model.yaml

base_element: c

tracers:
  o2:
    long_name: oxygen
    type: inorganic
    composition: [o]
    parameters:
      temperature_regulation:
        temp_limited: False
      surface_flux: True

      reaeration:
        d: 0.31
        k1: 1953.4
        k2: 128.0
        k3: 3.9918
        k4: 0.050091
        schmidt: 660.0
        saturation_conversion: ideal_gas    # options: "ideal_gas" or "stp"

  po4:
    long_name: phosphate
    type: inorganic
    composition: [p]
    parameters:
      temperature_regulation:
        temp_limited: False

  no3:
    long_name: nitrate
    type: inorganic
    composition: [n]
    parameters:
      temperature_regulation:
        temp_limited: True
        function: q10                       # options: arrhenius, eppley, or q10
        # arrhenius: needs "activation_energy" and "coefficient" as additional parameters
        # eppley: needs "coefficient" as additional parameter
        # q10: needs "base_temp" and "coefficient" as additional parameters
        coefficient: 2.
        base_temp: 20.

      denitrification:
        anoxic_mineralization_rate: 1.
        denitrification_rate: 0.35
        
  nh4:
    long_name: ammonium
    type: inorganic
    composition: [n]
    parameters:
      temperature_regulation:
        temp_limited: True
        function: q10                       # options: [1] arrhenius, [2] eppley, or [3] q10
        # arrhenius: needs "activation_energy" and "coefficient" as additional parameters
        # eppley: needs "coefficient" as additional parameter
        # q10: needs "base_temp" and "coefficient" as additional parameters
        coefficient: 2.
        base_temp: 20.

      nitrification:
        half_sat_oxygen: 10.0               # [mmol O2 / m^3]
        nitrification_rate: 0.01            # [1/d]
        convert_o2: 2.0

  n2:
    long_name: nitrogen sink
    type: inorganic
    composition: [n]
    parameters:
      temperature_regulation:
        temp_limited: False

  sio4:
    long_name: silicate
    type: inorganic
    composition: [si]
    parameters:
      temperature_regulation:
        temp_limited: True
        function: q10
        coefficient: 1.49
        base_temp: 20.

  hs:
    long_name: reduction equivalents
    type: inorganic
    composition: [s]
    parameters:
      temperature_regulation:
        temp_limited: False

      reoxidation:
        half_sat_oxygen: 10.0               # [mmol O2 / m^3]
        reoxidation_rate: 0.05              # [1/d]
        convert_o2: 2.                      # stoichiometric conversion [mmol O2 / mmol HS-]

  bac1:
    long_name: bacterioplankton
    type: bacteria
    composition: [c,n,p]
    parameters:
      cell_quota:
        min: {c: 1., n: 1.67E-02, p: 1.85E-03}
        opt: {c: 1., n: 1.67E-02, p: 1.85E-03}

      oxygen_inhibition:
        oxygen_limited: True
        half_sat: 30.                       # [mmol O2 / m^3]
        exponent: 3.                        # optional: Hill exponent for Monod function (default to 1. if not included)
      
      temperature_regulation:
        temp_limited: True
        function: q10
        coefficient: 2.95
        base_temp: 20.

      om_partition:
        dom1: {c: 0.60, n: 0.72, p: 0.832}  # c,n,p [-]
        pom1: {c: 0.40, n: 0.28, p: 0.168}  # c,n,p [-]

      excretion:                            # options: "activity", "relaxation", or constant
        # if "activity": uses uptake rate to calculate nutrient excretion
        #                requires "activity_respiration_frac" and "excretion_rate" as additional parameters
        # if "relaxation": uses relaxation time scale to calculate excess nutrient excretion above cell quota
        #                  requires "relaxation_timescale" as an additional parameter
        #                  requires "half_sat" if exretion to inorganic nutrient
        # if "constant": uses constant excretion rate
        #                requires "excretion_rate" as an additional parameter
        dom2:
          option: relaxation
          relaxation_timescale: 1.
        dom3:
          option: activity
          activity_respiration_frac: 0.6
          excretion_rate: 0.

      mortality:
        mortality_rate:
          linear: 0.1
          quadratic: 0.
        temp_limitation:
          linear: True
          quadratic: False

      respiration:
        activity_respiration_frac: 0.6
        anoxic_respiration_frac: 0.2
        basal_respiration_rate: 0.01
        convert_o2: 1/12
        convert_hs: 1/24

      uptake:
        potential_rich: {dom1: 0.3, dom2: 0., dom3: 0., pom1: 0.01}
        potential_poor: {dom1: 0., dom2: 0., dom3: 0., pom1: 0.}
        max_growth_rate: 8.38
        substrate_correction: False
        option: potential                  # options: direct or potential
        # direct: directly calculates uptake of nutrient
        #         requires dictionary for each nutrient which includes "strategy"
        #         if "strategy" == "coupled" --> requires "coupled_uptake" dictionary which includes "method" and "link", may include "convert_uptake"
        #         if "strategy" == "independent" --> requires "max_growth_rate", "basal_metabolic_rate", "max_growth_efficiency", and "half_sat", may include "convert_uptake"
        # potential: determines potential & realized uptake then calculates nutrient uptake based on those values
        #            requires "max_growth_rate", "potential_rich", "potential_poor", and "substrate_correction"

      uptake_release:
        nh4:
          half_sat: 5.
          relaxation_timescale: 1.
        po4:
          half_sat: 1.
          relaxation_timescale: 1.

  phyto1:
    long_name: diatoms
    type: phytoplankton
    composition: [c,n,p,chl,si]
    parameters:
      cell_quota:
        max: {c: 1., n: 1.26E-02, p: 7.86E-04, chl: 0.035, si: 8.5E-03}
        min: {c: 1., n: 6.87E-03, p: 4.29E-04, chl: 0.035, si: 4.3E-03}
        opt: {c: 1., n: 1.26E-02, p: 7.86E-04, chl: 0.035, si: 8.5E-03}

      nutrient_limitation:  
        colimitation: minimum               # [1] mininimum, [2] product, or [3] sum of all limiting nutrients
        include: ["no3","po4"]              # nutrients included for calculation of colimitation factor
        no3:
          type: internal
          function: droop
          nh4_inhibited: True
        nh4:
          type: external
          function: monod
          half_sat: 1.
        po4:
          type: internal
          function: droop
        sio4:
          type: external
          function: monod
          half_sat: 1.

