3) + R2: + long_name: semi-labile dissolved organic matter + model: ersem/pelagic_base + parameters: + composition: c # elemental composition + c0: 0.0033 # background carbon concentration (mg C/m^3), default = 0.0 + initialization: + c: 12.0 # carbon (mg C/m^3) + R3: + long_name: semi-refractory dissolved organic matter + model: ersem/pelagic_base + parameters: + composition: c # elemental composition + c0: 0.0033 # background carbon concentration (mg C/m^3), default = 0.0 + initialization: + c: 12.0 # carbon (mg C/m^3) + R4: + long_name: small-size pom + model: ersem/pelagic_base + parameters: + composition: cnpf # elemental composition + c0: 0.0033 # background carbon concentration (mg C/m^3), default = 0.0 + iopABS: 1e-05 # specific shortwave absorption (m^2/mg C), default = 0.0 + iopBBS: 1.6e-05 # specific shortwave backscatter (m^2/mg C), default = 0.0 + rm: 1.0 # sinking velocity (m/d), default = 0.0 + ndeposition: 2 # number of target pools for sedimentation, default = 1 + qxc2: 0.1 # fraction of carbon sinking into deposition target 2 (-) + qxn2: 0.1 # fraction of nitrogen sinking into deposition target 2 (-) + qxp2: 0.06 # fraction of phosphorus sinking into deposition target 2 (-) + initialization: + c: 7.2 # carbon (mg C/m^3) + n: 0.1 # nitrogen (mmol N/m^3) + p: 0.007 # phosphorus (mmol P/m^3) + coupling: + deposition_target1: Q6/surface + deposition_target2: Q7/surface + R6: + long_name: medium-size pom + model: ersem/pelagic_base + parameters: + composition: cnpsf # elemental composition + c0: 0.0033 # background carbon concentration (mg C/m^3), default = 0.0 + iopABS: 1e-05 # specific shortwave absorption (m^2/mg C), default = 0.0 + iopBBS: 1.6e-05 # specific shortwave backscatter (m^2/mg C), default = 0.0 + rm: 5.0 # sinking velocity (m/d), default = 0.0 + ndeposition: 2 # number of target pools for sedimentation, default = 1 + qxc2: 0.1 # fraction of carbon sinking into deposition target 2 (-) + qxn2: 0.1 # fraction of nitrogen sinking into deposition target 2 (-) + qxp2: 0.06 # fraction of phosphorus sinking into deposition target 2 (-) + qxs2: 0.0 # fraction of silicate sinking into deposition target 2 (-) + initialization: + c: 17.0 # carbon (mg C/m^3) + n: 0.24 # nitrogen (mmol N/m^3) + p: 0.02 # phosphorus (mmol P/m^3) + s: 0.1 # silicate (mmol Si/m^3) + coupling: + deposition_target1: Q6/surface + deposition_target2: Q7/surface + R8: + long_name: large-size pom + model: ersem/pelagic_base + parameters: + composition: cnps # elemental composition + c0: 0.0033 # background carbon concentration (mg C/m^3), default = 0.0 + iopABS: 1e-05 # specific shortwave absorption (m^2/mg C), default = 0.0 + iopBBS: 1.6e-05 # specific shortwave backscatter (m^2/mg C), default = 0.0 + rm: 10.0 # sinking velocity (m/d), default = 0.0 + ndeposition: 2 # number of target pools for sedimentation, default = 1 + qxc2: 0.1 # fraction of carbon sinking into deposition target 2 (-) + qxn2: 0.1 # fraction of nitrogen sinking into deposition target 2 (-) + qxp2: 0.06 # fraction of phosphorus sinking into deposition target 2 (-) + qxs2: 0.0 # fraction of silicate sinking into deposition target 2 (-) + initialization: + c: 0.17 # carbon (mg C/m^3) + n: 0.0024 # nitrogen (mmol N/m^3) + p: 0.0002 # phosphorus (mmol P/m^3) + s: 0.001 # silicate (mmol Si/m^3) + coupling: + deposition_target1: Q6/surface + deposition_target2: Q7/surface + Q1: + long_name: benthic dissolved organic matter + model: ersem/benthic_base + parameters: + composition: cnp # elemental composition + c0: 0.001 # background carbon concentration (mg C/m^2), default = 0.0 + initialization: + c: 18.9 # carbon (mg C/m^2) + n: 0.6 # nitrogen (mmol N/m^2) + p: 0.0035 # phosphorus (mmol P/m^2) + Q6: + long_name: benthic particulate organic matter + model: ersem/benthic_column_particulate_matter + parameters: + composition: cnpsf # elemental composition + c0: 0.001 # background carbon concentration (mg C/m^2), default = 0.0 + resuspension: true # enable resuspension, default = false + initialization: + c: 3052.0 # carbon (mg C/m^2) + n: 3.5 # nitrogen (mmol N/m^2) + p: 0.5 # phosphorus (mmol P/m^2) + s: 149.0 # silicate (mmol Si/m^2) + pen_depth_c: 0.0173 # penetration depth of carbon (m) + pen_depth_n: 0.02 # penetration depth of nitrogen (m) + pen_depth_p: 0.025 # penetration depth of phosphorus (m) + pen_depth_s: 0.0313 # penetration depth of silicate (m) + coupling: + RP: R6 + Q7: + long_name: benthic refractory matter + model: ersem/benthic_column_particulate_matter + parameters: + composition: cnp # elemental composition + c0: 0.001 # background carbon concentration (mg C/m^2), default = 0.0 + burial: true # enable burial, default = false + initialization: + c: 30520.0 # carbon (mg C/m^2) + n: 80.0 # nitrogen (mmol N/m^2) + p: 8.0 # phosphorus (mmol P/m^2) + pen_depth_c: 0.2 # penetration depth of carbon (m) + pen_depth_n: 0.25 # penetration depth of nitrogen (m) + pen_depth_p: 0.313 # penetration depth of phosphorus (m) + coupling: + burial_target: Q17 + Q17: + long_name: benthic buried matter + model: ersem/benthic_base + parameters: + composition: cnp # elemental composition + initialization: + c: 0.0 # carbon (mg C/m^2) + n: 0.0 # nitrogen (mmol N/m^2) + p: 0.0 # phosphorus (mmol P/m^2) + B1: + long_name: bacteria + model: ersem/bacteria_docdyn + parameters: + iswBlim: 2 # nutrient limitation (1: minimum of inorganic and organic availability, 2: additive availability) + q10: 2.0 # Q_10 temperature coefficient (-) + chdo: 0.31 # Michaelis-Menten constant for oxygen limitation (-) + chn: 0.5 # Michaelis-Menten constant for nitrate limitation (mmol N/m^3) + chp: 0.1 # Michaelis-Menten constant for phosphate limitation (mmol P/m^3) + sd: 0.05 # specific mortality at reference temperature (1/d) + sum: 2.2 # maximum specific uptake at reference temperature (1/d) + pu: 0.6 # efficiency at high oxygen levels (-) + puo: 0.2 # efficiency at low oxygen levels (-) + srs: 0.1 # specific rest respiration at reference temperature (1/d) + sR1: 1.0 # maximum turn-over rate of DOM (1/d), default = 1.0 + qpc: 0.0019 # maximum phosphorus to carbon ratio (mmol P/mg C) + qnc: 0.0167 # maximum nitrogen to carbon ratio (mmol N/mg C) + ur_O2: 0.1 # oxygen consumed per carbon respired (mmol O_2/mg C) + sR1N1: 0.0 # mineralisation rate of labile dissolved organic phosphorus (1/d) + sR1N4: 0.0 # mineralisation rate of labile dissolved organic nitrogen (1/d) + fsink: 7e-05 # scavenging rate for iron (1/d) + c0: 0.01 # background carbon concentration (mg C/m^3) + nRP: 3 # number of substrates, default = 0 + sRP1R1: 0.01 # remineralisation of substrate 1 to DOM (1/d) + sRP2R1: 0.0025 # remineralisation of substrate 2 to DOM (1/d) + sRP3R1: 0.001 # remineralisation of substrate 3 to DOM (1/d) + rR2: 0.0075 # fraction of semi-labile DOC available to bacteria (-) + rR3: 0.0025 # fraction of semi-refractory DOC available to bacteria (-) + frR3: 0.3 # fraction of activity respiration converted to semi-refractory DOC (-) + denit: 1 # denitrification switch (0: off, 1: on) + Denix: 0.35 # potential denitrification rate (1/d) + reox: 0.05 # specific reoxidation rate of reduction equivalents (d-1) + omroX: 0.5 # stoichiometric coefficient for reduction equivalent (mmol HS mmol O2-1) + omonX: 1.25 # stoichiometric coefficient for denitrification reaction (mmol O2 mmol N-1) + chN3o: 2700.0 # Michaelis-Menten constant for cubic oxygen dependence of denitrification ((mmol O_2/m^3)^3) + initialization: + c: 15.7 # carbon (mg C/m^3) + n: 0.26 # nitrogen (mmol N/m^3) + p: 0.029 # phosphorus (mmol P/m^3) + coupling: + RP1: R4 + RP2: R6 + RP3: R8 + N1p: N1/p # phosphate (mmol P/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # labile dissolved organic carbon (mg C/m^3) + R1p: R1/p # labile dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # labile dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + R3c: R3/c # semi-refractory DOC (mg C/m^3) + O3c: O3/c # carbon dioxide (mmol C/m^3) + O2o: O2/o # oxygen (mmol O_2/m^3) + N6: N6/h # reduction equivalent (mmol S/m^3) + N3n: N3/n # nitrate (mmol N /m^3) + pel_nit: + long_name: pelagic nitrification + model: ersem/nitrification + parameters: + q10: 2.0 # Q_10 temperature coefficient (-) + ISWph: 1 # pH impact on nitrification (0: off, 1: on) + sN4N3: 0.5 # specific nitrification rate (1/d) + chN3o: 2700.0 # Michaelis-Menten constant for cubic oxygen dependence of nitrification ((mmol O_2/m^3)^3) + chN4n: 0.5 # Michaelis-Menten constant for cubic ammonium dependence of nitrification ((mmol N/m^3)^3), default = 0.0 + coupling: + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + O2o: O2/o # oxygen (mmol O_2/m^3) + P1: + long_name: diatoms + model: ersem/primary_producer + parameters: + sum: 1.375 # maximum specific productivity at reference temperature (1/d) + q10: 2.0 # Q_10 temperature coefficient (-) + srs: 0.04 # specific rest respiration at reference temperature (1/d) + pu_ea: 0.2 # excreted fraction of primary production (-) + pu_ra: 0.2 # respired fraction of primary production (-) + qnlc: 0.0042 # minimum nitrogen to carbon ratio (mmol N/mg C) + qplc: 0.0001 # minimum phosphorus to carbon ratio (mmol P/mg C) + xqcp: 1.0 # threshold for phosphorus limitation (relative to Redfield ratio) (-) + xqcn: 1.0 # threshold for nitrogen limitation (relative to Redfield ratio) (-) + xqp: 2.0 # maximum phosphorus to carbon ratio (relative to Redfield ratio) (-) + xqn: 1.075 # maximum nitrogen to carbon ratio (relative to Redfield ratio) (-) + qun3: 0.0025 # nitrate affinity (m^3/mg C/d) + qun4: 0.0025 # ammonium affinity (m^3/mg C/d) + qurp: 0.003 # phosphate affinity (m^3/mg C/d) + snplux: 1.0 # specific tendency of luxury uptake of nutrients towards maximum quota (1/d), default = 1.0 + use_Si: true # use silicate, default = false + qsc: 0.0118 # maximum silicate to carbon ratio (mmol Si/mg C) + chs: 0.2 # Michaelis-Menten constant for silicate limitation (mmol/m^3) + sdo: 0.05 # 1.1 of minimal specific lysis rate (1/d) + alpha: 4.0 # initial slope of PI-curve (mg C m^2/mg Chl/W/d) + beta: 0.07 # photoinhibition parameter (mg C m^2/mg Chl/W/d) + phim: 0.06 # maximum effective chlorophyll to carbon photosynthesis ratio (mg Chl/mg C) + Limnut: 1 # nitrogen-phosphorus colimitation formulation (0: geometric mean, 1: minimum, 2: harmonic mean) + docdyn: true # use dynamic ratio of labile to semi-labile DOM production, default = false + uB1c_O2: 0.11 # oxygen produced per unit of carbon fixed (mmol O_2/mg C) + urB1_O2: 0.1 # oxygen consumed per unit of carbon respired (mmol O_2/mg C) + iopABS: 0.007 # specific shortwave absorption (m^2/mg Chl), default = 0.008 + iopBBS: 0.00048 # specific shortwave backscatter (m^2/mg Chl), default = 0.003 + c0: 0.0001 # background carbon concentration (mg C/m^3), default = 0.0 + resm: 5.0 # maximum nutrient-limitation-induced sinking velocity (m/d), default = 0.0 + esni: 0.7 # level of nutrient limitation below which sinking commences (-) + cenh: false # enable atmospheric CO2 influence on photosynthesis, default = false + ndeposition: 3 # number of target pools for sedimentation, default = 1 + qxc2: 0.2 # fraction of carbon sinking into deposition target 2 (-) + qxc3: 0.005 # fraction of carbon sinking into deposition target 3 (-) + qxn2: 0.2 # fraction of nitrogen sinking into deposition target 2 (-) + qxn3: 0.005 # fraction of nitrogen sinking into deposition target 3 (-) + qxp2: 0.24 # fraction of phosphorus sinking into deposition target 2 (-) + qxp3: 0.003 # fraction of phosphorus sinking into deposition target 3 (-) + qxs2: 0.0 # fraction of silicate sinking into deposition target 2 (-) + qxs3: 0.0 # fraction of silicate sinking into deposition target 3 (-) + initialization: + c: 8.0 # carbon (mg C/m^3) + n: 0.1114 # nitrogen (mmol N/m^3) + p: 0.009 # phosphorus (mmol P/m^3) + s: 0.128 # silicate (mmol Si/m^3) + Chl: 0.4 # chlorophyll a (mg/m^3) + coupling: + RP: R6 + deposition_target1: Q6/surface + deposition_target2: Q1 + deposition_target3: Q7/surface + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + N5s: N5/s # silicate (mmol Si/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + O2o: O2/o # oxygen (mmol O_2/m^3) + O3c: O3/c # carbon dioxide (mmol C/m^3) + P2: + long_name: nanophytoplankton + model: ersem/primary_producer + parameters: + sum: 1.625 # maximum specific productivity at reference temperature (1/d) + q10: 2.0 # Q_10 temperature coefficient (-) + srs: 0.04 # specific rest respiration at reference temperature (1/d) + pu_ea: 0.2 # excreted fraction of primary production (-) + pu_ra: 0.2 # respired fraction of primary production (-) + qnlc: 0.005 # minimum nitrogen to carbon ratio (mmol N/mg C) + qplc: 0.000225 # minimum phosphorus to carbon ratio (mmol P/mg C) + xqcp: 1.0 # threshold for phosphorus limitation (relative to Redfield ratio) (-) + xqcn: 1.0 # threshold for nitrogen limitation (relative to Redfield ratio) (-) + xqp: 2.0 # maximum phosphorus to carbon ratio (relative to Redfield ratio) (-) + xqn: 1.075 # maximum nitrogen to carbon ratio (relative to Redfield ratio) (-) + qun3: 0.004 # nitrate affinity (m^3/mg C/d) + qun4: 0.004 # ammonium affinity (m^3/mg C/d) + qurp: 0.004 # phosphate affinity (m^3/mg C/d) + snplux: 1.0 # specific tendency of luxury uptake of nutrients towards maximum quota (1/d), default = 1.0 + use_Si: false # use silicate, default = false + sdo: 0.05 # 1.1 of minimal specific lysis rate (1/d) + alpha: 5.0 # initial slope of PI-curve (mg C m^2/mg Chl/W/d) + beta: 0.1 # photoinhibition parameter (mg C m^2/mg