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fabm_monospectral.yaml
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check_conservation: false
require_initialization: true
log: true
instances:
zenith_angle:
model: ogs/zenith_angle
light:
model: ogs/light
parameters:
pEPSCHL: 0.080 # 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:
# P1chl: P1/Chl
# P2chl: P2/Chl
# P3chl: P3/Chl
# P4chl: P4/Chl
X1c: X1/c
X2c: X2/c
X3c: X3/c
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: Particulate Organic carbon
model: ogs/bfm_pelagic_base
parameters:
composition: cpns # elemental composition
rm: 4.25 # 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_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_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: 0.00057 # [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: 0.080 # [-] fraction of colored semi-labile DOC
# --------- Chlorophyll parameters -----------
p_switchChl: 2 # [1-4] Switch for Chla-a synthesis
p_sdchl: 0.2 # [1/d] Specific turnover rate for Chla
p_alpha_chl: 2.61e-5 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve
p_quantum_yield: 0.750e-3 # [mgC / uE] Photochemical efficiency
p_Esource: 6 # [1-6] source of light for PP, 1=absorbed by P1, 5=scalar, 6=mono
p_qlcPPY: 0.026 # [mgChla/mgC] Reference 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
# --------- 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:
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
X1c: X1/c
X2c: X2/c
O3h: O3h/h
O5c: O5/c
PAR: light/parEIR
# ---------------------- 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_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_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: 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: 0.000352 # [mmolN/mgC] minimum phosphorus to carbon ratio (mmol P/mg C)
p_qpcPPY: 0.000556 # [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 ----
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: 0.043 # [-] fraction of colored semi-labile DOC
# --------- Chlorophyll parameters -----------
p_switchChl: 2 # [1-4] Switch for Chla-a synthesis
p_sdchl: 0.2 # [1/d] Specific turnover rate for Chla
p_alpha_chl: 0.53e-5 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve
p_quantum_yield: 0.198e-3 # [mgC / uE] Photochemical efficiency
p_Esource: 6 # [1-6] source of light for PP, 2=absorbed by P2, 5=scalar, 6=mono
p_qlcPPY: 0.045 # [mgChla/mgC] Reference 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
# --------- 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:
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
X1c: X1/c
X2c: X2/c
O3h: O3h/h
O5c: O5/c
PAR: light/parEIR
# ---------------------- 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_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_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: 0.00072 # [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: 0.039 # [-] fraction of colored semi-labile DOC
# --------- Chlorophyll parameters -----------
p_switchChl: 2 # [1-4] Switch for Chla-a synthesis
p_sdchl: 0.2 # [1/d] Specific turnover rate for Chla
p_alpha_chl: 3.02e-5 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve
p_quantum_yield: 0.990e-3 # [mgC / uE] Photochemical efficiency
p_Esource: 6 # [1-6] source of light for PP, 3=absorbed by P3, 5=scalar, 6=mono
p_qlcPPY: 0.014 # [mgChla/mgC] Reference 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
# --------- 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:
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
X1c: X1/c
X2c: X2/c
O3h: O3h/h
O5c: O5/c
PAR: light/parEIR
# ---------------------- 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_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_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 ----
# Silicon absent in this PFT
# ---- 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: 0.053 # [-] fraction of colored semi-labile DOC
# --------- Chlorophyll parameters -----------
p_switchChl: 2 # [1-4] Switch for Chla-a synthesis
p_sdchl: 0.2 # [1/d] Specific turnover rate for Chla
p_alpha_chl: 0.68e-5 # [mgC s m2/mgChl/uE] Initial slope of the P-E curve
p_quantum_yield: 0.257e-3 # [mgC / uE] Photochemical efficiency
p_Esource: 6 # [1-6] source of light for PP, 4=absorbed by P4, 5=scalar, 6=mono
p_qlcPPY: 0.019 # [mgChla/mgC] Reference 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
# --------- 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:
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
X1c: X1/c
X2c: X2/c
O3h: O3h/h
O5c: O5/c
PAR: light/parEIR
# ---------------------- 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 : 0.1 # [1/d] Specific potential uptake for 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
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
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: 0.02 # [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: 30.0 # [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: 0.1 # [-] Availability of pelagic Bacteria group b
# to Zooplankton group z
suprey2: 0.7 # [-] Availability of PhytoPlankton group P1
# to Zooplankton group z
suprey3: 1.0 # [-] Availability of PhytoPlankton group P2
# to Zooplankton group z
suprey4: 0.1 # [-] 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_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)
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: 0.02 # [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_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)
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
#-----------------------------------------------------------------------------
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)
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
#-------------------------------------------------------------------------------
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)
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
p_q10R6N5: 1.49 # [-] Q10 factor for biogenic silica
p_bX1c: 0.167 # [1/d] photodegradation (bleaching) rate X1c
p_bX2c: 0.167 # [1/d] photodegradation (bleaching) rate X2c
p_bX3c: 0.00119 # [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: 6 # [5 or 6] source of light for CDOM bleaching, 5=spectral, 6=mono
initialization:
coupling:
N3n: N3/n # nitrate (mmol N/m^3)
N4n: N4/n # ammonium (mmol N/m^3)
O2o: O2/o # oxygen (mmol O_2/m^3)
O3h: O3h/h # alkalinity (mmol /m^3)
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)
PAR_tot: light/parEIR
## --------------------- 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 # background concentration (mg C/m^3), 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)