      sedimentation:
        sinking: True
        background_sinking_rate: 0.
        max_sinking_rate: 5.
        burial_velocity: 0.
        sinking_threshold: 0.7

      temperature_regulation:
        temp_limited: True
        function: q10                       # options: [1] arrhenius, [2] eppley, or [3] q10
        # arrhenius: needs "activation_energy" and "coefficient" as additional parameters
        # eppley: needs "coefficient" as additional parameter
        # q10: needs "base_temp" and "coefficient" as additional parameters
        coefficient: 2.
        base_temp: 20.

      exudation:
        method: photosynthesis              # options: uptake, photosynthesis
        # "photosynthesis": exudation rate calculated using excreted fraction of photosynthesis
        # "uptake": exudation rate calculated using constant excreted fraction of nutrient uptake
        excreted_fraction: 0.01             # [-]
        include_activity: True
        include_nutrient_stress: True

      growth:
        light_limitation: platt             # options: monod, geider, platt, or smith
        light_location: integrated          # options: top, middle, or integrated
        # top: light calculated at top of the cell
        # middle: light calculated in middle of cell
        # integrated: light integrated through cell
        light_attenuation: 0.03
        max_photo_rate: 2.5
        chl_quota: 0.035                    # [mg Chl / mg C]
        chl_relax_rate: 0.25                # [(mg C . m^2) / (mg Chl μE)]
        initial_PI_slope: 1.1E-05
        eps_PAR: 0.4
        convert_o2: 1/12                    # [mmol 02 / mg C]
        optimal_Epar_Ek: 3.
        silicate_limitation: True

      lysis:
        method: cell_quota                  # options: constant or cell_quota
        # constant: based on constant lysis rate
        # cell_quota: based on elemental ratios within zooplankton cell, requires "apportioning factor" as additional parameter
        extra_lysis_rate: 0.
        half_sat_stress_lysis: 0.1
        half_sat_extra_lysis: 0.0
        max_stress_lysis_rate: 0.01         # [1/d]
        apportioning_factor:  # list of elements of which to apply apportioning factor to, elements not included will not have dissolved/particulate apportioning factor applied
          dom1: [c,n,p]
          pom1: [c,n,p]

      respiration:
        activity_respiration_frac: 0.1      # [-]
        basal_respiration_rate: 0.05        # [1/d]
        convert_o2: 1/12                    # [mmol 02 / mg C]

      uptake:
        no3:
          basis: nutrient                   # (if strategy is "independent") options: constant, growth, or nutrient
          # constant: based on constant uptake rate
          # growth: based on photosynthesis and nutrient limitation
          # nutrient: based on nutrient availabilty
          strategy: independent             # options: independent or coupled
          # independent: calculates uptake rate based on the nutrient
          # coupled: uses conversion factor to calculate uptake rated based on uptake of a different nutrient
          form: affinity                    # options: affinity or constituent
          # affinity: uses specific affinity, based on cell quota w.r.t base element
          # constituent: uses concentration of phytoplankton constituent of nutrient element
          half_sat_nh4_preference: 1.
          luxury_storage: 2.
          specific_affinity: 0.025          # [m^3 / (mg C . d)]
        nh4:
          basis: nutrient                   # (if strategy is "independent") options: constant, growth, or nutrient
          # constant: based on constant uptake rate
          # growth: based on photosynthesis and nutrient limitation
          # nutrient: based on nutrient availabilty
          strategy: independent             # options: independent or coupled
          # independent: calculates uptake rate based on the nutrient
          # coupled: uses conversion factor to calculate uptake rated based on uptake of a different nutrient
          form: affinity                    # options: affinity or constituent
          # affinity: uses specific affinity, based on cell quota w.r.t base element
          # constituent: uses concentration of phytoplankton constituent of nutrient element
          half_sat_nh4_preference: 1.
          luxury_storage: 2.
          # max_photo_rate: 2.5               # [1/d]
          specific_affinity: 0.025          # [m^3 / (mg C . d)]
        po4:
          basis: nutrient                   # (if strategy is "independent") options: constant, growth, or nutrient
          # constant: based on constant uptake rate
          # growth: based on photosynthesis and nutrient limitation
          # nutrient: based on nutrient availabilty
          strategy: independent             # options: independent or coupled
          # independent: calculates uptake rate based on the nutrient
          # coupled: uses conversion factor to calculate uptake rated based on uptake of a different nutrient
          form: affinity                    # options: affinity or constituent
          # affinity: uses specific affinity, based on cell quota w.r.t base element
          # constituent: uses concentration of phytoplankton constituent of nutrient element
          luxury_storage: 2.
          specific_affinity: 0.0025         # [m^3 / (mg C . d)]
        sio4:
          basis: growth
          strategy: independent
          form: affinity
          half_sat_uptake: 1.
          numerator: cell_quota
          denominator: zero
          exclude_respiratory_cost: True

  phyto2:
    long_name: nanoflagellates
    type: phytoplankton
    composition: [c,n,p,chl]
    parameters:
      cell_quota:
        max: {c: 1., n: 1.26E-02, p: 7.86E-04, chl: 0.016}
        min: {c: 1., n: 6.87E-03, p: 4.29E-04, chl: 0.016}
        opt: {c: 1., n: 1.26E-02, p: 7.86E-04, chl: 0.016}

      nutrient_limitation:  
        colimitation: minimum               # [1] mininimum, [2] product, or [3] sum of all limiting nutrients
        include: ["no3","po4"]              # nutrients included for calculation of colimitation factor
        no3:
          type: internal
          function: droop
          nh4_inhibited: True
        nh4:
          type: external
          function: monod
          half_sat: 1.5
        po4:
          type: internal
          function: droop

      sedimentation:
        sinking: True
        background_sinking_rate: 0.
        max_sinking_rate: 0.5
        burial_velocity: 0.
        sinking_threshold: 0.75

      temperature_regulation:
        temp_limited: True
        function: q10                       # options: [1] arrhenius, [2] eppley, or [3] q10
        # arrhenius: needs "activation_energy" and "coefficient" as additional parameters
        # eppley: needs "coefficient" as additional parameter
        # q10: needs "base_temp" and "coefficient" as additional parameters
        coefficient: 2.
        base_temp: 20.