Chl/W/d) + phim: 0.025 # maximum effective chlorophyll to carbon photosynthesis ratio (mg Chl/mg C) + Limnut: 1 # nitrogen-phosphorus colimitation formulation (0: geometric mean, 1: minimum, 2: harmonic mean) + docdyn: true # use dynamic ratio of labile to semi-labile DOM production, default = false + uB1c_O2: 0.11 # oxygen produced per unit of carbon fixed (mmol O_2/mg C) + urB1_O2: 0.1 # oxygen consumed per unit of carbon respired (mmol O_2/mg C) + iopABS: 0.0041 # specific shortwave absorption (m^2/mg Chl), default = 0.008 + iopBBS: 0.003 # specific shortwave backscatter (m^2/mg Chl), default = 0.003 + c0: 0.001 # background carbon concentration (mg C/m^3), default = 0.0 + calcify: true # calcify, default = false + resm: 0.0 # maximum nutrient-limitation-induced sinking velocity (m/d), default = 0.0 + esni: 0.7 # level of nutrient limitation below which sinking commences (-) + cenh: false # enable atmospheric CO2 influence on photosynthesis, default = false + ndeposition: 3 # number of target pools for sedimentation, default = 1 + qxc2: 0.5 # fraction of carbon sinking into deposition target 2 (-) + qxc3: 0.05 # fraction of carbon sinking into deposition target 3 (-) + qxn2: 0.5 # fraction of nitrogen sinking into deposition target 2 (-) + qxn3: 0.05 # fraction of nitrogen sinking into deposition target 3 (-) + qxp2: 0.6 # fraction of phosphorus sinking into deposition target 2 (-) + qxp3: 0.03 # fraction of phosphorus sinking into deposition target 3 (-) + initialization: + c: 5.9 # carbon (mg C/m^3) + n: 0.0926 # nitrogen (mmol N/m^3) + p: 0.0036 # phosphorus (mmol P/m^3) + Chl: 0.3 # chlorophyll a (mg/m^3) + coupling: + RP: R4 + deposition_target1: Q6/surface + deposition_target2: Q1 + deposition_target3: Q7/surface + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + O2o: O2/o # oxygen (mmol O_2/m^3) + O3c: O3/c # carbon dioxide (mmol C/m^3) + RainR: L2/RainR # rain ratio (PIC : POC) (-) + L2c: L2/c # free calcite (mg C/m^3) + P3: + long_name: picophytoplankton + model: ersem/primary_producer + parameters: + sum: 2.0 # maximum specific productivity at reference temperature (1/d) + q10: 2.0 # Q_10 temperature coefficient (-) + srs: 0.045 # specific rest respiration at reference temperature (1/d) + pu_ea: 0.2 # excreted fraction of primary production (-) + pu_ra: 0.2 # respired fraction of primary production (-) + qnlc: 0.006 # minimum nitrogen to carbon ratio (mmol N/mg C) + qplc: 0.00035 # minimum phosphorus to carbon ratio (mmol P/mg C) + xqcp: 1.0 # threshold for phosphorus limitation (relative to Redfield ratio) (-) + xqcn: 1.0 # threshold for nitrogen limitation (relative to Redfield ratio) (-) + xqp: 1.5 # maximum phosphorus to carbon ratio (relative to Redfield ratio) (-) + xqn: 1.05 # maximum nitrogen to carbon ratio (relative to Redfield ratio) (-) + qun3: 0.006 # nitrate affinity (m^3/mg C/d) + qun4: 0.007 # ammonium affinity (m^3/mg C/d) + qurp: 0.006 # phosphate affinity (m^3/mg C/d) + snplux: 1.0 # specific tendency of luxury uptake of nutrients towards maximum quota (1/d), default = 1.0 + use_Si: false # use silicate, default = false + sdo: 0.055 # 1.1 of minimal specific lysis rate (1/d) + alpha: 6.0 # initial slope of PI-curve (mg C m^2/mg Chl/W/d) + beta: 0.12 # photoinhibition parameter (mg C m^2/mg Chl/W/d) + phim: 0.015 # maximum effective chlorophyll to carbon photosynthesis ratio (mg Chl/mg C) + Limnut: 1 # nitrogen-phosphorus colimitation formulation (0: geometric mean, 1: minimum, 2: harmonic mean) + docdyn: true # use dynamic ratio of labile to semi-labile DOM production, default = false + uB1c_O2: 0.11 # oxygen produced per unit of carbon fixed (mmol O_2/mg C) + urB1_O2: 0.1 # oxygen consumed per unit of carbon respired (mmol O_2/mg C) + iopABS: 0.023 # specific shortwave absorption (m^2/mg Chl), default = 0.008 + iopBBS: 0.003 # specific shortwave backscatter (m^2/mg Chl), default = 0.003 + c0: 0.0088 # background carbon concentration (mg C/m^3), default = 0.0 + resm: 0.0 # maximum nutrient-limitation-induced sinking velocity (m/d), default = 0.0 + esni: 0.7 # level of nutrient limitation below which sinking commences (-) + cenh: false # enable atmospheric CO2 influence on photosynthesis, default = false + ndeposition: 3 # number of target pools for sedimentation, default = 1 + qxc2: 0.5 # fraction of carbon sinking into deposition target 2 (-) + qxc3: 0.05 # fraction of carbon sinking into deposition target 3 (-) + qxn2: 0.5 # fraction of nitrogen sinking into deposition target 2 (-) + qxn3: 0.05 # fraction of nitrogen sinking into deposition target 3 (-) + qxp2: 0.6 # fraction of phosphorus sinking into deposition target 2 (-) + qxp3: 0.03 # fraction of phosphorus sinking into deposition target 3 (-) + initialization: + c: 5.9 # carbon (mg C/m^3) + n: 0.0926 # nitrogen (mmol N/m^3) + p: 0.0036 # phosphorus (mmol P/m^3) + Chl: 0.3 # chlorophyll a (mg/m^3) + coupling: + RP: R4 + deposition_target1: Q6/surface + deposition_target2: Q1 + deposition_target3: Q7/surface + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + O2o: O2/o # oxygen (mmol O_2/m^3) + O3c: O3/c # carbon dioxide (mmol C/m^3) + P4: + long_name: microphytoplankton + model: ersem/primary_producer + parameters: + sum: 1.125 # maximum specific productivity at reference temperature (1/d) + q10: 2.0 # Q_10 temperature coefficient (-) + srs: 0.035 # specific rest respiration at reference temperature (1/d) + pu_ea: 0.2 # excreted fraction of primary production (-) + pu_ra: 0.2 # respired fraction of primary production (-) + qnlc: 0.0042 # minimum nitrogen to carbon ratio (mmol N/mg C) + qplc: 0.0001 # minimum phosphorus to carbon ratio (mmol P/mg C) + xqcp: 1.0 # threshold for phosphorus limitation (relative to Redfield ratio) (-) + xqcn: 1.0 # threshold for nitrogen limitation (relative to Redfield ratio) (-) + xqp: 2.7 # maximum phosphorus to carbon ratio (relative to Redfield ratio) (-) + xqn: 1.1 # maximum nitrogen to carbon ratio (relative to Redfield ratio) (-) + qun3: 0.002 # nitrate affinity (m^3/mg C/d) + qun4: 0.002 # ammonium affinity (m^3/mg C/d) + qurp: 0.002 # phosphate affinity (m^3/mg C/d) + snplux: 1.0 # specific tendency of luxury uptake of nutrients towards maximum quota (1/d), default = 1.0 + use_Si: false # use silicate, default = false + sdo: 0.045 # 1.1 of minimal specific lysis rate (1/d) + alpha: 3.0 # initial slope of PI-curve (mg C m^2/mg Chl/W/d) + beta: 0.06 # photoinhibition parameter (mg C m^2/mg Chl/W/d) + phim: 0.045 # maximum effective chlorophyll to carbon photosynthesis ratio (mg Chl/mg C) + Limnut: 1 # nitrogen-phosphorus colimitation formulation (0: geometric mean, 1: minimum, 2: harmonic mean) + docdyn: true # use dynamic ratio of labile to semi-labile DOM production, default = false + uB1c_O2: 0.11 # oxygen produced per unit of carbon fixed (mmol O_2/mg C) + urB1_O2: 0.1 # oxygen consumed per unit of carbon respired (mmol O_2/mg C) + iopABS: 0.008 # specific shortwave absorption (m^2/mg Chl), default = 0.008 + iopBBS: 0.00048 # specific shortwave backscatter (m^2/mg Chl), default = 0.003 + c0: 0.0001 # background carbon concentration (mg C/m^3), default = 0.0 + resm: 5.0 # maximum nutrient-limitation-induced sinking velocity (m/d), default = 0.0 + esni: 0.7 # level of nutrient limitation below which sinking commences (-) + cenh: false # enable atmospheric CO2 influence on photosynthesis, default = false + ndeposition: 3 # number of target pools for sedimentation, default = 1 + qxc2: 0.5 # fraction of carbon sinking into deposition target 2 (-) + qxc3: 0.05 # fraction of carbon sinking into deposition target 3 (-) + qxn2: 0.5 # fraction of nitrogen sinking into deposition target 2 (-) + qxn3: 0.05 # fraction of nitrogen sinking into deposition target 3 (-) + qxp2: 0.6 # fraction of phosphorus sinking into deposition target 2 (-) + qxp3: 0.03 # fraction of phosphorus sinking into deposition target 3 (-) + initialization: + c: 5.9 # carbon (mg C/m^3) + n: 0.0926 # nitrogen (mmol N/m^3) + p: 0.0036 # phosphorus (mmol P/m^3) + Chl: 0.3 # chlorophyll a (mg/m^3) + coupling: + RP: R6 + deposition_target1: Q6/surface + deposition_target2: Q1 + deposition_target3: Q7/surface + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + O2o: O2/o # oxygen (mmol O_2/m^3) + O3c: O3/c # carbon dioxide (mmol C/m^3) + Z4: + long_name: mesozooplankton + model: ersem/mesozooplankton + parameters: + q10: 2.0 # Q_10 temperature coefficient (-) + minfood: 12.0 # Michaelis-Menten constant to perceive food (mg C/m^3) + chuc: 36.0 # Michaelis-Menten constant for food uptake (mg C/m^3) + sum: 1.0 # maximum specific uptake at reference temperature (1/d) + pu: 0.6 # assimilation efficiency (-) + pu_ea: 0.5 # fraction of unassimilated prey that is excreted (not respired) (-) + pu_eaR: 0.9 # fraction of unassimilated detritus that is excreted (not respired) (-) + pe_R1: 0.5 # dissolved fraction of excreted/dying matter (-) + srs: 0.015 # specific rest respiration at reference temperature (1/d) + sd: 0.05 # basal mortality (1/d) + sdo: 0.2 # maximum mortality due to oxygen limitation (1/d) + chro: 7.81 # Michaelis-Menten constant for oxygen limitation (-) + qpc: 0.000786 # phosphorus to carbon ratio (mmol P/mg C) + qnc: 0.0126 # nitrogen to carbon ratio (mmol N/mg C) + Minprey: 300.0 # food threshold for overwintering state (mg C/m^2) + repw: 0.0025 # specific overwintering respiration (1/d) + mort: 0.0025 # specific overwintering mortality (1/d) + R1R2: 1.0 # labile fraction of produced dissolved organic carbon (-) + xR1p: 1.2 # transfer of phosphorus to DOM, relative to POM (-), default = 0.0 + xR1n: 1.0 # transfer of nitrogen to DOM, relative to POM (-), default = 0.0 + urB1_O2: 0.1 # oxygen consumed per carbon respired (mmol O_2/mg C) + gutdiss: 0.5 # fraction of prey calcite that dissolves after ingestion (-) + c0: 0.0033 # background concentration (mg C/m^3) + nprey: 9 # number of prey types, default = 0 + suprey1: 0.15 # relative affinity for prey type 1 (-) + suprey2: 0.05 # relative affinity for prey type 2 (-) + suprey3: 0.0 # relative affinity for prey type 3 (-) + suprey4: 0.15 # relative affinity for prey type 4 (-) + suprey5: 0.25 # relative affinity for prey type 5 (-) + suprey6: 0.25 # relative affinity for prey type 6 (-) + suprey7: 0.05 # relative affinity for prey type 7 (-) + suprey8: 0.0 # relative affinity for prey type 8 (-) + suprey9: 0.1 # relative affinity for prey type 9 (-) + prey9ispom: true # prey type 9 is detritus, default = false + initialization: + c: 1.2 # carbon (mg C/m^3) + coupling: + prey1: P1 + prey2: P2 + prey3: P3 + prey4: P4 + prey5: Z4 + prey6: Z5 + prey7: Z6 + prey8: B1 + prey9: R6 + RP: R8 + N1p: N1/p # phosphate (mmol P/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + O2o: O2/o # oxygen source (mmol O_2/m^3) + O3c: O3/c # carbon dioxide sink (mmol C/m^3) + L2c: L2/c # calcite (mg C/m^3) + Z5: + long_name: microzooplankton + model: ersem/microzooplankton + parameters: + q10: 2.0 # Q_10 temperature coefficient (-) + minfood: 12.0 # Michaelis-Menten constant to perceive food (mg C/m^3) + chuc: 32.0 # Michaelis-Menten constant for food uptake (mg C/m^3) + sum: 1.25 # maximum specific uptake at reference temperature (1/d) + pu: 0.5 # assimilation efficiency (-) + pu_ea: 0.5 # fraction of unassimilated prey that is excreted (not respired) (-) + pe_R1: 0.5 # dissolved fraction of excreted/dying matter (-) + srs: 0.02 # specific rest respiration at reference temperature (1/d) + sd: 0.05 # basal mortality (1/d) + sdo: 0.25 # maximum mortality due to oxygen limitation (1/d) + chro: 7.81 # Michaelis-Menten constant for oxygen limitation (-) + qpc: 0.001 # maximum phosphorus to carbon ratio (mmol P/mg C) + qnc: 0.0167 # maximum nitrogen to carbon ratio (mmol N/mg C) + stempp: 0.5 # specific excretion rate of excess phosphorus (1/d) + stempn: 0.5 # specific excretion rate of excess nitrogen (1/d) + R1R2: 1.0 # labile fraction of produced dissolved organic carbon (-) + xR1p: 1.2 # transfer of phosphorus to DOM, relative to POM (-), default = 1.0 + xR1n: 1.0 # transfer of nitrogen to DOM, relative to POM (-), default = 1.0 + urB1_O2: 0.1 # oxygen consumed per carbon respired (mmol O_2/mg C) + gutdiss: 0.5 # fraction of prey calcite that dissolves after ingestion (-) + c0: 0.0033 # background concentration (mg C/m^3) + nprey: 7 # number of prey types, default = 0 + suprey1: 0.1 # relative affinity for prey type 1 (-) + suprey2: 0.15 # relative affinity for prey type 2 (-) + suprey3: 0.15 # relative affinity for prey type 3 (-) + suprey4: 0.15 # relative affinity for prey type 4 (-) + suprey5: 0.1 # relative affinity for prey type 5 (-) + suprey6: 0.15 # relative affinity for prey type 6 (-) + suprey7: 0.2 # relative affinity for prey type 7 (-) + initialization: + c: 7.2 # carbon (mg C/m^3) + n: 0.12 # nitrogen (mmol N/m^3) + p: 0.0113 # phosphorus (mmol P/m^3) + coupling: + prey1: B1 + prey2: P1 + prey3: P2 + prey4: P3 + prey5: P4 + prey6: Z5 + prey7: Z6 + RP: R6 + N1p: N1/p # phosphate (mmol P/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + O2o: O2/o # oxygen source (mmol O_2/m^3) + O3c: O3/c # carbon dioxide sink (mmol C/m^3) + L2c: L2/c # calcite (mg C/m^3) + Z6: + long_name: nanoflagellates + model: ersem/microzooplankton + parameters: + q10: 2.0 # Q_10 temperature coefficient (-) + minfood: 12.0 # Michaelis-Menten constant to perceive food (mg C/m^3) + chuc: 28.0 # Michaelis-Menten constant for food uptake (mg C/m^3) + sum: 1.5 # maximum specific uptake at reference temperature (1/d) + pu: 0.4 # assimilation