From 45eef14649be71e480ae517c7564ef684eef6156 Mon Sep 17 00:00:00 2001 From: Giovanni Galli Date: Fri, 5 Jun 2026 17:51:10 +0200 Subject: [PATCH 01/15] Phyto.F90 - added p_qlcmin, minimum Chl / C ratio --- Phyto.F90 | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/Phyto.F90 b/Phyto.F90 index b84ee87..dd139d8 100755 --- a/Phyto.F90 +++ b/Phyto.F90 @@ -149,7 +149,7 @@ module bfm_Phyto real(rk) :: p_chPs, p_Contois, p_qus, p_qslc ,p_qscPPY real(rk) :: p_esNI,p_res real(rk) :: p_caco3r - real(rk) :: p_sdchl, p_alpha_chl, p_quantum_yield, p_qlcPPY, p_epsChla, p_tochl_relt,p_EpEk_or + real(rk) :: p_sdchl, p_alpha_chl, p_quantum_yield, p_qlcPPY, p_qlcmin, p_epsChla, p_tochl_relt,p_EpEk_or real(rk) :: p_iswLtyp, p_chELiPPY, p_clELiPPY, p_ruELiPPY,p_addepth real(rk) :: p_rPIm real(rk) :: p_fX1p, p_fX2p @@ -267,6 +267,7 @@ subroutine initialize(self,configunit) call self%get_parameter(self%p_quantum_yield, 'p_quantum_yield','mgC/uE', 'Photochemical efficiency') call self%get_parameter(self%p_Esource, 'p_Esource', '1-6', 'source of light for PP') call self%get_parameter(self%p_qlcPPY, 'p_qlcPPY', 'mgChla/mgC','reference quotum Chla:C') + call self%get_parameter(self%p_qlcmin, 'p_qlcmin', 'mgChla/mgC','minimum quotum Chla:C') call self%get_parameter(self%p_epsChla, 'p_epsChla', 'm2/mgChla', 'Chla-specific extinction coefficient') call self%get_parameter(self%p_tochl_relt, 'p_tochl_relt', '1/d', 'Relaxation rate towards maximum Chla:C') call self%get_parameter(self%p_EpEk_or, 'p_EpEk_or', '-', 'Optimal value of E_PAR/E_K') @@ -1148,9 +1149,10 @@ subroutine do(self,_ARGUMENTS_DO_) photochem*( phytol+ p_small)* parEIR)) rate_Chl = rho_Chl*(sum - seo - sea - sra) * phytoc - sdo*phytol case (2) ! OPATM-BFM - rho_Chl = self%p_qlcPPY * sum/( photochem* qlcPPY * parEIR * et + p_small) - rate_Chl = iN* rho_Chl* run- max( self%p_sdchl * ( ONE - iN), sdo)* & - phytol+ min( ZERO, sum- slc+ sdo)* max( ZERO, phytol- self%p_qlcPPY * phytoc) + rho_Chl = self%p_qlcmin + ((self%p_qlcPPY - self%p_qlcmin) * sunPPY / & + (photochem * qlcPPY * parEIR * et + p_small)) + rate_Chl = iN * rho_Chl * run - max(self%p_sdchl * (ONE - iN), sdo) * & + phytol + min(ZERO, sum - slc + sdo) * max(ZERO, phytol - self%p_qlcPPY * phytoc) case (3) ! UNIBO rho_Chl = self%p_qlcPPY*min(ONE, & (sum-seo-sea-sra) *phytoc / & From f6b1409b76807b721db3ee905d806ae233e37b0c Mon Sep 17 00:00:00 2001 From: Giovanni Galli Date: Mon, 8 Jun 2026 11:23:18 +0200 Subject: [PATCH 02/15] added p_qo2cr and p_qo2cf coefficients, O2consumed per carbon respired / fixed. Values hard-coded in shared.F90 --- MesoZoo.F90 | 4 ++-- MicroZoo.F90 | 4 ++-- PelBac.F90 | 4 ++-- Phyto.F90 | 8 ++++---- shared.F90 | 2 ++ 5 files changed, 12 insertions(+), 10 deletions(-) diff --git a/MesoZoo.F90 b/MesoZoo.F90 index 6bf76be..83bd198 100644 --- a/MesoZoo.F90 +++ b/MesoZoo.F90 @@ -665,8 +665,8 @@ subroutine do(self,_ARGUMENTS_DO_) !-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- prI = ONE - self%p_puI - self%p_peI rrc = prI * rut_c + self%p_srs*et*zooc -! call flux_vector(iiPel, ppO2o, ppO2o, -rrc/MW_C) - _SET_ODE_(self%id_O2o,-(rrc/MW_C)) +! call flux_vector(iiPel, ppO2o, ppO2o, -rrc/MW_C*p_qo2cr) + _SET_ODE_(self%id_O2o,-(rrc/MW_C*p_qo2cr)) ! call quota_flux(iiPel, ppzooc, ppzooc, ppO3c, rrc, tfluxC) _SET_ODE_(self%id_c,-rrc) _SET_ODE_(self%id_O3c,rrc) diff --git a/MicroZoo.F90 b/MicroZoo.F90 index 9482091..e2b47be 100644 --- a/MicroZoo.F90 +++ b/MicroZoo.F90 @@ -571,8 +571,8 @@ subroutine do(self,_ARGUMENTS_DO_) ! call quota_flux(iiPel, ppzooc, ppzooc, ppO3c, rrtc, tfluxC) _SET_ODE_(self%id_c, -rrtc) _SET_ODE_(self%id_O3c,rrtc) - ! call flux_vector(iiPel, ppO2o, ppO2o, -rrtc/MW_C) - _SET_ODE_(self%id_O2o,-(rrtc/MW_C)) + ! call flux_vector(iiPel, ppO2o, ppO2o, -rrtc/MW_C*p_qo2cr) + _SET_ODE_(self%id_O2o,-(rrtc/MW_C*p_qo2cr)) _SET_DIAGNOSTIC_(self%id_rrsc,rrsc) _SET_DIAGNOSTIC_(self%id_rrac,rrac) diff --git a/PelBac.F90 b/PelBac.F90 index 2f9ba48..e685029 100644 --- a/PelBac.F90 +++ b/PelBac.F90 @@ -638,8 +638,8 @@ subroutine do(self,_ARGUMENTS_DO_) !SEAMLESS call quota_flux( iiPel, ppbacc, ppbacc, ppO3c, rrc, tfluxC) _SET_ODE_(self%id_O3c,rrc) _SET_ODE_(self%id_c,-rrc) -!SEAMLESS call flux_vector( iiPel, ppO2o, ppO2o, -eO2*rrc/MW_C ) - _SET_ODE_(self%id_O2o,-eO2*rrc/MW_C ) +!SEAMLESS call flux_vector( iiPel, ppO2o, ppO2o, -eO2*rrc/MW_C*p_qo2cr ) + _SET_ODE_(self%id_O2o,-eO2*rrc/MW_C*p_qo2cr ) flN6rPBA = (ONE- eO2)*rrc/ MW_C* self%p_qro !SEAMLESS call flux_vector( iiPel, ppN6r, ppN6r, flN6rPBA ) diff --git a/Phyto.F90 b/Phyto.F90 index dd139d8..680ed1a 100755 --- a/Phyto.F90 +++ b/Phyto.F90 @@ -845,10 +845,10 @@ subroutine do(self,_ARGUMENTS_DO_) !SEAMLESS call quota_flux( iiPel, ppphytoc, ppphytoc,ppO3c, rrc, tfluxC ) _SET_ODE_(self%id_c,-rrc) _SET_ODE_(self%id_O3c,rrc) -!SEAMLESS call flux_vector( iiPel, ppO2o,ppO2o,-( rrc/ MW_C) ) - _SET_ODE_(self%id_O2o,-(rrc/MW_C)) -!SEAMLESS call flux_vector( iiPel, ppO2o,ppO2o, rugc/ MW_C ) - _SET_ODE_(self%id_O2o,rugc/MW_C) +!SEAMLESS call flux_vector( iiPel, ppO2o,ppO2o,-( rrc/ MW_C * p_qo2cr) ) + _SET_ODE_(self%id_O2o,-(rrc/MW_C*p_qo2cr)) +!SEAMLESS call flux_vector( iiPel, ppO2o,ppO2o, rugc/ MW_C * p_qo2cf ) + _SET_ODE_(self%id_O2o,rugc/MW_C*p_qo2cf) !SEAMLESS !-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- diff --git a/shared.F90 b/shared.F90 index 907a8d5..40dcfae 100755 --- a/shared.F90 +++ b/shared.F90 @@ -14,6 +14,8 @@ module ogs_bfm_shared real(rk),parameter :: ZERO = 0._rk real(rk),parameter :: BASETEMP = 10._rk real(rk),parameter :: p_small = 1.0E-20_rk + real(rk),parameter :: p_qo2cr = 1.0_rk ! Oxygen consumed per unit of carbon respired [mol_O2/mol_C] + real(rk),parameter :: p_qo2cf = 1.0_rk ! Oxygen consumed per unit of carbon fixed [mol_O2/mol_C] real(rk),parameter :: qnRPIcX = 1.26E-02_rk real(rk),parameter :: qpRPIcX = 7.86E-04_rk real(rk),parameter :: qsRPIcX = 15._rk/106._rk/CMass From bec8fe36bc7f522fb4659de97d2ae6db2e1db847 Mon Sep 17 00:00:00 2001 From: Giovanni Galli Date: Tue, 9 Jun 2026 16:35:23 +0200 Subject: [PATCH 03/15] Phyto.F90 - added partition of nutrient stress excretion / respiration with p_pu_rn split parameter --- Phyto.F90 | 41 ++++++++++++++++++++--------------------- 1 file changed, 20 insertions(+), 21 deletions(-) diff --git a/Phyto.F90 b/Phyto.F90 index 680ed1a..180fac2 100755 --- a/Phyto.F90 +++ b/Phyto.F90 @@ -108,7 +108,7 @@ module bfm_Phyto type (type_diagnostic_variable_id) :: id_rugc ! gross primary production type (type_diagnostic_variable_id) :: id_flPIR2c ! release to semi-labile transparent DOC type (type_diagnostic_variable_id) :: id_flPIR2c_act ! activity release to semi-labile DOC - type (type_diagnostic_variable_id) :: id_flPIR2c_tot ! total release to semi-labile DOC + type (type_diagnostic_variable_id) :: id_flPIO3c ! extra respiration under nutrient stress type (type_diagnostic_variable_id) :: id_f2cdom ! fraction to CDOM type (type_diagnostic_variable_id) :: id_run ! net primary production type (type_diagnostic_variable_id) :: id_sadap ! adaptation @@ -145,7 +145,8 @@ module bfm_Phyto ! Parameters (described in subroutine initialize, below) real(rk) :: p_q10,p_temp,p_sum,p_srs,p_sdmo,p_thdo,p_seo,p_sheo,p_pu_ea,p_pu_ra - real(rk) :: p_qun,p_lN4, p_qnlc, p_qncPPY, p_xqn, p_qup, p_qplc,p_qpcPPY, p_xqp + real(rk) :: p_qun,p_lN4, p_qnlc, p_qncPPY, p_xqn, p_qup, p_qplc, p_qpcPPY, p_xqp + real(rk) :: p_pu_rn real(rk) :: p_chPs, p_Contois, p_qus, p_qslc ,p_qscPPY real(rk) :: p_esNI,p_res real(rk) :: p_caco3r @@ -289,6 +290,8 @@ subroutine initialize(self,configunit) call self%get_parameter(self%p_fR6, 'p_fR6', '-', 'fraction of lysis to R6 (small POC)', default=0.8_rk) ! --------- Optical type ------------ call self%get_parameter(self%p_OT, 'p_OT', '1-9', 'optical type label for absorption/scattering spectra') +! --------- nutrient stress respiration / excretion partition ------ + call self%get_parameter(self%p_pu_rn, 'p_pu_rn', '0.0', 'nutrient stress respiration fraction') ! Register state variables (handled by type_bfm_pelagic_base) @@ -415,9 +418,9 @@ subroutine initialize(self,configunit) call self%register_diagnostic_variable(self%id_rr1c, 'rr1c','mgC/m3/d','lysis fraction to labile DOC',output=output_none) call self%register_diagnostic_variable(self%id_rrc, 'rrc', 'mgC/m3/d','total respiration',output=output_none) call self%register_diagnostic_variable(self%id_rugc, 'rugc','mgC/m3/d','Gross primary production') - call self%register_diagnostic_variable(self%id_flPIR2c_tot,'flPIR2c_tot', 'mgC/m3/d', 'total flux to semilabile DOC',output=output_none) call self%register_diagnostic_variable(self%id_flPIR2c_act,'flPIR2c_act', 'mgC/m3/d', 'activity flux to semilabile DOC',output=output_none) call self%register_diagnostic_variable(self%id_flPIR2c, 'flPIR2c', 'mgC/m3/d', 'flux to transparent semilabile DOC',output=output_none) + call self%register_diagnostic_variable(self%id_flPIO3c, 'flPIO3c', 'mgC/m3/d', 'extra respiration under nutrient stress',output=output_none) call self%register_diagnostic_variable(self%id_f2cdom, 'f2cdom', '-', 'fraction to semilabile CDOM',output=output_none) call self%register_diagnostic_variable(self%id_run, 'run', 'mgC/m3/d','net primary production') call self%register_diagnostic_variable(self%id_sadap, 'sadap', 'mgC/m3/d',' adaptation',output=output_none) @@ -515,7 +518,7 @@ subroutine do(self,_ARGUMENTS_DO_) real(rk) :: sdo, sea, seo real(rk) :: pe_R6, rr1c, rr6c, rr8c real(rk) :: sra, srs, srt, rrc - real(rk) :: rugc, slc, flPIR2c, flPIR2c_tot, f2cdom + real(rk) :: rugc, slc, flPIR2c, flPIO3c, f2cdom real(rk) :: run, sadap real(rk) :: cqun3, rumn3, rumn4, rumn, rump real(rk) :: netgrowth, sunPPY @@ -882,6 +885,7 @@ subroutine do(self,_ARGUMENTS_DO_) _SET_DIAGNOSTIC_(self%id_rumn, rumn) _SET_DIAGNOSTIC_(self%id_rump, rump) + flPIO3c = ZERO if (self%p_netgrowth) then !-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- ! Check which fraction of fixed C can be used for new biomass @@ -894,31 +898,26 @@ subroutine do(self,_ARGUMENTS_DO_) 0.05_rk * rugc*( qpcPPY - self%p_qplc)))/ self%p_qplc) !-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- - ! Excrete C that cannot be used for growth as carbo-hydrates: + ! Excrete / respire C that cannot be used for growth as carbo-hydrates: ! Correct the net C uptake !-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- netgrowth = max( netgrowth, ZERO) - flPIR2c_tot = flPIR2c+ run- netgrowth - flPIR2c = ((1.00D0-f2cdom)*flPIR2c) + run - netgrowth + flPIR2c = ((1.00D0 - f2cdom) * flPIR2c) + (1.00D0 - self%p_pu_rn) * (run - netgrowth) + flPIO3c = self%p_pu_rn * (run - netgrowth) run = netgrowth end if - _SET_DIAGNOSTIC_(self%id_netgrowth, netgrowth) - -!!SEAMLESS call quota_flux( iiPel, ppphytoc, ppphytoc,ppR2c, 0.98D0 * flPIR2c, tfluxC ) ! flux to non CDOM -! _SET_ODE_(self%id_c, -(1.00D0-f2cdom) * flPIR2c_tot) -! _SET_ODE_(self%id_R2c,(1.00D0-f2cdom) * flPIR2c_tot) -!!SEAMLESS call quota_flux( iiPel, ppphytoc, ppphytoc,ppR2l, 0.02D0 * flPIR2c, tfluxC ) ! flux to CDOM -! _SET_ODE_(self%id_c, -f2cdom * flPIR2c_tot) -! _SET_ODE_(self%id_X2c,f2cdom * flPIR2c_tot) + _SET_DIAGNOSTIC_(self%id_flPIR2c, flPIR2c) + _SET_DIAGNOSTIC_(self%id_flPIO3c, flPIO3c) + _SET_DIAGNOSTIC_(self%id_netgrowth, netgrowth) ! CEA 98% of activity excretion + nutrient estress excretion produce only R2c - _SET_ODE_(self%id_c,-flPIR2c) - _SET_ODE_(self%id_R2c,flPIR2c) - - _SET_DIAGNOSTIC_(self%id_flPIR2c, flPIR2c) - _SET_DIAGNOSTIC_(self%id_flPIR2c_tot, flPIR2c_tot) - + _SET_ODE_(self%id_c, -flPIO3c) + _SET_ODE_(self%id_O3c, flPIO3c) + _SET_ODE_(self%id_O2o, flPIO3c * (self%p_qo2cr / MW_C)) + _SET_ODE_(self%id_c, -flPIR2c) + _SET_ODE_(self%id_R2c, flPIR2c) + !-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- ! Specific net growth rate (d-1) !-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From 0d68d692aa047ad7ac794910e8822d46383189f8 Mon Sep 17 00:00:00 2001 From: Giovanni Galli Date: Tue, 9 Jun 2026 17:03:53 +0200 Subject: [PATCH 04/15] typo in Phyto.F90 --- Phyto.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Phyto.F90 b/Phyto.F90 index 180fac2..f49cedf 100755 --- a/Phyto.F90 +++ b/Phyto.F90 @@ -914,7 +914,7 @@ subroutine do(self,_ARGUMENTS_DO_) ! CEA 98% of activity excretion + nutrient estress excretion produce only R2c _SET_ODE_(self%id_c, -flPIO3c) _SET_ODE_(self%id_O3c, flPIO3c) - _SET_ODE_(self%id_O2o, flPIO3c * (self%p_qo2cr / MW_C)) + _SET_ODE_(self%id_O2o, flPIO3c * (p_qo2cr / MW_C)) _SET_ODE_(self%id_c, -flPIR2c) _SET_ODE_(self%id_R2c, flPIR2c) From dcbbeb464d554b52df291ca1311b4c147c1fdb16 Mon Sep 17 00:00:00 2001 From: Giovanni Galli Date: Tue, 9 Jun 2026 17:09:31 +0200 Subject: [PATCH 05/15] fabm_multispectral_2xDetritus.yaml - with new parameters, p_pu_rn, p_qlcmin --- fabm_multispectral_2xDetritus.yaml | 40 ++++++++++++++++++------------ 1 file changed, 24 insertions(+), 16 deletions(-) diff --git a/fabm_multispectral_2xDetritus.yaml b/fabm_multispectral_2xDetritus.yaml index 74ca01d..b440050 100755 --- a/fabm_multispectral_2xDetritus.yaml +++ b/fabm_multispectral_2xDetritus.yaml @@ -8,17 +8,17 @@ instances: p_BenDepth: 12000.0 zenith_angle: model: ogs/zenith_angle - light: - model: ogs/light - parameters: - pEPSCHL: 0.0088 # attenuation by Chlorophyll (m^2/mg Chl), default= 0.0088 - pEPSCDOM: 0.01476 # attenuation by CDOM (m^2/mg C), default= 0.0646 - EPS0r: 0.04 # background shortwave attenuation (1/m), default = 0.04 - pEIR_eow: 0.4 # photosynthetically active fraction of shortwave radiation (-), default = 0.5 - coupling: - X1c: X1/c - X2c: X2/c - X3c: X3/c +# light: +# model: ogs/light +# parameters: +# pEPSCHL: 0.0088 # attenuation by Chlorophyll (m^2/mg Chl), default= 0.0088 +# pEPSCDOM: 0.01476 # attenuation by CDOM (m^2/mg C), default= 0.0646 +# EPS0r: 0.04 # background shortwave attenuation (1/m), default = 0.04 +# pEIR_eow: 0.4 # photosynthetically active fraction of shortwave radiation (-), default = 0.5 +# coupling: +# X1c: X1/c +# X2c: X2/c +# X3c: X3/c light_atm: model: spectral/atmosphere parameters: @@ -243,7 +243,7 @@ instances: model: ogs/bfm_pelagic_base parameters: composition: cpns # elemental composition - rm: 7.00 # Sinking Velocity + rm: 7.0 # Sinking Velocity initialization: c: 1.0 # POC (mg C /m^3) n: 1.260E-002 # PON (mmol N /m^3) @@ -298,6 +298,7 @@ instances: p_sheo: 0.0 # [mgC/3] Half saturation constant for extra lysis p_pu_ea: 0.10 # [-] Excreted fraction of primary production p_pu_ra: 0.1 # [-] Activity respiration fraction + p_pu_rn: 0.18 # [-] nutrient stress respiration fraction p_switchDOC: 2 # [1-3] Switch for the type of DOC excretion # This choice must be consistent with bacteria # 1. All DOC is released as R1c (Vichi et al., 2007) @@ -350,6 +351,7 @@ instances: p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono p_OT: 1 # [1-9] type of absorption/scattering spectra p_qlcPPY: 0.026 # [mgChla/mgC] Reference quotum Chla:C + p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K @@ -408,6 +410,7 @@ instances: p_sheo: 0.0 # [mgC/3] Half saturation constant for extra lysis p_pu_ea: 0.15 # [-] Excreted fraction of primary production p_pu_ra: 0.1 # [-] Activity respiration fraction + p_pu_rn: 0.18 # [-] nutrient stress respiration fraction p_switchDOC: 2 # [1-3] 2. Activity DOC is released as R2c (Vichi et al., 2004) # --------- Nutrient parameters in phytoplankton ----------------- p_netgrowth: .TRUE. # [T or F] .T. nutrient-balanced growth (Vichi et al.2004) @@ -439,7 +442,8 @@ instances: p_quantum_yield: 0.198e-3 # [mgC / uE] Photochemical efficiency p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono p_OT: 2 # [1-9] type of absorption/scattering spectra - p_qlcPPY: 0.045 # [mgChla/mgC] Reference quotum Chla:C + p_qlcPPY: 0.045 # [mgChla/mgC] Reference quotum Chla:C + p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K @@ -494,6 +498,7 @@ instances: p_sheo: 0.0 # [mgC/3] Half saturation constant for extra lysis p_pu_ea: 0.15 # [-] Excreted fraction of primary production p_pu_ra: 0.2 # [-] Activity respiration fraction + p_pu_rn: 0.18 # [-] nutrient stress respiration fraction p_switchDOC: 2 # [1-3] Switch for the type of DOC excretion # This choice must be consistent with bacteria # 1. All DOC is released as R1c (Vichi et al., 2007) @@ -510,7 +515,7 @@ instances: # 1. Threshold (Liebig-like) # 2. Combined # ---- N limitation control ---- - p_qun: 0.25 # [m3/mgC/d] Membrane affinity for N + p_qun: 0.025 # [m3/mgC/d] Membrane affinity for N p_lN4: 0.1 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C @@ -537,7 +542,8 @@ instances: p_quantum_yield: 0.990e-3 # [mgC / uE] Photochemical efficiency p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono p_OT: 3 # [1-9] type of absorption/scattering spectra - p_qlcPPY: 0.014 # [mgChla/mgC] Reference quotum Chla:C + p_qlcPPY: 0.014 # [mgChla/mgC] Reference quotum Chla:C + p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K @@ -592,6 +598,7 @@ instances: p_sheo: 100.0 # [mgC/3] Half saturation constant for extra lysis p_pu_ea: 0.20 # [-] Excreted fraction of primary production p_pu_ra: 0.1 # [-] Activity respiration fraction + p_pu_rn: 0.18 # [-] nutrient stress respiration fraction p_switchDOC: 2 # [1-3] 2. Activity DOC is released as R2c (Vichi et al., 2004) # --------- Nutrient parameters in phytoplankton ----------------- p_netgrowth: .TRUE. # [T or F] .T. nutrient-balanced growth (Vichi et al.2004) @@ -622,7 +629,8 @@ instances: p_quantum_yield: 0.257e-3 # [mgC / uE] Photochemical efficiency p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono p_OT: 4 # [1-9] type of absorption/scattering spectra - p_qlcPPY: 0.019 # [mgChla/mgC] Reference quotum Chla:C + p_qlcPPY: 0.019 # [mgChla/mgC] Reference quotum Chla:C + p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K From 1a7a466e0ed1e207a54d24f0ff8b4abee5621484 Mon Sep 17 00:00:00 2001 From: Giovanni Galli Date: Tue, 9 Jun 2026 17:43:48 +0200 Subject: [PATCH 06/15] shared.F90 - updated default (hard-coded) values of p_qo2cr (1.32) and p_qo2cf (1.36) --- shared.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/shared.F90 b/shared.F90 index 40dcfae..7f77397 100755 --- a/shared.F90 +++ b/shared.F90 @@ -14,8 +14,8 @@ module ogs_bfm_shared real(rk),parameter :: ZERO = 0._rk real(rk),parameter :: BASETEMP = 10._rk real(rk),parameter :: p_small = 1.0E-20_rk - real(rk),parameter :: p_qo2cr = 1.0_rk ! Oxygen consumed per unit of carbon respired [mol_O2/mol_C] - real(rk),parameter :: p_qo2cf = 1.0_rk ! Oxygen consumed per unit of carbon fixed [mol_O2/mol_C] + real(rk),parameter :: p_qo2cr = 1.32_rk ! Oxygen consumed per unit of carbon respired [mol_O2/mol_C] + real(rk),parameter :: p_qo2cf = 1.36_rk ! Oxygen consumed per unit of carbon fixed [mol_O2/mol_C] real(rk),parameter :: qnRPIcX = 1.26E-02_rk real(rk),parameter :: qpRPIcX = 7.86E-04_rk real(rk),parameter :: qsRPIcX = 15._rk/106._rk/CMass From 368d11c3a5c6e395a40993aafb26eff954a24548 Mon Sep 17 00:00:00 2001 From: ggalli00 <152898875+ggalli00@users.noreply.github.com> Date: Tue, 9 Jun 2026 17:54:02 +0200 Subject: [PATCH 07/15] Potential fix for pull request finding correct sign of O2 flux related to nutrient-stress respiration Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- Phyto.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Phyto.F90 b/Phyto.F90 index f49cedf..97e3e6a 100755 --- a/Phyto.F90 +++ b/Phyto.F90 @@ -914,7 +914,7 @@ subroutine do(self,_ARGUMENTS_DO_) ! CEA 98% of activity excretion + nutrient estress excretion produce only R2c _SET_ODE_(self%id_c, -flPIO3c) _SET_ODE_(self%id_O3c, flPIO3c) - _SET_ODE_(self%id_O2o, flPIO3c * (p_qo2cr / MW_C)) + _SET_ODE_(self%id_O2o, -flPIO3c * (p_qo2cr / MW_C)) _SET_ODE_(self%id_c, -flPIR2c) _SET_ODE_(self%id_R2c, flPIR2c) From bcc26ca40062d7d0c9d953cd0fd327d42d32a357 Mon Sep 17 00:00:00 2001 From: ggalli00 <152898875+ggalli00@users.noreply.github.com> Date: Tue, 9 Jun 2026 17:57:03 +0200 Subject: [PATCH 08/15] Potential fix for pull request finding initialise netgrowth (=run) outside if p_netgrowth (in case p_netgrowth=false) Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- Phyto.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Phyto.F90 b/Phyto.F90 index 97e3e6a..5d1400a 100755 --- a/Phyto.F90 +++ b/Phyto.F90 @@ -885,9 +885,9 @@ subroutine do(self,_ARGUMENTS_DO_) _SET_DIAGNOSTIC_(self%id_rumn, rumn) _SET_DIAGNOSTIC_(self%id_rump, rump) + netgrowth = run flPIO3c = ZERO if (self%p_netgrowth) then - !