      exudation:
        method: photosynthesis              # options: uptake, photosynthesis
        # "photosynthesis": exudation rate calculated using excreted fraction of photosynthesis, requires "include_activity" and "include_nutrient_stress" as additional parameters
        # "uptake": exudation rate calculated using constant excreted fraction of nutrient uptake
        excreted_fraction: 0.05             # [-]
        include_activity: True
        include_nutrient_stress: True

      growth:
        light_limitation: platt             # options: monod, geider, platt, or smith
        light_location: integrated          # options: top, middle, or integrated
        # top: light calculated at top of the cell
        # middle: light calculated in middle of cell
        # integrated: light integrated through cell
        light_attenuation: 0.03
        max_photo_rate: 1.6
        chl_quota: 0.016                    # [mg Chl / mg C]
        chl_relax_rate: 0.                  # [(mg C . m^2) / (mg Chl μE)]
        initial_PI_slope: 1.52E-05
        eps_PAR: 0.4
        convert_o2: 1/12                    # [mmol 02 / mg C]
        optimal_Epar_Ek: 0.
        silicate_limitation: False

      lysis:
        method: cell_quota                  # options: constant or cell_quota
        # constant: based on constant lysis rate
        # cell_quota: based on elemental ratios within zooplankton cell
        extra_lysis_rate: 0.
        half_sat_stress_lysis: 0.1
        half_sat_extra_lysis: 0.0
        max_stress_lysis_rate: 0.05         # [1/d]
        apportioning_factor:  # list of elements of which to apply apportioning factor to, elements not included will not have dissolved/particulate apportioning factor applied
          dom1: [c,n,p]
          pom1: [c,n,p]

      respiration:
        activity_respiration_frac: 0.05     # [-]
        basal_respiration_rate: 0.05        # [1/d]
        convert_o2: 1/12                    # [mmol 02 / mg C]

      uptake:
        no3:
          basis: nutrient                   # (if strategy is "independent") options: constant, growth, or nutrient
          # constant: based on constant uptake rate
          # growth: based on photosynthesis and nutrient limitation
          # nutrient: based on nutrient availabilty
          strategy: independent             # options: independent or coupled
          # independent: calculates uptake rate based on the nutrient
          # coupled: uses conversion factor to calculate uptake rated based on uptake of a different nutrient
          form: affinity                    # options: affinity or constituent
          # affinity: uses specific affinity, based on cell quota w.r.t base element
          # constituent: uses concentration of phytoplankton constituent of nutrient element
          half_sat_nh4_preference: 1.5
          luxury_storage: 1.
          specific_affinity: 0.025          # [m^3 / (mg C . d)]
        nh4:
          basis: nutrient                   # (if strategy is "independent") options: constant, growth, or nutrient
          # constant: based on constant uptake rate
          # growth: based on photosynthesis and nutrient limitation
          # nutrient: based on nutrient availabilty
          strategy: independent             # options: independent or coupled
          # independent: calculates uptake rate based on the nutrient
          # coupled: uses conversion factor to calculate uptake rated based on uptake of a different nutrient
          form: affinity                    # options: affinity or constituent
          # affinity: uses specific affinity, based on cell quota w.r.t base element
          # constituent: uses concentration of phytoplankton constituent of nutrient element
          half_sat_nh4_preference: 1.5
          luxury_storage: 1.
          specific_affinity: 0.025          # [m^3 / (mg C . d)]
        po4:
          basis: nutrient                   # (if strategy is "independent") options: constant, growth, or nutrient
          # constant: based on constant uptake rate
          # growth: based on photosynthesis and nutrient limitation
          # nutrient: based on nutrient availabilty
          strategy: independent             # options: independent or coupled
          # independent: calculates uptake rate based on the nutrient
          # coupled: uses conversion factor to calculate uptake rated based on uptake of a different nutrient
          form: affinity                    # options: affinity or constituent
          # affinity: uses specific affinity, based on cell quota w.r.t base element
          # constituent: uses concentration of phytoplankton constituent of nutrient element
          luxury_storage: 1.
          specific_affinity: 0.0025         # [m^3 / (mg C . d)]

  phyto3:
    long_name: picophytoplankton
    type: phytoplankton
    composition: [c,n,p,chl]
    parameters:
      cell_quota:
        max: {c: 1., n: 1.26E-02, p: 7.86E-04, chl: 0.02}
        min: {c: 1., n: 6.87E-03, p: 4.29E-04, chl: 0.02}
        opt: {c: 1., n: 1.26E-02, p: 7.86E-04, chl: 0.02}

      nutrient_limitation:  
        colimitation: minimum               # [1] mininimum, [2] product, or [3] sum of all limiting nutrients
        include: ["no3","po4"]              # nutrients included for calculation of colimitation factor
        no3:
          type: internal
          function: droop
          nh4_inhibited: True
        nh4:
          type: external
          function: monod
          half_sat: 1.
        po4:
          type: internal
          function: droop

      sedimentation:
        sinking: True
        background_sinking_rate: 0.
        max_sinking_rate: 0.5
        burial_velocity: 0.
        sinking_threshold: 0.75

      temperature_regulation:
        temp_limited: True
        function: q10                       # options: [1] arrhenius, [2] eppley, or [3] q10
        # arrhenius: needs "activation_energy" and "coefficient" as additional parameters
        # eppley: needs "coefficient" as additional parameter
        # q10: needs "base_temp" and "coefficient" as additional parameters
        coefficient: 2.
        base_temp: 20.