efficiency (-) + pu_ea: 0.5 # fraction of unassimilated prey that is excreted (not respired) (-) + pe_R1: 0.5 # dissolved fraction of excreted/dying matter (-) + srs: 0.025 # specific rest respiration at reference temperature (1/d) + sd: 0.05 # basal mortality (1/d) + sdo: 0.3 # maximum mortality due to oxygen limitation (1/d) + chro: 7.81 # Michaelis-Menten constant for oxygen limitation (-) + qpc: 0.001 # maximum phosphorus to carbon ratio (mmol P/mg C) + qnc: 0.0167 # maximum nitrogen to carbon ratio (mmol N/mg C) + stempp: 0.5 # specific excretion rate of excess phosphorus (1/d) + stempn: 0.5 # specific excretion rate of excess nitrogen (1/d) + R1R2: 1.0 # labile fraction of produced dissolved organic carbon (-) + xR1p: 1.2 # transfer of phosphorus to DOM, relative to POM (-), default = 1.0 + xR1n: 1.0 # transfer of nitrogen to DOM, relative to POM (-), default = 1.0 + urB1_O2: 0.1 # oxygen consumed per carbon respired (mmol O_2/mg C) + gutdiss: 0.5 # fraction of prey calcite that dissolves after ingestion (-) + c0: 0.0033 # background concentration (mg C/m^3) + nprey: 4 # number of prey types, default = 0 + suprey1: 0.45 # relative affinity for prey type 1 (-) + suprey2: 0.15 # relative affinity for prey type 2 (-) + suprey3: 0.25 # relative affinity for prey type 3 (-) + suprey4: 0.15 # relative affinity for prey type 4 (-) + initialization: + c: 2.421 # carbon (mg C/m^3) + n: 0.0505 # nitrogen (mmol N/m^3) + p: 0.047 # phosphorus (mmol P/m^3) + coupling: + prey1: B1 + prey2: P2 + prey3: P3 + prey4: Z6 + RP: R4 + N1p: N1/p # phosphate (mmol P/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + RPs: R6/s # particulate organic silicate (mmol Si/m^3) + O2o: O2/o # oxygen source (mmol O_2/m^3) + O3c: O3/c # carbon dioxide sink (mmol C/m^3) + L2c: L2/c # calcite (mg C/m^3) + L2: + long_name: calcite + model: ersem/calcification + parameters: + iswcal: 1 # calcification/dissolution dependence on calcite saturation (1: power law, 2: hyperbolic) + ncalc: 0.81 # power of the calcification law (Ridgwell et al. 2007, mineral calcite) (-) + ndiss: 2.22 # power of the dissolution law (Keir 1980) (-) + Rain0: 0.6 # maximum rain ratio from PISCES (-) + sedL2: 10.0 # sinking velocity (m/d) + sL2O3: 0.03 # maximum specific dissolution rate (1/d), default = 1.0 + c0: 1e-05 # background concentration (mg C/m^3), default = 0.0 + ndeposition: 1 # number of target pools for sedimentation, default = 1 + initialization: + c: 0.05 # carbon (mg C/m^3) + coupling: + deposition_target1: bL2 + om_cal: O3/Om_cal # calcite saturation (-) + O3c: O3/c # total dissolved inorganic carbon (mmol C/m^3) + bL2: + long_name: benthic calcite + model: ersem/benthic_calcite + parameters: + iswcal: 1 # dissolution dependence on calcite saturation (0: none, 1: power law, 2: hyperbolic) + ndiss: 2.22 # power of the dissolution law (Keir 1980) (-) + fdissmax: 30.0 # maximum specific dissolution rate (1/d), default = 0.0 + fdissmin: 0.05 # minimum specific dissolution rate (1/d), default = 0.03 + c0: 1e-05 # background calcite concentration (mg C/m^2), default = 0.0 + initialization: + c: 0.05 # carbon (mg C/m^2) + coupling: + Om_Cal: O3/Om_cal # calcite saturation (-) + O3c: O3/c # dissolved inorganic carbon (mmol/m^3) + ben_col: + long_name: benthic column + model: ersem/benthic_column + parameters: + qPW: 0.4 # sediment porosity (-) + EDZ_mix: 20.0 # equilibrium diffusive speed between sediment surface water (d/m) + d_tot: 0.3 # depth of sediment column (m) + Etur: 2e-06 # basal bioturbation rate (m^2/d) + mtur: 10.0 # maximum relative turbation enhancement (-) + htur: 116.0 # Michaelis-Menten constant for bioturbation (mg C/m^2/d) + dtur: 0.02 # bioturbation depth (m) + EDZ_1: 5e-05 # diffusivity in oxygenated layer (m^2/d) + EDZ_2: 5e-05 # diffusivity in oxidized layer (m^2/d) + EDZ_3: 5e-05 # diffusivity in anoxic layer (m^2/d) + irr_min: 2.0 # minimum diffusion enhancement through bioirrigation (-) + mirr: 10.0 # maximum relative diffusion enhancement due to bioirrigation (-) + hirr: 101.0 # Michaelis-Menten constant for bioirrigation (mg C/m^2/d) + initialization: + D1m: 0.009 # depth of bottom interface of oxygenated layer (m) + D2m: 0.05 # depth of bottom interface of oxidized layer (m) + K1: + long_name: benthic phosphate + model: ersem/benthic_column_dissolved_matter + parameters: + composition: p # composition (any combination of c,n,p,s,o,a) + c0: 0.0003 # background carbon concentration (mg C/m^2), default = 0.0 + ads1: 100.0 # adsorption in layer 1 (total:dissolved) (-), default = 1.0 + ads2: 100.0 # adsorption in layer 2 (total:dissolved) (-), default = 1.0 + ads3: 2.0 # adsorption in layer 3 (total:dissolved) (-), default = 1.0 + initialization: + p: 6.8 # phosphorus (mmol/m^2) + coupling: + p_pel: N1/p # pelagic phosphorus (mmol/m^3) + K3: + long_name: benthic nitrate + model: ersem/benthic_column_dissolved_matter + parameters: + composition: n # composition (any combination of c,n,p,s,o,a) + c0: 0.0003 # background carbon concentration (mg C/m^2), default = 0.0 + last_layer: 2 # sediment layer where concentration drops to zero, default = 3 + relax: 5.0 # rate of relaxation towards equilibrium concentration profile (1/d) + minD: 0.0001 # minimum depth of zero-concentration isocline (m) + initialization: + n: 0.584 # nitrogen (mmol/m^2) + coupling: + n_pel: N3/n # pelagic nitrogen (mmol/m^3) + K4: + long_name: benthic ammonium + model: ersem/benthic_column_dissolved_matter + parameters: + composition: n # composition (any combination of c,n,p,s,o,a) + c0: 0.0003 # background carbon concentration (mg C/m^2), default = 0.0 + ads1: 3.0 # adsorption in layer 1 (total:dissolved) (-), default = 1.0 + ads2: 3.0 # adsorption in layer 2 (total:dissolved) (-), default = 1.0 + ads3: 3.0 # adsorption in layer 3 (total:dissolved) (-), default = 1.0 + correction: true # move losses in oxygenic layer to deeper layers if pelagic concentration is limiting, default = false + initialization: + n: 25.0 # nitrogen (mmol/m^2) + coupling: + n_pel: N4/n # pelagic nitrogen (mmol/m^3) + K5: + long_name: benthic silicate + model: ersem/benthic_column_dissolved_matter + parameters: + composition: s # composition (any combination of c,n,p,s,o,a) + c0: 9e-05 # background carbon concentration (mg C/m^2), default = 0.0 + initialization: + s: 20.1 # silicate (mmol/m^2) + coupling: + s_pel: N5/s # pelagic silicate (mmol/m^3) + G2: + long_name: benthic oxygen + model: ersem/benthic_column_dissolved_matter + parameters: + composition: o # composition (any combination of c,n,p,s,o,a) + last_layer: 1 # sediment layer where concentration drops to zero, default = 3 + relax: 5.0 # rate of relaxation towards equilibrium concentration profile (1/d) + minD: 0.0001 # minimum depth of zero-concentration isocline (m) + initialization: + o: 0.0225 # oxygen (mmol/m^2) + coupling: + o_pel: O2/o # pelagic oxygen (mmol/m^3) + G3: + long_name: benthic dissolved inorganic carbon + model: ersem/benthic_column_dissolved_matter + parameters: + composition: c # composition (any combination of c,n,p,s,o,a) + initialization: + c: 375.0 # carbon (mmol/m^2) + coupling: + c_pel: O3/c # pelagic carbon (mmol/m^3) + Q6s_aerobic: + long_name: aerobic particulate silicate + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: s # elemental composition + minimum_depth: 0.0 # minimum depth (m), default = 0.0 + variable_maximum_depth: true # maximum depth is variable, default = false + remin: 0.007 # remineralization rate at 10 degrees Celsius (1/d), default = 0.0 + coupling: + Q: Q6 + s_remin_target: K5/per_layer/s1 + maximum_depth: ben_col/D1m # maximum depth (m) + Q6s_anaerobic: + long_name: anaerobic particulate silicate + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: s # elemental composition + variable_minimum_depth: true # minimum depth is variable, default = false + maximum_depth: 0.3 # maximum depth (m), default = 0.0 + remin: 0.007 # remineralization rate at 10 degrees Celsius (1/d), default = 0.0 + source_depth_distribution: 2 # vertical distribution of changes (1: constant absolute rate, 2: constant relative rate, 3: constant carbon-based relative rate), default = 1 + coupling: + Q: Q6 + s_remin_target: K5/per_layer/s2 + minimum_depth: ben_col/D1m # minimum depth (m) + ben_nit: + long_name: benthic nitrogen cycle + model: ersem/benthic_nitrogen_cycle + parameters: + q10nit: 2.0 # Q_10 temperature coefficient (-) + hM4M3: 10.0 # Michaelis-Menten constant for nitrate limitation (mmol/m^3) + ISWph: 1 # pH impact on nitrification (0: off, 1: on), default = 0 + sM4M3: 4.0 # maximum nitrification rate at 10 degrees Celsius (1/d) + xno3: 2.0 # oxygen consumed per nitrate produced (mol O_2/mol N) + pammon: 0.5 # fraction of oxygen demand fulfilled by denitrification under anaerobic conditions (-) + pdenit: 0.05 # fraction of denitrification producing dinitrogen gas (remainder produces ammonium) (-) + xn2: 1.25 # oxygen demand fulfilled by reduction of nitrate to dinitrogen gas (mol O_2/mol N) + hM3G4: 1.0 # Michaelis-Menten constant for nitrate limitation of denitrification (mmol N/m^3) + coupling: + K3n: K3/per_layer/n1 # benthic nitrate in 1st layer (mmol N/m^2) + K4n: K4/per_layer/n1 # benthic ammonium in 1st layer (mmol N/m^2) + G2o: G2/per_layer/o1 # benthic oxygen in 1st layer (mmol O_2/m^2) + N4n: N4/n # pelagic ammonium (mmol N/m^3) + benTA: zero_hz # benthic alkalinity in aerobic layer (mEq/m^2) + benTA2: zero_hz # benthic alkalinity in anaerobic layer (mEq/m^2) + K3n2: K3/per_layer/n2 # benthic nitrate in 2nd layer (mmol N/m^2) + K4n2: K4/per_layer/n2 # benthic ammonium in 2nd layer (mmol N/m^2) + G2o2: G2/per_layer/o2 # oxygen in 2nd layer (mmol O_2/m^2) + layer2_thickness: ben_col/layer2_thickness # thickness of 2nd layer (m) + H1: + long_name: benthic aerobic bacteria + model: ersem/benthic_bacteria + parameters: + qnc: 0.0167 # nitrogen to carbon ratio (mmol N/mg C) + qpc: 0.00125 # phosphorus to carbon ratio (mmol P/mg C) + c0: 1e-06 # background concentration (mg C/m^2), default = 0.0 + q10: 2.0 # Q_10 temperature coefficient (-) + dd: 0.001 # Michaelis-Menten constant for oxygen limitation through layer thickness (m) + nfood: 3 # number of food sources + su1: 0.0005 # base affinity for food source 1 (m^2/mg C/d) + su2: 2e-05 # base affinity for food source 2 (m^2/mg C/d) + suf2: 0.0002 # additional affinity for food source 2 subject to nutrient limitation (m^2/mg C/d), default = 0.0 + puinc2: 2.0 # affinity for nutrients relative to carbon in food source 2 (-), default = 1.0 + pue2: 0.1 # fraction of consumed food source 2 that is excreted (-), default = 0.0 + su3: 2e-06 # base affinity for food source 3 (m^2/mg C/d) + pue3: 0.1 # fraction of consumed food source 3 that is excreted (-), default = 0.0 + pur: 0.3 # fraction of consumed carbon that is respired (-) + sr: 0.02 # specific rest respiration (1/d) + pdQ1: 0.1 # fraction of dying matter that is dissolved (-) + sd: 0.05 # specific maximum mortality related to oxygen limitation (1/d) + initialization: + c: 25.0 # carbon (mg C/m^2) + coupling: + Q1: Q1 + Q6: H1_Q6 + food1: Q1 + food2: H1_Q6 + food3: H1_Q7 + Dm: ben_col/D1m # depth interval available to bacteria (m) + K4n: K4/per_layer/n1_pw # ammonium (mmol N/m^2) + K1p: K1/per_layer/p1_pw # phosphate (mmol N/m^2) + G2o: G2/per_layer/o1 # oxygen (mmol O_2/m^2) + G3c: G3/per_layer/c1 # dissolved inorganic carbon (mmol C/m^2) + benTA: zero_hz # benthic alkalinity (mEq/m^2) + H1_Q6: + long_name: benthic aerobic bacteria POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + minimum_depth: 0.0 # minimum depth (m), default = 0.0 + variable_maximum_depth: true # maximum depth is variable, default = false + coupling: + Q: Q6 + maximum_depth: ben_col/D1m # maximum depth (m) + H1_Q7: + long_name: benthic aerobic bacteria refractory POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnp # elemental composition + minimum_depth: 0.0 # minimum depth (m), default = 0.0 + variable_maximum_depth: true # maximum depth is variable, default = false + coupling: + Q: Q7 + maximum_depth: ben_col/D1m # maximum depth (m) + H2: + long_name: benthic anaerobic bacteria + model: ersem/benthic_bacteria + parameters: + qnc: 0.0167 # nitrogen to carbon ratio (mmol N/mg C) + qpc: 0.00125 # phosphorus to carbon ratio (mmol P/mg C) + c0: 1e-06 # background concentration (mg C/m^2), default = 0.0 + q10: 2.0 # Q_10 temperature coefficient (-) + dd: 0.01 # Michaelis-Menten constant for oxygen limitation through layer thickness (m) + nfood: 2 # number of food sources + su1: 2e-05 # base affinity for food source 1 (m^2/mg C/d) + suf1: 0.0002 # additional affinity for food source 1 subject to nutrient limitation (m^2/mg C/d), default = 0.0 + puinc1: 2.0 # affinity for nutrients relative to carbon in food source 1 (-), default = 1.0 + pue1: 0.0 # fraction of consumed food source 1 that is excreted (-), default = 0.0 + su2: 2e-06 # base affinity for food source 2 (m^2/mg C/d) + pue2: 0.0 # fraction of consumed food source 2 that is excreted (-), default = 0.0 + pur: 0.3 # fraction of consumed carbon that is respired (-) + sr: 0.02 # specific rest respiration (1/d) + pdQ1: 0.0 # fraction of dying matter that is dissolved (-) + sd: 0.05 # specific maximum mortality related to oxygen limitation (1/d) + initialization: + c: 400.0 # carbon (mg C/m^2) + coupling: + Q1: Q1 + Q6: H2_Q6 + food1: H2_Q6 + food2: H2_Q7 + Dm: ben_col/layer2_thickness # depth interval available to bacteria (m) + K4n: K4/per_layer/n2_pw # ammonium (mmol N/m^2) + K1p: K1/per_layer/p2_pw # phosphate (mmol N/m^2) + G2o: ben_nit/K6_calculator/K6 # oxygen (mmol O_2/m^2) + G3c: G3/per_layer/c2 # dissolved inorganic carbon (mmol C/m^2) + benTA: zero_hz # benthic alkalinity (mEq/m^2) + H2_Q6: + long_name: benthic anaerobic bacteria POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + variable_minimum_depth: true # minimum depth is variable, default = false + maximum_depth: 0.3 # maximum depth (m), default = 0.0 + source_depth_distribution: 3 # vertical distribution of changes (1: constant absolute rate, 2: constant relative rate, 3: constant carbon-based relative rate), default = 1 + coupling: + Q: Q6 + minimum_depth: ben_col/D1m # minimum depth (m) + H2_Q7: + long_name: benthic anaerobic bacteria refractory POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnp # elemental composition + variable_minimum_depth: true # minimum depth is variable, default = false + maximum_depth: 0.3 # maximum depth (m), default = 0.0 + source_depth_distribution: 3 # vertical distribution of changes (1: constant absolute rate, 2: constant relative rate, 3: constant carbon-based relative rate), default = 1 + coupling: + Q: Q7 + minimum_depth: ben_col/D1m # minimum depth (m) + Y2: + long_name: benthic deposit feeder + model: ersem/benthic_fauna + parameters: + qnc: 0.0119 # nitrogen to carbon ratio (mmol N/mg C) + qpc: 0.000792 # phosphorus to carbon ratio (mmol P/mg C) + c0: 0.001 # background concentration (mg C/m^2), default = 0.0 + q10: 2.0 # Q_10 temperature coefficient (-) + rlO2: 0.0 # minimum pelagic oxygen concentration (mmol O2/m^3) + hO2: 0.0 # Michaelis-Menten constant for oxygen limitation (mmol O2/m^3) + xcl: 2500.0 # abundance above which crowding reduces food uptake (mg C/m^2) + xcs: 3000.0 # Michaelis-Menten constant for the impact of crowding (mg C/m^2) + xch: 5000.0 # abundance determining asymptotic threshold of crowding limitation (-> xch/(Yc+xch) for Yc-> inf) (mg C/m^2) + su: 0.11 # specific maximum uptake at reference temperature (1/d) + lu: 250.0 # Michaelis-Menten constant for food preference as function of food concentration (mg C/m^2) + hu: 3000.0 # Michaelis-Menten constant for gross carbon uptake (mg C/m^2) + pue: 0.35 # fraction of carbon in consumed live food that goes to faeces (-) + pueQ: 0.8 # fraction of carbon in consumed detritus that goes to faeces (-) + pudil: 0.8 # relative nutrient content of faeces (-) + sd: 0.001 # specific mortality at reference temperature (1/d) + sdmO2: 1.0 # specific maximum additional mortality due to oxygen stress (1/d) + sdc: 0.022 # specific maximum additional mortality induced by cold temperature (1/d) + xdc: -0.7 # e-folding temperature factor of cold mortality response (1/degree_C) + sr: 0.0027 # specific rest respiration at reference temperature (1/d) + pur: 0.35 # fraction of assimilated food that is respired (-) + nfood: 4 # number of food sources, default = 0 + pufood1: 1.0 # preference for food source 1 (-) + pufood2: 1.0 # preference for food source 2 (-) + pufood3: 0.1 # preference for food source 3 (-) + pufood4: 1.0 # preference for food source 4 (-) + food3ispom: true # food source 3 is detritus, default = false + ptur: 1.0 # relative contribution to bioturbation (-), default = 0.0 + pirr: 1.0 # relative contribution to bioirrigation (-), default = 0.0 + initialization: + c: 3000.0 # carbon (mg C/m^2) + coupling: + food1: H1 + food2: H2 + food3: Y2_Q6_source + food4: Y4 + Q: Y2_Q6_sink + Dm: ben_col/D1m # depth of limiting layer for uptake (m) + O2o: O2/o # pelagic oxygen (mmol O_2/m^3) + G3c: G3/per_layer/c1 # carbon dioxide (mmol C/m^2) + G2o: G2/per_layer/o1 # oxygen (mmol O_2/m^2) + K1p: K1/per_layer/p1 # benthic phosphate in aerobic layer (mmol P/m^2) + K4n: K4/per_layer/n1 # benthic ammonium in aerobic layer (mmol N/m^2) + K1p2: K1/per_layer/p2 # benthic phosphate in anaerobic layer (mmol P/m^2) + K4n2: K4/per_layer/n2 # benthic ammonium in anaerobic layer (mmol N/m^2) + benTA: zero_hz # benthic alkalinity in aerobic layer (mEq/m^2) + benTA2: zero_hz # benthic alkalinity in anaerobic layer (mEq/m^2) + food2c_an: H2/c # food source 2 carbon in anaerobic layer (mg C/m^2) + food3c_an: Y2_Q6_source_anaerobic/c # food source 3 carbon in anaerobic layer (mg C/m^2) + Y2_Q6_source: + long_name: benthic deposit feeder total POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + minimum_depth: 0.0025 # minimum depth (m), default = 0.0 + maximum_depth: 0.3 # maximum depth (m), default = 0.0 + coupling: + Q: Q6 + Y2_Q6_source_anaerobic: + long_name: benthic deposit feeder anaerobic POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + variable_minimum_depth: true # minimum depth is variable, default = false + maximum_depth: 0.3 # maximum depth (m), default = 0.0 + coupling: + Q: Q6 + minimum_depth: ben_col/D1m # minimum depth (m) + Y2_Q6_sink: + long_name: benthic deposit feeder POM sink + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + minimum_depth: 0.0 # minimum depth (m), default = 0.0 + variable_maximum_depth: true # maximum depth is variable, default = false + coupling: + Q: Q6 + maximum_depth: Q6/pen_depth_c # maximum depth (m) + Y3: + long_name: benthic suspension feeder + model: ersem/benthic_fauna + parameters: + qnc: 0.0119 # nitrogen to carbon ratio (mmol N/mg C) + qpc: 0.000792 # phosphorus to carbon ratio (mmol P/mg C) + c0: 0.001 # background concentration (mg C/m^2), default = 0.0 + q10: 2.0 # Q_10 temperature coefficient (-) + rlO2: 0.0 # minimum pelagic oxygen concentration (mmol O2/m^3) + hO2: 0.0 # Michaelis-Menten constant for oxygen limitation (mmol O2/m^3) + xcl: 2500.0 # abundance above which crowding reduces food uptake (mg C/m^2) + xcs: 3000.0 # Michaelis-Menten constant for the impact of crowding (mg C/m^2) + xch: 5000.0 # abundance determining asymptotic threshold of crowding limitation (-> xch/(Yc+xch) for Yc-> inf) (mg C/m^2) + su: 0.09 # specific maximum uptake at reference temperature (1/d) + lu: 10.0 # Michaelis-Menten constant for food preference as function of food concentration (mg C/m^2) + hu: 300.0 # Michaelis-Menten constant for gross carbon uptake (mg C/m^2) + pue: 0.35 # fraction of carbon in consumed live food that goes to faeces (-) + pueQ: 0.85 # fraction of carbon in consumed detritus that goes to faeces (-) + pudil: 0.8 # relative nutrient content of faeces (-) + sd: 0.001 # specific mortality at reference temperature (1/d) + sdmO2: 1.0 # specific maximum additional mortality due to oxygen stress (1/d) + sdc: 0.022 # specific maximum additional mortality induced by cold temperature (1/d) + xdc: -0.7 # e-folding temperature factor of cold mortality response (1/degree_C) + sr: 0.0027 # specific rest respiration at reference temperature (1/d) + pur: 0.4 # fraction of assimilated food that is respired (-) + nfood: 6 # number of food sources, default = 0 + food1ispel: true # food source 1 is pelagic, default = false + food2ispel: true # food source 2 is pelagic, default = false + food3ispel: true # food source 3 is pelagic, default = false + food4ispel: true # food source 4 is pelagic, default = false + food5_ll: true # availability of food source 5 is limited by aerobic layer height, default = false + pufood1: 1.0 # preference for food source 1 (-) + pufood2: 1.0 # preference for food source 2 (-) + pufood3: 1.0 # preference for food source 3 (-) + pufood4: 1.0 # preference for food source 4 (-) + pufood5: 1.0 # preference for food source 5 (-) + pufood6: 0.1 # preference for food source 6 (-) + food4ispom: true # food source 4 is detritus, default = false + food6ispom: true # food source 6 is detritus, default = false + dwat: 1.0 # water layer accessible for pelagic food uptake (m), default = 1.0 + dQ6: 0.0025 # depth of available sediment layer (m), default = 0.0 + initialization: + c: 2000.0 # carbon (mg C/m^2) + coupling: + food1: P1 + food2: P2 + food3: P3 + food4: R6 + food5: H1 + food6: Y3_Q6 + Q: Y3_Q6 + Dm: ben_col/D1m # depth of limiting layer for uptake (m) + O2o: O2/o # pelagic oxygen (mmol O_2/m^3) + G3c: G3/per_layer/c1 # carbon dioxide (mmol C/m^2) + G2o: G2/per_layer/o1 # oxygen (mmol O_2/m^2) + K1p: K1/per_layer/p1 # benthic phosphate in aerobic layer (mmol P/m^2) + K4n: K4/per_layer/n1 # benthic ammonium in aerobic layer (mmol N/m^2) + K1p2: K1/per_layer/p2 # benthic phosphate in anaerobic layer (mmol P/m^2) + K4n2: K4/per_layer/n2 # benthic ammonium in anaerobic layer (mmol N/m^2) + benTA: zero_hz # benthic alkalinity in aerobic layer (mEq/m^2) + benTA2: zero_hz # benthic alkalinity in anaerobic layer (mEq/m^2) + Y3_Q6: + long_name: benthic suspension feeder POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + minimum_depth: 0.0 # minimum depth (m), default = 0.0 + maximum_depth: 0.0025 # maximum depth (m), default = 0.0 + coupling: + Q: Q6 + Y4: + long_name: benthic meiofauna + model: ersem/benthic_fauna + parameters: + qnc: 0.0119 # nitrogen to carbon ratio (mmol N/mg C) + qpc: 0.000792 # phosphorus to carbon ratio (mmol P/mg C) + c0: 0.001 # background concentration (mg C/m^2), default = 0.0 + q10: 2.0 # Q_10 temperature coefficient (-) + rlO2: 0.0 # minimum pelagic oxygen concentration (mmol O2/m^3) + hO2: 0.0 # Michaelis-Menten constant for oxygen limitation (mmol O2/m^3) + xcl: 25000.0 # abundance above which crowding reduces food uptake (mg C/m^2) + xcs: 3000.0 # Michaelis-Menten constant for the impact of crowding (mg C/m^2) + xch: 5000.0 # abundance determining asymptotic threshold of crowding limitation (-> xch/(Yc+xch) for Yc-> inf) (mg C/m^2) + su: 0.4 # specific maximum uptake at reference temperature (1/d) + lu: 50.0 # Michaelis-Menten constant for food preference as function of food concentration (mg C/m^2) + hu: 1000.0 # Michaelis-Menten constant for gross carbon uptake (mg C/m^2) + pue: 0.25 # fraction of carbon in consumed live food that goes to faeces (-) + pueQ: 0.4 # fraction of carbon in consumed detritus that goes to faeces (-) + pudil: 0.8 # relative nutrient content of faeces (-) + sd: 0.01 # specific mortality at reference temperature (1/d) + sdmO2: 1.0 # specific maximum additional mortality due to oxygen stress (1/d) + sdc: 0.02 # specific maximum additional mortality induced by cold temperature (1/d) + xdc: -0.7 # e-folding temperature factor of cold mortality response (1/degree_C) + sr: 0.01 # specific rest respiration at reference temperature (1/d) + pur: 0.45 # fraction of assimilated food that is respired (-) + nfood: 4 # number of food sources, default = 0 + pufood1: 1.0 # preference for food source 1 (-) + pufood2: 1.0 # preference for food source 2 (-) + pufood3: 1.0 # preference for food source 3 (-) + pufood4: 0.3 # preference for food source 4 (-) + food4ispom: true # food source 4 is detritus, default = false + pirr: 0.2 # relative contribution to bioirrigation (-), default = 0.0 + initialization: + c: 200.0 # carbon (mg C/m^2) + coupling: + food1: H1 + food2: H2 + food3: Y4 + food4: Y4_Q6 + Q: Y4_Q6 + Dm: ben_col/D1m # depth of limiting layer for uptake (m) + O2o: O2/o # pelagic oxygen (mmol O_2/m^3) + G3c: G3/per_layer/c1 # carbon dioxide (mmol C/m^2) + G2o: G2/per_layer/o1 # oxygen (mmol O_2/m^2) + K1p: K1/per_layer/p1 # benthic phosphate in aerobic layer (mmol P/m^2) + K4n: K4/per_layer/n1 # benthic ammonium in aerobic layer (mmol N/m^2) + K1p2: K1/per_layer/p2 # benthic phosphate in anaerobic layer (mmol P/m^2) + K4n2: K4/per_layer/n2 # benthic ammonium in anaerobic layer (mmol N/m^2) + benTA: zero_hz # benthic alkalinity in aerobic layer (mEq/m^2) + benTA2: zero_hz # benthic alkalinity in anaerobic layer (mEq/m^2) + Y4_Q6: + long_name: benthic meiofauna POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + minimum_depth: 0.0 # minimum depth (m), default = 0.0 + maximum_depth: 0.03 # maximum depth (m), default = 0.0 + coupling: + Q: Q6 + erosion: + model: ersem/benthic_erosion diff --git a/testcases/fabm-ersem-15.06-L4-ben-docdyn-iop-n2o.yaml b/testcases/fabm-ersem-15.06-L4-ben-docdyn-iop-n2o.yaml new file mode 100644 index 0000000..5e9dfee --- /dev/null +++ b/testcases/fabm-ersem-15.06-L4-ben-docdyn-iop-n2o.yaml @@ -0,0 +1,1193 @@ +check_conservation: false +require_initialization: true +instances: + zenithAngle: + model: ersem/zenith_angle + light: + model: ersem/light_iop + parameters: + a0w: 0.03 # absorption coefficient of clear water (1/m), default = 0.036 + b0w: 0.0015 # backscatter coefficient of clear water (1/m), default = 0.0016 + pEIR_eow: 0.5 # photosynthetically active fraction of shortwave radiation (-), default = 0.5 + N1: + long_name: phosphate + model: ersem/pelagic_base + parameters: + composition: p # elemental composition + c0: 0.001 # background carbon concentration (mg C/m^3), default = 0.0 + initialization: + p: 0.4 # phosphorus (mmol P/m^3) + N3: + long_name: nitrate + model: ersem/pelagic_base + parameters: + composition: n # elemental composition + c0: 0.001 # background carbon concentration (mg C/m^3), default = 0.0 + initialization: + n: 8.0 # nitrogen (mmol N/m^3) + N4: + long_name: ammonium + model: ersem/pelagic_base + parameters: + composition: n # elemental composition + c0: 0.001 # background carbon concentration (mg C/m^3), default = 0.0 + initialization: + n: 0.1 # nitrogen (mmol N/m^3) + N5: + long_name: silicate + model: ersem/pelagic_base + parameters: + composition: s # elemental composition + s0: 0.0003 # background silicon concentration (mmol Si/m^3), default = 0.0 + initialization: + s: 4.5 # silicate (mmol Si/m^3) + O5: + long_name: nitrous oxide + model: ersem/nitrous_oxide + parameters: + initialization: + n: 0.02 + O2: + long_name: oxygen + model: ersem/oxygen + parameters: + iswO2: 2 # saturation formulation (1: legacy ERSEM, 2: Weiss 1970, 3: Nightingale et al. 2000, 4: Wanninkhof 2014) + initialization: + o: 300.0 # oxygen (mmol O_2/m^3) + O3: + long_name: carbonate + model: ersem/carbonate + parameters: + iswCO2: 1 # carbonate system diagnostics (0: off, 1: on), default = 1 + iswASFLUX: 1 # air-sea CO2 exchange (0: none, 1: Nightingale et al. 2000, 2: Wanninkhof 1992 without chemical enhancement, 3: Wanninkhof 1992 with chemical enhancement, 4: Wanninkhof and McGillis 1999, 5: Wanninkhof 1992 switching to Wanninkhof and McGillis 1999, 6: Wan, default = 6 + iswtalk: 2 # alkalinity formulation (1-4: from salinity and temperature, 5: dynamic alkalinity), default = 5 + pHscale: 1 # pH scale (1: total, 0: SWS, -1: SWS backward compatible), default = 1 + iswbioalk: 1 # use bioalkalinity (0: off, 1: on), default = 1 + initialization: + c: 2130.0 # total dissolved inorganic carbon (mmol C/m^3) + R1: + long_name: labile dissolved organic matter + model: ersem/pelagic_base + parameters: + composition: cnp # elemental composition + c0: 0.0034 # background carbon concentration (mg C/m^3), default = 0.0 + initialization: + c: 10.0 # carbon (mg C/m^3) + n: 0.14 # nitrogen (mmol N/m^3) + p: 0.01 # phosphorus (mmol P/m^3) + R2: + long_name: semi-labile dissolved organic matter + model: ersem/pelagic_base + parameters: + composition: c # elemental composition + c0: 0.0033 # background carbon concentration (mg C/m^3), default = 0.0 + initialization: + c: 12.0 # carbon (mg C/m^3) + R3: + long_name: semi-refractory dissolved organic matter + model: ersem/pelagic_base + parameters: + composition: c # elemental composition + c0: 0.0033 # background carbon concentration (mg C/m^3), default = 0.0 + initialization: + c: 12.0 # carbon (mg C/m^3) + R4: + long_name: small-size pom + model: ersem/pelagic_base + parameters: + composition: cnpf # elemental composition + c0: 0.0033 # background carbon concentration (mg C/m^3), default = 0.0 + iopABS: 1e-05 # specific shortwave absorption (m^2/mg C), default = 0.0 + iopBBS: 1.6e-05 # specific shortwave backscatter (m^2/mg C), default = 0.0 + rm: 1.0 # sinking velocity (m/d), default = 0.0 + ndeposition: 2 # number of target pools for sedimentation, default = 1 + qxc2: 0.1 # fraction of carbon sinking into deposition target 2 (-) + qxn2: 0.1 # fraction of nitrogen sinking into deposition target 2 (-) + qxp2: 0.06 # fraction of phosphorus sinking into deposition target 2 (-) + initialization: + c: 7.2 # carbon (mg C/m^3) + n: 0.1 # nitrogen (mmol N/m^3) + p: 0.007 # phosphorus (mmol P/m^3) + coupling: + deposition_target1: Q6/surface + deposition_target2: Q7/surface + R6: + long_name: medium-size pom + model: ersem/pelagic_base + parameters: + composition: cnpsf # elemental composition + c0: 0.0033 # background carbon concentration (mg C/m^3), default = 0.0 + iopABS: 1e-05 # specific shortwave absorption (m^2/mg C), default = 0.0 + iopBBS: 1.6e-05 # specific shortwave backscatter (m^2/mg C), default = 0.0 + rm: 5.0 # sinking velocity (m/d), default = 0.0 + ndeposition: 2 # number of target pools for sedimentation, default = 1 + qxc2: 0.1 # fraction of carbon sinking into deposition target 2 (-) + qxn2: 0.1 # fraction of nitrogen sinking into deposition target 2 (-) + qxp2: 0.06 # fraction of phosphorus sinking into deposition target 2 (-) + qxs2: 0.0 # fraction of silicate sinking into deposition target 2 (-) + initialization: + c: 17.0 # carbon (mg C/m^3) + n: 0.24 # nitrogen (mmol N/m^3) + p: 0.02 # phosphorus (mmol P/m^3) + s: 0.1 # silicate (mmol Si/m^3) + coupling: + deposition_target1: Q6/surface + deposition_target2: Q7/surface + R8: + long_name: large-size pom + model: ersem/pelagic_base + parameters: + composition: cnps # elemental composition + c0: 0.0033 # background carbon concentration (mg C/m^3), default = 0.0 + iopABS: 1e-05 # specific shortwave absorption (m^2/mg C), default = 0.0 + iopBBS: 1.6e-05 # specific shortwave backscatter (m^2/mg C), default = 0.0 + rm: 10.0 # sinking velocity (m/d), default = 0.0 + ndeposition: 2 # number of target pools for sedimentation, default = 1 + qxc2: 0.1 # fraction of carbon sinking into deposition target 2 (-) + qxn2: 0.1 # fraction of nitrogen sinking into deposition target 2 (-) + qxp2: 0.06 # fraction of phosphorus sinking into deposition target 2 (-) + qxs2: 0.0 # fraction of silicate sinking into deposition target 2 (-) + initialization: + c: 0.17 # carbon (mg C/m^3) + n: 0.0024 # nitrogen (mmol N/m^3) + p: 0.0002 # phosphorus (mmol P/m^3) + s: 0.001 # silicate (mmol Si/m^3) + coupling: + deposition_target1: Q6/surface + deposition_target2: Q7/surface + Q1: + long_name: benthic dissolved organic matter + model: ersem/benthic_base + parameters: + composition: cnp # elemental composition + c0: 0.001 # background carbon concentration (mg C/m^2), default = 0.0 + initialization: + c: 18.9 # carbon (mg C/m^2) + n: 0.6 # nitrogen (mmol N/m^2) + p: 0.0035 # phosphorus (mmol P/m^2) + Q6: + long_name: benthic particulate organic matter + model: ersem/benthic_column_particulate_matter + parameters: + composition: cnpsf # elemental composition + c0: 0.001 # background carbon concentration (mg C/m^2), default = 0.0 + resuspension: true # enable resuspension, default = false + initialization: + c: 3052.0 # carbon (mg C/m^2) + n: 3.5 # nitrogen (mmol N/m^2) + p: 0.5 # phosphorus (mmol P/m^2) + s: 149.0 # silicate (mmol Si/m^2) + pen_depth_c: 0.0173 # penetration depth of carbon (m) + pen_depth_n: 0.02 # penetration depth of nitrogen (m) + pen_depth_p: 0.025 # penetration depth of phosphorus (m) + pen_depth_s: 0.0313 # penetration depth of silicate (m) + coupling: + RP: R6 + Q7: + long_name: benthic refractory matter + model: ersem/benthic_column_particulate_matter + parameters: + composition: cnp # elemental composition + c0: 0.001 # background carbon concentration (mg C/m^2), default = 0.0 + burial: true # enable burial, default = false + initialization: + c: 30520.0 # carbon (mg C/m^2) + n: 80.0 # nitrogen (mmol N/m^2) + p: 8.0 # phosphorus (mmol P/m^2) + pen_depth_c: 0.2 # penetration depth of carbon (m) + pen_depth_n: 0.25 # penetration depth of nitrogen (m) + pen_depth_p: 0.313 # penetration depth of phosphorus (m) + coupling: + burial_target: Q17 + Q17: + long_name: benthic buried matter + model: ersem/benthic_base + parameters: + composition: cnp # elemental composition + initialization: + c: 0.0 # carbon (mg C/m^2) + n: 0.0 # nitrogen (mmol N/m^2) + p: 0.0 # phosphorus (mmol P/m^2) + B1: + long_name: bacteria + model: ersem/bacteria_docdyn + parameters: + iswBlim: 2 # nutrient limitation (1: minimum of inorganic and organic availability, 2: additive availability) + q10: 2.0 # Q_10 temperature coefficient (-) + chdo: 0.31 # Michaelis-Menten constant for oxygen limitation (-) + chn: 0.5 # Michaelis-Menten constant for nitrate limitation (mmol N/m^3) + chp: 0.1 # Michaelis-Menten constant for phosphate limitation (mmol P/m^3) + sd: 0.05 # specific mortality at reference temperature (1/d) + sum: 2.2 # maximum specific uptake at reference temperature (1/d) + pu: 0.6 # efficiency at high oxygen levels (-) + puo: 0.2 # efficiency at low oxygen levels (-) + srs: 0.1 # specific rest respiration at reference temperature (1/d) + sR1: 1.0 # maximum turn-over rate of DOM (1/d), default = 1.0 + qpc: 0.0019 # maximum phosphorus to carbon ratio (mmol P/mg C) + qnc: 0.0167 # maximum nitrogen to carbon ratio (mmol N/mg C) + ur_O2: 0.1 # oxygen consumed per carbon respired (mmol O_2/mg C) + sR1N1: 0.0 # mineralisation rate of labile dissolved organic phosphorus (1/d) + sR1N4: 0.0 # mineralisation rate of labile dissolved organic nitrogen (1/d) + fsink: 7e-05 # scavenging rate for iron (1/d) + c0: 0.01 # background carbon concentration (mg C/m^3) + nRP: 3 # number of substrates, default = 0 + sRP1R1: 0.01 # remineralisation of substrate 1 to DOM (1/d) + sRP2R1: 0.0025 # remineralisation of substrate 2 to DOM (1/d) + sRP3R1: 0.001 # remineralisation of substrate 3 to DOM (1/d) + rR2: 0.0075 # fraction of semi-labile DOC available to bacteria (-) + rR3: 0.0025 # fraction of semi-refractory DOC available to bacteria (-) + frR3: 0.3 # fraction of activity respiration converted to semi-refractory DOC (-) + initialization: + c: 15.7 # carbon (mg C/m^3) + n: 0.26 # nitrogen (mmol N/m^3) + p: 0.029 # phosphorus (mmol P/m^3) + coupling: + RP1: R4 + RP2: R6 + RP3: R8 + N1p: N1/p # phosphate (mmol P/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # labile dissolved organic carbon (mg C/m^3) + R1p: R1/p # labile dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # labile dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + R3c: R3/c # semi-refractory DOC (mg C/m^3) + O3c: O3/c # carbon dioxide (mmol C/m^3) + O2o: O2/o # oxygen (mmol O_2/m^3) + pel_nit: + long_name: pelagic nitrification + model: ersem/nitrification + parameters: + q10: 2.0 # Q_10 temperature coefficient (-) + ISWph: 1 # pH impact on nitrification (0: off, 1: on) + sN4N3: 0.5 # specific nitrification rate (1/d) + chN3o: 2700.0 # Michaelis-Menten constant for cubic oxygen dependence of nitrification ((mmol O_2/m^3)^3) + chN4n: 0.5 # Michaelis-Menten constant for cubic ammonium dependence of nitrification ((mmol N/m^3)^3), default = 0.0 + ISWn2o: true # activate production of nitrous oxide (default = false) + N4O5minX: 0.001 # fraction of N going to N2O during nitrification + coupling: + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + O2o: O2/o # oxygen (mmol O_2/m^3) + O5n: O5/n # nitrous oxide (mmol N/m^3) + P1: + long_name: diatoms + model: ersem/primary_producer + parameters: + sum: 1.375 # maximum specific productivity at reference temperature (1/d) + q10: 2.0 # Q_10 temperature coefficient (-) + srs: 0.04 # specific rest respiration at reference temperature (1/d) + pu_ea: 0.2 # excreted fraction of primary production (-) + pu_ra: 0.2 # respired fraction of primary production (-) + qnlc: 0.0042 # minimum nitrogen to carbon ratio (mmol N/mg C) + qplc: 0.0001 # minimum phosphorus to carbon ratio (mmol P/mg C) + xqcp: 1.0 # threshold for phosphorus limitation (relative to Redfield ratio) (-) + xqcn: 1.0 # threshold for nitrogen limitation (relative to Redfield ratio) (-) + xqp: 2.0 # maximum phosphorus to carbon ratio (relative to Redfield ratio) (-) + xqn: 1.075 # maximum nitrogen to carbon ratio (relative to Redfield ratio) (-) + qun3: 0.0025 # nitrate affinity (m^3/mg C/d) + qun4: 0.0025 # ammonium affinity (m^3/mg C/d) + qurp: 0.003 # phosphate affinity (m^3/mg C/d) + snplux: 1.0 # specific tendency of luxury uptake of nutrients towards maximum quota (1/d), default = 1.0 + use_Si: true # use silicate, default = false + qsc: 0.0118 # maximum silicate to carbon ratio (mmol Si/mg C) + chs: 0.2 # Michaelis-Menten constant for silicate limitation (mmol/m^3) + sdo: 0.05 # 1.1 of minimal specific lysis rate (1/d) + alpha: 4.0 # initial slope of PI-curve (mg C m^2/mg Chl/W/d) + beta: 0.07 # photoinhibition parameter (mg C m^2/mg Chl/W/d) + phim: 0.06 # maximum effective chlorophyll to carbon photosynthesis ratio (mg Chl/mg C) + Limnut: 1 # nitrogen-phosphorus colimitation formulation (0: geometric mean, 1: minimum, 2: harmonic mean) + docdyn: true # use dynamic ratio of labile to semi-labile DOM production, default = false + uB1c_O2: 0.11 # oxygen produced per unit of carbon fixed (mmol O_2/mg C) + urB1_O2: 0.1 # oxygen consumed per unit of carbon respired (mmol O_2/mg C) + iopABS: 0.007 # specific shortwave absorption (m^2/mg Chl), default = 0.008 + iopBBS: 0.00048 # specific shortwave backscatter (m^2/mg Chl), default = 0.003 + c0: 0.0001 # background carbon concentration (mg C/m^3), default = 0.0 + resm: 5.0 # maximum nutrient-limitation-induced sinking velocity (m/d), default = 0.0 + esni: 0.7 # level of nutrient limitation below which sinking commences (-) + cenh: false # enable atmospheric CO2 influence on photosynthesis, default = false + ndeposition: 3 # number of target pools for sedimentation, default = 1 + qxc2: 0.2 # fraction of carbon sinking into deposition target 2 (-) + qxc3: 0.005 # fraction of carbon sinking into deposition target 3 (-) + qxn2: 0.2 # fraction of nitrogen sinking into deposition target 2 (-) + qxn3: 0.005 # fraction of nitrogen sinking into deposition target 3 (-) + qxp2: 0.24 # fraction of phosphorus sinking into deposition target 2 (-) + qxp3: 0.003 # fraction of phosphorus sinking into deposition target 3 (-) + qxs2: 0.0 # fraction of silicate sinking into deposition target 2 (-) + qxs3: 0.0 # fraction of silicate sinking into deposition target 3 (-) + initialization: + c: 8.0 # carbon (mg C/m^3) + n: 0.1114 # nitrogen (mmol N/m^3) + p: 0.009 # phosphorus (mmol P/m^3) + s: 0.128 # silicate (mmol Si/m^3) + Chl: 0.4 # chlorophyll a (mg/m^3) + coupling: + RP: R6 + deposition_target1: Q6/surface + deposition_target2: Q1 + deposition_target3: Q7/surface + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + N5s: N5/s # silicate (mmol Si/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + O2o: O2/o # oxygen (mmol O_2/m^3) + O3c: O3/c # carbon dioxide (mmol C/m^3) + P2: + long_name: nanophytoplankton + model: ersem/primary_producer + parameters: + sum: 1.625 # maximum specific productivity at reference temperature (1/d) + q10: 2.0 # Q_10 temperature coefficient (-) + srs: 0.04 # specific rest respiration at reference temperature (1/d) + pu_ea: 0.2 # excreted fraction of primary production (-) + pu_ra: 0.2 # respired fraction of