-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- ! Check which fraction of fixed C can be used for new biomass ! given the internal storage. ! N and P uptake are compared sequentially From 5f43d06d71ee03bbcc1abc2f7f71dffe556c85c0 Mon Sep 17 00:00:00 2001 From: ggalli00 <152898875+ggalli00@users.noreply.github.com> Date: Tue, 9 Jun 2026 17:58:37 +0200 Subject: [PATCH 09/15] Potential fix for pull request finding initialise units of p_pu_rn + default=0.0 Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- Phyto.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Phyto.F90 b/Phyto.F90 index 5d1400a..c8f36b9 100755 --- a/Phyto.F90 +++ b/Phyto.F90 @@ -291,7 +291,7 @@ subroutine initialize(self,configunit) ! --------- Optical type ------------ call self%get_parameter(self%p_OT, 'p_OT', '1-9', 'optical type label for absorption/scattering spectra') ! --------- nutrient stress respiration / excretion partition ------ - call self%get_parameter(self%p_pu_rn, 'p_pu_rn', '0.0', 'nutrient stress respiration fraction') + call self%get_parameter(self%p_pu_rn, 'p_pu_rn', '-', 'nutrient stress respiration fraction', default=0.0_rk) ! Register state variables (handled by type_bfm_pelagic_base) From 89ca9369b22857950de2208997dd671bf9744922 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 10 Jun 2026 08:03:13 +0000 Subject: [PATCH 10/15] Fix p_qun typo in multispectral 2xDetritus preset --- fabm_multispectral_2xDetritus.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fabm_multispectral_2xDetritus.yaml b/fabm_multispectral_2xDetritus.yaml index b440050..0d16f77 100755 --- a/fabm_multispectral_2xDetritus.yaml +++ b/fabm_multispectral_2xDetritus.yaml @@ -515,7 +515,7 @@ instances: # 1. Threshold (Liebig-like) # 2. Combined # ---- N limitation control ---- - p_qun: 0.025 # [m3/mgC/d] Membrane affinity for N + p_qun: 0.25 # [m3/mgC/d] Membrane affinity for N p_lN4: 0.1 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C From ee623fcf7f33e373a9d910a1482bfaa6a8f88042 Mon Sep 17 00:00:00 2001 From: Giovanni Galli Date: Wed, 10 Jun 2026 10:03:24 +0200 Subject: [PATCH 11/15] shared.F90 - typo in comment --- shared.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shared.F90 b/shared.F90 index 7f77397..bef0514 100755 --- a/shared.F90 +++ b/shared.F90 @@ -15,7 +15,7 @@ module ogs_bfm_shared real(rk),parameter :: BASETEMP = 10._rk real(rk),parameter :: p_small = 1.0E-20_rk real(rk),parameter :: p_qo2cr = 1.32_rk ! Oxygen consumed per unit of carbon respired [mol_O2/mol_C] - real(rk),parameter :: p_qo2cf = 1.36_rk ! Oxygen consumed per unit of carbon fixed [mol_O2/mol_C] + real(rk),parameter :: p_qo2cf = 1.36_rk ! Oxygen produced per unit of carbon fixed [mol_O2/mol_C] real(rk),parameter :: qnRPIcX = 1.26E-02_rk real(rk),parameter :: qpRPIcX = 7.86E-04_rk real(rk),parameter :: qsRPIcX = 15._rk/106._rk/CMass From 38316958ba6167ecb2ee707729fec7c18e3c2947 Mon Sep 17 00:00:00 2001 From: Giovanni Galli Date: Thu, 11 Jun 2026 10:58:38 +0200 Subject: [PATCH 12/15] Phyto.F90 - deleted unused ERSEM-II light parameters --- Phyto.F90 | 7 ------- fabm_multispectral_2xDetritus.yaml | 24 ------------------------ 2 files changed, 31 deletions(-) diff --git a/Phyto.F90 b/Phyto.F90 index c8f36b9..80023f7 100755 --- a/Phyto.F90 +++ b/Phyto.F90 @@ -151,7 +151,6 @@ module bfm_Phyto real(rk) :: p_esNI,p_res real(rk) :: p_caco3r real(rk) :: p_sdchl, p_alpha_chl, p_quantum_yield, p_qlcPPY, p_qlcmin, p_epsChla, p_tochl_relt,p_EpEk_or - real(rk) :: p_iswLtyp, p_chELiPPY, p_clELiPPY, p_ruELiPPY,p_addepth real(rk) :: p_rPIm real(rk) :: p_fX1p, p_fX2p real(rk) :: p_fR6 @@ -272,12 +271,6 @@ subroutine initialize(self,configunit) call self%get_parameter(self%p_epsChla, 'p_epsChla', 'm2/mgChla', 'Chla-specific extinction coefficient') call self%get_parameter(self%p_tochl_relt, 'p_tochl_relt', '1/d', 'Relaxation rate towards maximum Chla:C') call self%get_parameter(self%p_EpEk_or, 'p_EpEk_or', '-', 'Optimal value of E_PAR/E_K') -! --------- Light parameters ERSEM-II ----------- - call self%get_parameter(self%p_iswLtyp, 'p_iswLtyp', '0-6', 'Shape of the productivity function') - call self%get_parameter(self%p_chELiPPY, 'p_chELiPPY', 'W/m2', 'Maximum Iopt') - call self%get_parameter(self%p_clELiPPY, 'p_clELiPPY', 'W/m2', 'Minimum Iopt') - call self%get_parameter(self%p_ruELiPPY, 'p_ruELiPPY', '1/d', 'Maximum daily shift in Iopt (1/d)') - call self%get_parameter(self%p_addepth, 'p_addepth', 'm', 'Adaptation depth. Meaningless with high-res models') ! --------- Sinking parameters ----------- call self%get_parameter(self%p_rPIm, 'p_rPIm', 'm/d', 'Phytoplankton background sinking rate') ! --------- Calcite parameters only for P2 ------------ diff --git a/fabm_multispectral_2xDetritus.yaml b/fabm_multispectral_2xDetritus.yaml index 0d16f77..b21b7d4 100755 --- a/fabm_multispectral_2xDetritus.yaml +++ b/fabm_multispectral_2xDetritus.yaml @@ -355,12 +355,6 @@ instances: p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K -# --------- Light parameters ERSEM-II ----------- - p_iswLtyp: 5 # [0-6] Shape of the productivity function - p_chELiPPY: 50.0 # [W/m2] Maximum Iopt - p_clELiPPY: 100.0 # [W/m2] Minimum Iopt - p_ruELiPPY: 8.0 # [1/d] Maximum daily shift in Iopt (1/d) - p_addepth: 0.2 # [m] Adaptation depth. Meaningless with high-res models # --------- Sinking parameters ----------- p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate initialization: @@ -447,12 +441,6 @@ instances: p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K -# --------- Light parameters ERSEM-II ----------- - p_iswLtyp: 5 # [0-6] Shape of the productivity function - p_chELiPPY: 50.0 # [W/m2] Maximum Iopt - p_clELiPPY: 100.0 # [W/m2] Minimum Iopt - p_ruELiPPY: 10.0 # [1/d] Maximum daily shift in Iopt (1/d) - p_addepth: 0.25 # [m] Adaptation depth. Meaningless with high-res models # --------- Sinking parameters ----------- p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate initialization: @@ -547,12 +535,6 @@ instances: p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K -# --------- Light parameters ERSEM-II ----------- - p_iswLtyp: 5 # [0-6] Shape of the productivity function - p_chELiPPY: 50.0 # [W/m2] Maximum Iopt - p_clELiPPY: 100.0 # [W/m2] Minimum Iopt - p_ruELiPPY: 10.0 # [1/d] Maximum daily shift in Iopt (1/d) - p_addepth: 0.25 # [m] Adaptation depth. Meaningless with high-res models # --------- Sinking parameters ----------- p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate initialization: @@ -634,12 +616,6 @@ instances: p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K -# --------- Light parameters ERSEM-II ----------- - p_iswLtyp: 5 # [0-6] Shape of the productivity function - p_chELiPPY: 50.0 # [W/m2] Maximum Iopt - p_clELiPPY: 100.0 # [W/m2] Minimum Iopt - p_ruELiPPY: 10.0 # [1/d] Maximum daily shift in Iopt (1/d) - p_addepth: 0.25 # [m] Adaptation depth. Meaningless with high-res models # --------- Sinking parameters ----------- p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate initialization: From 322634107268a676d1a4200da155cd001af0090b Mon Sep 17 00:00:00 2001 From: Giovanni Galli Date: Thu, 11 Jun 2026 11:08:16 +0200 Subject: [PATCH 13/15] fabm_V13C.yaml - new parameters, synced with EIS_2026_11 V13C run --- fabm_V13C.yaml | 1108 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 1108 insertions(+) create mode 100755 fabm_V13C.yaml diff --git a/fabm_V13C.yaml b/fabm_V13C.yaml new file mode 100755 index 0000000..9198e42 --- /dev/null +++ b/fabm_V13C.yaml @@ -0,0 +1,1108 @@ +check_conservation: false +require_initialization: true +log: true +instances: + Benthic_layer: + model: ogs/BenthicLayer + parameters: + p_BenDepth: 12000.0 + zenith_angle: + model: ogs/zenith_angle +# light: +# model: ogs/light +# parameters: +# pEPSCHL: 0.0088 # attenuation by Chlorophyll (m^2/mg Chl), default= 0.0088 +# pEPSCDOM: 0.01476 # attenuation by CDOM (m^2/mg C), default= 0.0646 +# EPS0r: 0.04 # background shortwave attenuation (1/m), default = 0.04 +# pEIR_eow: 0.4 # photosynthetically active fraction of shortwave radiation (-), default = 0.5 +# coupling: +# X1c: X1/c +# X2c: X2/c +# X3c: X3/c + light_atm: + model: spectral/atmosphere + parameters: + lambda_method: 1 + compute_mean_wind: true + spectral_output: 1 + relhum: + model: spectral/relhum + ozone: + model: spectral/ozone + lightspectral: + model: ogs/light_spectral_OASIM + parameters: + nlt: 33 # number of wavelenghts considered + npft: 4 # number of PFT considered + SdomX1: 0.0175 # spectral slope acdom of X1c [nm-1] + X1coeff: 0.015 # acdom coeff of X1c at lambda_aCDOM [m2/mgC] + SdomX2: 0.0162 # spectral slope acdom of X2c [nm-1] + X2coeff: 0.015 # acdom coeff of X2c at lambda_aCDOM [m2/mgC] + SdomX3: 0.0180 # spectral slope acdom of X3c [nm-1] + X3coeff: 0.015 # acdom coeff of X3c at lambda_aCDOM [m2/mgC] + Xmincoeff: 0.00 # minimum aCDOM [m-1] at 450nm + lambda_aCDOM: 450 # lambda at which reference acdom is given [nm] + compute_acdom: .FALSE. # logical [T=compute coeffs, F=use file] + Sapar: 0.013 # spectral slope anap [nm-1] + lambda_aPart: 440 # lambda at which reference anap is given [nm] + aparcoeff: 0.00058 # anap coeff at lambda_aPart [m2/mgC] + Sbpar: 0.5 # exponent bnap [-] + lambda_bPart: 550 # lambda at which reference bnap is given [nm] + bparcoeff: 0.0120 # bnap coeff at lambda_bPart [m2/mgC] + bb_to_b: 0.005 # back to total scatter POC [-] + compute_anap: .FALSE. # logical [T=comptute coeffs, F=use file] + p_epsP1: 0.0152 # mean absorption coefficient from 400-700nm for P1 [m2 mgChl-1] + p_epsP2: 0.0293 # mean absorption coefficient from 400-700nm for P2 [m2 mgChl-1] + p_epsP3: 0.0443 # mean absorption coefficient from 400-700nm for P3 [m2 mgChl-1] + p_epsP4: 0.0178 # mean absorption coefficient from 400-700nm for P4 [m2 mgChl-1] + compute_aph: .FALSE. # logical flag to scale aph [T=use file scaled to p_epsPn or F=use file unscaled] + p_bpsP1: 0.0140 # mean scattering coefficient from 400-700nm for P1 [m2 mgC-1] + p_bpsP2: 0.0077 # mean scattering coefficient from 400-700nm for P2 [m2 mgC-1] + p_bpsP3: 0.0101 # mean scattering coefficient from 400-700nm for P3 [m2 mgC-1] + p_bpsP4: 0.0112 # mean scattering coefficient from 400-700nm for P4 [m2 mgC-1] + compute_bph: .FALSE. # logical flag to scale bph [T=use file scaled to p_bpsPn or F=use file unscaled] + p_bbrP1: 0.0020 # non-spectral backscattering to total scattering ratio for P1 [-] + p_bbrP2: 0.0071 # non-spectral backscattering to total scattering ratio for P2 [-] + p_bbrP3: 0.0039 # non-spectral backscattering to total scattering ratio for P3 [-] + p_bbrP4: 0.0030 # non-spectral backscattering to total scattering ratio for P4 [-] + compute_bbc: .FALSE. # logical flag to compute bbc or read it from file [T=compute bc*bbr or F=use file] + p_useSPM: .FALSE. # if true requires input data specification in gotm.yaml + p_spmc1: 0.016 # basal absorption for minimal absorption at long wavelengths [m2 g-1] + p_spmc2: 0.054 # specific absorption at the reference wavelength [m2 g-1] + p_spmS: 0.012 # slope for exponential decline of aSPM with wavelength [nm-1] + lambda_aSPM: 440 # wavelength where reference aSPM (c2) is given + p_spmb: 0.7 # specific scattering at 555nm [m2 g-1] + p_spmbb: 0.008 # specific backscattering at 555nm [m2 g-1] + coupling: + X1c : X1/c + X2c : X2/c + X3c : X3/c + R6c : R6/c + R8c : R8/c + direct_band1 : light_atm/dir_sf_band1 + diffuse_band1 : light_atm/dif_sf_band1 + direct_band2 : light_atm/dir_sf_band2 + diffuse_band2 : light_atm/dif_sf_band2 + direct_band3 : light_atm/dir_sf_band3 + diffuse_band3 : light_atm/dif_sf_band3 + direct_band4 : light_atm/dir_sf_band4 + diffuse_band4 : light_atm/dif_sf_band4 + direct_band5 : light_atm/dir_sf_band5 + diffuse_band5 : light_atm/dif_sf_band5 + direct_band6 : light_atm/dir_sf_band6 + diffuse_band6 : light_atm/dif_sf_band6 + direct_band7 : light_atm/dir_sf_band7 + diffuse_band7 : light_atm/dif_sf_band7 + direct_band8 : light_atm/dir_sf_band8 + diffuse_band8 : light_atm/dif_sf_band8 + direct_band9 : light_atm/dir_sf_band9 + diffuse_band9 : light_atm/dif_sf_band9 + direct_band10 : light_atm/dir_sf_band10 + diffuse_band10 : light_atm/dif_sf_band10 + direct_band11 : light_atm/dir_sf_band11 + diffuse_band11 : light_atm/dif_sf_band11 + direct_band12 : light_atm/dir_sf_band12 + diffuse_band12 : light_atm/dif_sf_band12 + direct_band13 : light_atm/dir_sf_band13 + diffuse_band13 : light_atm/dif_sf_band13 + direct_band14 : light_atm/dir_sf_band14 + diffuse_band14 : light_atm/dif_sf_band14 + direct_band15 : light_atm/dir_sf_band15 + diffuse_band15 : light_atm/dif_sf_band15 + direct_band16 : light_atm/dir_sf_band16 + diffuse_band16 : light_atm/dif_sf_band16 + direct_band17 : light_atm/dir_sf_band17 + diffuse_band17 : light_atm/dif_sf_band17 + direct_band18 : light_atm/dir_sf_band18 + diffuse_band18 : light_atm/dif_sf_band18 + direct_band19 : light_atm/dir_sf_band19 + diffuse_band19 : light_atm/dif_sf_band19 + direct_band20 : light_atm/dir_sf_band20 + diffuse_band20 : light_atm/dif_sf_band20 + direct_band21 : light_atm/dir_sf_band21 + diffuse_band21 : light_atm/dif_sf_band21 + direct_band22 : light_atm/dir_sf_band22 + diffuse_band22 : light_atm/dif_sf_band22 + direct_band23 : light_atm/dir_sf_band23 + diffuse_band23 : light_atm/dif_sf_band23 + direct_band24 : light_atm/dir_sf_band24 + diffuse_band24 : light_atm/dif_sf_band24 + direct_band25 : light_atm/dir_sf_band25 + diffuse_band25 : light_atm/dif_sf_band25 + direct_band26 : light_atm/dir_sf_band26 + diffuse_band26 : light_atm/dif_sf_band26 + direct_band27 : light_atm/dir_sf_band27 + diffuse_band27 : light_atm/dif_sf_band27 + direct_band28 : light_atm/dir_sf_band28 + diffuse_band28 : light_atm/dif_sf_band28 + direct_band29 : light_atm/dir_sf_band29 + diffuse_band29 : light_atm/dif_sf_band29 + direct_band30 : light_atm/dir_sf_band30 + diffuse_band30 : light_atm/dif_sf_band30 + direct_band31 : light_atm/dir_sf_band31 + diffuse_band31 : light_atm/dif_sf_band31 + direct_band32 : light_atm/dir_sf_band32 + diffuse_band32 : light_atm/dif_sf_band32 + direct_band33 : light_atm/dir_sf_band33 + diffuse_band33 : light_atm/dif_sf_band33 + costheta_r : light_atm/costheta_r + N1: + long_name: phosphate + model: ogs/bfm_pelagic_base + parameters: + composition: p # elemental composition + initialization: + p: 0.4 # phosphorus (mmol P/m^3) + N3: + long_name: nitrate + model: ogs/bfm_pelagic_base + parameters: + composition: n # elemental composition + initialization: + n: 8.0 # nitrogen (mmol N/m^3) + N4: + long_name: ammonium + model: ogs/bfm_pelagic_base + parameters: + composition: n # elemental composition + initialization: + n: 0.1 # nitrogen (mmol N/m^3) + N5: + long_name: silicate + model: ogs/bfm_pelagic_base + parameters: + composition: s # elemental composition + initialization: + s: 4.5 # silicate (mmol Si/m^3) + N6: + long_name: Reduction equivalent + model: ogs/bfm_pelagic_base + parameters: + composition: r # elemental composition + initialization: + r: 1.0 # Reduction equivalent (mmol Eq/m^3) + O3: + long_name: dissolved inorganic carbon + model: ogs/PelagicCSYS +# parameters: +# composition: c # elemental composition + initialization: + c: 28500.00 # Dissolved Inorganic Carbon (mg C /m^3) + coupling: + N1p: N1/p # phosphate (mmol P/m^3) + N5s: N5/s # silicate (mmol Si/m^3) + O3h: O3h/h + O2: + long_name: Dissolved Oxygen + model: ogs/PelOxygen +# parameters: +# composition: o # elemental composition + initialization: + o: 300.0 + O3h: + long_name: alkalinity + model: ogs/bfm_pelagic_base + parameters: + composition: h # elemental composition + initialization: + h: 2660.0 # alkalinity (mmol m3) + O4: + long_name: Nitrogen Sink + model: ogs/bfm_pelagic_base + parameters: + composition: n # elemental composition + initialization: + n: 200.0 + R1: + long_name: Dissolved Organic carbon Labile + model: ogs/bfm_pelagic_base + parameters: + composition: cnp # elemental composition + initialization: + c: 80.0 # Dissolved Organic Carbon (mg C /m^3) +# n: 1.260E-002 # Dissolved Organic Nitrogen (mmol N /m^3) +# p: 7.8620E-004 # Dissolved Organic Phosphorus (mmol P /m^3) + n: 1.008 # adjusted for c=80 instead c=1 + p: 0.062 # adjusted for c=80 instead c=1 + R2: + long_name: Dissolved Organic carbon semi-Labile + model: ogs/bfm_pelagic_base + parameters: + composition: c # elemental composition + initialization: + c: 400.0 # Dissolved Organic Carbon (mg C /m^3) + R3: + long_name: Dissolved Organic carbon semi-refractory + model: ogs/bfm_pelagic_base + parameters: + composition: c # elemental composition + initialization: + c: 480.0 # Dissolved Organic Carbon (mg C /m^3) + R6: + long_name: Small Particulate Organic carbon + model: ogs/bfm_pelagic_base + parameters: + composition: cpns # elemental composition + rm: 7.0 # Sinking Velocity + initialization: + c: 1.0 # POC (mg C /m^3) + n: 1.260E-002 # PON (mmol N /m^3) + p: 7.8620E-004 # POP (mmol P /m^3) + s: 1.260E-002 # POS (mmol S /m^3) + R8: + long_name: Large Particulate Organic carbon + model: ogs/bfm_pelagic_base + parameters: + composition: cpns # elemental composition + rm: 15.00 # Sinking Velocity + initialization: + c: 1.0 # POC (mg C /m^3) + n: 1.260E-002 # PON (mmol N /m^3) + p: 7.8620E-004 # POP (mmol P /m^3) + s: 1.260E-002 # POS (mmol S /m^3) + X1: + long_name: labile CDOM + model: ogs/bfm_pelagic_base + parameters: + composition: c # elemental composition + initialization: + c: 1.000000000000000E-000 + X2: + long_name: semi labile CDOM + model: ogs/bfm_pelagic_base + parameters: + composition: c # elemental composition + initialization: + c: 3.000000000000000E-000 + X3: + long_name: semi refractory CDOM + model: ogs/bfm_pelagic_base + parameters: + composition: c # elemental composition + initialization: + c: 1.250000000000000E-000 +# ---------------------- P1 Diatom ---------------------- + P1: + long_name: diatoms + model: ogs/Phyto + parameters: +# --------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Characteristic Q10 coefficient + p_temp: 0.0 # [-] Cut-off threshold for temperature factor + p_sum: 2.5 # [1/d] maximum specific productivity at reference temperature (1/d) + p_srs: 0.076 # [1/d] Respiration rate at 10 degrees C + p_fR6: 0.5 # [-] fraction of lysis to small POC (R6) + p_sdmo: 0.0 # [1/d] Max.specific nutrient-stress lysis rate + p_thdo: 0.0 # [-] Half saturation constant for nutrient stress lysis + p_seo: 0.0 # [1/d] Extra lysis rate (biomass density-dependent) + p_sheo: 0.0 # [mgC/3] Half saturation constant for extra lysis + p_pu_ea: 0.10 # [-] Excreted fraction of primary production + p_pu_ra: 0.1 # [-] Activity respiration fraction + p_pu_rn: 0.35 # [-] nutrient stress respiration fraction + p_switchDOC: 2 # [1-3] Switch for the type of DOC excretion + # This choice must be consistent with bacteria + # 1. All DOC is released as R1c (Vichi et al., 2007) + # 2. Activity DOC is released as R2c (Vichi et al., 2004) + # (there is no nutrient-stress excretion) + # 3. All DOC is released as R2c (Polimene et al., 2006) +# --------- Nutrient parameters in phytoplankton ----------------- + p_netgrowth: .TRUE. # [T or F] Logical switch for nutrient-limited growth + # .T. nutrient-balanced growth (Vichi et al.2004) + # .F. nutrient-stress carbon excretion + # (Baretta-Bekker et al.1995 and Vichi et al.2007) + p_limnut: 1 # Switch for N-P co-limitation + # 0. Geometric mean + # 1. Threshold (Liebig-like) + # 2. Combined +# ---- N limitation control ---- + p_qun: 0.025 # [m3/mgC/d] Membrane affinity for N + p_lN4: 1.0 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 + p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) + p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C + p_xqn: 2.0 # [-] Multiplication factor for luxury storage +# ---- P limitation control ---- + p_qup: 0.0025 # [m3/mgC/d] Membrane affinity for P + p_qplc: 0.0004288 # [mmolN/mgC] minimum phosphorus to carbon ratio (mmol P/mg C) + p_qpcPPY: 0.000786 # [mmolP/mgC] Reference quotum P:C + p_xqp: 2.0 # [-] Multiplication factor for luxury storage +# ---- Si limitation control ---- + p_switchSi: 2 # [1-2] Switch for