      exudation:
        method: photosynthesis              # options: uptake, photosynthesis
        # "photosynthesis": exudation rate calculated using excreted fraction of photosynthesis
        # "uptake": exudation rate calculated using constant excreted fraction of nutrient uptake
        excreted_fraction: 0.1              # [-]
        include_activity: True
        include_nutrient_stress: True

      growth:
        light_limitation: platt             # options: monod, geider, platt, or smith
        light_location: integrated          # options: top, middle, or integrated
        # top: light calculated at top of the cell
        # middle: light calculated in middle of cell
        # integrated: light integrated through cell
        light_attenuation: 0.03
        max_photo_rate: 1.02
        chl_quota: 0.02                     # [mg Chl / mg C]
        chl_relax_rate: 0.25                # [(mg C . m^2) / (mg Chl μE)]
        initial_PI_slope: 0.7E-05
        eps_PAR: 0.4
        convert_o2: 1/12                    # [mmol 02 / mg C]
        optimal_Epar_Ek: 3.
        silicate_limitation: False

      lysis:
        method: cell_quota                  # options: constant or cell_quota
        # constant: based on constant lysis rate
        # cell_quota: based on elemental ratios within zooplankton cell
        extra_lysis_rate: 0.
        half_sat_stress_lysis: 0.1
        half_sat_extra_lysis: 0.0
        max_stress_lysis_rate: 0.01         # [1/d]
        apportioning_factor:  # list of elements of which to apply apportioning factor to, elements not included will not have dissolved/particulate apportioning factor applied
          dom1: [c,n,p]
          pom1: [c,n,p]

      respiration:
        activity_respiration_frac: 0.2      # [-]
        basal_respiration_rate: 0.05        # [1/d]
        convert_o2: 1/12                    # [mmol 02 / mg C]

      uptake:
        no3:
          basis: nutrient                   # (if strategy is "independent") options: constant, growth, or nutrient
          # constant: based on constant uptake rate
          # growth: based on photosynthesis and nutrient limitation
          # nutrient: based on nutrient availabilty
          strategy: independent             # options: independent or coupled
          # independent: calculates uptake rate based on the nutrient
          # coupled: uses conversion factor to calculate uptake rated based on uptake of a different nutrient
          form: affinity                    # options: affinity or constituent
          # affinity: uses specific affinity, based on cell quota w.r.t base element
          # constituent: uses concentration of phytoplankton constituent of nutrient element
          half_sat_nh4_preference: 0.1
          luxury_storage: 2.
          specific_affinity: 0.025          # [m^3 / (mg C . d)]
        nh4:
          basis: nutrient                   # (if strategy is "independent") options: constant, growth, or nutrient
          # constant: based on constant uptake rate
          # growth: based on photosynthesis and nutrient limitation
          # nutrient: based on nutrient availabilty
          strategy: independent             # options: independent or coupled
          # independent: calculates uptake rate based on the nutrient
          # coupled: uses conversion factor to calculate uptake rated based on uptake of a different nutrient
          form: affinity                    # options: affinity or constituent
          # affinity: uses specific affinity, based on cell quota w.r.t base element
          # constituent: uses concentration of phytoplankton constituent of nutrient element
          half_sat_nh4_preference: 0.1
          luxury_storage: 2.
          specific_affinity: 0.025          # [m^3 / (mg C . d)]
        po4:
          basis: nutrient                   # (if strategy is "independent") options: constant, growth, or nutrient
          # constant: based on constant uptake rate
          # growth: based on photosynthesis and nutrient limitation
          # nutrient: based on nutrient availabilty
          strategy: independent             # options: independent or coupled
          # independent: calculates uptake rate based on the nutrient
          # coupled: uses conversion factor to calculate uptake rated based on uptake of a different nutrient
          form: affinity                    # options: affinity or constituent
          # affinity: uses specific affinity, based on cell quota w.r.t base element
          # constituent: uses concentration of phytoplankton constituent of nutrient element
          luxury_storage: 2.
          specific_affinity: 0.0025         # [m^3 / (mg C . d)]

  phyto4:
    long_name: large phytoplankton
    type: phytoplankton
    composition: [c,n,p,chl]
    parameters:
      cell_quota:
        max: {c: 1., n: 1.26E-02, p: 7.86E-04, chl: 0.035}
        min: {c: 1., n: 6.87E-03, p: 4.29E-04, chl: 0.035}
        opt: {c: 1., n: 1.26E-02, p: 7.86E-04, chl: 0.035}

      nutrient_limitation:  
        colimitation: minimum               # [1] mininimum, [2] product, or [3] sum of all limiting nutrients
        include: ["no3","po4"]              # nutrients included for calculation of colimitation factor
        no3:
          type: internal
          function: droop
          nh4_inhibited: True
        nh4:
          type: external
          function: monod
          half_sat: 1.
        po4:
          type: internal
          function: droop

      sedimentation:
        sinking: True
        background_sinking_rate: 0.
        max_sinking_rate: 5.
        burial_velocity: 0.
        sinking_threshold: 0.75

      temperature_regulation:
        temp_limited: True
        function: q10                       # options: [1] arrhenius, [2] eppley, or [3] q10
        # arrhenius: needs "activation_energy" and "coefficient" as additional parameters
        # eppley: needs "coefficient" as additional parameter
        # q10: needs "base_temp" and "coefficient" as additional parameters
        coefficient: 2.
        base_temp: 20.

      exudation:
        method: photosynthesis              # options: uptake, photosynthesis
        # "photosynthesis": exudation rate calculated using excreted fraction of photosynthesis
        # "uptake": exudation rate calculated using constant excreted fraction of nutrient uptake
        excreted_fraction: 0.15             # [-]
        include_activity: True
        include_nutrient_stress: True

      growth:
        light_limitation: platt             # options: monod, geider, platt, or smith
        light_location: integrated          # options: top, middle, or integrated
        # top: light calculated at top of the cell
        # middle: light calculated in middle of cell
        # integrated: light integrated through cell
        light_attenuation: 0.03
        max_photo_rate: 0.83
        chl_quota: 0.035                    # [mg Chl / mg C]
        chl_relax_rate: 0.25                # [(mg C . m^2) / (mg Chl μE)]
        initial_PI_slope: 6.8E-06
        eps_PAR: 0.4
        convert_o2: 1/12                    # [mmol 02 / mg C]
        optimal_Epar_Ek: 3.
        silicate_limitation: False

      lysis:
        method: cell_quota                  # options: constant or cell_quota
        # constant: based on constant lysis rate
        # cell_quota: based on elemental ratios within zooplankton cell
        extra_lysis_rate: 0.5
        half_sat_stress_lysis: 0.5
        half_sat_extra_lysis: 100.
        max_stress_lysis_rate: 0.2          # [1/d]
        apportioning_factor:  # list of elements of which to apply apportioning factor to, elements not included will not have dissolved/particulate apportioning factor applied
          dom1: [c,n,p]
          pom1: [c,n,p]