primary production (-) + qnlc: 0.005 # minimum nitrogen to carbon ratio (mmol N/mg C) + qplc: 0.000225 # minimum phosphorus to carbon ratio (mmol P/mg C) + xqcp: 1.0 # threshold for phosphorus limitation (relative to Redfield ratio) (-) + xqcn: 1.0 # threshold for nitrogen limitation (relative to Redfield ratio) (-) + xqp: 2.0 # maximum phosphorus to carbon ratio (relative to Redfield ratio) (-) + xqn: 1.075 # maximum nitrogen to carbon ratio (relative to Redfield ratio) (-) + qun3: 0.004 # nitrate affinity (m^3/mg C/d) + qun4: 0.004 # ammonium affinity (m^3/mg C/d) + qurp: 0.004 # phosphate affinity (m^3/mg C/d) + snplux: 1.0 # specific tendency of luxury uptake of nutrients towards maximum quota (1/d), default = 1.0 + use_Si: false # use silicate, default = false + sdo: 0.05 # 1.1 of minimal specific lysis rate (1/d) + alpha: 5.0 # initial slope of PI-curve (mg C m^2/mg Chl/W/d) + beta: 0.1 # photoinhibition parameter (mg C m^2/mg Chl/W/d) + phim: 0.025 # maximum effective chlorophyll to carbon photosynthesis ratio (mg Chl/mg C) + Limnut: 1 # nitrogen-phosphorus colimitation formulation (0: geometric mean, 1: minimum, 2: harmonic mean) + docdyn: true # use dynamic ratio of labile to semi-labile DOM production, default = false + uB1c_O2: 0.11 # oxygen produced per unit of carbon fixed (mmol O_2/mg C) + urB1_O2: 0.1 # oxygen consumed per unit of carbon respired (mmol O_2/mg C) + iopABS: 0.0041 # specific shortwave absorption (m^2/mg Chl), default = 0.008 + iopBBS: 0.003 # specific shortwave backscatter (m^2/mg Chl), default = 0.003 + c0: 0.001 # background carbon concentration (mg C/m^3), default = 0.0 + calcify: true # calcify, default = false + resm: 0.0 # maximum nutrient-limitation-induced sinking velocity (m/d), default = 0.0 + esni: 0.7 # level of nutrient limitation below which sinking commences (-) + cenh: false # enable atmospheric CO2 influence on photosynthesis, default = false + ndeposition: 3 # number of target pools for sedimentation, default = 1 + qxc2: 0.5 # fraction of carbon sinking into deposition target 2 (-) + qxc3: 0.05 # fraction of carbon sinking into deposition target 3 (-) + qxn2: 0.5 # fraction of nitrogen sinking into deposition target 2 (-) + qxn3: 0.05 # fraction of nitrogen sinking into deposition target 3 (-) + qxp2: 0.6 # fraction of phosphorus sinking into deposition target 2 (-) + qxp3: 0.03 # fraction of phosphorus sinking into deposition target 3 (-) + initialization: + c: 5.9 # carbon (mg C/m^3) + n: 0.0926 # nitrogen (mmol N/m^3) + p: 0.0036 # phosphorus (mmol P/m^3) + Chl: 0.3 # chlorophyll a (mg/m^3) + coupling: + RP: R4 + deposition_target1: Q6/surface + deposition_target2: Q1 + deposition_target3: Q7/surface + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + O2o: O2/o # oxygen (mmol O_2/m^3) + O3c: O3/c # carbon dioxide (mmol C/m^3) + RainR: L2/RainR # rain ratio (PIC : POC) (-) + L2c: L2/c # free calcite (mg C/m^3) + P3: + long_name: picophytoplankton + model: ersem/primary_producer + parameters: + sum: 2.0 # maximum specific productivity at reference temperature (1/d) + q10: 2.0 # Q_10 temperature coefficient (-) + srs: 0.045 # specific rest respiration at reference temperature (1/d) + pu_ea: 0.2 # excreted fraction of primary production (-) + pu_ra: 0.2 # respired fraction of primary production (-) + qnlc: 0.006 # minimum nitrogen to carbon ratio (mmol N/mg C) + qplc: 0.00035 # minimum phosphorus to carbon ratio (mmol P/mg C) + xqcp: 1.0 # threshold for phosphorus limitation (relative to Redfield ratio) (-) + xqcn: 1.0 # threshold for nitrogen limitation (relative to Redfield ratio) (-) + xqp: 1.5 # maximum phosphorus to carbon ratio (relative to Redfield ratio) (-) + xqn: 1.05 # maximum nitrogen to carbon ratio (relative to Redfield ratio) (-) + qun3: 0.006 # nitrate affinity (m^3/mg C/d) + qun4: 0.007 # ammonium affinity (m^3/mg C/d) + qurp: 0.006 # phosphate affinity (m^3/mg C/d) + snplux: 1.0 # specific tendency of luxury uptake of nutrients towards maximum quota (1/d), default = 1.0 + use_Si: false # use silicate, default = false + sdo: 0.055 # 1.1 of minimal specific lysis rate (1/d) + alpha: 6.0 # initial slope of PI-curve (mg C m^2/mg Chl/W/d) + beta: 0.12 # photoinhibition parameter (mg C m^2/mg Chl/W/d) + phim: 0.015 # maximum effective chlorophyll to carbon photosynthesis ratio (mg Chl/mg C) + Limnut: 1 # nitrogen-phosphorus colimitation formulation (0: geometric mean, 1: minimum, 2: harmonic mean) + docdyn: true # use dynamic ratio of labile to semi-labile DOM production, default = false + uB1c_O2: 0.11 # oxygen produced per unit of carbon fixed (mmol O_2/mg C) + urB1_O2: 0.1 # oxygen consumed per unit of carbon respired (mmol O_2/mg C) + iopABS: 0.023 # specific shortwave absorption (m^2/mg Chl), default = 0.008 + iopBBS: 0.003 # specific shortwave backscatter (m^2/mg Chl), default = 0.003 + c0: 0.0088 # background carbon concentration (mg C/m^3), default = 0.0 + resm: 0.0 # maximum nutrient-limitation-induced sinking velocity (m/d), default = 0.0 + esni: 0.7 # level of nutrient limitation below which sinking commences (-) + cenh: false # enable atmospheric CO2 influence on photosynthesis, default = false + ndeposition: 3 # number of target pools for sedimentation, default = 1 + qxc2: 0.5 # fraction of carbon sinking into deposition target 2 (-) + qxc3: 0.05 # fraction of carbon sinking into deposition target 3 (-) + qxn2: 0.5 # fraction of nitrogen sinking into deposition target 2 (-) + qxn3: 0.05 # fraction of nitrogen sinking into deposition target 3 (-) + qxp2: 0.6 # fraction of phosphorus sinking into deposition target 2 (-) + qxp3: 0.03 # fraction of phosphorus sinking into deposition target 3 (-) + initialization: + c: 5.9 # carbon (mg C/m^3) + n: 0.0926 # nitrogen (mmol N/m^3) + p: 0.0036 # phosphorus (mmol P/m^3) + Chl: 0.3 # chlorophyll a (mg/m^3) + coupling: + RP: R4 + deposition_target1: Q6/surface + deposition_target2: Q1 + deposition_target3: Q7/surface + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + O2o: O2/o # oxygen (mmol O_2/m^3) + O3c: O3/c # carbon dioxide (mmol C/m^3) + P4: + long_name: microphytoplankton + model: ersem/primary_producer + parameters: + sum: 1.125 # maximum specific productivity at reference temperature (1/d) + q10: 2.0 # Q_10 temperature coefficient (-) + srs: 0.035 # specific rest respiration at reference temperature (1/d) + pu_ea: 0.2 # excreted fraction of primary production (-) + pu_ra: 0.2 # respired fraction of primary production (-) + qnlc: 0.0042 # minimum nitrogen to carbon ratio (mmol N/mg C) + qplc: 0.0001 # minimum phosphorus to carbon ratio (mmol P/mg C) + xqcp: 1.0 # threshold for phosphorus limitation (relative to Redfield ratio) (-) + xqcn: 1.0 # threshold for nitrogen limitation (relative to Redfield ratio) (-) + xqp: 2.7 # maximum phosphorus to carbon ratio (relative to Redfield ratio) (-) + xqn: 1.1 # maximum nitrogen to carbon ratio (relative to Redfield ratio) (-) + qun3: 0.002 # nitrate affinity (m^3/mg C/d) + qun4: 0.002 # ammonium affinity (m^3/mg C/d) + qurp: 0.002 # phosphate affinity (m^3/mg C/d) + snplux: 1.0 # specific tendency of luxury uptake of nutrients towards maximum quota (1/d), default = 1.0 + use_Si: false # use silicate, default = false + sdo: 0.045 # 1.1 of minimal specific lysis rate (1/d) + alpha: 3.0 # initial slope of PI-curve (mg C m^2/mg Chl/W/d) + beta: 0.06 # photoinhibition parameter (mg C m^2/mg Chl/W/d) + phim: 0.045 # maximum effective chlorophyll to carbon photosynthesis ratio (mg Chl/mg C) + Limnut: 1 # nitrogen-phosphorus colimitation formulation (0: geometric mean, 1: minimum, 2: harmonic mean) + docdyn: true # use dynamic ratio of labile to semi-labile DOM production, default = false + uB1c_O2: 0.11 # oxygen produced per unit of carbon fixed (mmol O_2/mg C) + urB1_O2: 0.1 # oxygen consumed per unit of carbon respired (mmol O_2/mg C) + iopABS: 0.008 # specific shortwave absorption (m^2/mg Chl), default = 0.008 + iopBBS: 0.00048 # specific shortwave backscatter (m^2/mg Chl), default = 0.003 + c0: 0.0001 # background carbon concentration (mg C/m^3), default = 0.0 + resm: 5.0 # maximum nutrient-limitation-induced sinking velocity (m/d), default = 0.0 + esni: 0.7 # level of nutrient limitation below which sinking commences (-) + cenh: false # enable atmospheric CO2 influence on photosynthesis, default = false + ndeposition: 3 # number of target pools for sedimentation, default = 1 + qxc2: 0.5 # fraction of carbon sinking into deposition target 2 (-) + qxc3: 0.05 # fraction of carbon sinking into deposition target 3 (-) + qxn2: 0.5 # fraction of nitrogen sinking into deposition target 2 (-) + qxn3: 0.05 # fraction of nitrogen sinking into deposition target 3 (-) + qxp2: 0.6 # fraction of phosphorus sinking into deposition target 2 (-) + qxp3: 0.03 # fraction of phosphorus sinking into deposition target 3 (-) + initialization: + c: 5.9 # carbon (mg C/m^3) + n: 0.0926 # nitrogen (mmol N/m^3) + p: 0.0036 # phosphorus (mmol P/m^3) + Chl: 0.3 # chlorophyll a (mg/m^3) + coupling: + RP: R6 + deposition_target1: Q6/surface + deposition_target2: Q1 + deposition_target3: Q7/surface + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + O2o: O2/o # oxygen (mmol O_2/m^3) + O3c: O3/c # carbon dioxide (mmol C/m^3) + Z4: + long_name: mesozooplankton + model: ersem/mesozooplankton + parameters: + q10: 2.0 # Q_10 temperature coefficient (-) + minfood: 12.0 # Michaelis-Menten constant to perceive food (mg C/m^3) + chuc: 36.0 # Michaelis-Menten constant for food uptake (mg C/m^3) + sum: 1.0 # maximum specific uptake at reference temperature (1/d) + pu: 0.6 # assimilation efficiency (-) + pu_ea: 0.5 # fraction of unassimilated prey that is excreted (not respired) (-) + pu_eaR: 0.9 # fraction of unassimilated detritus that is excreted (not respired) (-) + pe_R1: 0.5 # dissolved fraction of excreted/dying matter (-) + srs: 0.015 # specific rest respiration at reference temperature (1/d) + sd: 0.05 # basal mortality (1/d) + sdo: 0.2 # maximum mortality due to oxygen limitation (1/d) + chro: 7.81 # Michaelis-Menten constant for oxygen limitation (-) + qpc: 0.000786 # phosphorus to carbon ratio (mmol P/mg C) + qnc: 0.0126 # nitrogen to carbon ratio (mmol N/mg C) + Minprey: 300.0 # food threshold for overwintering state (mg C/m^2) + repw: 0.0025 # specific overwintering respiration (1/d) + mort: 0.0025 # specific overwintering mortality (1/d) + R1R2: 1.0 # labile fraction of produced dissolved organic carbon (-) + xR1p: 1.2 # transfer of phosphorus to DOM, relative to POM (-), default = 0.0 + xR1n: 1.0 # transfer of nitrogen to DOM, relative to POM (-), default = 0.0 + urB1_O2: 0.1 # oxygen consumed per carbon respired (mmol O_2/mg C) + gutdiss: 0.5 # fraction of prey calcite that dissolves after ingestion (-) + c0: 0.0033 # background concentration (mg C/m^3) + nprey: 9 # number of prey types, default = 0 + suprey1: 0.15 # relative affinity for prey type 1 (-) + suprey2: 0.05 # relative affinity for prey type 2 (-) + suprey3: 0.0 # relative affinity for prey type 3 (-) + suprey4: 0.15 # relative affinity for prey type 4 (-) + suprey5: 0.25 # relative affinity for prey type 5 (-) + suprey6: 0.25 # relative affinity for prey type 6 (-) + suprey7: 0.05 # relative affinity for prey type 7 (-) + suprey8: 0.0 # relative affinity for prey type 8 (-) + suprey9: 0.1 # relative affinity for prey type 9 (-) + prey9ispom: true # prey type 9 is detritus, default = false + initialization: + c: 1.2 # carbon (mg C/m^3) + coupling: + prey1: P1 + prey2: P2 + prey3: P3 + prey4: P4 + prey5: Z4 + prey6: Z5 + prey7: Z6 + prey8: B1 + prey9: R6 + RP: R8 + N1p: N1/p # phosphate (mmol P/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + O2o: O2/o # oxygen source (mmol O_2/m^3) + O3c: O3/c # carbon dioxide sink (mmol C/m^3) + L2c: L2/c # calcite (mg C/m^3) + Z5: + long_name: microzooplankton + model: ersem/microzooplankton + parameters: + q10: 2.0 # Q_10 temperature coefficient (-) + minfood: 12.0 # Michaelis-Menten constant to perceive food (mg C/m^3) + chuc: 32.0 # Michaelis-Menten constant for food uptake (mg C/m^3) + sum: 1.25 # maximum specific uptake at reference temperature (1/d) + pu: 0.5 # assimilation efficiency (-) + pu_ea: 0.5 # fraction of unassimilated prey that is excreted (not respired) (-) + pe_R1: 0.5 # dissolved fraction of excreted/dying matter (-) + srs: 0.02 # specific rest respiration at reference temperature (1/d) + sd: 0.05 # basal mortality (1/d) + sdo: 0.25 # maximum mortality due to oxygen limitation (1/d) + chro: 7.81 # Michaelis-Menten constant for oxygen limitation (-) + qpc: 0.001 # maximum phosphorus to carbon ratio (mmol P/mg C) + qnc: 0.0167 # maximum nitrogen to carbon ratio (mmol N/mg C) + stempp: 0.5 # specific excretion rate of excess phosphorus (1/d) + stempn: 0.5 # specific excretion rate of excess nitrogen (1/d) + R1R2: 1.0 # labile fraction of produced dissolved organic carbon (-) + xR1p: 1.2 # transfer of phosphorus to DOM, relative to POM (-), default = 1.0 + xR1n: 1.0 # transfer of nitrogen to DOM, relative to POM (-), default = 1.0 + urB1_O2: 0.1 # oxygen consumed per carbon respired (mmol O_2/mg C) + gutdiss: 0.5 # fraction of prey calcite that dissolves after ingestion (-) + c0: 0.0033 # background concentration (mg C/m^3) + nprey: 7 # number of prey types, default = 0 + suprey1: 0.1 # relative affinity for prey type 1 (-) + suprey2: 0.15 # relative affinity for prey type 2 (-) + suprey3: 0.15 # relative affinity for prey type 3 (-) + suprey4: 0.15 # relative affinity for prey type 4 (-) + suprey5: 0.1 # relative affinity for prey type 5 (-) + suprey6: 0.15 # relative affinity for prey type 6 (-) + suprey7: 0.2 # relative affinity for prey type 7 (-) + initialization: + c: 7.2 # carbon (mg C/m^3) + n: 0.12 # nitrogen (mmol N/m^3) + p: 0.0113 # phosphorus (mmol P/m^3) + coupling: + prey1: B1 + prey2: P1 + prey3: P2 + prey4: P3 + prey5: P4 + prey6: Z5 + prey7: Z6 + RP: R6 + N1p: N1/p # phosphate (mmol P/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + O2o: O2/o # oxygen source (mmol O_2/m^3) + O3c: O3/c # carbon dioxide sink (mmol C/m^3) + L2c: L2/c # calcite (mg C/m^3) + Z6: + long_name: nanoflagellates + model: ersem/microzooplankton + parameters: + q10: 2.0 # Q_10 temperature coefficient (-) + minfood: 12.0 # Michaelis-Menten constant to perceive food (mg C/m^3) + chuc: 28.0 # Michaelis-Menten constant for food uptake (mg C/m^3) + sum: 1.5 # maximum specific uptake at reference temperature (1/d) + pu: 0.4 # assimilation efficiency (-) + pu_ea: 0.5 # fraction of unassimilated prey that is excreted (not respired) (-) + pe_R1: 0.5 # dissolved fraction of excreted/dying matter (-) + srs: 0.025 # specific rest respiration at reference temperature (1/d) + sd: 0.05 # basal mortality (1/d) + sdo: 0.3 # maximum mortality due to oxygen limitation (1/d) + chro: 7.81 # Michaelis-Menten constant for oxygen limitation (-) + qpc: 0.001 # maximum phosphorus to carbon ratio (mmol P/mg C) + qnc: 0.0167 # maximum nitrogen to carbon ratio (mmol N/mg C) + stempp: 0.5 # specific excretion rate of excess phosphorus (1/d) + stempn: 0.5 # specific excretion rate of excess nitrogen (1/d) + R1R2: 1.0 # labile fraction of produced dissolved organic carbon (-) + xR1p: 1.2 # transfer of phosphorus to DOM, relative to POM (-), default = 1.0 + xR1n: 1.0 # transfer of nitrogen to DOM, relative to POM (-), default = 1.0 + urB1_O2: 0.1 # oxygen consumed per carbon respired (mmol O_2/mg C) + gutdiss: 0.5 # fraction of prey calcite that dissolves after ingestion (-) + c0: 0.0033 # background concentration (mg C/m^3) + nprey: 4 # number of prey types, default = 0 + suprey1: 0.45 # relative affinity for prey type 1 (-) + suprey2: 0.15 # relative affinity for prey type 2 (-) + suprey3: 0.25 # relative affinity for prey type 3 (-) + suprey4: 0.15 # relative affinity for prey type 4 (-) + initialization: + c: 2.421 # carbon (mg C/m^3) + n: 0.0505 # nitrogen (mmol N/m^3) + p: 0.047 # phosphorus (mmol P/m^3) + coupling: + prey1: B1 + prey2: P2 + prey3: P3 + prey4: Z6 + RP: R4 + N1p: N1/p # phosphate (mmol P/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R1c: R1/c # dissolved organic carbon (mg C/m^3) + R1p: R1/p # dissolved organic phosphorus (mmol P/m^3) + R1n: R1/n # dissolved organic nitrogen (mmol N/m^3) + R2c: R2/c # semi-labile dissolved organic carbon (mg C/m^3) + RPs: R6/s # particulate organic silicate (mmol Si/m^3) + O2o: O2/o # oxygen source (mmol O_2/m^3) + O3c: O3/c # carbon dioxide sink (mmol C/m^3) + L2c: L2/c # calcite (mg C/m^3) + L2: + long_name: calcite + model: ersem/calcification + parameters: + iswcal: 1 # calcification/dissolution dependence on calcite saturation (1: power law, 2: hyperbolic) + ncalc: 0.81 # power of the calcification law (Ridgwell et al. 2007, mineral calcite) (-) + ndiss: 2.22 # power of the dissolution law (Keir 1980) (-) + Rain0: 0.6 # maximum rain ratio from PISCES (-) + sedL2: 10.0 # sinking velocity (m/d) + sL2O3: 0.03 # maximum specific dissolution rate (1/d), default = 1.0 + c0: 1e-05 # background concentration (mg C/m^3), default = 0.0 + ndeposition: 1 # number of target pools for sedimentation, default = 1 + initialization: + c: 0.05 # carbon (mg C/m^3) + coupling: + deposition_target1: bL2 + om_cal: O3/Om_cal # calcite saturation (-) + O3c: O3/c # total dissolved inorganic carbon (mmol C/m^3) + bL2: + long_name: benthic calcite + model: ersem/benthic_calcite + parameters: + iswcal: 1 # dissolution dependence on calcite saturation (0: none, 1: power law, 2: hyperbolic) + ndiss: 2.22 # power of the dissolution law (Keir 1980) (-) + fdissmax: 30.0 # maximum specific dissolution rate (1/d), default = 0.0 + fdissmin: 0.05 # minimum specific dissolution rate (1/d), default = 0.03 + c0: 1e-05 # background calcite concentration (mg C/m^2), default = 0.0 + initialization: + c: 0.05 # carbon (mg C/m^2) + coupling: + Om_Cal: O3/Om_cal # calcite saturation (-) + O3c: O3/c # dissolved inorganic carbon (mmol/m^3) + ben_col: + long_name: benthic column + model: ersem/benthic_column + parameters: + qPW: 0.4 # sediment porosity (-) + EDZ_mix: 20.0 # equilibrium diffusive speed between sediment surface water (d/m) + d_tot: 0.3 # depth of sediment column (m) + Etur: 2e-06 # basal bioturbation rate (m^2/d) + mtur: 10.0 # maximum relative turbation enhancement (-) + htur: 116.0 # Michaelis-Menten constant for bioturbation (mg C/m^2/d) + dtur: 0.02 # bioturbation depth (m) + EDZ_1: 5e-05 # diffusivity in oxygenated layer (m^2/d) + EDZ_2: 5e-05 # diffusivity in oxidized layer (m^2/d) + EDZ_3: 5e-05 # diffusivity in anoxic layer (m^2/d) + irr_min: 2.0 # minimum diffusion enhancement through bioirrigation (-) + mirr: 10.0 # maximum relative diffusion enhancement due to bioirrigation (-) + hirr: 101.0 # Michaelis-Menten constant for bioirrigation (mg C/m^2/d) + initialization: + D1m: 0.009 # depth of bottom interface of oxygenated layer (m) + D2m: 0.05 # depth of bottom interface of oxidized layer (m) + K1: + long_name: benthic phosphate + model: ersem/benthic_column_dissolved_matter + parameters: + composition: p # composition (any combination of c,n,p,s,o,a) + c0: 0.0003 # background carbon concentration (mg C/m^2), default = 0.0 + ads1: 100.0 # adsorption in layer 1 (total:dissolved) (-), default = 1.0 + ads2: 100.0 # adsorption in layer 2 (total:dissolved) (-), default = 1.0 + ads3: 2.0 # adsorption in layer 3 (total:dissolved) (-), default = 1.0 + initialization: + p: 6.8 # phosphorus (mmol/m^2) + coupling: + p_pel: N1/p # pelagic phosphorus (mmol/m^3) + K3: + long_name: benthic nitrate + model: ersem/benthic_column_dissolved_matter + parameters: + composition: n # composition (any combination of c,n,p,s,o,a) + c0: 0.0003 # background carbon concentration (mg C/m^2), default = 0.0 + last_layer: 2 # sediment layer where concentration drops to zero, default = 3 + relax: 5.0 # rate of relaxation towards equilibrium concentration profile (1/d) + minD: 0.0001 # minimum depth of zero-concentration isocline (m) + initialization: + n: 0.584 # nitrogen (mmol/m^2) + coupling: + n_pel: N3/n # pelagic nitrogen (mmol/m^3) + K4: + long_name: benthic ammonium + model: ersem/benthic_column_dissolved_matter + parameters: + composition: n # composition (any combination of c,n,p,s,o,a) + c0: 0.0003 # background carbon concentration (mg C/m^2), default = 0.0 + ads1: 3.0 # adsorption in layer 1 (total:dissolved) (-), default = 1.0 + ads2: 3.0 # adsorption in layer 2 (total:dissolved) (-), default = 1.0 + ads3: 3.0 # adsorption in layer 3 (total:dissolved) (-), default = 1.0 + correction: true # move losses in oxygenic layer to deeper layers if pelagic concentration is limiting, default = false + initialization: + n: 25.0 # nitrogen (mmol/m^2) + coupling: + n_pel: N4/n # pelagic nitrogen (mmol/m^3) + K5: + long_name: benthic silicate + model: ersem/benthic_column_dissolved_matter + parameters: + composition: s # composition (any combination of c,n,p,s,o,a) + c0: 9e-05 # background carbon concentration (mg C/m^2), default = 0.0 + initialization: + s: 20.1 # silicate (mmol/m^2) + coupling: + s_pel: N5/s # pelagic silicate (mmol/m^3) + G2: + long_name: benthic oxygen + model: ersem/benthic_column_dissolved_matter + parameters: + composition: o # composition (any combination of c,n,p,s,o,a) + last_layer: 1 # sediment layer where concentration drops to zero, default = 3 + relax: 5.0 # rate of relaxation towards equilibrium concentration profile (1/d) + minD: 0.0001 # minimum depth of zero-concentration isocline (m) + initialization: + o: 0.0225 # oxygen (mmol/m^2) + coupling: + o_pel: O2/o # pelagic oxygen (mmol/m^3) + G5: + long_name: benthic nitrous oxide + model: ersem/benthic_column_dissolved_matter + parameters: + composition: n # composition (any combination of c,n,p,s,o,a) + last_layer: 2 # sediment layer where concentration drops to zero, default = 3 + relax: 5.0 # rate of relaxation towards equilibrium concentration profile (1/d) + minD: 0.0001 # minimum depth of zero-concentration isocline (m) + initialization: + n: 0.0 # nitrogen (mmol/m^2) + coupling: + n_pel: O5/n # pelagic nitrous oxide (mmol/m^3) + G3: + long_name: benthic dissolved inorganic carbon + model: ersem/benthic_column_dissolved_matter + parameters: + composition: c # composition (any combination of c,n,p,s,o,a) + initialization: + c: 375.0 # carbon (mmol/m^2) + coupling: + c_pel: O3/c # pelagic carbon (mmol/m^3) + Q6s_aerobic: + long_name: aerobic particulate silicate + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: s # elemental composition + minimum_depth: 0.0 # minimum depth (m), default = 0.0 + variable_maximum_depth: true # maximum depth is variable, default = false + remin: 0.007 # remineralization rate at 10 degrees Celsius (1/d), default = 0.0 + coupling: + Q: Q6 + s_remin_target: K5/per_layer/s1 + maximum_depth: ben_col/D1m # maximum depth (m) + Q6s_anaerobic: + long_name: anaerobic particulate silicate + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: s # elemental composition + variable_minimum_depth: true # minimum depth is variable, default = false + maximum_depth: 0.3 # maximum depth (m), default = 0.0 + remin: 0.007 # remineralization rate at 10 degrees Celsius (1/d), default = 0.0 + source_depth_distribution: 2 # vertical distribution of changes (1: constant absolute rate, 2: constant relative rate, 3: constant carbon-based relative rate), default = 1 + coupling: + Q: Q6 + s_remin_target: K5/per_layer/s2 + minimum_depth: ben_col/D1m # minimum depth (m) + ben_nit: + long_name: benthic nitrogen cycle + model: ersem/benthic_nitrogen_cycle + parameters: + q10nit: 2.0 # Q_10 temperature coefficient (-) + hM4M3: 10.0 # Michaelis-Menten constant for nitrate limitation (mmol/m^3) + ISWph: 1 # pH impact on nitrification (0: off, 1: on), default = 0 + sM4M3: 4.0 # maximum nitrification rate at 10 degrees Celsius (1/d) + xno3: 2.0 # oxygen consumed per nitrate produced (mol O_2/mol N) + pammon: 0.5 # fraction of oxygen demand fulfilled by denitrification under anaerobic conditions (-) + pdenit: 0.05 # fraction of denitrification producing dinitrogen gas (remainder produces ammonium) (-) + xn2: 1.25 # oxygen demand fulfilled by reduction of nitrate to dinitrogen gas (mol O_2/mol N) + hM3G4: 1.0 # Michaelis-Menten constant for nitrate limitation of denitrification (mmol N/m^3) + coupling: + K3n: K3/per_layer/n1 # benthic nitrate in 1st layer (mmol N/m^2) + K4n: K4/per_layer/n1 # benthic ammonium in 1st layer (mmol N/m^2) + G2o: G2/per_layer/o1 # benthic oxygen in 1st layer (mmol O_2/m^2) + N4n: N4/n # pelagic ammonium (mmol N/m^3) + benTA: zero_hz # benthic alkalinity in aerobic layer (mEq/m^2) + benTA2: zero_hz # benthic alkalinity in anaerobic layer (mEq/m^2) + K3n2: K3/per_layer/n2 # benthic nitrate in 2nd layer (mmol N/m^2) + K4n2: K4/per_layer/n2 # benthic ammonium in 2nd layer (mmol N/m^2) + G2o2: G2/per_layer/o2 # oxygen in 2nd layer (mmol O_2/m^2) + layer2_thickness: ben_col/layer2_thickness # thickness of 2nd layer (m) + H1: + long_name: benthic aerobic bacteria + model: ersem/benthic_bacteria + parameters: + qnc: 0.0167 # nitrogen to carbon ratio (mmol N/mg C) + qpc: 0.00125 # phosphorus to carbon ratio (mmol P/mg C) + c0: 1e-06 # background concentration (mg C/m^2), default = 0.0 + q10: 2.0 # Q_10 temperature coefficient (-) + dd: 0.001 # Michaelis-Menten constant for oxygen limitation through layer thickness (m) + nfood: 3 # number of food sources + su1: 0.0005 # base affinity for food source 1 (m^2/mg C/d) + su2: 2e-05 # base affinity for food source 2 (m^2/mg C/d) + suf2: 0.0002 # additional affinity for food source 2 subject to nutrient limitation (m^2/mg C/d), default = 0.0 + puinc2: 2.0 # affinity for nutrients relative to carbon in food source 2 (-), default = 1.0 + pue2: 0.1 # fraction of consumed food source 2 that is excreted (-), default = 0.0 + su3: 2e-06 # base affinity for food source 3 (m^2/mg C/d) + pue3: 0.1 # fraction of consumed food source 3 that is excreted (-), default = 0.0 + pur: 0.3 # fraction of consumed carbon that is respired (-) + sr: 0.02 # specific rest respiration (1/d) + pdQ1: 0.1 # fraction of dying matter that is dissolved (-) + sd: 0.05 # specific maximum mortality related to oxygen limitation (1/d) + initialization: + c: 25.0 # carbon (mg C/m^2) + coupling: + Q1: Q1 + Q6: H1_Q6 + food1: Q1 + food2: H1_Q6 + food3: H1_Q7 + Dm: ben_col/D1m # depth interval available to bacteria (m) + K4n: K4/per_layer/n1_pw # ammonium (mmol N/m^2) + K1p: K1/per_layer/p1_pw # phosphate (mmol N/m^2) + G2o: G2/per_layer/o1 # oxygen (mmol O_2/m^2) + G3c: G3/per_layer/c1 # dissolved inorganic carbon (mmol C/m^2) + benTA: zero_hz # benthic alkalinity (mEq/m^2) + H1_Q6: + long_name: benthic aerobic bacteria POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + minimum_depth: 0.0 # minimum depth (m), default = 0.0 + variable_maximum_depth: true # maximum depth is variable, default = false + coupling: + Q: Q6 + maximum_depth: ben_col/D1m # maximum depth (m) + H1_Q7: + long_name: benthic aerobic bacteria refractory POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnp # elemental composition + minimum_depth: 0.0 # minimum depth (m), default = 0.0 + variable_maximum_depth: true # maximum depth is variable, default = false + coupling: + Q: Q7 + maximum_depth: ben_col/D1m # maximum depth (m) + H2: + long_name: benthic anaerobic bacteria + model: ersem/benthic_bacteria + parameters: + qnc: 0.0167 # nitrogen to carbon ratio (mmol N/mg C) + qpc: 0.00125 # phosphorus to carbon ratio (mmol P/mg C) + c0: 1e-06 # background concentration (mg C/m^2), default = 0.0 + q10: 2.0 # Q_10 temperature coefficient (-) + dd: 0.01 # Michaelis-Menten constant for oxygen limitation through layer thickness (m) + nfood: 2 # number of food sources + su1: 2e-05 # base affinity for food source 1 (m^2/mg C/d) + suf1: 0.0002 # additional affinity for food source 1 subject to nutrient limitation (m^2/mg C/d), default = 0.0 + puinc1: 2.0 # affinity for nutrients relative to carbon in food source 1 (-), default = 1.0 + pue1: 0.0 # fraction of consumed food source 1 that is excreted (-), default = 0.0 + su2: 2e-06 # base affinity for food source 2 (m^2/mg C/d) + pue2: 0.0 # fraction of consumed food source 2 that is excreted (-), default = 0.0 + pur: 0.3 # fraction of consumed carbon that is respired (-) + sr: 0.02 # specific rest respiration (1/d) + pdQ1: 0.0 # fraction of dying matter that is dissolved (-) + sd: 0.05 # specific maximum mortality related to oxygen limitation (1/d) + initialization: + c: 400.0 # carbon (mg C/m^2) + coupling: + Q1: Q1 + Q6: H2_Q6 + food1: H2_Q6 + food2: H2_Q7 + Dm: ben_col/layer2_thickness # depth interval available to bacteria (m) + K4n: K4/per_layer/n2_pw # ammonium (mmol N/m^2) + K1p: K1/per_layer/p2_pw # phosphate (mmol N/m^2) + G2o: ben_nit/K6_calculator/K6 # oxygen (mmol O_2/m^2) + G3c: G3/per_layer/c2 # dissolved inorganic carbon (mmol C/m^2) + benTA: zero_hz # benthic alkalinity (mEq/m^2) + H2_Q6: + long_name: benthic anaerobic bacteria POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + variable_minimum_depth: true # minimum depth is variable, default = false + maximum_depth: 0.3 # maximum depth (m), default = 0.0 + source_depth_distribution: 3 # vertical distribution of changes (1: constant absolute rate, 2: constant relative rate, 3: constant carbon-based relative rate), default = 1 + coupling: + Q: Q6 + minimum_depth: ben_col/D1m # minimum depth (m) + H2_Q7: + long_name: benthic anaerobic bacteria refractory POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnp # elemental composition + variable_minimum_depth: true # minimum depth is variable, default = false + maximum_depth: 0.3 # maximum depth (m), default = 0.0 + source_depth_distribution: 3 # vertical distribution of changes (1: constant absolute rate, 2: constant relative rate, 3: constant carbon-based relative rate), default = 1 + coupling: + Q: Q7 + minimum_depth: ben_col/D1m # minimum depth (m) + Y2: + long_name: benthic deposit feeder + model: ersem/benthic_fauna + parameters: + qnc: 0.0119 # nitrogen to carbon ratio (mmol N/mg C) + qpc: 0.000792 # phosphorus to carbon ratio (mmol P/mg C) + c0: 0.001 # background concentration (mg C/m^2), default = 0.0 + q10: 2.0 # Q_10 temperature coefficient (-) + rlO2: 0.0 # minimum pelagic oxygen concentration (mmol O2/m^3) + hO2: 0.0 # Michaelis-Menten constant for oxygen limitation (mmol O2/m^3) + xcl: 2500.0 # abundance above which crowding reduces food uptake (mg C/m^2) + xcs: 3000.0 # Michaelis-Menten constant for the impact of crowding (mg C/m^2) + xch: 5000.0 # abundance determining asymptotic threshold of crowding limitation (-> xch/(Yc+xch) for Yc-> inf) (mg C/m^2) + su: 0.11 # specific maximum uptake at reference temperature (1/d) + lu: 250.0 # Michaelis-Menten constant for food preference as function of food concentration (mg C/m^2) + hu: 3000.0 # Michaelis-Menten constant for gross carbon uptake (mg C/m^2) + pue: 0.35 # fraction of carbon in consumed live food that goes to faeces (-) + pueQ: 0.8 # fraction of carbon in consumed detritus that goes to faeces (-) + pudil: 0.8 # relative nutrient content of faeces (-) + sd: 0.001 # specific mortality at reference temperature (1/d) + sdmO2: 1.0 # specific maximum additional mortality due to oxygen stress (1/d) + sdc: 0.022 # specific maximum additional mortality induced by cold temperature (1/d) + xdc: -0.7 # e-folding temperature factor of cold mortality response (1/degree_C) + sr: 0.0027 # specific rest respiration at reference temperature (1/d) + pur: 0.35 # fraction of assimilated food that is respired (-) + nfood: 4 # number of food sources, default = 0 + pufood1: 1.0 # preference for food source 1 (-) + pufood2: 1.0 # preference for food source 2 (-) + pufood3: 0.1 # preference for food source 3 (-) + pufood4: 1.0 # preference for food source 4 (-) + food3ispom: true # food source 3 is detritus, default = false + ptur: 1.0 # relative contribution to bioturbation (-), default = 0.0 + pirr: 1.0 # relative contribution to bioirrigation (-), default = 0.0 + initialization: + c: 3000.0 # carbon (mg C/m^2) + coupling: + food1: H1 + food2: H2 + food3: Y2_Q6_source + food4: Y4 + Q: Y2_Q6_sink + Dm: ben_col/D1m # depth of limiting layer for uptake (m) + O2o: O2/o # pelagic oxygen (mmol O_2/m^3) + G3c: G3/per_layer/c1 # carbon dioxide (mmol C/m^2) + G2o: G2/per_layer/o1 # oxygen (mmol O_2/m^2) + K1p: K1/per_layer/p1 # benthic phosphate in aerobic layer (mmol P/m^2) + K4n: K4/per_layer/n1 # benthic ammonium in aerobic layer (mmol N/m^2) + K1p2: K1/per_layer/p2 # benthic phosphate in anaerobic layer (mmol P/m^2) + K4n2: K4/per_layer/n2 # benthic ammonium in anaerobic layer (mmol N/m^2) + benTA: zero_hz # benthic alkalinity in aerobic layer (mEq/m^2) + benTA2: zero_hz # benthic alkalinity in anaerobic layer (mEq/m^2) + food2c_an: H2/c # food source 2 carbon in anaerobic layer (mg C/m^2) + food3c_an: Y2_Q6_source_anaerobic/c # food source 3 carbon in anaerobic layer (mg C/m^2) + Y2_Q6_source: + long_name: benthic deposit feeder total POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + minimum_depth: 0.0025 # minimum depth (m), default = 0.0 + maximum_depth: 0.3 # maximum depth (m), default = 0.0 + coupling: + Q: Q6 + Y2_Q6_source_anaerobic: + long_name: benthic deposit feeder anaerobic POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + variable_minimum_depth: true # minimum depth is variable, default = false + maximum_depth: 0.3 # maximum depth (m), default = 0.0 + coupling: + Q: Q6 + minimum_depth: ben_col/D1m # minimum depth (m) + Y2_Q6_sink: + long_name: benthic deposit feeder POM sink + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + minimum_depth: 0.0 # minimum depth (m), default = 0.0 + variable_maximum_depth: true # maximum depth is variable, default = false + coupling: + Q: Q6 + maximum_depth: Q6/pen_depth_c # maximum depth (m) + Y3: + long_name: benthic suspension feeder + model: ersem/benthic_fauna + parameters: + qnc: 0.0119 # nitrogen to carbon ratio (mmol N/mg C) + qpc: 0.000792 # phosphorus to carbon ratio (mmol P/mg C) + c0: 0.001 # background concentration (mg C/m^2), default = 0.0 + q10: 2.0 # Q_10 temperature coefficient (-) + rlO2: 0.0 # minimum pelagic oxygen concentration (mmol O2/m^3) + hO2: 0.0 # Michaelis-Menten constant for oxygen limitation (mmol O2/m^3) + xcl: 2500.0 # abundance above which crowding reduces food uptake (mg C/m^2) + xcs: 3000.0 # Michaelis-Menten constant for the impact of crowding (mg C/m^2) + xch: 5000.0 # abundance determining asymptotic threshold of crowding limitation (-> xch/(Yc+xch) for Yc-> inf) (mg C/m^2) + su: 0.09 # specific maximum uptake at reference temperature (1/d) + lu: 10.0 # Michaelis-Menten constant for food preference as function of food concentration (mg C/m^2) + hu: 300.0 # Michaelis-Menten constant for gross carbon uptake (mg C/m^2) + pue: 0.35 # fraction of carbon in consumed live food that goes to faeces (-) + pueQ: 0.85 # fraction of carbon in consumed detritus that goes to faeces (-) + pudil: 0.8 # relative nutrient content of faeces (-) + sd: 0.001 # specific mortality at reference temperature (1/d) + sdmO2: 1.0 # specific maximum additional mortality due to oxygen stress (1/d) + sdc: 0.022 # specific maximum additional mortality induced by cold temperature (1/d) + xdc: -0.7 # e-folding temperature factor of cold mortality response (1/degree_C) + sr: 0.0027 # specific rest respiration at reference temperature (1/d) + pur: 0.4 # fraction of assimilated food that is respired (-) + nfood: 6 # number of food sources, default = 0 + food1ispel: true # food source 1 is pelagic, default = false + food2ispel: true # food source 2 is pelagic, default = false + food3ispel: true # food source 3 is pelagic, default = false + food4ispel: true # food source 4 is pelagic, default = false + food5_ll: true # availability of food source 5 is limited by aerobic layer height, default = false + pufood1: 1.0 # preference for food source 1 (-) + pufood2: 1.0 # preference for food source 2 (-) + pufood3: 1.0 # preference for food source 3 (-) + pufood4: 1.0 # preference for food source 4 (-) + pufood5: 1.0 # preference for food source 5 (-) + pufood6: 0.1 # preference for food source 6 (-) + food4ispom: true # food source 4 is detritus, default = false + food6ispom: true # food source 6 is detritus, default = false + dwat: 1.0 # water layer accessible for pelagic food uptake (m), default = 1.0 + dQ6: 0.0025 # depth of available sediment layer (m), default = 0.0 + initialization: + c: 2000.0 # carbon (mg C/m^2) + coupling: + food1: P1 + food2: P2 + food3: P3 + food4: R6 + food5: H1 + food6: Y3_Q6 + Q: Y3_Q6 + Dm: ben_col/D1m # depth of limiting layer for uptake (m) + O2o: O2/o # pelagic oxygen (mmol O_2/m^3) + G3c: G3/per_layer/c1 # carbon dioxide (mmol C/m^2) + G2o: G2/per_layer/o1 # oxygen (mmol O_2/m^2) + K1p: K1/per_layer/p1 # benthic phosphate in aerobic layer (mmol P/m^2) + K4n: K4/per_layer/n1 # benthic ammonium in aerobic layer (mmol N/m^2) + K1p2: K1/per_layer/p2 # benthic phosphate in anaerobic layer (mmol P/m^2) + K4n2: K4/per_layer/n2 # benthic ammonium in anaerobic layer (mmol N/m^2) + benTA: zero_hz # benthic alkalinity in aerobic layer (mEq/m^2) + benTA2: zero_hz # benthic alkalinity in anaerobic layer (mEq/m^2) + Y3_Q6: + long_name: benthic suspension feeder POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + minimum_depth: 0.0 # minimum depth (m), default = 0.0 + maximum_depth: 0.0025 # maximum depth (m), default = 0.0 + coupling: + Q: Q6 + Y4: + long_name: benthic meiofauna + model: ersem/benthic_fauna + parameters: + qnc: 0.0119 # nitrogen to carbon ratio (mmol N/mg C) + qpc: 0.000792 # phosphorus to carbon ratio (mmol P/mg C) + c0: 0.001 # background concentration (mg C/m^2), default = 0.0 + q10: 2.0 # Q_10 temperature coefficient (-) + rlO2: 0.0 # minimum pelagic oxygen concentration (mmol O2/m^3) + hO2: 0.0 # Michaelis-Menten constant for oxygen limitation (mmol O2/m^3) + xcl: 25000.0 # abundance above which crowding reduces food uptake (mg C/m^2) + xcs: 3000.0 # Michaelis-Menten constant for the impact of crowding (mg C/m^2) + xch: 5000.0 # abundance determining asymptotic threshold of crowding limitation (-> xch/(Yc+xch) for Yc-> inf) (mg C/m^2) + su: 0.4 # specific maximum uptake at reference temperature (1/d) + lu: 50.0 # Michaelis-Menten constant for food preference as function of food concentration (mg C/m^2) + hu: 1000.0 # Michaelis-Menten constant for gross carbon uptake (mg C/m^2) + pue: 0.25 # fraction of carbon in consumed live food that goes to faeces (-) + pueQ: 0.4 # fraction of carbon in consumed detritus that goes to faeces (-) + pudil: 0.8 # relative nutrient content of faeces (-) + sd: 0.01 # specific mortality at reference temperature (1/d) + sdmO2: 1.0 # specific maximum additional mortality due to oxygen stress (1/d) + sdc: 0.02 # specific maximum additional mortality induced by cold temperature (1/d) + xdc: -0.7 # e-folding temperature factor of cold mortality response (1/degree_C) + sr: 0.01 # specific rest respiration at reference temperature (1/d) + pur: 0.45 # fraction of assimilated food that is respired (-) + nfood: 4 # number of food sources, default = 0 + pufood1: 1.0 # preference for food source 1 (-) + pufood2: 1.0 # preference for food source 2 (-) + pufood3: 1.0 # preference for food source 3 (-) + pufood4: 0.3 # preference for food source 4 (-) + food4ispom: true # food source 4 is detritus, default = false + pirr: 0.2 # relative contribution to bioirrigation (-), default = 0.0 + initialization: + c: 200.0 # carbon (mg C/m^2) + coupling: + food1: H1 + food2: H2 + food3: Y4 + food4: Y4_Q6 + Q: Y4_Q6 + Dm: ben_col/D1m # depth of limiting layer for uptake (m) + O2o: O2/o # pelagic oxygen (mmol O_2/m^3) + G3c: G3/per_layer/c1 # carbon dioxide (mmol C/m^2) + G2o: G2/per_layer/o1 # oxygen (mmol O_2/m^2) + K1p: K1/per_layer/p1 # benthic phosphate in aerobic layer (mmol P/m^2) + K4n: K4/per_layer/n1 # benthic ammonium in aerobic layer (mmol N/m^2) + K1p2: K1/per_layer/p2 # benthic phosphate in anaerobic layer (mmol P/m^2) + K4n2: K4/per_layer/n2 # benthic ammonium in anaerobic layer (mmol N/m^2) + benTA: zero_hz # benthic alkalinity in aerobic layer (mEq/m^2) + benTA2: zero_hz # benthic alkalinity in anaerobic layer (mEq/m^2) + Y4_Q6: + long_name: benthic meiofauna POM + model: ersem/benthic_column_particulate_matter_layer + parameters: + composition: cnps # elemental composition + minimum_depth: 0.0 # minimum depth (m), default = 0.0 + maximum_depth: 0.03 # maximum depth (m), default = 0.0 + coupling: + Q: Q6 + erosion: + model: ersem/benthic_erosion