Silica limitation + # 1. Si limitation is controlled by external Si conc. + # 2. Si limitation is controlled by internal quota + p_chPs: 0.3 # [mmolSi/m3] Half saturation conc. for dissolved Si limitation + p_Contois: 0.0 # [>=0] If >0, use Contois formulation + p_qus: 0.0025 # [m3/mgC/d] Membrane affinity for Si + p_qslc: 0.007 # [mmolSi/mgC] minimum silicate to carbon ratio (mmol Si/mg C) + use_Si: .TRUE. # use silicate, default = false + p_qscPPY: 0.01 # [mmolSi/mgC] Reference quotum Si:C +# ---- nutrient stressed sinking ---- + p_esNI: 0.7 # [-] Nutrient stress threshold for sinking + p_res: 5.0 # [m/d] Maximum Sinking vel city (m/d) +# ---- Calcification ---- + p_caco3r: 0.0 # [-] Reference PIC:POC (rain) ratio +# ---- CDOM production ---- + p_fX1p: 0.00 # [-] fraction of colored labile DOC + p_fX2p: 0.053 # [-] fraction of colored semi-labile DOC +# --------- Chlorophyll parameters ----------- + p_switchChl: 2 # [1-4] Switch for Chla-a synthesis + p_sdchl: 0.0 # [1/d] Specific turnover rate for Chla + p_alpha_chl: 0.000768 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve + p_quantum_yield: 0.750e-3 # [mgC / uE] Photochemical efficiency + p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono + p_OT: 1 # [1-9] type of absorption/scattering spectra + p_qlcPPY: 0.026 # [mgChla/mgC] Reference quotum Chla:C + p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C + p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient + p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C + p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K +# --------- Sinking parameters ----------- + p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate + initialization: + c: 8.0 # carbon (mg C/m^3) + n: 0.1008 # nitrogen (mmol N/m^3) + p: 0.006288 # phosphate (mmol N/m^3) + s: 0.08 # silicate (mmol Si/m^3) + Chl: 0.16 # chlorophyll a (mg/m^3) + coupling: + 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) + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + O2o: O2/o # Oxygen (mmol O/m^3) + R1c: R1/c + R1n: R1/n + R1p: R1/p + R2c: R2/c + R6c: R6/c + R6n: R6/n + R6s: R6/s + R6p: R6/p + R8c: R8/c + R8n: R8/n + R8s: R8/s + R8p: R8/p + X1c: X1/c + X2c: X2/c + O3h: O3h/h + O5c: O5/c + PAR: lightspectral/PAR_P1 +# ---------------------- P2 nanoflagellates ---------------------- + P2: + long_name: nanoflagellates + model: ogs/Phyto + parameters: +# --------- Physiological parameters ----------------- + p_q10: 2.25 # [-] Characteristic Q10 coefficient + p_temp: 0.0 # [-] Cut-off threshold for temperature factor + p_sum: 2.6 # [1/d] maximum specific productivity at reference temperature (1/d) + p_srs: 0.09 # [1/d] Respiration rate at 10 degrees C + p_fR6: 1.0 # [-] fraction of lysis to small POC (R6) + p_sdmo: 0.0 # [1/d] Max.specific nutrient-stress lysis rate + p_thdo: 0.0 # [-] Half saturation constant for nutrient stress lysis + p_seo: 0.0 # [1/d] Extra lysis rate (biomass density-dependent) + p_sheo: 0.0 # [mgC/3] Half saturation constant for extra lysis + p_pu_ea: 0.15 # [-] Excreted fraction of primary production + p_pu_ra: 0.1 # [-] Activity respiration fraction + p_pu_rn: 0.35 # [-] nutrient stress respiration fraction + p_switchDOC: 2 # [1-3] 2. Activity DOC is released as R2c (Vichi et al., 2004) +# --------- Nutrient parameters in phytoplankton ----------------- + p_netgrowth: .TRUE. # [T or F] .T. nutrient-balanced growth (Vichi et al.2004) + p_limnut: 1 # Switch for N-P co-limitation, 1. Threshold (Liebig-like) +# ---- N limitation control ---- + p_qun: 0.025 # [m3/mgC/d] Membrane affinity for N + p_lN4: 0.5 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 + p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) + p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C + p_xqn: 2.0 # [-] Multiplication factor for luxury storage +# ---- P limitation control ---- + p_qup: 0.0035 # [m3/mgC/d] Membrane affinity for P + p_qplc: 0.00035 # [mmolN/mgC] minimum phosphorus to carbon ratio (mmol P/mg C) + p_qpcPPY: 0.000786 # [mmolP/mgC] Reference quotum P:C + p_xqp: 2.0 # [-] Multiplication factor for luxury storage +# ---- nutrient stressed sinking ---- + p_esNI: 0.75 # [-] Nutrient stress threshold for sinking + p_res: 0.0 # [m/d] Maximum Sinking vel city (m/d) +# ---- Calcification ---- + use_CaCO3: .TRUE. # use CaCO3, default = false + p_caco3r: 0.3 # [-] Reference PIC:POC (rain) ratio +# ---- CDOM production ---- + p_fX1p: 0.00 # [-] fraction of colored labile DOC + p_fX2p: 0.029 # [-] fraction of colored semi-labile DOC +# --------- Chlorophyll parameters ----------- + p_switchChl: 2 # [1-4] Switch for Chla-a synthesis + p_sdchl: 0.0 # [1/d] Specific turnover rate for Chla + p_alpha_chl: 0.0002016 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve + p_quantum_yield: 0.2016e-3 # [mgC / uE] Photochemical efficiency + p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono + p_OT: 2 # [1-9] type of absorption/scattering spectra + p_qlcPPY: 0.045 # [mgChla/mgC] Reference quotum Chla:C + p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C + p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient + p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C + p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K +# --------- Sinking parameters ----------- + p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate + initialization: + c: 8.0 # carbon (mg C/m^3) + n: 0.1008 # nitrogen (mmol N/m^3) + p: 0.006288 # phosphate (mmol N/m^3) + Chl: 0.16 # chlorophyll a (mg/m^3) + coupling: + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + O2o: O2/o # Oxygen (mmol O/m^3) + R1c: R1/c + R1n: R1/n + R1p: R1/p + R2c: R2/c + R6c: R6/c + R6n: R6/n + R6p: R6/p + R8c: R8/c + R8n: R8/n + R8p: R8/p + X1c: X1/c + X2c: X2/c + O3h: O3h/h + O5c: O5/c + PAR: lightspectral/PAR_P2 +# ---------------------- P3 Picophytoplankton ---------------------- + P3: + long_name: Picoplankton + model: ogs/Phyto + parameters: +# --------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Characteristic Q10 coefficient + p_temp: 0.75 # [-] Cut-off threshold for temperature factor + p_sum: 3.5 # [1/d] maximum specific productivity at reference temperature (1/d) + p_srs: 0.1 # [1/d] Respiration rate at 10 degrees C + p_fR6: 1.0 # [-] fraction of lysis to small POC (R6) + p_sdmo: 0.0 # [1/d] Max.specific nutrient-stress lysis rate + p_thdo: 0.0 # [-] Half saturation constant for nutrient stress lysis + p_seo: 0.0 # [1/d] Extra lysis rate (biomass density-dependent) + p_sheo: 0.0 # [mgC/3] Half saturation constant for extra lysis + p_pu_ea: 0.15 # [-] Excreted fraction of primary production + p_pu_ra: 0.2 # [-] Activity respiration fraction + p_pu_rn: 0.35 # [-] nutrient stress respiration fraction + p_switchDOC: 2 # [1-3] Switch for the type of DOC excretion + # This choice must be consistent with bacteria + # 1. All DOC is released as R1c (Vichi et al., 2007) + # 2. Activity DOC is released as R2c (Vichi et al., 2004) + # (there is no nutrient-stress excretion) + # 3. All DOC is released as R2c (Polimene et al., 2006) +# --------- Nutrient parameters in phytoplankton ----------------- + p_netgrowth: .TRUE. # [T or F] Logical switch for nutrient-limited growth + # .T. nutrient-balanced growth (Vichi et al.2004) + # .F. nutrient-stress carbon excretion + # (Baretta-Bekker et al.1995 and Vichi et al.2007) + p_limnut: 1 # Switch for N-P co-limitation + # 0. Geometric mean + # 1. Threshold (Liebig-like) + # 2. Combined +# ---- N limitation control ---- + p_qun: 0.25 # [m3/mgC/d] Membrane affinity for N + p_lN4: 0.1 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 + p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) + p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C + p_xqn: 2.0 # [-] Multiplication factor for luxury storage +# ---- P limitation control ---- + p_qup: 0.0025 # [m3/mgC/d] Membrane affinity for P + p_qplc: 0.0004288 # [mmolN/mgC] minimum phosphorus to carbon ratio (mmol P/mg C) + p_qpcPPY: 0.000786 # [mmolP/mgC] Reference quotum P:C + p_xqp: 2.0 # [-] Multiplication factor for luxury storage +# ---- Si limitation control ---- +# Silicon absent in this PFT +# ---- nutrient stressed sinking ---- + p_esNI: 0.75 # [-] Nutrient stress threshold for sinking + p_res: 0.0 # [m/d] Maximum Sinking vel city (m/d) +# ---- Calcification ---- + p_caco3r: 0.0 # [-] Reference PIC:POC (rain) ratio +# ---- CDOM production ---- + p_fX1p: 0.00 # [-] fraction of colored labile DOC + p_fX2p: 0.026 # [-] fraction of colored semi-labile DOC +# --------- Chlorophyll parameters ----------- + p_switchChl: 2 # [1-4] Switch for Chla-a synthesis + p_sdchl: 0.0 # [1/d] Specific turnover rate for Chla + p_alpha_chl: 0.0010104 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve + p_quantum_yield: 1.0104e-3 # [mgC / uE] Photochemical efficiency + p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono + p_OT: 3 # [1-9] type of absorption/scattering spectra + p_qlcPPY: 0.014 # [mgChla/mgC] Reference quotum Chla:C + p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C + p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient + p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C + p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K +# --------- Sinking parameters ----------- + p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate + initialization: + c: 8.0 # carbon (mg C/m^3) + n: 0.1008 # nitrogen (mmol N/m^3) + p: 0.006288 # phosphate (mmol N/m^3) + Chl: 0.16 # chlorophyll a (mg/m^3) + coupling: + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + O2o: O2/o # Oxygen (mmol O/m^3) + R1c: R1/c + R1n: R1/n + R1p: R1/p + R2c: R2/c + R6c: R6/c + R6n: R6/n + R6p: R6/p + R8c: R8/c + R8n: R8/n + R8p: R8/p + X1c: X1/c + X2c: X2/c + O3h: O3h/h + O5c: O5/c + PAR: lightspectral/PAR_P3 +# ---------------------- P4 dinoflagellates ---------------------- + P4: + long_name: dinoflagellates + model: ogs/Phyto + parameters: +# --------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Characteristic Q10 coefficient + p_temp: 0.0 # [-] Cut-off threshold for temperature factor + p_sum: 1.5 # [1/d] maximum specific productivity at reference temperature (1/d) + p_srs: 0.1 # [1/d] Respiration rate at 10 degrees C + p_fR6: 0.5 # [-] fraction of lysis to small POC (R6) + p_sdmo: 0.0 # [1/d] Max.specific nutrient-stress lysis rate + p_thdo: 0.0 # [-] Half saturation constant for nutrient stress lysis + p_seo: 0.0 # [1/d] Extra lysis rate (biomass density-dependent) + p_sheo: 100.0 # [mgC/3] Half saturation constant for extra lysis + p_pu_ea: 0.20 # [-] Excreted fraction of primary production + p_pu_ra: 0.1 # [-] Activity respiration fraction + p_pu_rn: 0.35 # [-] nutrient stress respiration fraction + p_switchDOC: 2 # [1-3] 2. Activity DOC is released as R2c (Vichi et al., 2004) +# --------- Nutrient parameters in phytoplankton ----------------- + p_netgrowth: .TRUE. # [T or F] .T. nutrient-balanced growth (Vichi et al.2004) + p_limnut: 1 # Switch for N-P co-limitation, 1. Threshold (Liebig-like) +# ---- N limitation control ---- + p_qun: 0.025 # [m3/mgC/d] Membrane affinity for N + p_lN4: 1.0 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 + p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) + p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C + p_xqn: 2.0 # [-] Multiplication factor for luxury storage +# ---- P limitation control ---- + p_qup: 0.0025 # [m3/mgC/d] Membrane affinity for P + p_qplc: 0.0004288 # [mmolN/mgC] minimum phosphorus to carbon ratio (mmol P/mg C) + p_qpcPPY: 0.000786 # [mmolP/mgC] Reference quotum P:C + p_xqp: 2.0 # [-] Multiplication factor for luxury storage +# ---- nutrient stressed sinking ---- + p_esNI: 0.75 # [-] Nutrient stress threshold for sinking + p_res: 2.5 # [m/d] Maximum Sinking vel city (m/d) +# ---- Calcification ---- + p_caco3r: 0.0 # [-] Reference PIC:POC (rain) ratio +# ---- CDOM production ---- + p_fX1p: 0.00 # [-] fraction of colored labile DOC + p_fX2p: 0.035 # [-] fraction of colored semi-labile DOC +# --------- Chlorophyll parameters ----------- + p_switchChl: 2 # [1-4] Switch for Chla-a synthesis + p_sdchl: 0.0 # [1/d] Specific turnover rate for Chla + p_alpha_chl: 0.0002616 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve + p_quantum_yield: 0.2616e-3 # [mgC / uE] Photochemical efficiency + p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono + p_OT: 4 # [1-9] type of absorption/scattering spectra + p_qlcPPY: 0.019 # [mgChla/mgC] Reference quotum Chla:C + p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C + p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient + p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C + p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K +# --------- Sinking parameters ----------- + p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate + initialization: + c: 8.0 # carbon (mg C/m^3) + n: 0.1008 # nitrogen (mmol N/m^3) + p: 0.006288 # phosphate (mmol N/m^3) + Chl: 0.16 # chlorophyll a (mg/m^3) + coupling: + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + O2o: O2/o # Oxygen (mmol O/m^3) + R1c: R1/c + R1n: R1/n + R1p: R1/p + R2c: R2/c + R6c: R6/c + R6n: R6/n + R6p: R6/p + R8c: R8/c + R8n: R8/n + R8p: R8/p + X1c: X1/c + X2c: X2/c + O3h: O3h/h + O5c: O5/c + PAR: lightspectral/PAR_P4 +# ---------------------- B1 Pelagic heteretrophic bacteria ---------------------- +# + B1: + long_name: Bacteria + model: ogs/PelBac + parameters: +# --------- Physiological parameters ----------------- + p_version : 2 # Switch for bacteria parameterization +# 1 : Baretta-Bekker et al. 1995; +# Vichi et al., 2007 +# 2 : Vichi et al., 2004 +# 3 : Polimene et al., 2006 + p_q10 : 2.95 # [-] Q10-value (temperature dependency) + p_chdo : 30.0 # [mmol/m3] Half-saturation constant for O2 limitation + p_sd : 0.0 # [1/d] Specific mortality rate + p_sd2 : 0.0 # [1/d] Density dependent specific mortality rate + p_suhR1 : 0.5 # [1/d] Specific potential uptake for nutrient-rich DOM + p_sulR1 : 0.0 # [1/d] Specific potential uptake for nutrient-poor DOM + p_suR2 : 0.05 # [1/d] Specific potential uptake for semi-labile DOC + p_suR3 : 0.0 # [1/d] Specific potential uptake for semi-refractory DOC + p_suR6 : 0.012 # [1/d] Specific potential uptake for small POM (1/d) + p_suR8 : 0.03 # [1/d] Specific potential uptake for large POM (1/d) + p_sum : 8.38 # [1/d] Potential specific growth rate + p_pu_ra : 0.76 # [-] Activity respiration fraction + p_pu_ra_o : 0.2 # [-] Additional respiration fraction at low O2 conc + p_srs : 0.01 # [1/d] Specific rest respiration + p_qncPBA : 0.017 # [mmolN/mgC] Optimal N/C ratio + p_qpcPBA : 0.0019 # [mmolP/mgC] Optimal P/C ratio + p_qlnc : 0.0085 # [mmolN/mgC] Minimal N/C ratio + p_qlpc : 0.00095 # [mmolP/mgC] Minimal P/C ratio + p_qun : 0.05 # [mmolN/mgC/day] Membrane affinity for N + p_qup : 0.005 # [mmolP/mgC/day] Membrane affinity for P + p_chn : 0.05 # [mmolN/m3] Half saturation ammonium conc. for uptake + p_chp : 1.00 # [mmolP/m3] Half saturation phosphate conc. for uptake + p_rec : 1.0 # [1/d] Relaxation timescale for semi-labile excretion + p_ruen : 1.0 # [1/d] Relaxation timescale for N uptake/remin. + p_ruep : 1.0 # [1/d] Relaxation timescale for P uptake/remin. + p_pu_ea_R3 : 0.0 # [-] Excretion of semi-refractory DOC + p_qro : 0.5 # [mmolHS-/mmolO2] Stoichiometric coefficient for anaerobic reactions + p_pe_R1c: 0.60 # [-] Fractional content of C in cytoplasm + p_pe_R1n: 0.72 # [-] Fractional content of N in cytoplasm + p_pe_R1p: 0.832 # [-] Fractional content of P in cytoplasm +# ---- CDOM production ---- + p_fX1b: 0.00 # [-] fraction of colored labile DOC + p_fX2b: 0.02 # [-] fraction of colored semi-labile DOC + p_fX3b: 0.018 # [-] fraction of colored semi-refractory DOC +# ---- POM split ---- + p_fR6: 0.0 # [-] fraction of lysis to small POC (R6) + initialization: + c: 1.0 # carbon (mg C/m^3) + n: 1.700000000000000E-002 # nitrogen (mmol N/m^3) + p: 1.900000000000000E-003 # phosphate (mmol N/m^3) + coupling: + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + N6r: N6/r + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + O3h: O3h/h + O2o: O2/o # Oxygen (mmol O/m^3) + R1c: R1/c + R1n: R1/n + R1p: R1/p + R2c: R2/c + R3c: R3/c + R6c: R6/c + R6n: R6/n + R6p: R6/p + R6s: R6/s + R8c: R8/c + R8n: R8/n + R8p: R8/p + R8s: R8/s + X1c: X1/c + X2c: X2/c + X3c: X3/c +# ---------------------- Z5 Microzooplankton ---------------------- + Z5: +# use: false + long_name: Microzooplankton + model: ogs/MicroZoo + parameters: +# --------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Characteristic Q10 coefficient + p_srs: 0.01 # [1/d] Respiration rate at 10 degrees Celsius + p_sum: 2.71 # [1/d] Potential growth rate + p_sdo: 0.05 # [1/d] Mortality rate due to oxygen limitation + p_sd: 0.0 # [1/d] Temperature independent mortality rate + p_pu: 0.5 # [-] Assimilation efficiency + p_pu_ea: 0.5 # [-] Fraction of activity excretion + p_chro: 8 # [mmolO2/m3] Half-saturation oxygen concentration + p_chuc: 15.0 # [mgC/m3] Half-saturation Food concentration for Type II + p_minfood: 37.5 # [mgC/m3] Half-saturation food concentration for + # preference factor + p_pecaco3: 0.5 # [-] Portion of egested calcified shells during grazing + p_qpcMIZ: 1.85e-3 # [mmolN/mgC] Maximum quotum P:C + p_qncMIZ: 1.67e-2 # [mmolN/mgC] Maximum quotum N:C + nprey: 7 # [-] Number of preys + suprey1: 0.1 # [-] Availability of pelagic Bacteria group b + # to Zooplankton group z + suprey2: 0.35 # [-] Availability of PhytoPlankton group P1 + # to Zooplankton group z + suprey3: 0.5 # [-] Availability of PhytoPlankton group P2 + # to Zooplankton group z + suprey4: 0.3 # [-] Availability of PhytoPlankton group P3 + # to Zooplankton group z + suprey5: 0.1 # [-] Availability of PhytoPlankton group P4 + # to Zooplankton group z + suprey6: 1.0 # [-] Availability of MicroZooplankton group Z5 + # to Zooplankton group z + suprey7: 1.0 # [-] Availability of MicroZooplankton group Z6 + # to Zooplankton group z +#-------------------------------------------------------------------- + isP21: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP22: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP23: 1 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP24: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP25: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP26: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP27: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] +#-------------------------------------------------------------------- + p_fR6: 0.5 # [-] Fraction of lysis and sloppy predation to small POC (R6) + p_pe_R1c: 0.60 # [-] Fractional content of C in cytoplasm + p_pe_R1n: 0.72 # [-] Fractional content of C in cytoplasm + p_pe_R1p: 0.832 # [-] Fractional content of C in cytoplasm + p_fX1z: 0.018 # [-] fraction of colored labile DOC + initialization: + c: 1.0 # carbon (mg C/m^3) + n: 0.0167 # nitrogen (mmol N/m^3) + p: 0.00185 # phosphate (mmol N/m^3) + coupling: + O2o: O2/o # Oxygen (mmol O2/m^3) + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + N1p: N1/p # phosphate (mmol P/m^3) + R6c: R6/c # POC (mgC/m3) + R6s: R6/s # POSi (mgSi/m3) + R6n: R6/n # PON (mmolN/m3) + R6p: R6/p # POP (mmolP/m3) + R8c: R8/c # POC (mgC/m3) + R8s: R8/s # POSi (mgSi/m3) + R8n: R8/n # PON (mmolN/m3) + R8p: R8/p # POP (mmolP/m3) + X1c: X1/c # labile CDOM + R1c: R1/c # labile DOC + R1n: R1/n # labile DON + R1p: R1/p # labile DOP + prey1: B1 + prey2: P1 + prey3: P2 + prey4: P3 + prey5: P4 + prey6: Z5 + prey7: Z6 + O3h: O3h/h + O5c: O5/c +# ---------------------- Z6 Microzooplankton ---------------------- + Z6: +# use: false + long_name: Heterotrophic Nanoflagellates (HNAN) + model: ogs/MicroZoo + parameters: +# --------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Characteristic Q10 coefficient + p_srs: 0.01 # [1/d] Respiration rate at 10 degrees Celsius + p_sum: 3.88 # [1/d] Potential growth rate + p_sdo: 0.05 # [1/d] Mortality rate due to oxygen limitation + p_sd: 0.0 # [1/d] Temperature independent mortality rate + p_pu: 0.3 # [-] Assimilation efficiency + p_pu_ea: 0.5 # [-] Fraction of activity excretion + p_chro: 8 # [mmolO2/m3] Half-saturation oxygen concentration + p_chuc: 100.0 # [mgC/m3] Half-saturation Food concentration for Type II + p_minfood: 50.0 # [mgC/m3] Half-saturation food concentration for + # preference factor + p_pecaco3: 0.5 # [-] Portion of egested calcified shells during grazing + p_qpcMIZ: 1.85e-3 # [mmolN/mgC] Maximum quotum P:C + p_qncMIZ: 1.67e-2 # [mmolN/mgC] Maximum quotum N:C + nprey: 7 # [-] Number of preys + suprey1: 1.0 # [-] Availability of pelagic Bacteria group b + # to Zooplankton group z + suprey2: 0.0 # [-] Availability of PhytoPlankton group P1 + # to Zooplankton group z + suprey3: 0.2 # [-] Availability of PhytoPlankton group P2 + # to Zooplankton group z + suprey4: 1.0 # [-] Availability of PhytoPlankton group P3 + # to Zooplankton group z + suprey5: 0.0 # [-] Availability of PhytoPlankton group P4 + # to Zooplankton group z + suprey6: 0.0 # [-] Availability of MicroZooplankton group Z5 + # to Zooplankton group z + suprey7: 0.2 # [-] Availability of MicroZooplankton group Z6 + # to Zooplankton group z +#-------------------------------------------------------------------- + isP21: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP22: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP23: 1 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP24: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP25: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP26: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP27: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] +#-------------------------------------------------------------------- + p_fR6: 1.0 # [-] Fraction of lysis and sloppy predation to small POC (R6) + p_pe_R1c: 0.60 # [-] Fractional content of C in cytoplasm + p_pe_R1n: 0.72 # [-] Fractional content of C in cytoplasm + p_pe_R1p: 0.832 # [-] Fractional content of C in cytoplasm + p_fX1z: 0.030 # [-] fraction of colored labile DOC + initialization: + c: 1.0 # carbon (mg C/m^3) + n: 0.0167 # nitrogen (mmol N/m^3) + p: 0.00185 # phosphate (mmol N/m^3) + coupling: + O2o: O2/o # Oxygen (mmol O2/m^3) + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + N1p: N1/p # phosphate (mmol P/m^3) + R6c: R6/c # POC (mgC/m3) + R6s: R6/s # POSi (mgSi/m3) + R6n: R6/n # PON (mmolN/m3) + R6p: R6/p # POP (mmolP/m3) + R8c: R8/c # POC (mgC/m3) + R8s: R8/s # POSi (mgSi/m3) + R8n: R8/n # PON (mmolN/m3) + R8p: R8/p # POP (mmolP/m3) + X1c: X1/c # labile CDOM + R1c: R1/c # labile DOC + R1n: R1/n # labile DON + R1p: R1/p # labile DOP + prey1: B1 + prey2: P1 + prey3: P2 + prey4: P3 + prey5: P4 + prey6: Z5 + prey7: Z6 + O3h: O3h/h + O5c: O5/c +# ---------------------- Z3 Carnivorous Mesozooplankton ---------------------- + Z3: +# use: false + long_name: Carnivorous Mesozooplankton + model: ogs/MesoZoo + parameters: +# --------------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Q10 value for physiological rates + p_srs: 0.01 # [1/d] Respiration rate at 10 degrees C + p_sum: 2.0 # [1/d] Maximal productivity at 10 degrees C + p_sd: 0.02 # [1/d] Background natural mortality + p_vum: 0.008 # [m3/mgC/d] Specific search volume + p_puI: 0.6 # [-] Assimilation efficiency + p_peI: 0.3 # [-] Fraction of Faeces production + p_sdo: 0.01 # [m3/mgC/d] Specific density-dependent mortality + p_sds: 2.0 # [-] Exponent of density-dependent mortality + p_pecaco3: 0.75 # [-] Portion of egested calcified shells during grazing + p_qpcMEZ: 1.67e-3 # [mmolP/mgC] Maximum quotum P:C + p_qncMEZ: 0.015 # [mmolN/mgC] Maximum quotum N:C + p_clO2o: 30.0 # [mmolO2/m3] Half-saturation oxygen concentration + p_fR6: 0.5 # [-] Fraction of lysis and sloppy predation to small POC (R6) +#----------------------------------------------------------------------------- + nprey: 3 # [-] Number of preys + suprey1: 1.0 # [-] Availability of PhytoPlankton group P4 + # to Zooplankton group z + suprey2: 1.0 # [-] Availability of MicroZooplankton group Z3 + # to Zooplankton group z + suprey3: 1.0 # [-] Availability of MicroZooplankton group Z4 + # to Zooplankton group z +#------------------------------------------------------------------------------ + isP21: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP22: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP23: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] +#------------------------------------------------------------------------------ + initialization: + c: 1.0 # carbon (mg C/m^3) + n: 0.015 # nitrogen (mmol N/m^3) + p: 0.00167 # phosphate (mmol N/m^3) + coupling: + O2o: O2/o # dissolved oxygen + O3c: O3/c # DIC + N1p: N1/p # phosphate (mmol P/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R6c: R6/c # POC + R6n: R6/n # PON + R6p: R6/p # POP + R6s: R6/s # biogenic silica (mmol Si/m^3) + R8c: R8/c # POC + R8n: R8/n # PON + R8p: R8/p # POP + R8s: R8/s # biogenic silica (mmol Si/m^3 + prey1: P4 + prey2: Z3 + prey3: Z4 + O3h: O3h/h + O5c: O5/c +# --------------------------------------------------------------------------- +# ---------------------- Z4 Omnivorous Mesozooplankton ---------------------- + Z4: +# use: false + long_name: Omnivorous Mesozooplankton + model: ogs/MesoZoo + parameters: +# ----------------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Q10 value for physiological rates + p_srs: 0.02 # [1/d] Respiration rate at 10 degrees C + p_sum: 2.0 # [1/d] Maximal productivity at 10 degrees C + p_sd: 0.02 # [1/d] Background natural mortality + p_vum: 0.02 # [m3/mgC/d] Specific search volume + p_puI: 0.6 # [-] Assimilation efficiency + p_peI: 0.35 # [-] Fraction of Faeces production + p_sdo: 0.01 # [m3/mgC/d] Specific density-dependent mortality + p_sds: 2.0 # [-] Exponent of density-dependent mortality + p_pecaco3: 0.75 # [-] Portion of egested calcified shells during grazing + p_qpcMEZ: 1.67e-3 # [mmolP/mgC] Maximum quotum P:C + p_qncMEZ: 0.015 # [mmolN/mgC] Maximum quotum N:C + p_clO2o: 30.0 # [mmolO2/m3] Half-saturation oxygen concentration + p_fR6: 0.5 # [-] Fraction of lysis and sloppy predation to small POC (R6) +#------------------------------------------------------------------------------- + nprey: 5 # [-] Number of preys + suprey1: 1.0 # [-] Availability of PhytoPlankton group P1 + # to Zooplankton group z + suprey2: 0.75 # [-] Availability of PhytoPlankton group P2 + # to Zooplankton group z + suprey3: 1.0 # [-] Availability of PhytoPlankton group P4 + # to Zooplankton group z + suprey4: 1.0 # [-] Availability of MicroZooplankton group Z5 + # to Zooplankton group z + suprey5: 1.0 # [-] Availability of MicroZooplankton group Z4 + # to Zooplankton group z +#------------------------------------------------------------------------------- + isP21: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP22: 1 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP23: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP24: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP25: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] +#------------------------------------------------------------------------------- + initialization: + c: 1.0 # carbon (mg C/m^3) + n: 0.015 # nitrogen (mmol N/m^3) + p: 0.00167 # phosphate (mmol N/m^3) + coupling: + O2o: O2/o # dissolved oxygen + O3c: O3/c # DIC + N1p: N1/p # phosphate (mmol P/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R6c: R6/c # POC + R6n: R6/n # PON + R6p: R6/p # POP + R6s: R6/s # biogenic silica (mmol Si/m^3) + R8c: R8/c # POC + R8n: R8/n # PON + R8p: R8/p # POP + R8s: R8/s # biogenic silica (mmol Si/m^3) + prey1: P1 + prey2: P2 + prey3: P4 + prey4: Z5 + prey5: Z4 + O3h: O3h/h + O5c: O5/c +# ---------------------- Pelagic chemistry ---------------------- +# + PelChem: + long_name: pelagic chemistry + model: ogs/PelChem + parameters: + p_clO2o: 10.0 # [mmolO2/m3] Half-saturation O2 concentration for nitrification and reoxidation + p_clN6r: 1.0 # [mmolHS/m3] Half-saturation concentration of reduction equivalents for denitrification[mmolO2/m3] + p_sN4N3: 0.01 # [1/d] Specific nitrification rate at 10 degC + p_q10N4N3: 2.367 # [-] Q10 factor for nitrification/denit + p_qon_nitri: 2.0 # [mmolO2/mmolN] stoichiometric coefficient for nitrification + p_qro: 0.5 # [mmolHS-/mmolO2] Stoichiometric coefficient for anaerobic reactions + p_sN3O4n: 0.35 # [1/d] Specific denitrification rate + p_rPAo: 1.0 # [mmolO2/m3/d] Reference anoxic mineralization rate + p_qon_dentri: 1.25 # [mmolO2/mmolN] Stoichiometric coefficient for denitrification + p_rOS: 0.05 # [1/d] Specific reoxidation rate of reduction equivalents + p_sR6N5: 0.1 # [1/d] Specific remineralization rate of biogenic silica (small POC) + p_q10R6N5: 1.49 # [-] Q10 factor for biogenic silica (small POC) + p_sR8N5: 0.1 # [1/d] Specific remineralization rate of biogenic silica (large POC) + p_q10R8N5: 1.49 # [-] Q10 factor for biogenic silica (large POC) + p_bX1c: 0.1 # [1/d] photodegradation (bleaching) rate X1c + p_bX2c: 0.03 # [1/d] photodegradation (bleaching) rate X2c + p_bX3c: 0.01 # [1/d] photodegradation (bleaching) rate X3c + p_IX1: 60.0 # [uE m-2 s-1] light threshold for X1c bleaching + p_IX2: 60.0 # [uE m-2 s-1] light threshold for X2c bleaching + p_IX3: 50.0 # [uE m-2 s-1] light threshold for X3c bleaching + p_rX3c: 0.00003 # [1/d] remineralization rate X3c and R3c + p_q10X: 2.95 # [-] q10 for CDOM degradation + p_Esource: 5 # [5 or 6] source of light for CDOM bleaching, 5=spectral, 6=mono + p_use_benthic: 0 #[0=F or 1=T] activate first-order benthic return + p_TauC: 1.0 #[d] remineralization of Carbon in detritus + p_TauN: 0.5 #[d] remineralization of Nitrogen in detritus + p_TauP: 1.0 #[d] remineralization of Phosphorus in detritus + p_Amm_rem: 0.2 #[0 to 1] fraction of detritus remineralized to NH4 + initialization: + coupling: + N1p: N1/p # phosphate (mmol P/m^3) + 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) + O3h: O3h/h # alkalinity (mmol /m^3) + O3c: O3/c # DIC + O4n: O4/n # N2 (mmol N/m^3) + N6r: N6/r # reduction equivalent (mmol HS/m^3) + N5s: N5/s # silicate (mmol Si/m^3) + X1c: X1/c # cdom X1c (mgC/m^3) + X2c: X2/c # cdom X2c (mgC/m^3) + X3c: X3/c # cdom X3c (mgC/m^3) + R3c: R3/c # cdom R3c (mgC/m^3) + R6s: R6/s # POSi (mgSi/m3) + R6c: R6/c # POC (mgC/m3) + R6n: R6/n # PON (mmolN/m3) + R6p: R6/p # POP (mmolP/m3) + R8s: R8/s # POSi (mgSi/m3) + R8c: R8/c # POC (mgC/m3) + R8n: R8/n # PON (mmolN/m3) + R8p: R8/p # POP (mmolP/m3) + PAR_tot: lightspectral/PAR_tot + isBen: Benthic_layer/isBen +## --------------------- CalciteDissolution + O5: +# use: false + long_name: calcite + model: ogs/CalciteDissolution + parameters: + p_kdca: 10.9 # [d-1] Calcite dissolution rate constant + p_nomega: 1.0 # [-] Order of the dissolution rate dependence on Omega + p_wsinkPIC: 30 # [m d-1] sinking velocity of PIC (Calcite) + c0: 1.0e-05 # [mg C/m^3] background concentration, default = 0.0 + initialization: + c: 1.0 # carbon (mg C/m^3) + coupling: + OCalc: O3/OCalc # calcite saturation (-) + O3c: O3/c # total dissolved inorganic carbon (mgC/m^3) + O3h: O3h/h # alkalinity (mmol/m^3) + Phyto_c: + long_name: total + model: weighted_sum + parameters: + n: 4 + coupling: + term1: P1_c + term2: P2_c + term3: P3_c + term4: P4_c + Phyto_Chl: + long_name: total + model: weighted_sum + parameters: + n: 4 + coupling: + term1: P1_Chl + term2: P2_Chl + term3: P3_Chl + term4: P4_Chl +# Phyto_NPP: +# long_name: total +# model: weighted_sum +# parameters: +# n: 4 +# coupling: +# term1: P1_run_result +# term2: P2_run_result +# term3: P3_run_result +# term4: P4_run_result From 5688bf11eb68359e78392e8c17448bae127e9e86 Mon Sep 17 00:00:00 2001 From: Giovanni Galli Date: Thu, 11 Jun 2026 11:10:19 +0200 Subject: [PATCH 14/15] renamed yaml file to fabm_EIS_2026_11_V13C.yaml --- fabm_EIS_2026_11_V13C.yaml | 1108 ++++++++++++++++++++++++++++++++++++ 1 file changed, 1108 insertions(+) create mode 100755 fabm_EIS_2026_11_V13C.yaml diff --git a/fabm_EIS_2026_11_V13C.yaml b/fabm_EIS_2026_11_V13C.yaml new file mode 100755 index 0000000..9198e42 --- /dev/null +++ b/fabm_EIS_2026_11_V13C.yaml @@ -0,0 +1,1108 @@ +check_conservation: false +require_initialization: true +log: true +instances: + Benthic_layer: + model: ogs/BenthicLayer + parameters: + p_BenDepth: 12000.0 + zenith_angle: + model: ogs/zenith_angle +# light: +# model: ogs/light +# parameters: +# pEPSCHL: 0.0088 # attenuation by Chlorophyll (m^2/mg Chl), default= 0.0088 +# pEPSCDOM: 0.01476 # attenuation by CDOM (m^2/mg C), default= 0.0646 +# EPS0r: 0.04 # background shortwave attenuation (1/m), default = 0.04 +# pEIR_eow: 0.4 # photosynthetically active fraction of shortwave radiation (-), default = 0.5 +# coupling: +# X1c: X1/c +# X2c: X2/c +# X3c: X3/c + light_atm: + model: spectral/atmosphere + parameters: + lambda_method: 1 + compute_mean_wind: true + spectral_output: 1 + relhum: + model: spectral/relhum + ozone: + model: spectral/ozone + lightspectral: + model: ogs/light_spectral_OASIM + parameters: + nlt: 33 # number of wavelenghts considered + npft: 4 # number of PFT considered + SdomX1: 0.0175 # spectral slope acdom of X1c [nm-1] + X1coeff: 0.015 # acdom coeff of X1c at lambda_aCDOM [m2/mgC] + SdomX2: 0.0162 # spectral slope acdom of X2c [nm-1] + X2coeff: 0.015 # acdom coeff of X2c at lambda_aCDOM [m2/mgC] + SdomX3: 0.0180 # spectral slope acdom of X3c [nm-1] + X3coeff: 0.015 # acdom coeff of X3c at lambda_aCDOM [m2/mgC] + Xmincoeff: 0.00 # minimum aCDOM [m-1] at 450nm + lambda_aCDOM: 450 # lambda at which reference acdom is given [nm] + compute_acdom: .FALSE. # logical [T=compute coeffs, F=use file] + Sapar: 0.013 # spectral slope anap [nm-1] + lambda_aPart: 440 # lambda at which reference anap is given [nm] + aparcoeff: 0.00058 # anap coeff at lambda_aPart [m2/mgC] + Sbpar: 0.5 # exponent bnap [-] + lambda_bPart: 550 # lambda at which reference bnap is given [nm] + bparcoeff: 0.0120 # bnap coeff at lambda_bPart [m2/mgC] + bb_to_b: 0.005 # back to total scatter POC [-] + compute_anap: .FALSE. # logical [T=comptute coeffs, F=use file] + p_epsP1: 0.0152 # mean absorption coefficient from 400-700nm for P1 [m2 mgChl-1] + p_epsP2: 0.0293 # mean absorption coefficient from 400-700nm for P2 [m2 mgChl-1] + p_epsP3: 0.0443 # mean absorption coefficient from 400-700nm for P3 [m2 mgChl-1] + p_epsP4: 0.0178 # mean absorption coefficient from 400-700nm for P4 [m2 mgChl-1] + compute_aph: .FALSE. # logical flag to scale aph [T=use file scaled to p_epsPn or F=use file unscaled] + p_bpsP1: 0.0140 # mean scattering coefficient from 400-700nm for P1 [m2 mgC-1] + p_bpsP2: 0.0077 # mean scattering coefficient from 400-700nm for P2 [m2 mgC-1] + p_bpsP3: 0.0101 # mean scattering coefficient from 400-700nm for P3 [m2 mgC-1] + p_bpsP4: 0.0112 # mean scattering coefficient from 400-700nm for P4 [m2 mgC-1] + compute_bph: .FALSE. # logical flag to scale bph [T=use file scaled to p_bpsPn or F=use file unscaled] + p_bbrP1: 0.0020 # non-spectral backscattering to total scattering ratio for P1 [-] + p_bbrP2: 0.0071 # non-spectral backscattering to total scattering ratio for P2 [-] + p_bbrP3: 0.0039 # non-spectral backscattering to total scattering ratio for P3 [-] + p_bbrP4: 0.0030 # non-spectral backscattering to total scattering ratio for P4 [-] + compute_bbc: .FALSE. # logical flag to compute bbc or read it from file [T=compute bc*bbr or F=use file] + p_useSPM: .FALSE. # if true requires input data specification in gotm.yaml + p_spmc1: 0.016 # basal absorption for minimal absorption at long wavelengths [m2 g-1] + p_spmc2: 0.054 # specific absorption at the reference wavelength [m2 g-1] + p_spmS: 0.012 # slope for exponential decline of aSPM with wavelength [nm-1] + lambda_aSPM: 440 # wavelength where reference aSPM (c2) is given + p_spmb: 0.7 # specific scattering at 555nm [m2 g-1] + p_spmbb: 0.008 # specific backscattering at 555nm [m2 g-1] + coupling: + X1c : X1/c + X2c : X2/c + X3c : X3/c + R6c : R6/c + R8c : R8/c + direct_band1 : light_atm/dir_sf_band1 + diffuse_band1 : light_atm/dif_sf_band1 + direct_band2 : light_atm/dir_sf_band2 + diffuse_band2 : light_atm/dif_sf_band2 + direct_band3 : light_atm/dir_sf_band3 + diffuse_band3 : light_atm/dif_sf_band3 + direct_band4 : light_atm/dir_sf_band4 + diffuse_band4 : light_atm/dif_sf_band4 + direct_band5 : light_atm/dir_sf_band5 + diffuse_band5 : light_atm/dif_sf_band5 + direct_band6 : light_atm/dir_sf_band6 + diffuse_band6 : light_atm/dif_sf_band6 + direct_band7 : light_atm/dir_sf_band7 + diffuse_band7 : light_atm/dif_sf_band7 + direct_band8 : light_atm/dir_sf_band8 + diffuse_band8 : light_atm/dif_sf_band8 + direct_band9 : light_atm/dir_sf_band9 + diffuse_band9 : light_atm/dif_sf_band9 + direct_band10 : light_atm/dir_sf_band10 + diffuse_band10 : light_atm/dif_sf_band10 + direct_band11 : light_atm/dir_sf_band11 + diffuse_band11 : light_atm/dif_sf_band11 + direct_band12 : light_atm/dir_sf_band12 + diffuse_band12 : light_atm/dif_sf_band12 + direct_band13 : light_atm/dir_sf_band13 + diffuse_band13 : light_atm/dif_sf_band13 + direct_band14 : light_atm/dir_sf_band14 + diffuse_band14 : light_atm/dif_sf_band14 + direct_band15 : light_atm/dir_sf_band15 + diffuse_band15 : light_atm/dif_sf_band15 + direct_band16 : light_atm/dir_sf_band16 + diffuse_band16 : light_atm/dif_sf_band16 + direct_band17 : light_atm/dir_sf_band17 + diffuse_band17 : light_atm/dif_sf_band17 + direct_band18 : light_atm/dir_sf_band18 + diffuse_band18 : light_atm/dif_sf_band18 + direct_band19 : light_atm/dir_sf_band19 + diffuse_band19 : light_atm/dif_sf_band19 + direct_band20 : light_atm/dir_sf_band20 + diffuse_band20 : light_atm/dif_sf_band20 + direct_band21 : light_atm/dir_sf_band21 + diffuse_band21 : light_atm/dif_sf_band21 + direct_band22 : light_atm/dir_sf_band22 + diffuse_band22 : light_atm/dif_sf_band22 + direct_band23 : light_atm/dir_sf_band23 + diffuse_band23 : light_atm/dif_sf_band23 + direct_band24 : light_atm/dir_sf_band24 + diffuse_band24 : light_atm/dif_sf_band24 + direct_band25 : light_atm/dir_sf_band25 + diffuse_band25 : light_atm/dif_sf_band25 + direct_band26 : light_atm/dir_sf_band26 + diffuse_band26 : light_atm/dif_sf_band26 + direct_band27 : light_atm/dir_sf_band27 + diffuse_band27 : light_atm/dif_sf_band27 + direct_band28 : light_atm/dir_sf_band28 + diffuse_band28 : light_atm/dif_sf_band28 + direct_band29 : light_atm/dir_sf_band29 + diffuse_band29 : light_atm/dif_sf_band29 + direct_band30 : light_atm/dir_sf_band30 + diffuse_band30 : light_atm/dif_sf_band30 + direct_band31 : light_atm/dir_sf_band31 + diffuse_band31 : light_atm/dif_sf_band31 + direct_band32 : light_atm/dir_sf_band32 + diffuse_band32 : light_atm/dif_sf_band32 + direct_band33 : light_atm/dir_sf_band33 + diffuse_band33 : light_atm/dif_sf_band33 + costheta_r : light_atm/costheta_r + N1: + long_name: phosphate + model: ogs/bfm_pelagic_base + parameters: + composition: p # elemental composition + initialization: + p: 0.4 # phosphorus (mmol P/m^3) + N3: + long_name: nitrate + model: ogs/bfm_pelagic_base + parameters: + composition: n # elemental composition + initialization: + n: 8.0 # nitrogen (mmol N/m^3) + N4: + long_name: ammonium + model: ogs/bfm_pelagic_base + parameters: + composition: n # elemental composition + initialization: + n: 0.1 # nitrogen (mmol N/m^3) + N5: + long_name: silicate + model: ogs/bfm_pelagic_base + parameters: + composition: s # elemental composition + initialization: + s: 4.5 # silicate (mmol Si/m^3) + N6: + long_name: Reduction equivalent + model: ogs/bfm_pelagic_base + parameters: + composition: r # elemental composition + initialization: + r: 1.0 # Reduction equivalent (mmol Eq/m^3) + O3: + long_name: dissolved inorganic carbon + model: ogs/PelagicCSYS +# parameters: +# composition: c # elemental composition + initialization: + c: 28500.00 # Dissolved Inorganic Carbon (mg C /m^3) + coupling: + N1p: N1/p # phosphate (mmol P/m^3) + N5s: N5/s # silicate (mmol Si/m^3) + O3h: O3h/h + O2: + long_name: Dissolved Oxygen + model: ogs/PelOxygen +# parameters: +# composition: o # elemental composition + initialization: + o: 300.0 + O3h: + long_name: alkalinity + model: ogs/bfm_pelagic_base + parameters: + composition: h # elemental composition + initialization: + h: 2660.0 # alkalinity (mmol m3) + O4: + long_name: Nitrogen Sink + model: ogs/bfm_pelagic_base + parameters: + composition: n # elemental composition + initialization: + n: 200.0 + R1: + long_name: Dissolved Organic carbon Labile + model: ogs/bfm_pelagic_base + parameters: + composition: cnp # elemental composition + initialization: + c: 80.0 # Dissolved Organic Carbon (mg C /m^3) +# n: 1.260E-002 # Dissolved Organic Nitrogen (mmol N /m^3) +# p: 7.8620E-004 # Dissolved Organic Phosphorus (mmol P /m^3) + n: 1.008 # adjusted for c=80 instead c=1 + p: 0.062 # adjusted for c=80 instead c=1 + R2: + long_name: Dissolved Organic carbon semi-Labile + model: ogs/bfm_pelagic_base + parameters: + composition: c # elemental composition + initialization: + c: 400.0 # Dissolved Organic Carbon (mg C /m^3) + R3: + long_name: Dissolved Organic carbon semi-refractory + model: ogs/bfm_pelagic_base + parameters: + composition: c # elemental composition + initialization: + c: 480.0 # Dissolved Organic Carbon (mg C /m^3) + R6: + long_name: Small Particulate Organic carbon + model: ogs/bfm_pelagic_base + parameters: + composition: cpns # elemental composition + rm: 7.0 # Sinking Velocity + initialization: + c: 1.0 # POC (mg C /m^3) + n: 1.260E-002 # PON (mmol N /m^3) + p: 7.8620E-004 # POP (mmol P /m^3) + s: 1.260E-002 # POS (mmol S /m^3) + R8: + long_name: Large Particulate Organic carbon + model: ogs/bfm_pelagic_base + parameters: + composition: cpns # elemental composition + rm: 15.00 # Sinking Velocity + initialization: + c: 1.0 # POC (mg C /m^3) + n: 1.260E-002 # PON (mmol N /m^3) + p: 7.8620E-004 # POP (mmol P /m^3) + s: 1.260E-002 # POS (mmol S /m^3) + X1: + long_name: labile CDOM + model: ogs/bfm_pelagic_base + parameters: + composition: c # elemental composition + initialization: + c: 1.000000000000000E-000 + X2: + long_name: semi labile CDOM + model: ogs/bfm_pelagic_base + parameters: + composition: c # elemental composition + initialization: + c: 3.000000000000000E-000 + X3: + long_name: semi refractory CDOM + model: ogs/bfm_pelagic_base + parameters: + composition: c # elemental composition + initialization: + c: 1.250000000000000E-000 +# ---------------------- P1 Diatom ---------------------- + P1: + long_name: diatoms + model: ogs/Phyto + parameters: +# --------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Characteristic Q10 coefficient + p_temp: 0.0 # [-] Cut-off threshold for temperature factor + p_sum: 2.5 # [1/d] maximum specific productivity at reference temperature (1/d) + p_srs: 0.076 # [1/d] Respiration rate at 10 degrees C + p_fR6: 0.5 # [-] fraction of lysis to small POC (R6) + p_sdmo: 0.0 # [1/d] Max.specific nutrient-stress lysis rate + p_thdo: 0.0 # [-] Half saturation constant for nutrient stress lysis + p_seo: 0.0 # [1/d] Extra lysis rate (biomass density-dependent) + p_sheo: 0.0 # [mgC/3] Half saturation constant for extra lysis + p_pu_ea: 0.10 # [-] Excreted fraction of primary production + p_pu_ra: 0.1 # [-] Activity respiration fraction + p_pu_rn: 0.35 # [-] nutrient stress respiration fraction + p_switchDOC: 2 # [1-3] Switch for the type of DOC excretion + # This choice must be consistent with bacteria + # 1. All DOC is released as R1c (Vichi et al., 2007) + # 2. Activity DOC is released as R2c (Vichi et al., 2004) + # (there is no nutrient-stress excretion) + # 3. All DOC is released as R2c (Polimene et al., 2006) +# --------- Nutrient parameters in phytoplankton ----------------- + p_netgrowth: .TRUE. # [T or F] Logical switch for nutrient-limited growth + # .T. nutrient-balanced growth (Vichi et al.2004) + # .F. nutrient-stress carbon excretion + # (Baretta-Bekker et al.1995 and Vichi et al.2007) + p_limnut: 1 # Switch for N-P co-limitation + # 0. Geometric mean + # 1. Threshold (Liebig-like) + # 2. Combined +# ---- N limitation control ---- + p_qun: 0.025 # [m3/mgC/d] Membrane affinity for N + p_lN4: 1.0 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 + p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) + p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C + p_xqn: 2.0 # [-] Multiplication factor for luxury storage +# ---- P limitation control ---- + p_qup: 0.0025 # [m3/mgC/d] Membrane affinity for P + p_qplc: 0.0004288 # [mmolN/mgC] minimum phosphorus to carbon ratio (mmol P/mg C) + p_qpcPPY: 0.000786 # [mmolP/mgC] Reference quotum P:C + p_xqp: 2.0 # [-] Multiplication factor for luxury storage +# ---- Si limitation control ---- + p_switchSi: 2 # [1-2] Switch for Silica limitation + # 1. Si limitation is controlled by external Si conc. + # 2. Si limitation is controlled by internal quota + p_chPs: 0.3 # [mmolSi/m3] Half saturation conc. for dissolved Si limitation + p_Contois: 0.0 # [>=0] If >0, use Contois formulation + p_qus: 0.0025 # [m3/mgC/d] Membrane affinity for Si + p_qslc: 0.007 # [mmolSi/mgC] minimum silicate to carbon ratio (mmol Si/mg C) + use_Si: .TRUE. # use silicate, default = false + p_qscPPY: 0.01 # [mmolSi/mgC] Reference quotum Si:C +# ---- nutrient stressed sinking ---- + p_esNI: 0.7 # [-] Nutrient stress threshold for sinking + p_res: 5.0 # [m/d] Maximum Sinking vel city (m/d) +# ---- Calcification ---- + p_caco3r: 0.0 # [-] Reference PIC:POC (rain) ratio +# ---- CDOM production ---- + p_fX1p: 0.00 # [-] fraction of colored labile DOC + p_fX2p: 0.053 # [-] fraction of colored semi-labile DOC +# --------- Chlorophyll parameters ----------- + p_switchChl: 2 # [1-4] Switch for Chla-a synthesis + p_sdchl: 0.0 # [1/d] Specific turnover rate for Chla + p_alpha_chl: 0.000768 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve + p_quantum_yield: 0.750e-3 # [mgC / uE] Photochemical efficiency + p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono + p_OT: 1 # [1-9] type of absorption/scattering spectra + p_qlcPPY: 0.026 # [mgChla/mgC] Reference quotum Chla:C + p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C + p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient + p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C + p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K +# --------- Sinking parameters ----------- + p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate + initialization: + c: 8.0 # carbon (mg C/m^3) + n: 0.1008 # nitrogen (mmol N/m^3) + p: 0.006288 # phosphate (mmol N/m^3) + s: 0.08 # silicate (mmol Si/m^3) + Chl: 0.16 # chlorophyll a (mg/m^3) + coupling: + 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) + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + O2o: O2/o # Oxygen (mmol O/m^3) + R1c: R1/c + R1n: R1/n + R1p: R1/p + R2c: R2/c + R6c: R6/c + R6n: R6/n + R6s: R6/s + R6p: R6/p + R8c: R8/c + R8n: R8/n + R8s: R8/s + R8p: R8/p + X1c: X1/c + X2c: X2/c + O3h: O3h/h + O5c: O5/c + PAR: lightspectral/PAR_P1 +# ---------------------- P2 nanoflagellates ---------------------- + P2: + long_name: nanoflagellates + model: ogs/Phyto + parameters: +# --------- Physiological parameters ----------------- + p_q10: 2.25 # [-] Characteristic Q10 coefficient + p_temp: 0.0 # [-] Cut-off threshold for temperature factor + p_sum: 2.6 # [1/d] maximum specific productivity at reference temperature (1/d) + p_srs: 0.09 # [1/d] Respiration rate at 10 degrees C + p_fR6: 1.0 # [-] fraction of lysis to small POC (R6) + p_sdmo: 0.0 # [1/d] Max.specific nutrient-stress lysis rate + p_thdo: 0.0 # [-] Half saturation constant for nutrient stress lysis + p_seo: 0.0 # [1/d] Extra lysis rate (biomass density-dependent) + p_sheo: 0.0 # [mgC/3] Half saturation constant for extra lysis + p_pu_ea: 0.15 # [-] Excreted fraction of primary production + p_pu_ra: 0.1 # [-] Activity respiration fraction + p_pu_rn: 0.35 # [-] nutrient stress respiration fraction + p_switchDOC: 2 # [1-3] 2. Activity DOC is released as R2c (Vichi et al., 2004) +# --------- Nutrient parameters in phytoplankton ----------------- + p_netgrowth: .TRUE. # [T or F] .T. nutrient-balanced growth (Vichi et al.2004) + p_limnut: 1 # Switch for N-P co-limitation, 1. Threshold (Liebig-like) +# ---- N limitation control ---- + p_qun: 0.025 # [m3/mgC/d] Membrane affinity for N + p_lN4: 0.5 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 + p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) + p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C + p_xqn: 2.0 # [-] Multiplication factor for luxury storage +# ---- P limitation control ---- + p_qup: 0.0035 # [m3/mgC/d] Membrane affinity for P + p_qplc: 0.00035 # [mmolN/mgC] minimum phosphorus to carbon ratio (mmol P/mg C) + p_qpcPPY: 0.000786 # [mmolP/mgC] Reference quotum P:C + p_xqp: 2.0 # [-] Multiplication factor for luxury storage +# ---- nutrient stressed sinking ---- + p_esNI: 0.75 # [-] Nutrient stress threshold for sinking + p_res: 0.0 # [m/d] Maximum Sinking vel city (m/d) +# ---- Calcification ---- + use_CaCO3: .TRUE. # use CaCO3, default = false + p_caco3r: 0.3 # [-] Reference PIC:POC (rain) ratio +# ---- CDOM production ---- + p_fX1p: 0.00 # [-] fraction of colored labile DOC + p_fX2p: 0.029 # [-] fraction of colored semi-labile DOC +# --------- Chlorophyll parameters ----------- + p_switchChl: 2 # [1-4] Switch for Chla-a synthesis + p_sdchl: 0.0 # [1/d] Specific turnover rate for Chla + p_alpha_chl: 0.0002016 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve + p_quantum_yield: 0.2016e-3 # [mgC / uE] Photochemical efficiency + p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono + p_OT: 2 # [1-9] type of absorption/scattering spectra + p_qlcPPY: 0.045 # [mgChla/mgC] Reference quotum Chla:C + p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C + p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient + p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C + p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K +# --------- Sinking parameters ----------- + p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate + initialization: + c: 8.0 # carbon (mg C/m^3) + n: 0.1008 # nitrogen (mmol N/m^3) + p: 0.006288 # phosphate (mmol N/m^3) + Chl: 0.16 # chlorophyll a (mg/m^3) + coupling: + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + O2o: O2/o # Oxygen (mmol O/m^3) + R1c: R1/c + R1n: R1/n + R1p: R1/p + R2c: R2/c + R6c: R6/c + R6n: R6/n + R6p: R6/p + R8c: R8/c + R8n: R8/n + R8p: R8/p + X1c: X1/c + X2c: X2/c + O3h: O3h/h + O5c: O5/c + PAR: lightspectral/PAR_P2 +# ---------------------- P3 Picophytoplankton ---------------------- + P3: + long_name: Picoplankton + model: ogs/Phyto + parameters: +# --------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Characteristic Q10 coefficient + p_temp: 0.75 # [-] Cut-off threshold for temperature factor + p_sum: 3.5 # [1/d] maximum specific productivity at reference temperature (1/d) + p_srs: 0.1 # [1/d] Respiration rate at 10 degrees C + p_fR6: 1.0 # [-] fraction of lysis to small POC (R6) + p_sdmo: 0.0 # [1/d] Max.specific nutrient-stress lysis rate + p_thdo: 0.0 # [-] Half saturation constant for nutrient stress lysis + p_seo: 0.0 # [1/d] Extra lysis rate (biomass density-dependent) + p_sheo: 0.0 # [mgC/3] Half saturation constant for extra lysis + p_pu_ea: 0.15 # [-] Excreted fraction of primary production + p_pu_ra: 0.2 # [-] Activity respiration fraction + p_pu_rn: 0.35 # [-] nutrient stress respiration fraction + p_switchDOC: 2 # [1-3] Switch for the type of DOC excretion + # This choice must be consistent with bacteria + # 1. All DOC is released as R1c (Vichi et al., 2007) + # 2. Activity DOC is released as R2c (Vichi et al., 2004) + # (there is no nutrient-stress excretion) + # 3. All DOC is released as R2c (Polimene et al., 2006) +# --------- Nutrient parameters in phytoplankton ----------------- + p_netgrowth: .TRUE. # [T or F] Logical switch for nutrient-limited growth + # .T. nutrient-balanced growth (Vichi et al.2004) + # .F. nutrient-stress carbon excretion + # (Baretta-Bekker et al.1995 and Vichi et al.2007) + p_limnut: 1 # Switch for N-P co-limitation + # 0. Geometric mean + # 1. Threshold (Liebig-like) + # 2. Combined +# ---- N limitation control ---- + p_qun: 0.25 # [m3/mgC/d] Membrane affinity for N + p_lN4: 0.1 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 + p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) + p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C + p_xqn: 2.0 # [-] Multiplication factor for luxury storage +# ---- P limitation control ---- + p_qup: 0.0025 # [m3/mgC/d] Membrane affinity for P + p_qplc: 0.0004288 # [mmolN/mgC] minimum phosphorus to carbon ratio (mmol P/mg C) + p_qpcPPY: 0.000786 # [mmolP/mgC] Reference quotum P:C + p_xqp: 2.0 # [-] Multiplication factor for luxury storage +# ---- Si limitation control ---- +# Silicon absent in this PFT +# ---- nutrient stressed sinking ---- + p_esNI: 0.75 # [-] Nutrient stress threshold for sinking + p_res: 0.0 # [m/d] Maximum Sinking vel city (m/d) +# ---- Calcification ---- + p_caco3r: 0.0 # [-] Reference PIC:POC (rain) ratio +# ---- CDOM production ---- + p_fX1p: 0.00 # [-] fraction of colored labile DOC + p_fX2p: 0.026 # [-] fraction of colored semi-labile DOC +# --------- Chlorophyll parameters ----------- + p_switchChl: 2 # [1-4] Switch for Chla-a synthesis + p_sdchl: 0.0 # [1/d] Specific turnover rate for Chla + p_alpha_chl: 0.0010104 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve + p_quantum_yield: 1.0104e-3 # [mgC / uE] Photochemical efficiency + p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono + p_OT: 3 # [1-9] type of absorption/scattering spectra + p_qlcPPY: 0.014 # [mgChla/mgC] Reference quotum Chla:C + p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C + p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient + p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C + p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K +# --------- Sinking parameters ----------- + p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate + initialization: + c: 8.0 # carbon (mg C/m^3) + n: 0.1008 # nitrogen (mmol N/m^3) + p: 0.006288 # phosphate (mmol N/m^3) + Chl: 0.16 # chlorophyll a (mg/m^3) + coupling: + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + O2o: O2/o # Oxygen (mmol O/m^3) + R1c: R1/c + R1n: R1/n + R1p: R1/p + R2c: R2/c + R6c: R6/c + R6n: R6/n + R6p: R6/p + R8c: R8/c + R8n: R8/n + R8p: R8/p + X1c: X1/c + X2c: X2/c + O3h: O3h/h + O5c: O5/c + PAR: lightspectral/PAR_P3 +# ---------------------- P4 dinoflagellates ---------------------- + P4: + long_name: dinoflagellates + model: ogs/Phyto + parameters: +# --------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Characteristic Q10 coefficient + p_temp: 0.0 # [-] Cut-off threshold for temperature factor + p_sum: 1.5 # [1/d] maximum specific productivity at reference temperature (1/d) + p_srs: 0.1 # [1/d] Respiration rate at 10 degrees C + p_fR6: 0.5 # [-] fraction of lysis to small POC (R6) + p_sdmo: 0.0 # [1/d] Max.specific nutrient-stress lysis rate + p_thdo: 0.0 # [-] Half saturation constant for nutrient stress lysis + p_seo: 0.0 # [1/d] Extra lysis rate (biomass density-dependent) + p_sheo: 100.0 # [mgC/3] Half saturation constant for extra lysis + p_pu_ea: 0.20 # [-] Excreted fraction of primary production + p_pu_ra: 0.1 # [-] Activity respiration fraction + p_pu_rn: 0.35 # [-] nutrient stress respiration fraction + p_switchDOC: 2 # [1-3] 2. Activity DOC is released as R2c (Vichi et al., 2004) +# --------- Nutrient parameters in phytoplankton ----------------- + p_netgrowth: .TRUE. # [T or F] .T. nutrient-balanced growth (Vichi et al.2004) + p_limnut: 1 # Switch for N-P co-limitation, 1. Threshold (Liebig-like) +# ---- N limitation control ---- + p_qun: 0.025 # [m3/mgC/d] Membrane affinity for N + p_lN4: 1.0 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 + p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) + p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C + p_xqn: 2.0 # [-] Multiplication factor for luxury storage +# ---- P limitation control ---- + p_qup: 0.0025 # [m3/mgC/d] Membrane affinity for P + p_qplc: 0.0004288 # [mmolN/mgC] minimum phosphorus to carbon ratio (mmol P/mg C) + p_qpcPPY: 0.000786 # [mmolP/mgC] Reference quotum P:C + p_xqp: 2.0 # [-] Multiplication factor for luxury storage +# ---- nutrient stressed sinking ---- + p_esNI: 0.75 # [-] Nutrient stress threshold for sinking + p_res: 2.5 # [m/d] Maximum Sinking vel city (m/d) +# ---- Calcification ---- + p_caco3r: 0.0 # [-] Reference PIC:POC (rain) ratio +# ---- CDOM production ---- + p_fX1p: 0.00 # [-] fraction of colored labile DOC + p_fX2p: 0.035 # [-] fraction of colored semi-labile DOC +# --------- Chlorophyll parameters ----------- + p_switchChl: 2 # [1-4] Switch for Chla-a synthesis + p_sdchl: 0.0 # [1/d] Specific turnover rate for Chla + p_alpha_chl: 0.0002616 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve + p_quantum_yield: 0.2616e-3 # [mgC / uE] Photochemical efficiency + p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono + p_OT: 4 # [1-9] type of absorption/scattering spectra + p_qlcPPY: 0.019 # [mgChla/mgC] Reference quotum Chla:C + p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C + p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient + p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C + p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K +# --------- Sinking parameters ----------- + p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate + initialization: + c: 8.0 # carbon (mg C/m^3) + n: 0.1008 # nitrogen (mmol N/m^3) + p: 0.006288 # phosphate (mmol N/m^3) + Chl: 0.16 # chlorophyll a (mg/m^3) + coupling: + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + O2o: O2/o # Oxygen (mmol O/m^3) + R1c: R1/c + R1n: R1/n + R1p: R1/p + R2c: R2/c + R6c: R6/c + R6n: R6/n + R6p: R6/p + R8c: R8/c + R8n: R8/n + R8p: R8/p + X1c: X1/c + X2c: X2/c + O3h: O3h/h + O5c: O5/c + PAR: lightspectral/PAR_P4 +# ---------------------- B1 Pelagic heteretrophic bacteria ---------------------- +# + B1: + long_name: Bacteria + model: ogs/PelBac + parameters: +# --------- Physiological parameters ----------------- + p_version : 2 # Switch for bacteria parameterization +# 1 : Baretta-Bekker et al. 1995; +# Vichi et al., 2007 +# 2 : Vichi et al., 2004 +# 3 : Polimene et al., 2006 + p_q10 : 2.95 # [-] Q10-value (temperature dependency) + p_chdo : 30.0 # [mmol/m3] Half-saturation constant for O2 limitation + p_sd : 0.0 # [1/d] Specific mortality rate + p_sd2 : 0.0 # [1/d] Density dependent specific mortality rate + p_suhR1 : 0.5 # [1/d] Specific potential uptake for nutrient-rich DOM + p_sulR1 : 0.0 # [1/d] Specific potential uptake for nutrient-poor DOM + p_suR2 : 0.05 # [1/d] Specific potential uptake for semi-labile DOC + p_suR3 : 0.0 # [1/d] Specific potential uptake for semi-refractory DOC + p_suR6 : 0.012 # [1/d] Specific potential uptake for small POM (1/d) + p_suR8 : 0.03 # [1/d] Specific potential uptake for large POM (1/d) + p_sum : 8.38 # [1/d] Potential specific growth rate + p_pu_ra : 0.76 # [-] Activity respiration fraction + p_pu_ra_o : 0.2 # [-] Additional respiration fraction at low O2 conc + p_srs : 0.01 # [1/d] Specific rest respiration + p_qncPBA : 0.017 # [mmolN/mgC] Optimal N/C ratio + p_qpcPBA : 0.0019 # [mmolP/mgC] Optimal P/C ratio + p_qlnc : 0.0085 # [mmolN/mgC] Minimal N/C ratio + p_qlpc : 0.00095 # [mmolP/mgC] Minimal P/C ratio + p_qun : 0.05 # [mmolN/mgC/day] Membrane affinity for N + p_qup : 0.005 # [mmolP/mgC/day] Membrane affinity for P + p_chn : 0.05 # [mmolN/m3] Half saturation ammonium conc. for uptake + p_chp : 1.00 # [mmolP/m3] Half saturation phosphate conc. for uptake + p_rec : 1.0 # [1/d] Relaxation timescale for semi-labile excretion + p_ruen : 1.0 # [1/d] Relaxation timescale for N uptake/remin. + p_ruep : 1.0 # [1/d] Relaxation timescale for P uptake/remin. + p_pu_ea_R3 : 0.0 # [-] Excretion of semi-refractory DOC + p_qro : 0.5 # [mmolHS-/mmolO2] Stoichiometric coefficient for anaerobic reactions + p_pe_R1c: 0.60 # [-] Fractional content of C in cytoplasm + p_pe_R1n: 0.72 # [-] Fractional content of N in cytoplasm + p_pe_R1p: 0.832 # [-] Fractional content of P in cytoplasm +# ---- CDOM production ---- + p_fX1b: 0.00 # [-] fraction of colored labile DOC + p_fX2b: 0.02 # [-] fraction of colored semi-labile DOC + p_fX3b: 0.018 # [-] fraction of colored semi-refractory DOC +# ---- POM split ---- + p_fR6: 0.0 # [-] fraction of lysis to small POC (R6) + initialization: + c: 1.0 # carbon (mg C/m^3) + n: 1.700000000000000E-002 # nitrogen (mmol N/m^3) + p: 1.900000000000000E-003 # phosphate (mmol N/m^3) + coupling: + N1p: N1/p # phosphate (mmol P/m^3) + N3n: N3/n # nitrate (mmol N/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + N6r: N6/r + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + O3h: O3h/h + O2o: O2/o # Oxygen (mmol O/m^3) + R1c: R1/c + R1n: R1/n + R1p: R1/p + R2c: R2/c + R3c: R3/c + R6c: R6/c + R6n: R6/n + R6p: R6/p + R6s: R6/s + R8c: R8/c + R8n: R8/n + R8p: R8/p + R8s: R8/s + X1c: X1/c + X2c: X2/c + X3c: X3/c +# ---------------------- Z5 Microzooplankton ---------------------- + Z5: +# use: false + long_name: Microzooplankton + model: ogs/MicroZoo + parameters: +# --------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Characteristic Q10 coefficient + p_srs: 0.01 # [1/d] Respiration rate at 10 degrees Celsius + p_sum: 2.71 # [1/d] Potential growth rate + p_sdo: 0.05 # [1/d] Mortality rate due to oxygen limitation + p_sd: 0.0 # [1/d] Temperature independent mortality rate + p_pu: 0.5 # [-] Assimilation efficiency + p_pu_ea: 0.5 # [-] Fraction of activity excretion + p_chro: 8 # [mmolO2/m3] Half-saturation oxygen concentration + p_chuc: 15.0 # [mgC/m3] Half-saturation Food concentration for Type II + p_minfood: 37.5 # [mgC/m3] Half-saturation food concentration for + # preference factor + p_pecaco3: 0.5 # [-] Portion of egested calcified shells during grazing + p_qpcMIZ: 1.85e-3 # [mmolN/mgC] Maximum quotum P:C + p_qncMIZ: 1.67e-2 # [mmolN/mgC] Maximum quotum N:C + nprey: 7 # [-] Number of preys + suprey1: 0.1 # [-] Availability of pelagic Bacteria group b + # to Zooplankton group z + suprey2: 0.35 # [-] Availability of PhytoPlankton group P1 + # to Zooplankton group z + suprey3: 0.5 # [-] Availability of PhytoPlankton group P2 + # to Zooplankton group z + suprey4: 0.3 # [-] Availability of PhytoPlankton group P3 + # to Zooplankton group z + suprey5: 0.1 # [-] Availability of PhytoPlankton group P4 + # to Zooplankton group z + suprey6: 1.0 # [-] Availability of MicroZooplankton group Z5 + # to Zooplankton group z + suprey7: 1.0 # [-] Availability of MicroZooplankton group Z6 + # to Zooplankton group z +#-------------------------------------------------------------------- + isP21: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP22: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP23: 1 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP24: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP25: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP26: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP27: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] +#-------------------------------------------------------------------- + p_fR6: 0.5 # [-] Fraction of lysis and sloppy predation to small POC (R6) + p_pe_R1c: 0.60 # [-] Fractional content of C in cytoplasm + p_pe_R1n: 0.72 # [-] Fractional content of C in cytoplasm + p_pe_R1p: 0.832 # [-] Fractional content of C in cytoplasm + p_fX1z: 0.018 # [-] fraction of colored labile DOC + initialization: + c: 1.0 # carbon (mg C/m^3) + n: 0.0167 # nitrogen (mmol N/m^3) + p: 0.00185 # phosphate (mmol N/m^3) + coupling: + O2o: O2/o # Oxygen (mmol O2/m^3) + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + N1p: N1/p # phosphate (mmol P/m^3) + R6c: R6/c # POC (mgC/m3) + R6s: R6/s # POSi (mgSi/m3) + R6n: R6/n # PON (mmolN/m3) + R6p: R6/p # POP (mmolP/m3) + R8c: R8/c # POC (mgC/m3) + R8s: R8/s # POSi (mgSi/m3) + R8n: R8/n # PON (mmolN/m3) + R8p: R8/p # POP (mmolP/m3) + X1c: X1/c # labile CDOM + R1c: R1/c # labile DOC + R1n: R1/n # labile DON + R1p: R1/p # labile DOP + prey1: B1 + prey2: P1 + prey3: P2 + prey4: P3 + prey5: P4 + prey6: Z5 + prey7: Z6 + O3h: O3h/h + O5c: O5/c +# ---------------------- Z6 Microzooplankton ---------------------- + Z6: +# use: false + long_name: Heterotrophic Nanoflagellates (HNAN) + model: ogs/MicroZoo + parameters: +# --------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Characteristic Q10 coefficient + p_srs: 0.01 # [1/d] Respiration rate at 10 degrees Celsius + p_sum: 3.88 # [1/d] Potential growth rate + p_sdo: 0.05 # [1/d] Mortality rate due to oxygen limitation + p_sd: 0.0 # [1/d] Temperature independent mortality rate + p_pu: 0.3 # [-] Assimilation efficiency + p_pu_ea: 0.5 # [-] Fraction of activity excretion + p_chro: 8 # [mmolO2/m3] Half-saturation oxygen concentration + p_chuc: 100.0 # [mgC/m3] Half-saturation Food concentration for Type II + p_minfood: 50.0 # [mgC/m3] Half-saturation food concentration for + # preference factor + p_pecaco3: 0.5 # [-] Portion of egested calcified shells during grazing + p_qpcMIZ: 1.85e-3 # [mmolN/mgC] Maximum quotum P:C + p_qncMIZ: 1.67e-2 # [mmolN/mgC] Maximum quotum N:C + nprey: 7 # [-] Number of preys + suprey1: 1.0 # [-] Availability of pelagic Bacteria group b + # to Zooplankton group z + suprey2: 0.0 # [-] Availability of PhytoPlankton group P1 + # to Zooplankton group z + suprey3: 0.2 # [-] Availability of PhytoPlankton group P2 + # to Zooplankton group z + suprey4: 1.0 # [-] Availability of PhytoPlankton group P3 + # to Zooplankton group z + suprey5: 0.0 # [-] Availability of PhytoPlankton group P4 + # to Zooplankton group z + suprey6: 0.0 # [-] Availability of MicroZooplankton group Z5 + # to Zooplankton group z + suprey7: 0.2 # [-] Availability of MicroZooplankton group Z6 + # to Zooplankton group z +#-------------------------------------------------------------------- + isP21: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP22: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP23: 1 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP24: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP25: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP26: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP27: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] +#-------------------------------------------------------------------- + p_fR6: 1.0 # [-] Fraction of lysis and sloppy predation to small POC (R6) + p_pe_R1c: 0.60 # [-] Fractional content of C in cytoplasm + p_pe_R1n: 0.72 # [-] Fractional content of C in cytoplasm + p_pe_R1p: 0.832 # [-] Fractional content of C in cytoplasm + p_fX1z: 0.030 # [-] fraction of colored labile DOC + initialization: + c: 1.0 # carbon (mg C/m^3) + n: 0.0167 # nitrogen (mmol N/m^3) + p: 0.00185 # phosphate (mmol N/m^3) + coupling: + O2o: O2/o # Oxygen (mmol O2/m^3) + O3c: O3/c # dissolved inorganic carbon (mg C/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + N1p: N1/p # phosphate (mmol P/m^3) + R6c: R6/c # POC (mgC/m3) + R6s: R6/s # POSi (mgSi/m3) + R6n: R6/n # PON (mmolN/m3) + R6p: R6/p # POP (mmolP/m3) + R8c: R8/c # POC (mgC/m3) + R8s: R8/s # POSi (mgSi/m3) + R8n: R8/n # PON (mmolN/m3) + R8p: R8/p # POP (mmolP/m3) + X1c: X1/c # labile CDOM + R1c: R1/c # labile DOC + R1n: R1/n # labile DON + R1p: R1/p # labile DOP + prey1: B1 + prey2: P1 + prey3: P2 + prey4: P3 + prey5: P4 + prey6: Z5 + prey7: Z6 + O3h: O3h/h + O5c: O5/c +# ---------------------- Z3 Carnivorous Mesozooplankton ---------------------- + Z3: +# use: false + long_name: Carnivorous Mesozooplankton + model: ogs/MesoZoo + parameters: +# --------------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Q10 value for physiological rates + p_srs: 0.01 # [1/d] Respiration rate at 10 degrees C + p_sum: 2.0 # [1/d] Maximal productivity at 10 degrees C + p_sd: 0.02 # [1/d] Background natural mortality + p_vum: 0.008 # [m3/mgC/d] Specific search volume + p_puI: 0.6 # [-] Assimilation efficiency + p_peI: 0.3 # [-] Fraction of Faeces production + p_sdo: 0.01 # [m3/mgC/d] Specific density-dependent mortality + p_sds: 2.0 # [-] Exponent of density-dependent mortality + p_pecaco3: 0.75 # [-] Portion of egested calcified shells during grazing + p_qpcMEZ: 1.67e-3 # [mmolP/mgC] Maximum quotum P:C + p_qncMEZ: 0.015 # [mmolN/mgC] Maximum quotum N:C + p_clO2o: 30.0 # [mmolO2/m3] Half-saturation oxygen concentration + p_fR6: 0.5 # [-] Fraction of lysis and sloppy predation to small POC (R6) +#----------------------------------------------------------------------------- + nprey: 3 # [-] Number of preys + suprey1: 1.0 # [-] Availability of PhytoPlankton group P4 + # to Zooplankton group z + suprey2: 1.0 # [-] Availability of MicroZooplankton group Z3 + # to Zooplankton group z + suprey3: 1.0 # [-] Availability of MicroZooplankton group Z4 + # to Zooplankton group z +#------------------------------------------------------------------------------ + isP21: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP22: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP23: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] +#------------------------------------------------------------------------------ + initialization: + c: 1.0 # carbon (mg C/m^3) + n: 0.015 # nitrogen (mmol N/m^3) + p: 0.00167 # phosphate (mmol N/m^3) + coupling: + O2o: O2/o # dissolved oxygen + O3c: O3/c # DIC + N1p: N1/p # phosphate (mmol P/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R6c: R6/c # POC + R6n: R6/n # PON + R6p: R6/p # POP + R6s: R6/s # biogenic silica (mmol Si/m^3) + R8c: R8/c # POC + R8n: R8/n # PON + R8p: R8/p # POP + R8s: R8/s # biogenic silica (mmol Si/m^3 + prey1: P4 + prey2: Z3 + prey3: Z4 + O3h: O3h/h + O5c: O5/c +# --------------------------------------------------------------------------- +# ---------------------- Z4 Omnivorous Mesozooplankton ---------------------- + Z4: +# use: false + long_name: Omnivorous Mesozooplankton + model: ogs/MesoZoo + parameters: +# ----------------- Physiological parameters ----------------- + p_q10: 2.0 # [-] Q10 value for physiological rates + p_srs: 0.02 # [1/d] Respiration rate at 10 degrees C + p_sum: 2.0 # [1/d] Maximal productivity at 10 degrees C + p_sd: 0.02 # [1/d] Background natural mortality + p_vum: 0.02 # [m3/mgC/d] Specific search volume + p_puI: 0.6 # [-] Assimilation efficiency + p_peI: 0.35 # [-] Fraction of Faeces production + p_sdo: 0.01 # [m3/mgC/d] Specific density-dependent mortality + p_sds: 2.0 # [-] Exponent of density-dependent mortality + p_pecaco3: 0.75 # [-] Portion of egested calcified shells during grazing + p_qpcMEZ: 1.67e-3 # [mmolP/mgC] Maximum quotum P:C + p_qncMEZ: 0.015 # [mmolN/mgC] Maximum quotum N:C + p_clO2o: 30.0 # [mmolO2/m3] Half-saturation oxygen concentration + p_fR6: 0.5 # [-] Fraction of lysis and sloppy predation to small POC (R6) +#------------------------------------------------------------------------------- + nprey: 5 # [-] Number of preys + suprey1: 1.0 # [-] Availability of PhytoPlankton group P1 + # to Zooplankton group z + suprey2: 0.75 # [-] Availability of PhytoPlankton group P2 + # to Zooplankton group z + suprey3: 1.0 # [-] Availability of PhytoPlankton group P4 + # to Zooplankton group z + suprey4: 1.0 # [-] Availability of MicroZooplankton group Z5 + # to Zooplankton group z + suprey5: 1.0 # [-] Availability of MicroZooplankton group Z4 + # to Zooplankton group z +#------------------------------------------------------------------------------- + isP21: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP22: 1 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP23: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP24: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] + isP25: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] +#------------------------------------------------------------------------------- + initialization: + c: 1.0 # carbon (mg C/m^3) + n: 0.015 # nitrogen (mmol N/m^3) + p: 0.00167 # phosphate (mmol N/m^3) + coupling: + O2o: O2/o # dissolved oxygen + O3c: O3/c # DIC + N1p: N1/p # phosphate (mmol P/m^3) + N4n: N4/n # ammonium (mmol N/m^3) + R6c: R6/c # POC + R6n: R6/n # PON + R6p: R6/p # POP + R6s: R6/s # biogenic silica (mmol Si/m^3) + R8c: R8/c # POC + R8n: R8/n # PON + R8p: R8/p # POP + R8s: R8/s # biogenic silica (mmol Si/m^3) + prey1: P1 + prey2: P2 + prey3: P4 + prey4: Z5 + prey5: Z4 + O3h: O3h/h + O5c: O5/c +# ---------------------- Pelagic chemistry ---------------------- +# + PelChem: + long_name: pelagic chemistry + model: ogs/PelChem + parameters: + p_clO2o: 10.0 # [mmolO2/m3] Half-saturation O2 concentration for nitrification and reoxidation + p_clN6r: 1.0 # [mmolHS/m3] Half-saturation concentration of reduction equivalents for denitrification[mmolO2/m3] + p_sN4N3: 0.01 # [1/d] Specific nitrification rate at 10 degC + p_q10N4N3: 2.367 # [-] Q10 factor for nitrification/denit + p_qon_nitri: 2.0 # [mmolO2/mmolN] stoichiometric coefficient for nitrification + p_qro: 0.5 # [mmolHS-/mmolO2] Stoichiometric coefficient for anaerobic reactions + p_sN3O4n: 0.35 # [1/d] Specific denitrification rate + p_rPAo: 1.0 # [mmolO2/m3/d] Reference anoxic mineralization rate + p_qon_dentri: 1.25 # [mmolO2/mmolN] Stoichiometric coefficient for denitrification + p_rOS: 0.05 # [1/d] Specific reoxidation rate of reduction equivalents + p_sR6N5: 0.1 # [1/d] Specific remineralization rate of biogenic silica (small POC) + p_q10R6N5: 1.49 # [-] Q10 factor for biogenic silica (small POC) + p_sR8N5: 0.1 # [1/d] Specific remineralization rate of biogenic silica (large POC) + p_q10R8N5: 1.49 # [-] Q10 factor for biogenic silica (large POC) + p_bX1c: 0.1 # [1/d] photodegradation (bleaching) rate X1c + p_bX2c: 0.03 # [1/d] photodegradation (bleaching) rate X2c + p_bX3c: 0.01 # [1/d] photodegradation (bleaching) rate X3c + p_IX1: 60.0 # [uE m-2 s-1] light threshold for X1c bleaching + p_IX2: 60.0 # [uE m-2 s-1] light threshold for X2c bleaching + p_IX3: 50.0 # [uE m-2 s-1] light threshold for X3c bleaching + p_rX3c: 0.00003 # [1/d] remineralization rate X3c and R3c + p_q10X: 2.95 # [-] q10 for CDOM degradation + p_Esource: 5 # [5 or 6] source of light for CDOM bleaching, 5=spectral, 6=mono + p_use_benthic: 0 #[0=F or 1=T] activate first-order benthic return + p_TauC: 1.0 #[d] remineralization of Carbon in detritus + p_TauN: 0.5 #[d] remineralization of Nitrogen in detritus + p_TauP: 1.0 #[d] remineralization of Phosphorus in detritus + p_Amm_rem: 0.2 #[0 to 1] fraction of detritus remineralized to NH4 + initialization: + coupling: + N1p: N1/p # phosphate (mmol P/m^3) + 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) + O3h: O3h/h # alkalinity (mmol /m^3) + O3c: O3/c # DIC + O4n: O4/n # N2 (mmol N/m^3) + N6r: N6/r # reduction equivalent (mmol HS/m^3) + N5s: N5/s # silicate (mmol Si/m^3) + X1c: X1/c # cdom X1c (mgC/m^3) + X2c: X2/c # cdom X2c (mgC/m^3) + X3c: X3/c # cdom X3c (mgC/m^3) + R3c: R3/c # cdom R3c (mgC/m^3) + R6s: R6/s # POSi (mgSi/m3) + R6c: R6/c # POC (mgC/m3) + R6n: R6/n # PON (mmolN/m3) + R6p: R6/p # POP (mmolP/m3) + R8s: R8/s # POSi (mgSi/m3) + R8c: R8/c # POC (mgC/m3) + R8n: R8/n # PON (mmolN/m3) + R8p: R8/p # POP (mmolP/m3) + PAR_tot: lightspectral/PAR_tot + isBen: Benthic_layer/isBen +## --------------------- CalciteDissolution + O5: +# use: false + long_name: calcite + model: ogs/CalciteDissolution + parameters: + p_kdca: 10.9 # [d-1] Calcite dissolution rate constant + p_nomega: 1.0 # [-] Order of the dissolution rate dependence on Omega + p_wsinkPIC: 30 # [m d-1] sinking velocity of PIC (Calcite) + c0: 1.0e-05 # [mg C/m^3] background concentration, default = 0.0 + initialization: + c: 1.0 # carbon (mg C/m^3) + coupling: + OCalc: O3/OCalc # calcite saturation (-) + O3c: O3/c # total dissolved inorganic carbon (mgC/m^3) + O3h: O3h/h # alkalinity (mmol/m^3) + Phyto_c: + long_name: total + model: weighted_sum + parameters: + n: 4 + coupling: + term1: P1_c + term2: P2_c + term3: P3_c + term4: P4_c + Phyto_Chl: + long_name: total + model: weighted_sum + parameters: + n: 4 + coupling: + term1: P1_Chl + term2: P2_Chl + term3: P3_Chl + term4: P4_Chl +# Phyto_NPP: +# long_name: total +# model: weighted_sum +# parameters: +# n: 4 +# coupling: +# term1: P1_run_result +# term2: P2_run_result +# term3: P3_run_result +# term4: P4_run_result From 98f47a18c548d396d886657f6a4bb626f722d5d6 Mon Sep 17 00:00:00 2001 From: Giovanni Galli Date: Thu, 11 Jun 2026 11:11:09 +0200 Subject: [PATCH 15/15] removed fabm_V13C.yaml --- fabm_V13C.yaml | 1108 ------------------------------------------------ 1 file changed, 1108 deletions(-) delete mode 100755 fabm_V13C.yaml diff --git a/fabm_V13C.yaml b/fabm_V13C.yaml deleted file mode 100755 index 9198e42..0000000 --- a/fabm_V13C.yaml +++ /dev/null @@ -1,1108 +0,0 @@ -check_conservation: false -require_initialization: true -log: true -instances: - Benthic_layer: - model: ogs/BenthicLayer - parameters: - p_BenDepth: 12000.0 - zenith_angle: - model: ogs/zenith_angle -# light: -# model: ogs/light -# parameters: -# pEPSCHL: 0.0088 # attenuation by Chlorophyll (m^2/mg Chl), default= 0.0088 -# pEPSCDOM: 0.01476 # attenuation by CDOM (m^2/mg C), default= 0.0646 -# EPS0r: 0.04 # background shortwave attenuation (1/m), default = 0.04 -# pEIR_eow: 0.4 # photosynthetically active fraction of shortwave radiation (-), default = 0.5 -# coupling: -# X1c: X1/c -# X2c: X2/c -# X3c: X3/c - light_atm: - model: spectral/atmosphere - parameters: - lambda_method: 1 - compute_mean_wind: true - spectral_output: 1 - relhum: - model: spectral/relhum - ozone: - model: spectral/ozone - lightspectral: - model: ogs/light_spectral_OASIM - parameters: - nlt: 33 # number of wavelenghts considered - npft: 4 # number of PFT considered - SdomX1: 0.0175 # spectral slope acdom of X1c [nm-1] - X1coeff: 0.015 # acdom coeff of X1c at lambda_aCDOM [m2/mgC] - SdomX2: 0.0162 # spectral slope acdom of X2c [nm-1] - X2coeff: 0.015 # acdom coeff of X2c at lambda_aCDOM [m2/mgC] - SdomX3: 0.0180 # spectral slope acdom of X3c [nm-1] - X3coeff: 0.015 # acdom coeff of X3c at lambda_aCDOM [m2/mgC] - Xmincoeff: 0.00 # minimum aCDOM [m-1] at 450nm - lambda_aCDOM: 450 # lambda at which reference acdom is given [nm] - compute_acdom: .FALSE. # logical [T=compute coeffs, F=use file] - Sapar: 0.013 # spectral slope anap [nm-1] - lambda_aPart: 440 # lambda at which reference anap is given [nm] - aparcoeff: 0.00058 # anap coeff at lambda_aPart [m2/mgC] - Sbpar: 0.5 # exponent bnap [-] - lambda_bPart: 550 # lambda at which reference bnap is given [nm] - bparcoeff: 0.0120 # bnap coeff at lambda_bPart [m2/mgC] - bb_to_b: 0.005 # back to total scatter POC [-] - compute_anap: .FALSE. # logical [T=comptute coeffs, F=use file] - p_epsP1: 0.0152 # mean absorption coefficient from 400-700nm for P1 [m2 mgChl-1] - p_epsP2: 0.0293 # mean absorption coefficient from 400-700nm for P2 [m2 mgChl-1] - p_epsP3: 0.0443 # mean absorption coefficient from 400-700nm for P3 [m2 mgChl-1] - p_epsP4: 0.0178 # mean absorption coefficient from 400-700nm for P4 [m2 mgChl-1] - compute_aph: .FALSE. # logical flag to scale aph [T=use file scaled to p_epsPn or F=use file unscaled] - p_bpsP1: 0.0140 # mean scattering coefficient from 400-700nm for P1 [m2 mgC-1] - p_bpsP2: 0.0077 # mean scattering coefficient from 400-700nm for P2 [m2 mgC-1] - p_bpsP3: 0.0101 # mean scattering coefficient from 400-700nm for P3 [m2 mgC-1] - p_bpsP4: 0.0112 # mean scattering coefficient from 400-700nm for P4 [m2 mgC-1] - compute_bph: .FALSE. # logical flag to scale bph [T=use file scaled to p_bpsPn or F=use file unscaled] - p_bbrP1: 0.0020 # non-spectral backscattering to total scattering ratio for P1 [-] - p_bbrP2: 0.0071 # non-spectral backscattering to total scattering ratio for P2 [-] - p_bbrP3: 0.0039 # non-spectral backscattering to total scattering ratio for P3 [-] - p_bbrP4: 0.0030 # non-spectral backscattering to total scattering ratio for P4 [-] - compute_bbc: .FALSE. # logical flag to compute bbc or read it from file [T=compute bc*bbr or F=use file] - p_useSPM: .FALSE. # if true requires input data specification in gotm.yaml - p_spmc1: 0.016 # basal absorption for minimal absorption at long wavelengths [m2 g-1] - p_spmc2: 0.054 # specific absorption at the reference wavelength [m2 g-1] - p_spmS: 0.012 # slope for exponential decline of aSPM with wavelength [nm-1] - lambda_aSPM: 440 # wavelength where reference aSPM (c2) is given - p_spmb: 0.7 # specific scattering at 555nm [m2 g-1] - p_spmbb: 0.008 # specific backscattering at 555nm [m2 g-1] - coupling: - X1c : X1/c - X2c : X2/c - X3c : X3/c - R6c : R6/c - R8c : R8/c - direct_band1 : light_atm/dir_sf_band1 - diffuse_band1 : light_atm/dif_sf_band1 - direct_band2 : light_atm/dir_sf_band2 - diffuse_band2 : light_atm/dif_sf_band2 - direct_band3 : light_atm/dir_sf_band3 - diffuse_band3 : light_atm/dif_sf_band3 - direct_band4 : light_atm/dir_sf_band4 - diffuse_band4 : light_atm/dif_sf_band4 - direct_band5 : light_atm/dir_sf_band5 - diffuse_band5 : light_atm/dif_sf_band5 - direct_band6 : light_atm/dir_sf_band6 - diffuse_band6 : light_atm/dif_sf_band6 - direct_band7 : light_atm/dir_sf_band7 - diffuse_band7 : light_atm/dif_sf_band7 - direct_band8 : light_atm/dir_sf_band8 - diffuse_band8 : light_atm/dif_sf_band8 - direct_band9 : light_atm/dir_sf_band9 - diffuse_band9 : light_atm/dif_sf_band9 - direct_band10 : light_atm/dir_sf_band10 - diffuse_band10 : light_atm/dif_sf_band10 - direct_band11 : light_atm/dir_sf_band11 - diffuse_band11 : light_atm/dif_sf_band11 - direct_band12 : light_atm/dir_sf_band12 - diffuse_band12 : light_atm/dif_sf_band12 - direct_band13 : light_atm/dir_sf_band13 - diffuse_band13 : light_atm/dif_sf_band13 - direct_band14 : light_atm/dir_sf_band14 - diffuse_band14 : light_atm/dif_sf_band14 - direct_band15 : light_atm/dir_sf_band15 - diffuse_band15 : light_atm/dif_sf_band15 - direct_band16 : light_atm/dir_sf_band16 - diffuse_band16 : light_atm/dif_sf_band16 - direct_band17 : light_atm/dir_sf_band17 - diffuse_band17 : light_atm/dif_sf_band17 - direct_band18 : light_atm/dir_sf_band18 - diffuse_band18 : light_atm/dif_sf_band18 - direct_band19 : light_atm/dir_sf_band19 - diffuse_band19 : light_atm/dif_sf_band19 - direct_band20 : light_atm/dir_sf_band20 - diffuse_band20 : light_atm/dif_sf_band20 - direct_band21 : light_atm/dir_sf_band21 - diffuse_band21 : light_atm/dif_sf_band21 - direct_band22 : light_atm/dir_sf_band22 - diffuse_band22 : light_atm/dif_sf_band22 - direct_band23 : light_atm/dir_sf_band23 - diffuse_band23 : light_atm/dif_sf_band23 - direct_band24 : light_atm/dir_sf_band24 - diffuse_band24 : light_atm/dif_sf_band24 - direct_band25 : light_atm/dir_sf_band25 - diffuse_band25 : light_atm/dif_sf_band25 - direct_band26 : light_atm/dir_sf_band26 - diffuse_band26 : light_atm/dif_sf_band26 - direct_band27 : light_atm/dir_sf_band27 - diffuse_band27 : light_atm/dif_sf_band27 - direct_band28 : light_atm/dir_sf_band28 - diffuse_band28 : light_atm/dif_sf_band28 - direct_band29 : light_atm/dir_sf_band29 - diffuse_band29 : light_atm/dif_sf_band29 - direct_band30 : light_atm/dir_sf_band30 - diffuse_band30 : light_atm/dif_sf_band30 - direct_band31 : light_atm/dir_sf_band31 - diffuse_band31 : light_atm/dif_sf_band31 - direct_band32 : light_atm/dir_sf_band32 - diffuse_band32 : light_atm/dif_sf_band32 - direct_band33 : light_atm/dir_sf_band33 - diffuse_band33 : light_atm/dif_sf_band33 - costheta_r : light_atm/costheta_r - N1: - long_name: phosphate - model: ogs/bfm_pelagic_base - parameters: - composition: p # elemental composition - initialization: - p: 0.4 # phosphorus (mmol P/m^3) - N3: - long_name: nitrate - model: ogs/bfm_pelagic_base - parameters: - composition: n # elemental composition - initialization: - n: 8.0 # nitrogen (mmol N/m^3) - N4: - long_name: ammonium - model: ogs/bfm_pelagic_base - parameters: - composition: n # elemental composition - initialization: - n: 0.1 # nitrogen (mmol N/m^3) - N5: - long_name: silicate - model: ogs/bfm_pelagic_base - parameters: - composition: s # elemental composition - initialization: - s: 4.5 # silicate (mmol Si/m^3) - N6: - long_name: Reduction equivalent - model: ogs/bfm_pelagic_base - parameters: - composition: r # elemental composition - initialization: - r: 1.0 # Reduction equivalent (mmol Eq/m^3) - O3: - long_name: dissolved inorganic carbon - model: ogs/PelagicCSYS -# parameters: -# composition: c # elemental composition - initialization: - c: 28500.00 # Dissolved Inorganic Carbon (mg C /m^3) - coupling: - N1p: N1/p # phosphate (mmol P/m^3) - N5s: N5/s # silicate (mmol Si/m^3) - O3h: O3h/h - O2: - long_name: Dissolved Oxygen - model: ogs/PelOxygen -# parameters: -# composition: o # elemental composition - initialization: - o: 300.0 - O3h: - long_name: alkalinity - model: ogs/bfm_pelagic_base - parameters: - composition: h # elemental composition - initialization: - h: 2660.0 # alkalinity (mmol m3) - O4: - long_name: Nitrogen Sink - model: ogs/bfm_pelagic_base - parameters: - composition: n # elemental composition - initialization: - n: 200.0 - R1: - long_name: Dissolved Organic carbon Labile - model: ogs/bfm_pelagic_base - parameters: - composition: cnp # elemental composition - initialization: - c: 80.0 # Dissolved Organic Carbon (mg C /m^3) -# n: 1.260E-002 # Dissolved Organic Nitrogen (mmol N /m^3) -# p: 7.8620E-004 # Dissolved Organic Phosphorus (mmol P /m^3) - n: 1.008 # adjusted for c=80 instead c=1 - p: 0.062 # adjusted for c=80 instead c=1 - R2: - long_name: Dissolved Organic carbon semi-Labile - model: ogs/bfm_pelagic_base - parameters: - composition: c # elemental composition - initialization: - c: 400.0 # Dissolved Organic Carbon (mg C /m^3) - R3: - long_name: Dissolved Organic carbon semi-refractory - model: ogs/bfm_pelagic_base - parameters: - composition: c # elemental composition - initialization: - c: 480.0 # Dissolved Organic Carbon (mg C /m^3) - R6: - long_name: Small Particulate Organic carbon - model: ogs/bfm_pelagic_base - parameters: - composition: cpns # elemental composition - rm: 7.0 # Sinking Velocity - initialization: - c: 1.0 # POC (mg C /m^3) - n: 1.260E-002 # PON (mmol N /m^3) - p: 7.8620E-004 # POP (mmol P /m^3) - s: 1.260E-002 # POS (mmol S /m^3) - R8: - long_name: Large Particulate Organic carbon - model: ogs/bfm_pelagic_base - parameters: - composition: cpns # elemental composition - rm: 15.00 # Sinking Velocity - initialization: - c: 1.0 # POC (mg C /m^3) - n: 1.260E-002 # PON (mmol N /m^3) - p: 7.8620E-004 # POP (mmol P /m^3) - s: 1.260E-002 # POS (mmol S /m^3) - X1: - long_name: labile CDOM - model: ogs/bfm_pelagic_base - parameters: - composition: c # elemental composition - initialization: - c: 1.000000000000000E-000 - X2: - long_name: semi labile CDOM - model: ogs/bfm_pelagic_base - parameters: - composition: c # elemental composition - initialization: - c: 3.000000000000000E-000 - X3: - long_name: semi refractory CDOM - model: ogs/bfm_pelagic_base - parameters: - composition: c # elemental composition - initialization: - c: 1.250000000000000E-000 -# ---------------------- P1 Diatom ---------------------- - P1: - long_name: diatoms - model: ogs/Phyto - parameters: -# --------- Physiological parameters ----------------- - p_q10: 2.0 # [-] Characteristic Q10 coefficient - p_temp: 0.0 # [-] Cut-off threshold for temperature factor - p_sum: 2.5 # [1/d] maximum specific productivity at reference temperature (1/d) - p_srs: 0.076 # [1/d] Respiration rate at 10 degrees C - p_fR6: 0.5 # [-] fraction of lysis to small POC (R6) - p_sdmo: 0.0 # [1/d] Max.specific nutrient-stress lysis rate - p_thdo: 0.0 # [-] Half saturation constant for nutrient stress lysis - p_seo: 0.0 # [1/d] Extra lysis rate (biomass density-dependent) - p_sheo: 0.0 # [mgC/3] Half saturation constant for extra lysis - p_pu_ea: 0.10 # [-] Excreted fraction of primary production - p_pu_ra: 0.1 # [-] Activity respiration fraction - p_pu_rn: 0.35 # [-] nutrient stress respiration fraction - p_switchDOC: 2 # [1-3] Switch for the type of DOC excretion - # This choice must be consistent with bacteria - # 1. All DOC is released as R1c (Vichi et al., 2007) - # 2. Activity DOC is released as R2c (Vichi et al., 2004) - # (there is no nutrient-stress excretion) - # 3. All DOC is released as R2c (Polimene et al., 2006) -# --------- Nutrient parameters in phytoplankton ----------------- - p_netgrowth: .TRUE. # [T or F] Logical switch for nutrient-limited growth - # .T. nutrient-balanced growth (Vichi et al.2004) - # .F. nutrient-stress carbon excretion - # (Baretta-Bekker et al.1995 and Vichi et al.2007) - p_limnut: 1 # Switch for N-P co-limitation - # 0. Geometric mean - # 1. Threshold (Liebig-like) - # 2. Combined -# ---- N limitation control ---- - p_qun: 0.025 # [m3/mgC/d] Membrane affinity for N - p_lN4: 1.0 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 - p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) - p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C - p_xqn: 2.0 # [-] Multiplication factor for luxury storage -# ---- P limitation control ---- - p_qup: 0.0025 # [m3/mgC/d] Membrane affinity for P - p_qplc: 0.0004288 # [mmolN/mgC] minimum phosphorus to carbon ratio (mmol P/mg C) - p_qpcPPY: 0.000786 # [mmolP/mgC] Reference quotum P:C - p_xqp: 2.0 # [-] Multiplication factor for luxury storage -# ---- Si limitation control ---- - p_switchSi: 2 # [1-2] Switch for Silica limitation - # 1. Si limitation is controlled by external Si conc. - # 2. Si limitation is controlled by internal quota - p_chPs: 0.3 # [mmolSi/m3] Half saturation conc. for dissolved Si limitation - p_Contois: 0.0 # [>=0] If >0, use Contois formulation - p_qus: 0.0025 # [m3/mgC/d] Membrane affinity for Si - p_qslc: 0.007 # [mmolSi/mgC] minimum silicate to carbon ratio (mmol Si/mg C) - use_Si: .TRUE. # use silicate, default = false - p_qscPPY: 0.01 # [mmolSi/mgC] Reference quotum Si:C -# ---- nutrient stressed sinking ---- - p_esNI: 0.7 # [-] Nutrient stress threshold for sinking - p_res: 5.0 # [m/d] Maximum Sinking vel city (m/d) -# ---- Calcification ---- - p_caco3r: 0.0 # [-] Reference PIC:POC (rain) ratio -# ---- CDOM production ---- - p_fX1p: 0.00 # [-] fraction of colored labile DOC - p_fX2p: 0.053 # [-] fraction of colored semi-labile DOC -# --------- Chlorophyll parameters ----------- - p_switchChl: 2 # [1-4] Switch for Chla-a synthesis - p_sdchl: 0.0 # [1/d] Specific turnover rate for Chla - p_alpha_chl: 0.000768 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve - p_quantum_yield: 0.750e-3 # [mgC / uE] Photochemical efficiency - p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono - p_OT: 1 # [1-9] type of absorption/scattering spectra - p_qlcPPY: 0.026 # [mgChla/mgC] Reference quotum Chla:C - p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C - p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient - p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C - p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K -# --------- Sinking parameters ----------- - p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate - initialization: - c: 8.0 # carbon (mg C/m^3) - n: 0.1008 # nitrogen (mmol N/m^3) - p: 0.006288 # phosphate (mmol N/m^3) - s: 0.08 # silicate (mmol Si/m^3) - Chl: 0.16 # chlorophyll a (mg/m^3) - coupling: - 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) - O3c: O3/c # dissolved inorganic carbon (mg C/m^3) - O2o: O2/o # Oxygen (mmol O/m^3) - R1c: R1/c - R1n: R1/n - R1p: R1/p - R2c: R2/c - R6c: R6/c - R6n: R6/n - R6s: R6/s - R6p: R6/p - R8c: R8/c - R8n: R8/n - R8s: R8/s - R8p: R8/p - X1c: X1/c - X2c: X2/c - O3h: O3h/h - O5c: O5/c - PAR: lightspectral/PAR_P1 -# ---------------------- P2 nanoflagellates ---------------------- - P2: - long_name: nanoflagellates - model: ogs/Phyto - parameters: -# --------- Physiological parameters ----------------- - p_q10: 2.25 # [-] Characteristic Q10 coefficient - p_temp: 0.0 # [-] Cut-off threshold for temperature factor - p_sum: 2.6 # [1/d] maximum specific productivity at reference temperature (1/d) - p_srs: 0.09 # [1/d] Respiration rate at 10 degrees C - p_fR6: 1.0 # [-] fraction of lysis to small POC (R6) - p_sdmo: 0.0 # [1/d] Max.specific nutrient-stress lysis rate - p_thdo: 0.0 # [-] Half saturation constant for nutrient stress lysis - p_seo: 0.0 # [1/d] Extra lysis rate (biomass density-dependent) - p_sheo: 0.0 # [mgC/3] Half saturation constant for extra lysis - p_pu_ea: 0.15 # [-] Excreted fraction of primary production - p_pu_ra: 0.1 # [-] Activity respiration fraction - p_pu_rn: 0.35 # [-] nutrient stress respiration fraction - p_switchDOC: 2 # [1-3] 2. Activity DOC is released as R2c (Vichi et al., 2004) -# --------- Nutrient parameters in phytoplankton ----------------- - p_netgrowth: .TRUE. # [T or F] .T. nutrient-balanced growth (Vichi et al.2004) - p_limnut: 1 # Switch for N-P co-limitation, 1. Threshold (Liebig-like) -# ---- N limitation control ---- - p_qun: 0.025 # [m3/mgC/d] Membrane affinity for N - p_lN4: 0.5 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 - p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) - p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C - p_xqn: 2.0 # [-] Multiplication factor for luxury storage -# ---- P limitation control ---- - p_qup: 0.0035 # [m3/mgC/d] Membrane affinity for P - p_qplc: 0.00035 # [mmolN/mgC] minimum phosphorus to carbon ratio (mmol P/mg C) - p_qpcPPY: 0.000786 # [mmolP/mgC] Reference quotum P:C - p_xqp: 2.0 # [-] Multiplication factor for luxury storage -# ---- nutrient stressed sinking ---- - p_esNI: 0.75 # [-] Nutrient stress threshold for sinking - p_res: 0.0 # [m/d] Maximum Sinking vel city (m/d) -# ---- Calcification ---- - use_CaCO3: .TRUE. # use CaCO3, default = false - p_caco3r: 0.3 # [-] Reference PIC:POC (rain) ratio -# ---- CDOM production ---- - p_fX1p: 0.00 # [-] fraction of colored labile DOC - p_fX2p: 0.029 # [-] fraction of colored semi-labile DOC -# --------- Chlorophyll parameters ----------- - p_switchChl: 2 # [1-4] Switch for Chla-a synthesis - p_sdchl: 0.0 # [1/d] Specific turnover rate for Chla - p_alpha_chl: 0.0002016 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve - p_quantum_yield: 0.2016e-3 # [mgC / uE] Photochemical efficiency - p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono - p_OT: 2 # [1-9] type of absorption/scattering spectra - p_qlcPPY: 0.045 # [mgChla/mgC] Reference quotum Chla:C - p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C - p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient - p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C - p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K -# --------- Sinking parameters ----------- - p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate - initialization: - c: 8.0 # carbon (mg C/m^3) - n: 0.1008 # nitrogen (mmol N/m^3) - p: 0.006288 # phosphate (mmol N/m^3) - Chl: 0.16 # chlorophyll a (mg/m^3) - coupling: - N1p: N1/p # phosphate (mmol P/m^3) - N3n: N3/n # nitrate (mmol N/m^3) - N4n: N4/n # ammonium (mmol N/m^3) - O3c: O3/c # dissolved inorganic carbon (mg C/m^3) - O2o: O2/o # Oxygen (mmol O/m^3) - R1c: R1/c - R1n: R1/n - R1p: R1/p - R2c: R2/c - R6c: R6/c - R6n: R6/n - R6p: R6/p - R8c: R8/c - R8n: R8/n - R8p: R8/p - X1c: X1/c - X2c: X2/c - O3h: O3h/h - O5c: O5/c - PAR: lightspectral/PAR_P2 -# ---------------------- P3 Picophytoplankton ---------------------- - P3: - long_name: Picoplankton - model: ogs/Phyto - parameters: -# --------- Physiological parameters ----------------- - p_q10: 2.0 # [-] Characteristic Q10 coefficient - p_temp: 0.75 # [-] Cut-off threshold for temperature factor - p_sum: 3.5 # [1/d] maximum specific productivity at reference temperature (1/d) - p_srs: 0.1 # [1/d] Respiration rate at 10 degrees C - p_fR6: 1.0 # [-] fraction of lysis to small POC (R6) - p_sdmo: 0.0 # [1/d] Max.specific nutrient-stress lysis rate - p_thdo: 0.0 # [-] Half saturation constant for nutrient stress lysis - p_seo: 0.0 # [1/d] Extra lysis rate (biomass density-dependent) - p_sheo: 0.0 # [mgC/3] Half saturation constant for extra lysis - p_pu_ea: 0.15 # [-] Excreted fraction of primary production - p_pu_ra: 0.2 # [-] Activity respiration fraction - p_pu_rn: 0.35 # [-] nutrient stress respiration fraction - p_switchDOC: 2 # [1-3] Switch for the type of DOC excretion - # This choice must be consistent with bacteria - # 1. All DOC is released as R1c (Vichi et al., 2007) - # 2. Activity DOC is released as R2c (Vichi et al., 2004) - # (there is no nutrient-stress excretion) - # 3. All DOC is released as R2c (Polimene et al., 2006) -# --------- Nutrient parameters in phytoplankton ----------------- - p_netgrowth: .TRUE. # [T or F] Logical switch for nutrient-limited growth - # .T. nutrient-balanced growth (Vichi et al.2004) - # .F. nutrient-stress carbon excretion - # (Baretta-Bekker et al.1995 and Vichi et al.2007) - p_limnut: 1 # Switch for N-P co-limitation - # 0. Geometric mean - # 1. Threshold (Liebig-like) - # 2. Combined -# ---- N limitation control ---- - p_qun: 0.25 # [m3/mgC/d] Membrane affinity for N - p_lN4: 0.1 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 - p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) - p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C - p_xqn: 2.0 # [-] Multiplication factor for luxury storage -# ---- P limitation control ---- - p_qup: 0.0025 # [m3/mgC/d] Membrane affinity for P - p_qplc: 0.0004288 # [mmolN/mgC] minimum phosphorus to carbon ratio (mmol P/mg C) - p_qpcPPY: 0.000786 # [mmolP/mgC] Reference quotum P:C - p_xqp: 2.0 # [-] Multiplication factor for luxury storage -# ---- Si limitation control ---- -# Silicon absent in this PFT -# ---- nutrient stressed sinking ---- - p_esNI: 0.75 # [-] Nutrient stress threshold for sinking - p_res: 0.0 # [m/d] Maximum Sinking vel city (m/d) -# ---- Calcification ---- - p_caco3r: 0.0 # [-] Reference PIC:POC (rain) ratio -# ---- CDOM production ---- - p_fX1p: 0.00 # [-] fraction of colored labile DOC - p_fX2p: 0.026 # [-] fraction of colored semi-labile DOC -# --------- Chlorophyll parameters ----------- - p_switchChl: 2 # [1-4] Switch for Chla-a synthesis - p_sdchl: 0.0 # [1/d] Specific turnover rate for Chla - p_alpha_chl: 0.0010104 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve - p_quantum_yield: 1.0104e-3 # [mgC / uE] Photochemical efficiency - p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono - p_OT: 3 # [1-9] type of absorption/scattering spectra - p_qlcPPY: 0.014 # [mgChla/mgC] Reference quotum Chla:C - p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C - p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient - p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C - p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K -# --------- Sinking parameters ----------- - p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate - initialization: - c: 8.0 # carbon (mg C/m^3) - n: 0.1008 # nitrogen (mmol N/m^3) - p: 0.006288 # phosphate (mmol N/m^3) - Chl: 0.16 # chlorophyll a (mg/m^3) - coupling: - N1p: N1/p # phosphate (mmol P/m^3) - N3n: N3/n # nitrate (mmol N/m^3) - N4n: N4/n # ammonium (mmol N/m^3) - O3c: O3/c # dissolved inorganic carbon (mg C/m^3) - O2o: O2/o # Oxygen (mmol O/m^3) - R1c: R1/c - R1n: R1/n - R1p: R1/p - R2c: R2/c - R6c: R6/c - R6n: R6/n - R6p: R6/p - R8c: R8/c - R8n: R8/n - R8p: R8/p - X1c: X1/c - X2c: X2/c - O3h: O3h/h - O5c: O5/c - PAR: lightspectral/PAR_P3 -# ---------------------- P4 dinoflagellates ---------------------- - P4: - long_name: dinoflagellates - model: ogs/Phyto - parameters: -# --------- Physiological parameters ----------------- - p_q10: 2.0 # [-] Characteristic Q10 coefficient - p_temp: 0.0 # [-] Cut-off threshold for temperature factor - p_sum: 1.5 # [1/d] maximum specific productivity at reference temperature (1/d) - p_srs: 0.1 # [1/d] Respiration rate at 10 degrees C - p_fR6: 0.5 # [-] fraction of lysis to small POC (R6) - p_sdmo: 0.0 # [1/d] Max.specific nutrient-stress lysis rate - p_thdo: 0.0 # [-] Half saturation constant for nutrient stress lysis - p_seo: 0.0 # [1/d] Extra lysis rate (biomass density-dependent) - p_sheo: 100.0 # [mgC/3] Half saturation constant for extra lysis - p_pu_ea: 0.20 # [-] Excreted fraction of primary production - p_pu_ra: 0.1 # [-] Activity respiration fraction - p_pu_rn: 0.35 # [-] nutrient stress respiration fraction - p_switchDOC: 2 # [1-3] 2. Activity DOC is released as R2c (Vichi et al., 2004) -# --------- Nutrient parameters in phytoplankton ----------------- - p_netgrowth: .TRUE. # [T or F] .T. nutrient-balanced growth (Vichi et al.2004) - p_limnut: 1 # Switch for N-P co-limitation, 1. Threshold (Liebig-like) -# ---- N limitation control ---- - p_qun: 0.025 # [m3/mgC/d] Membrane affinity for N - p_lN4: 1.0 # [mmolN/m3] Half saturation constant for NH4 uptake preference over NO3 - p_qnlc: 0.00687 # [mmolN/mgC] minimum nitrogen to carbon ratio (mmol N/mg C) - p_qncPPY: 0.0126 # [mmolN/mgC] Reference quotum N:C - p_xqn: 2.0 # [-] Multiplication factor for luxury storage -# ---- P limitation control ---- - p_qup: 0.0025 # [m3/mgC/d] Membrane affinity for P - p_qplc: 0.0004288 # [mmolN/mgC] minimum phosphorus to carbon ratio (mmol P/mg C) - p_qpcPPY: 0.000786 # [mmolP/mgC] Reference quotum P:C - p_xqp: 2.0 # [-] Multiplication