      respiration:
        activity_respiration_frac: 0.1      # [-]
        basal_respiration_rate: 0.1         # [1/d]
        convert_o2: 1/12                    # [mmol 02 / mg C]

      uptake:
        no3:
          basis: nutrient                   # (if strategy is "independent") options: constant, growth, or nutrient
          # constant: based on constant uptake rate
          # growth: based on photosynthesis and nutrient limitation
          # nutrient: based on nutrient availabilty
          strategy: independent             # options: independent or coupled
          # independent: calculates uptake rate based on the nutrient
          # coupled: uses conversion factor to calculate uptake rated based on uptake of a different nutrient
          form: affinity                    # options: affinity or constituent
          # affinity: uses specific affinity, based on cell quota w.r.t base element
          # constituent: uses concentration of phytoplankton constituent of nutrient element
          half_sat_nh4_preference: 1.
          luxury_storage: 2.
          specific_affinity: 0.025          # [m^3 / (mg C . d)]
        nh4:
          basis: nutrient                   # (if strategy is "independent") options: constant, growth, or nutrient
          # constant: based on constant uptake rate
          # growth: based on photosynthesis and nutrient limitation
          # nutrient: based on nutrient availabilty
          strategy: independent             # options: independent or coupled
          # independent: calculates uptake rate based on the nutrient
          # coupled: uses conversion factor to calculate uptake rated based on uptake of a different nutrient
          form: affinity                    # options: affinity or constituent
          # affinity: uses specific affinity, based on cell quota w.r.t base element
          # constituent: uses concentration of phytoplankton constituent of nutrient element
          half_sat_nh4_preference: 1.
          luxury_storage: 2.
          specific_affinity: 0.025          # [m^3 / (mg C . d)]
        po4:
          basis: nutrient                   # (if strategy is "independent") options: constant, growth, or nutrient
          # constant: based on constant uptake rate
          # growth: based on photosynthesis and nutrient limitation
          # nutrient: based on nutrient availabilty
          strategy: independent             # options: independent or coupled
          # independent: calculates uptake rate based on the nutrient
          # coupled: uses conversion factor to calculate uptake rated based on uptake of a different nutrient
          form: affinity                    # options: affinity or constituent
          # affinity: uses specific affinity, based on cell quota w.r.t base element
          # constituent: uses concentration of phytoplankton constituent of nutrient element
          luxury_storage: 2.
          specific_affinity: 0.0025         # [m^3 / (mg C . d)]   
        
  mesozoo1:
    long_name: carnivorous mesozooplankton
    type: zooplankton
    composition: [c,n,p]
    parameters:
      cell_quota:
        opt: {c: 1., n: 1.258E-02, p: 7.862E-04}
      
      temperature_regulation:
        temp_limited: True
        function: q10                       # options: arrhenius, eppley, or q10
        # arrhenius: needs "activation_energy" and "coefficient" as additional parameters
        # eppley: needs "coefficient" as additional parameter
        # q10: needs "base_temp" and "coefficient" as additional parameters
        coefficient: 2.0
        base_temp: 20.

      oxygen_inhibition:
        oxygen_limited: True
        half_sat: 30.                       # [mmol O2 / m^3]
        exponent: 3.                        # optional: Hill exponent for Monod function (default to 1. if not included)
      
      efficiency:
        assimilation: 0.6
        ingestion: 0.3

      egestion:
        unassimilated: []

      grazing:
        grazing_preferences: {mesozoo1: 1., mesozoo2: 1.}
        function: holling-2
        # feeding_threshold: 50.0             # [mg C / m^3]
        max_grazing_rate: 2.0               # [1/d]
        search_volume: 2.5E-03              # [m^3 / (predator . d)]
        feeding_model: clearance_rate       # options: "half_saturation" and "clearance_rate"
        # if feeding_model: "half_saturation" --> requires "half_sat_grazing" as additional parameter
        # if feeding_model: "clearance_rate"  --> requires "search_volume" as additional parameter

      metabolic_release:
        basal_metabolic_rate: 0.01
        destination:
          c: pom1
          n: nh4
          p: po4
        function:
        # "activity"      --> calculates excretion based on total ingestion and respiratory costs
        # "excess_only"   --> only applies excess excretion from variable limitation correction term
          c: excess_only
          n: activity
          p: activity

      mortality:
        mortality_rate: 
          linear: 0.                        # linear [1/d]
          quadratic: 0.02                   # quadratic [1/d^2]
          oxygen: 0.01                      # [1/d]
        temp_limitation:
          linear: False
          quadratic: False
          oxygen: True

      respiration:
        respiration_rate: 0.01              # [1/d]
        convert_o2: 1/12                    # [mmol 02 / mg C]

  mesozoo2:
    long_name: omnivorous mesozooplankton
    type: zooplankton
    composition: [c,n,p]
    parameters:
      cell_quota:
        opt: {c: 1., n: 1.258E-02, p: 7.862E-04}
      
      temperature_regulation:
        temp_limited: True
        function: q10                       # options: arrhenius, eppley, or q10
        # arrhenius: needs "activation_energy" and "coefficient" as additional parameters
        # eppley: needs "coefficient" as additional parameter
        # q10: needs "base_temp" and "coefficient" as additional parameters
        coefficient: 2.0
        base_temp: 20.

      oxygen_inhibition:
        oxygen_limited: True
        half_sat: 30.                       # [mmol O2 / m^3]
        exponent: 3.                        # optional: Hill exponent for Monod function (default to 1. if not included)
      
      efficiency:
        assimilation: 0.6
        ingestion: 0.35

      egestion:
        unassimilated: []

      grazing:
        grazing_preferences: {phyto1: 1., phyto2: 0.1, phyto4: 0.7, mesozoo2: 1., microzoo1: 1.}
        function: holling-2
        # feeding_threshold: 50.0             # [mg C / m^3]
        max_grazing_rate: 2.0               # [1/d]
        search_volume: 2.5E-02              # [m^3 / (predator . d)]
        feeding_model: clearance_rate       # options: "half_saturation" and "clearance_rate"
        # if feeding_model: "half_saturation" --> requires "half_sat_grazing" as additional parameter
        # if feeding_model: "clearance_rate"  --> requires "search_volume" as additional parameter

      metabolic_release:
        basal_metabolic_rate: 0.02
        destination:
          c: pom1
          n: nh4
          p: po4
        function:
        # "activity"      --> calculates excretion based on total ingestion and respiratory costs
        # "excess_only"   --> only applies excess excretion from variable limitation correction term
          c: excess_only
          n: activity
          p: activity

      mortality:
        mortality_rate: 
          linear: 0.                        # linear [1/d]
          quadratic: 0.02                   # quadratic [1/d^2]
          oxygen: 0.01                      # [1/d]
        temp_limitation:
          linear: False
          quadratic: False
          oxygen: True

      respiration:
        respiration_rate: 0.02              # [1/d]
        convert_o2: 1/12                    # [mmol 02 / mg C]

  microzoo1:
    long_name: microzooplankton
    type: zooplankton
    composition: [c,n,p]
    parameters:
      cell_quota:
        opt: {c: 1., n: 1.258E-02, p: 7.862E-04}
      
      temperature_regulation:
        temp_limited: True
        function: q10                       # options: arrhenius, eppley, or q10
        # arrhenius: needs "activation_energy" and "coefficient" as additional parameters
        # eppley: needs "coefficient" as additional parameter
        # q10: needs "base_temp" and "coefficient" as additional parameters
        coefficient: 2.0
        base_temp: 20.

      oxygen_inhibition:
        oxygen_limited: True
        half_sat: 0.5                       # [mmol O2 / m^3]
        exponent: 1.                        # optional: Hill exponent for Monod function (default to 1. if not included)
      
      om_partition:
        dom1: {c: 0.60, n: 0.72, p: 0.832}  # c,n,p [-]
        pom1: {c: 0.40, n: 0.28, p: 0.168}  # c,n,p [-]

      efficiency:
        assimilation: 0.5
        ingestion: 0.25

      egestion:
        unassimilated: [c]

      excretion:  # requires "destination" and "function"
        destination:
          n: nh4
          p: po4
        function:
        # "activity"      --> calculates excretion based on total ingestion and respiratory costs
        # numerical value --> constant excretion rate
          n: activity
          p: activity


      grazing:
        grazing_preferences: {bac1: 0.1, phyto1: 0.5, phyto2: 1., phyto3: 0.5, microzoo1: 1., microzoo2: 0.8}
        function: holling-2
        feeding_threshold: 50.0             # [mg C / m^3]
        max_grazing_rate: 2.0               # [1/d]
        half_sat_grazing: 200.0             # [mg C / m^3]
        feeding_model: half_saturation      # options: "half_saturation" and "clearance_rate"
        # if feeding_model: "half_saturation" --> requires "half_sat_grazing" as additional parameter
        # if feeding_model: "clearance_rate"  --> requires "search_volume" as additional parameter

      mortality:
        mortality_rate: 
          linear: 1.E-06                    # linear [1/d]
          quadratic: 0.                     # quadratic [1/d^2]
          oxygen: 0.25                      # [1/d]
        temp_limitation:
          linear: False
          quadratic: False
          oxygen: False

      respiration:
        respiration_rate: 0.02              # [1/d]
        convert_o2: 1/12                    # [mmol 02 / mg C]

  microzoo2:
    long_name: heterotrophic flagellates
    type: zooplankton
    composition: [c,n,p]
    parameters:
      cell_quota:
        opt: {c: 1., n: 1.258E-02, p: 7.862E-04}
      
      temperature_regulation:
        temp_limited: True
        function: q10                       # options: arrhenius, eppley, or q10
        # arrhenius: needs "activation_energy" and "coefficient" as additional parameters
        # eppley: needs "coefficient" as additional parameter
        # q10: needs "base_temp" and "coefficient" as additional parameters
        coefficient: 2.0
        base_temp: 20.

      oxygen_inhibition:  # optional, if included requires "oxygen_limited" boolean
        oxygen_limited: True                # if "True", requires "half_sat" as additional parameter and optional "exponent", no additional parameters needed if False
        half_sat: 0.5                       # [mmol O2 / m^3]
        exponent: 1.                        # optional: Hill exponent for Monod function (default to 1. if not included)
      
      om_partition:
        dom1: {c: 0.60, n: 0.72, p: 0.832}  # c,n,p [-]
        pom1: {c: 0.40, n: 0.28, p: 0.168}  # c,n,p [-]

      efficiency:
        assimilation: 0.3
        ingestion: 0.35

      egestion:
        unassimilated: [c]

      excretion:  # requires "destination" and "function"
        destination:
          n: nh4
          p: po4
        function:
        # "activity"      --> calculates excretion based on total ingestion and respiratory costs
        # numerical value --> constant excretion rate
          n: activity
          p: activity

      grazing:
        grazing_preferences: {bac1: 1., phyto2: 0.1, phyto3: 1., microzoo2: 0.2}
        function: holling-2
        feeding_threshold: 50.0             # [mg C / m^3]
        max_grazing_rate: 5.0               # [1/d]
        half_sat_grazing: 200.0             # [mg C / m^3]
        feeding_model: half_saturation      # options: "half_saturation" and "clearance_rate"
        # if feeding_model: "half_saturation" --> requires "half_sat_grazing" as additional parameter
        # if feeding_model: "clearance_rate"  --> requires "search_volume" as additional parameter

      mortality:
        mortality_rate: 
          linear: 1.E-06                    # linear [1/d]
          quadratic: 0.                     # quadratic [1/d^2]
          oxygen: 0.25                      # [1/d]
        temp_limitation:
          linear: False
          quadratic: False
          oxygen: False

      respiration:
        respiration_rate: 0.02              # [1/d]
        convert_o2: 1/12                    # [mmol 02 / mg C]

  dom1:
    long_name: labile dissolved organic matter
    type: detritus
    form: dissolved
    composition: [c,n,p]
    parameters:
      light_attenuation: 0.0                # [m^2 / mg C]

      # remineralization:
      #   remineralization_rate: {c: 0.05}         # [1/d]
      #   convert_o2: 1/12                    # [mmol 02 / mg C]

      sedimentation:
        sinking: False
        background_sinking_rate: 0.                    # [m/d]
        burial_velocity: 0.                 # [m/d]

  dom2:
    long_name: semi-labile dissolved organic matter
    type: detritus
    form: dissolved
    composition: [c]
    parameters:
      light_attenuation: 0.0                # [m^2 / mg C]