factor for luxury storage -# ---- nutrient stressed sinking ---- - p_esNI: 0.75 # [-] Nutrient stress threshold for sinking - p_res: 2.5 # [m/d] Maximum Sinking vel city (m/d) -# ---- Calcification ---- - p_caco3r: 0.0 # [-] Reference PIC:POC (rain) ratio -# ---- CDOM production ---- - p_fX1p: 0.00 # [-] fraction of colored labile DOC - p_fX2p: 0.035 # [-] fraction of colored semi-labile DOC -# --------- Chlorophyll parameters ----------- - p_switchChl: 2 # [1-4] Switch for Chla-a synthesis - p_sdchl: 0.0 # [1/d] Specific turnover rate for Chla - p_alpha_chl: 0.0002616 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve - p_quantum_yield: 0.2616e-3 # [mgC / uE] Photochemical efficiency - p_Esource: 1 # [1-6] source of light for PP, 1=multi, 5=scalar, 6=mono - p_OT: 4 # [1-9] type of absorption/scattering spectra - p_qlcPPY: 0.019 # [mgChla/mgC] Reference quotum Chla:C - p_qlcmin: 0.00625 # [mgChla/mgC] Minimum quotum Chla:C - p_epsChla: 0.03 # [m2/mgChla] Chla-specific extinction coefficient - p_tochl_relt: 0.0 # [1/d] Relaxation rate towards maximum Chla:C - p_EpEk_or: 0.0 # [-] Optimal value of E_PAR/E_K -# --------- Sinking parameters ----------- - p_rPIm: 0.0 # [m/d] Phytoplankton background sinking rate - initialization: - c: 8.0 # carbon (mg C/m^3) - n: 0.1008 # nitrogen (mmol N/m^3) - p: 0.006288 # phosphate (mmol N/m^3) - Chl: 0.16 # chlorophyll a (mg/m^3) - coupling: - N1p: N1/p # phosphate (mmol P/m^3) - N3n: N3/n # nitrate (mmol N/m^3) - N4n: N4/n # ammonium (mmol N/m^3) - O3c: O3/c # dissolved inorganic carbon (mg C/m^3) - O2o: O2/o # Oxygen (mmol O/m^3) - R1c: R1/c - R1n: R1/n - R1p: R1/p - R2c: R2/c - R6c: R6/c - R6n: R6/n - R6p: R6/p - R8c: R8/c - R8n: R8/n - R8p: R8/p - X1c: X1/c - X2c: X2/c - O3h: O3h/h - O5c: O5/c - PAR: lightspectral/PAR_P4 -# ---------------------- B1 Pelagic heteretrophic bacteria ---------------------- -# - B1: - long_name: Bacteria - model: ogs/PelBac - parameters: -# --------- Physiological parameters ----------------- - p_version : 2 # Switch for bacteria parameterization -# 1 : Baretta-Bekker et al. 1995; -# Vichi et al., 2007 -# 2 : Vichi et al., 2004 -# 3 : Polimene et al., 2006 - p_q10 : 2.95 # [-] Q10-value (temperature dependency) - p_chdo : 30.0 # [mmol/m3] Half-saturation constant for O2 limitation - p_sd : 0.0 # [1/d] Specific mortality rate - p_sd2 : 0.0 # [1/d] Density dependent specific mortality rate - p_suhR1 : 0.5 # [1/d] Specific potential uptake for nutrient-rich DOM - p_sulR1 : 0.0 # [1/d] Specific potential uptake for nutrient-poor DOM - p_suR2 : 0.05 # [1/d] Specific potential uptake for semi-labile DOC - p_suR3 : 0.0 # [1/d] Specific potential uptake for semi-refractory DOC - p_suR6 : 0.012 # [1/d] Specific potential uptake for small POM (1/d) - p_suR8 : 0.03 # [1/d] Specific potential uptake for large POM (1/d) - p_sum : 8.38 # [1/d] Potential specific growth rate - p_pu_ra : 0.76 # [-] Activity respiration fraction - p_pu_ra_o : 0.2 # [-] Additional respiration fraction at low O2 conc - p_srs : 0.01 # [1/d] Specific rest respiration - p_qncPBA : 0.017 # [mmolN/mgC] Optimal N/C ratio - p_qpcPBA : 0.0019 # [mmolP/mgC] Optimal P/C ratio - p_qlnc : 0.0085 # [mmolN/mgC] Minimal N/C ratio - p_qlpc : 0.00095 # [mmolP/mgC] Minimal P/C ratio - p_qun : 0.05 # [mmolN/mgC/day] Membrane affinity for N - p_qup : 0.005 # [mmolP/mgC/day] Membrane affinity for P - p_chn : 0.05 # [mmolN/m3] Half saturation ammonium conc. for uptake - p_chp : 1.00 # [mmolP/m3] Half saturation phosphate conc. for uptake - p_rec : 1.0 # [1/d] Relaxation timescale for semi-labile excretion - p_ruen : 1.0 # [1/d] Relaxation timescale for N uptake/remin. - p_ruep : 1.0 # [1/d] Relaxation timescale for P uptake/remin. - p_pu_ea_R3 : 0.0 # [-] Excretion of semi-refractory DOC - p_qro : 0.5 # [mmolHS-/mmolO2] Stoichiometric coefficient for anaerobic reactions - p_pe_R1c: 0.60 # [-] Fractional content of C in cytoplasm - p_pe_R1n: 0.72 # [-] Fractional content of N in cytoplasm - p_pe_R1p: 0.832 # [-] Fractional content of P in cytoplasm -# ---- CDOM production ---- - p_fX1b: 0.00 # [-] fraction of colored labile DOC - p_fX2b: 0.02 # [-] fraction of colored semi-labile DOC - p_fX3b: 0.018 # [-] fraction of colored semi-refractory DOC -# ---- POM split ---- - p_fR6: 0.0 # [-] fraction of lysis to small POC (R6) - initialization: - c: 1.0 # carbon (mg C/m^3) - n: 1.700000000000000E-002 # nitrogen (mmol N/m^3) - p: 1.900000000000000E-003 # phosphate (mmol N/m^3) - coupling: - N1p: N1/p # phosphate (mmol P/m^3) - N3n: N3/n # nitrate (mmol N/m^3) - N4n: N4/n # ammonium (mmol N/m^3) - N6r: N6/r - O3c: O3/c # dissolved inorganic carbon (mg C/m^3) - O3h: O3h/h - O2o: O2/o # Oxygen (mmol O/m^3) - R1c: R1/c - R1n: R1/n - R1p: R1/p - R2c: R2/c - R3c: R3/c - R6c: R6/c - R6n: R6/n - R6p: R6/p - R6s: R6/s - R8c: R8/c - R8n: R8/n - R8p: R8/p - R8s: R8/s - X1c: X1/c - X2c: X2/c - X3c: X3/c -# ---------------------- Z5 Microzooplankton ---------------------- - Z5: -# use: false - long_name: Microzooplankton - model: ogs/MicroZoo - parameters: -# --------- Physiological parameters ----------------- - p_q10: 2.0 # [-] Characteristic Q10 coefficient - p_srs: 0.01 # [1/d] Respiration rate at 10 degrees Celsius - p_sum: 2.71 # [1/d] Potential growth rate - p_sdo: 0.05 # [1/d] Mortality rate due to oxygen limitation - p_sd: 0.0 # [1/d] Temperature independent mortality rate - p_pu: 0.5 # [-] Assimilation efficiency - p_pu_ea: 0.5 # [-] Fraction of activity excretion - p_chro: 8 # [mmolO2/m3] Half-saturation oxygen concentration - p_chuc: 15.0 # [mgC/m3] Half-saturation Food concentration for Type II - p_minfood: 37.5 # [mgC/m3] Half-saturation food concentration for - # preference factor - p_pecaco3: 0.5 # [-] Portion of egested calcified shells during grazing - p_qpcMIZ: 1.85e-3 # [mmolN/mgC] Maximum quotum P:C - p_qncMIZ: 1.67e-2 # [mmolN/mgC] Maximum quotum N:C - nprey: 7 # [-] Number of preys - suprey1: 0.1 # [-] Availability of pelagic Bacteria group b - # to Zooplankton group z - suprey2: 0.35 # [-] Availability of PhytoPlankton group P1 - # to Zooplankton group z - suprey3: 0.5 # [-] Availability of PhytoPlankton group P2 - # to Zooplankton group z - suprey4: 0.3 # [-] Availability of PhytoPlankton group P3 - # to Zooplankton group z - suprey5: 0.1 # [-] Availability of PhytoPlankton group P4 - # to Zooplankton group z - suprey6: 1.0 # [-] Availability of MicroZooplankton group Z5 - # to Zooplankton group z - suprey7: 1.0 # [-] Availability of MicroZooplankton group Z6 - # to Zooplankton group z -#-------------------------------------------------------------------- - isP21: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP22: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP23: 1 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP24: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP25: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP26: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP27: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] -#-------------------------------------------------------------------- - p_fR6: 0.5 # [-] Fraction of lysis and sloppy predation to small POC (R6) - p_pe_R1c: 0.60 # [-] Fractional content of C in cytoplasm - p_pe_R1n: 0.72 # [-] Fractional content of C in cytoplasm - p_pe_R1p: 0.832 # [-] Fractional content of C in cytoplasm - p_fX1z: 0.018 # [-] fraction of colored labile DOC - initialization: - c: 1.0 # carbon (mg C/m^3) - n: 0.0167 # nitrogen (mmol N/m^3) - p: 0.00185 # phosphate (mmol N/m^3) - coupling: - O2o: O2/o # Oxygen (mmol O2/m^3) - O3c: O3/c # dissolved inorganic carbon (mg C/m^3) - N4n: N4/n # ammonium (mmol N/m^3) - N1p: N1/p # phosphate (mmol P/m^3) - R6c: R6/c # POC (mgC/m3) - R6s: R6/s # POSi (mgSi/m3) - R6n: R6/n # PON (mmolN/m3) - R6p: R6/p # POP (mmolP/m3) - R8c: R8/c # POC (mgC/m3) - R8s: R8/s # POSi (mgSi/m3) - R8n: R8/n # PON (mmolN/m3) - R8p: R8/p # POP (mmolP/m3) - X1c: X1/c # labile CDOM - R1c: R1/c # labile DOC - R1n: R1/n # labile DON - R1p: R1/p # labile DOP - prey1: B1 - prey2: P1 - prey3: P2 - prey4: P3 - prey5: P4 - prey6: Z5 - prey7: Z6 - O3h: O3h/h - O5c: O5/c -# ---------------------- Z6 Microzooplankton ---------------------- - Z6: -# use: false - long_name: Heterotrophic Nanoflagellates (HNAN) - model: ogs/MicroZoo - parameters: -# --------- Physiological parameters ----------------- - p_q10: 2.0 # [-] Characteristic Q10 coefficient - p_srs: 0.01 # [1/d] Respiration rate at 10 degrees Celsius - p_sum: 3.88 # [1/d] Potential growth rate - p_sdo: 0.05 # [1/d] Mortality rate due to oxygen limitation - p_sd: 0.0 # [1/d] Temperature independent mortality rate - p_pu: 0.3 # [-] Assimilation efficiency - p_pu_ea: 0.5 # [-] Fraction of activity excretion - p_chro: 8 # [mmolO2/m3] Half-saturation oxygen concentration - p_chuc: 100.0 # [mgC/m3] Half-saturation Food concentration for Type II - p_minfood: 50.0 # [mgC/m3] Half-saturation food concentration for - # preference factor - p_pecaco3: 0.5 # [-] Portion of egested calcified shells during grazing - p_qpcMIZ: 1.85e-3 # [mmolN/mgC] Maximum quotum P:C - p_qncMIZ: 1.67e-2 # [mmolN/mgC] Maximum quotum N:C - nprey: 7 # [-] Number of preys - suprey1: 1.0 # [-] Availability of pelagic Bacteria group b - # to Zooplankton group z - suprey2: 0.0 # [-] Availability of PhytoPlankton group P1 - # to Zooplankton group z - suprey3: 0.2 # [-] Availability of PhytoPlankton group P2 - # to Zooplankton group z - suprey4: 1.0 # [-] Availability of PhytoPlankton group P3 - # to Zooplankton group z - suprey5: 0.0 # [-] Availability of PhytoPlankton group P4 - # to Zooplankton group z - suprey6: 0.0 # [-] Availability of MicroZooplankton group Z5 - # to Zooplankton group z - suprey7: 0.2 # [-] Availability of MicroZooplankton group Z6 - # to Zooplankton group z -#-------------------------------------------------------------------- - isP21: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP22: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP23: 1 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP24: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP25: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP26: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP27: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] -#-------------------------------------------------------------------- - p_fR6: 1.0 # [-] Fraction of lysis and sloppy predation to small POC (R6) - p_pe_R1c: 0.60 # [-] Fractional content of C in cytoplasm - p_pe_R1n: 0.72 # [-] Fractional content of C in cytoplasm - p_pe_R1p: 0.832 # [-] Fractional content of C in cytoplasm - p_fX1z: 0.030 # [-] fraction of colored labile DOC - initialization: - c: 1.0 # carbon (mg C/m^3) - n: 0.0167 # nitrogen (mmol N/m^3) - p: 0.00185 # phosphate (mmol N/m^3) - coupling: - O2o: O2/o # Oxygen (mmol O2/m^3) - O3c: O3/c # dissolved inorganic carbon (mg C/m^3) - N4n: N4/n # ammonium (mmol N/m^3) - N1p: N1/p # phosphate (mmol P/m^3) - R6c: R6/c # POC (mgC/m3) - R6s: R6/s # POSi (mgSi/m3) - R6n: R6/n # PON (mmolN/m3) - R6p: R6/p # POP (mmolP/m3) - R8c: R8/c # POC (mgC/m3) - R8s: R8/s # POSi (mgSi/m3) - R8n: R8/n # PON (mmolN/m3) - R8p: R8/p # POP (mmolP/m3) - X1c: X1/c # labile CDOM - R1c: R1/c # labile DOC - R1n: R1/n # labile DON - R1p: R1/p # labile DOP - prey1: B1 - prey2: P1 - prey3: P2 - prey4: P3 - prey5: P4 - prey6: Z5 - prey7: Z6 - O3h: O3h/h - O5c: O5/c -# ---------------------- Z3 Carnivorous Mesozooplankton ---------------------- - Z3: -# use: false - long_name: Carnivorous Mesozooplankton - model: ogs/MesoZoo - parameters: -# --------------- Physiological parameters ----------------- - p_q10: 2.0 # [-] Q10 value for physiological rates - p_srs: 0.01 # [1/d] Respiration rate at 10 degrees C - p_sum: 2.0 # [1/d] Maximal productivity at 10 degrees C - p_sd: 0.02 # [1/d] Background natural mortality - p_vum: 0.008 # [m3/mgC/d] Specific search volume - p_puI: 0.6 # [-] Assimilation efficiency - p_peI: 0.3 # [-] Fraction of Faeces production - p_sdo: 0.01 # [m3/mgC/d] Specific density-dependent mortality - p_sds: 2.0 # [-] Exponent of density-dependent mortality - p_pecaco3: 0.75 # [-] Portion of egested calcified shells during grazing - p_qpcMEZ: 1.67e-3 # [mmolP/mgC] Maximum quotum P:C - p_qncMEZ: 0.015 # [mmolN/mgC] Maximum quotum N:C - p_clO2o: 30.0 # [mmolO2/m3] Half-saturation oxygen concentration - p_fR6: 0.5 # [-] Fraction of lysis and sloppy predation to small POC (R6) -#----------------------------------------------------------------------------- - nprey: 3 # [-] Number of preys - suprey1: 1.0 # [-] Availability of PhytoPlankton group P4 - # to Zooplankton group z - suprey2: 1.0 # [-] Availability of MicroZooplankton group Z3 - # to Zooplankton group z - suprey3: 1.0 # [-] Availability of MicroZooplankton group Z4 - # to Zooplankton group z -#------------------------------------------------------------------------------ - isP21: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP22: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP23: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] -#------------------------------------------------------------------------------ - initialization: - c: 1.0 # carbon (mg C/m^3) - n: 0.015 # nitrogen (mmol N/m^3) - p: 0.00167 # phosphate (mmol N/m^3) - coupling: - O2o: O2/o # dissolved oxygen - O3c: O3/c # DIC - N1p: N1/p # phosphate (mmol P/m^3) - N4n: N4/n # ammonium (mmol N/m^3) - R6c: R6/c # POC - R6n: R6/n # PON - R6p: R6/p # POP - R6s: R6/s # biogenic silica (mmol Si/m^3) - R8c: R8/c # POC - R8n: R8/n # PON - R8p: R8/p # POP - R8s: R8/s # biogenic silica (mmol Si/m^3 - prey1: P4 - prey2: Z3 - prey3: Z4 - O3h: O3h/h - O5c: O5/c -# --------------------------------------------------------------------------- -# ---------------------- Z4 Omnivorous Mesozooplankton ---------------------- - Z4: -# use: false - long_name: Omnivorous Mesozooplankton - model: ogs/MesoZoo - parameters: -# ----------------- Physiological parameters ----------------- - p_q10: 2.0 # [-] Q10 value for physiological rates - p_srs: 0.02 # [1/d] Respiration rate at 10 degrees C - p_sum: 2.0 # [1/d] Maximal productivity at 10 degrees C - p_sd: 0.02 # [1/d] Background natural mortality - p_vum: 0.02 # [m3/mgC/d] Specific search volume - p_puI: 0.6 # [-] Assimilation efficiency - p_peI: 0.35 # [-] Fraction of Faeces production - p_sdo: 0.01 # [m3/mgC/d] Specific density-dependent mortality - p_sds: 2.0 # [-] Exponent of density-dependent mortality - p_pecaco3: 0.75 # [-] Portion of egested calcified shells during grazing - p_qpcMEZ: 1.67e-3 # [mmolP/mgC] Maximum quotum P:C - p_qncMEZ: 0.015 # [mmolN/mgC] Maximum quotum N:C - p_clO2o: 30.0 # [mmolO2/m3] Half-saturation oxygen concentration - p_fR6: 0.5 # [-] Fraction of lysis and sloppy predation to small POC (R6) -#------------------------------------------------------------------------------- - nprey: 5 # [-] Number of preys - suprey1: 1.0 # [-] Availability of PhytoPlankton group P1 - # to Zooplankton group z - suprey2: 0.75 # [-] Availability of PhytoPlankton group P2 - # to Zooplankton group z - suprey3: 1.0 # [-] Availability of PhytoPlankton group P4 - # to Zooplankton group z - suprey4: 1.0 # [-] Availability of MicroZooplankton group Z5 - # to Zooplankton group z - suprey5: 1.0 # [-] Availability of MicroZooplankton group Z4 - # to Zooplankton group z -#------------------------------------------------------------------------------- - isP21: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP22: 1 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP23: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP24: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] - isP25: 0 # [-] identify P2 among the preys [1 for P2 otherwise 0] -#------------------------------------------------------------------------------- - initialization: - c: 1.0 # carbon (mg C/m^3) - n: 0.015 # nitrogen (mmol N/m^3) - p: 0.00167 # phosphate (mmol N/m^3) - coupling: - O2o: O2/o # dissolved oxygen - O3c: O3/c # DIC - N1p: N1/p # phosphate (mmol P/m^3) - N4n: N4/n # ammonium (mmol N/m^3) - R6c: R6/c # POC - R6n: R6/n # PON - R6p: R6/p # POP - R6s: R6/s # biogenic silica (mmol Si/m^3) - R8c: R8/c # POC - R8n: R8/n # PON - R8p: R8/p # POP - R8s: R8/s # biogenic silica (mmol Si/m^3) - prey1: P1 - prey2: P2 - prey3: P4 - prey4: Z5 - prey5: Z4 - O3h: O3h/h - O5c: O5/c -# ---------------------- Pelagic chemistry ---------------------- -# - PelChem: - long_name: pelagic chemistry - model: ogs/PelChem - parameters: - p_clO2o: 10.0 # [mmolO2/m3] Half-saturation O2 concentration for nitrification and reoxidation - p_clN6r: 1.0 # [mmolHS/m3] Half-saturation concentration of reduction equivalents for denitrification[mmolO2/m3] - p_sN4N3: 0.01 # [1/d] Specific nitrification rate at 10 degC - p_q10N4N3: 2.367 # [-] Q10 factor for nitrification/denit - p_qon_nitri: 2.0 # [mmolO2/mmolN] stoichiometric coefficient for nitrification - p_qro: 0.5 # [mmolHS-/mmolO2] Stoichiometric coefficient for anaerobic reactions - p_sN3O4n: 0.35 # [1/d] Specific denitrification rate - p_rPAo: 1.0 # [mmolO2/m3/d] Reference anoxic mineralization rate - p_qon_dentri: 1.25 # [mmolO2/mmolN] Stoichiometric coefficient for denitrification - p_rOS: 0.05 # [1/d] Specific reoxidation rate of reduction equivalents - p_sR6N5: 0.1 # [1/d] Specific remineralization rate of biogenic silica (small POC) - p_q10R6N5: 1.49 # [-] Q10 factor for biogenic silica (small POC) - p_sR8N5: 0.1 # [1/d] Specific remineralization rate of biogenic silica (large POC) - p_q10R8N5: 1.49 # [-] Q10 factor for biogenic silica (large POC) - p_bX1c: 0.1 # [1/d] photodegradation (bleaching) rate X1c - p_bX2c: 0.03 # [1/d] photodegradation (bleaching) rate X2c - p_bX3c: 0.01 # [1/d] photodegradation (bleaching) rate X3c - p_IX1: 60.0 # [uE m-2 s-1] light threshold for X1c bleaching - p_IX2: 60.0 # [uE m-2 s-1] light threshold for X2c bleaching - p_IX3: 50.0 # [uE m-2 s-1] light threshold for X3c bleaching - p_rX3c: 0.00003 # [1/d] remineralization rate X3c and R3c - p_q10X: 2.95 # [-] q10 for CDOM degradation - p_Esource: 5 # [5 or 6] source of light for CDOM bleaching, 5=spectral, 6=mono - p_use_benthic: 0 #[0=F or 1=T] activate first-order benthic return - p_TauC: 1.0 #[d] remineralization of Carbon in detritus - p_TauN: 0.5 #[d] remineralization of Nitrogen in detritus - p_TauP: 1.0 #[d] remineralization of Phosphorus in detritus - p_Amm_rem: 0.2 #[0 to 1] fraction of detritus remineralized to NH4 - initialization: - coupling: - N1p: N1/p # phosphate (mmol P/m^3) - 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) - O3h: O3h/h # alkalinity (mmol /m^3) - O3c: O3/c # DIC - O4n: O4/n # N2 (mmol N/m^3) - N6r: N6/r # reduction equivalent (mmol HS/m^3) - N5s: N5/s # silicate (mmol Si/m^3) - X1c: X1/c # cdom X1c (mgC/m^3) - X2c: X2/c # cdom X2c (mgC/m^3) - X3c: X3/c # cdom X3c (mgC/m^3) - R3c: R3/c # cdom R3c (mgC/m^3) - R6s: R6/s # POSi (mgSi/m3) - R6c: R6/c # POC (mgC/m3) - R6n: R6/n # PON (mmolN/m3) - R6p: R6/p # POP (mmolP/m3) - R8s: R8/s # POSi (mgSi/m3) - R8c: R8/c # POC (mgC/m3) - R8n: R8/n # PON (mmolN/m3) - R8p: R8/p # POP (mmolP/m3) - PAR_tot: lightspectral/PAR_tot - isBen: Benthic_layer/isBen -## --------------------- CalciteDissolution - O5: -# use: false - long_name: calcite - model: ogs/CalciteDissolution - parameters: - p_kdca: 10.9 # [d-1] Calcite dissolution rate constant - p_nomega: 1.0 # [-] Order of the dissolution rate dependence on Omega - p_wsinkPIC: 30 # [m d-1] sinking velocity of PIC (Calcite) - c0: 1.0e-05 # [mg C/m^3] background concentration, default = 0.0 - initialization: - c: 1.0 # carbon (mg C/m^3) - coupling: - OCalc: O3/OCalc # calcite saturation (-) - O3c: O3/c # total dissolved inorganic carbon (mgC/m^3) - O3h: O3h/h # alkalinity (mmol/m^3) - Phyto_c: - long_name: total - model: weighted_sum - parameters: - n: 4 - coupling: - term1: P1_c - term2: P2_c - term3: P3_c - term4: P4_c - Phyto_Chl: - long_name: total - model: weighted_sum - parameters: - n: 4 - coupling: - term1: P1_Chl - term2: P2_Chl - term3: P3_Chl - term4: P4_Chl -# Phyto_NPP: -# long_name: total -# model: weighted_sum -# parameters: -# n: 4 -# coupling: -# term1: P1_run_result -# term2: P2_run_result -# term3: P3_run_result -# term4: P4_run_result