      # remineralization:
      #   remineralization_rate: {c: 0.05}         # [1/d]
      #   convert_o2: 1/12                    # [mmol 02 / mg C]

      sedimentation:
        sinking: False
        background_sinking_rate: 0.                    # [m/d]
        burial_velocity: 0.                 # [m/d]

  dom3:
    long_name: semi-refractory dissolved organic matter
    type: detritus
    form: dissolved
    composition: [c]
    parameters:
      light_attenuation: 0.0                # [m^2 / mg C]

      # remineralization:
      #   remineralization_rate: {c: 0.05, n: 0.05, p: 0.05}          # [1/d]
      #   # remineralization_rate: 0.05         # [1/d]
      #   convert_o2: 1/12                    # [mmol 02 / mg C]

      sedimentation:
        sinking: False
        background_sinking_rate: 0.                    # [m/d]
        burial_velocity: 0.                 # [m/d]

  pom1:
    long_name: particulate organic matter
    type: detritus
    form: particulate
    composition: [c,n,p,si]
    parameters:
      light_attenuation: 1.0E-04            # [m^2 / mg C]

      dissolution:
        dissolution_rate: {si: 0.02}

      # remineralization:
      #   remineralization_rate: {c: 0.1, n: 0.1, p: 0.1}          # [1/d]
      #   # remineralization_rate: 0.1          # [1/d]
      #   convert_o2: 1/12                    # [mmol 02 / mg C]
        
      sedimentation:
        sinking: True
        background_sinking_rate: 1.                    # [m/d]
        burial_velocity: 1.                 # [m/d]

      temperature_regulation:
        temp_limited: True
        function: q10                       # options: arrhenius, eppley, or q10
        # arrhenius: needs "activation_energy" and "coefficient" as additional parameters
        # eppley: needs "coefficient" as additional parameter
        # q10: needs "base_temp" and "coefficient" as additional parameters
        coefficient: 1.49
        base_temp: 20.

  co2:
    long_name: carbon dioxide
    type: inorganic
    composition: [c]
    parameters:
      temperature_regulation:
        temp_limited: False
      surface_flux: True

      air_sea_flux:
        atmospheric_pco2: 370.0
        d: 0.31
        c1: 2073.1
        c2: 125.62
        c3: 3.6276
        c4: 0.043219
        schmidt: 660.0
        pH: 8.12
        # the following parameters are optional, default values will be used if not provided in input file
        OCMIP_accuracy: 1.E-10              # default: 1.E-10
        OCMIP_max_iters: 100.               # default: 100
        OCMIP_max_delta_pH: 0.3             # default: 0.5

  ta:
    long_name: total alkalinity
    type: inorganic
    composition: [eq]
    parameters:
      calc_alkalinity: False

# -------------------------------------------------------------------------------------------------
reactions:
  # inorganic rates -------------------------------------------------------------------------------------------------
  - type: co2_flux
    consumed:
    produced:
      co2: [c]

  - type: denitrification
    consumed:
      no3: [n]
      hs: [s]
    produced: 
      n2: [n]

  - type: nitrification
    consumed:
      nh4: [n]
      o2: [o]
    produced: 
      no3: [n]

  - type: reaeration
    consumed:
    produced:
      o2: [o]

  - type: reoxidation
    consumed:
      hs: [s]
      o2: [o]
    produced:
  
  # bac1 rates -------------------------------------------------------------------------------------------------
  - type: excretion
    consumed:
      bac1: [c]
    produced:
      dom2: [c]

  - type: excretion
    consumed:
      bac1: [c]
    produced:
      dom3: [c]

  - type: mortality
    consumed:
      bac1: [c,n,p]
    produced:
      dom1: [c,n,p]

  - type: mortality
    consumed:
      bac1: [c,n,p]
    produced:
      pom1: [c,n,p]

  - type: respiration
    consumed:
      bac1: [c]
      o2: [o]
    produced:
      co2: [c]
      hs: [s]

  - type: uptake
    consumed:
      dom1: [c,n,p]
    produced:
      bac1: [c,n,p]
  
  - type: uptake
    consumed:
      dom2: [c]
    produced:
      bac1: [c]
  
  - type: uptake
    consumed:
      dom3: [c]
    produced:
      bac1: [c]
  
  - type: uptake
    consumed:
      pom1: [c,n,p]
    produced:
      bac1: [c,n,p]

  - type: uptake_release
    consumed:
      bac1: [n]
    produced:
      nh4: [n]

  - type: uptake_release
    consumed:
      bac1: [p]
    produced:
      po4: [p]

  # phyto1 rates -------------------------------------------------------------------------------------------------
  - type: chlorophyll_synthesis
    consumed:
    produced:
      phyto1: [chl]

  - type: exudation
    consumed:
      phyto1: [c]
    produced:
      dom1: [c]

  - type: gross_primary_production
    consumed:
      co2: [c]
    produced:
      phyto1: [c]
      o2: [o]

  - type: lysis
    consumed:
      phyto1: [c,n,p]
    produced:
      dom1: [c,n,p]

  - type: lysis
    consumed:
      phyto1: [c,n,p,si]
    produced:
      pom1: [c,n,p,si]

  - type: photosynthesis
    consumed:
      phyto1: [c]
    produced:

  - type: respiration
    consumed:
      phyto1: [c]
      o2: [o]
    produced:
      co2: [c]

  - type: sedimentation
    consumed:
      phyto1: [c,n,p,chl,si]
    produced:

  - type: uptake
    consumed:
      no3: [n]
    produced:
      phyto1: [n]
      dom1: [n]

  - type: uptake
    consumed:
      nh4: [n]
    produced:
      phyto1: [n]
      dom1: [n]

  - type: uptake
    consumed:
      po4: [p]
    produced:
      phyto1: [p]
      dom1: [p]

  - type: uptake
    consumed:
      sio4: [si]
    produced:
      phyto1: [si]

  # phyto2 rates -------------------------------------------------------------------------------------------------
  - type: chlorophyll_synthesis
    consumed:
    produced:
      phyto2: [chl]

  - type: exudation
    consumed:
      phyto2: [c]
    produced:
      dom1: [c]

  - type: gross_primary_production
    consumed:
      co2: [c]
    produced:
      phyto2: [c]
      o2: [o]

  - type: lysis
    consumed:
      phyto2: [c,n,p]
    produced:
      dom1: [c,n,p]

  - type: lysis
    consumed:
      phyto2: [c,n,p]
    produced:
      pom1: [c,n,p]

  - type: photosynthesis
    consumed:
      phyto2: [c]
    produced:

  - type: respiration
    consumed:
      phyto2: [c]
      o2: [o]
    produced:
      co2: [c]

  - type: sedimentation
    consumed:
      phyto2: [c,n,p,chl]
    produced:

  - type: uptake
    consumed:
      no3: [n]
    produced:
      phyto2: [n]
      dom1: [n]

  - type: uptake
    consumed:
      nh4: [n]
    produced:
      phyto2: [n]
      dom1: [n]

  - type: uptake
    consumed:
      po4: [p]
    produced:
      phyto2: [p]
      dom1: [p]

  # phyto3 rates -------------------------------------------------------------------------------------------------
  - type: chlorophyll_synthesis
    consumed:
    produced:
      phyto3: [chl]

  - type: exudation
    consumed:
      phyto3: [c]
    produced:
      dom1: [c]

  - type: gross_primary_production
    consumed:
      co2: [c]
    produced:
      phyto3: [c]
      o2: [o]

  - type: lysis
    consumed:
      phyto3: [c,n,p]
    produced:
      dom1: [c,n,p]

  - type: lysis
    consumed:
      phyto3: [c,n,p]
    produced:
      pom1: [c,n,p]

  - type: photosynthesis
    consumed:
      phyto3: [c]
    produced:

  - type: respiration
    consumed:
      phyto3: [c]
      o2: [o]
    produced:
      co2: [c]

  - type: sedimentation
    consumed:
      phyto3: [c,n,p,chl]
    produced:

  - type: uptake
    consumed:
      no3: [n]
    produced:
      phyto3: [n]
      dom1: [n]

  - type: uptake
    consumed:
      nh4: [n]
    produced:
      phyto3: [n]
      dom1: [n]

  - type: uptake
    consumed:
      po4: [p]
    produced:
      phyto3: [p]
      dom1: [p]

  # phyto4 rates -------------------------------------------------------------------------------------------------
  - type: chlorophyll_synthesis
    consumed:
    produced:
      phyto4: [chl]

  - type: exudation
    consumed:
      phyto4: [c]
    produced:
      dom1: [c]

  - type: gross_primary_production
    consumed:
      co2: [c]
    produced:
      phyto4: [c]
      o2: [o]

  - type: lysis
    consumed:
      phyto4: [c,n,p]
    produced:
      dom1: [c,n,p]

  - type: lysis
    consumed:
      phyto4: [c,n,p]
    produced:
      pom1: [c,n,p]

  - type: photosynthesis
    consumed:
      phyto4: [c]
    produced:

  - type: respiration
    consumed:
      phyto4: [c]
      o2: [o]
    produced:
      co2: [c]

  - type: sedimentation
    consumed:
      phyto4: [c,n,p,chl]
    produced:

  - type: uptake
    consumed:
      no3: [n]
    produced:
      phyto4: [n]
      dom1: [n]

  - type: uptake
    consumed:
      nh4: [n]
    produced:
      phyto4: [n]
      dom1: [n]

  - type: uptake
    consumed:
      po4: [p]
    produced:
      phyto4: [p]
      dom1: [p]

  # mesozoo1 rates -------------------------------------------------------------------------------------------------
  - type: egestion
    consumed: 
      mesozoo1: [c,n,p]
    produced:
      pom1: [c,n,p]

  - type: grazing
    consumed:
      mesozoo2: [c,n,p]
    produced:
      mesozoo1: [c,n,p]

  - type: metabolic_release
    consumed:
      mesozoo1: [c]
    produced:
      pom1: [c]

  - type: metabolic_release
    consumed:
      mesozoo1: [n]
    produced:
      nh4: [n]

  - type: metabolic_release
    consumed:
      mesozoo1: [p]
    produced:
      po4: [p]

  - type: mortality
    consumed:
      mesozoo1: [c,n,p]
    produced:
      pom1: [c,n,p]

  - type: respiration
    consumed:
      mesozoo1: [c]
      o2: [o]
    produced:
      co2: [c]

  # mesozoo2 rates -------------------------------------------------------------------------------------------------
  - type: egestion
    consumed: 
      mesozoo2: [c,n,p]
    produced:
      pom1: [c,n,p]

  - type: grazing
    consumed:
      phyto1: [c,n,p,chl,si]
    produced:
      mesozoo2: [c,n,p]
      pom1: [si]

  - type: grazing
    consumed:
      phyto2: [c,n,p,chl]
    produced:
      mesozoo2: [c,n,p]

  - type: grazing
    consumed:
      phyto4: [c,n,p,chl]
    produced:
      mesozoo2: [c,n,p]

  - type: grazing
    consumed:
      microzoo1: [c,n,p]
    produced:
      mesozoo2: [c,n,p]

  - type: metabolic_release
    consumed:
      mesozoo2: [c]
    produced:
      pom1: [c]

  - type: metabolic_release
    consumed:
      mesozoo2: [n]
    produced:
      nh4: [n]

  - type: metabolic_release
    consumed:
      mesozoo2: [p]
    produced:
      po4: [p]

  - type: mortality
    consumed:
      mesozoo2: [c,n,p]
    produced:
      pom1: [c,n,p]

  - type: respiration
    consumed:
      mesozoo2: [c]
      o2: [o]
    produced:
      co2: [c]

  # microzoo1 rates -------------------------------------------------------------------------------------------------
  - type: excretion
    consumed:
      microzoo1: [n]
    produced:
      nh4: [n]

  - type: excretion
    consumed:
      microzoo1: [p]
    produced:
      po4: [p]

  - type: egestion
    consumed: 
      microzoo1: [c,n,p]
    produced:
      dom1: [c,n,p]

  - type: egestion
    consumed: 
      microzoo1: [c,n,p]
    produced:
      pom1: [c,n,p]

  - type: grazing
    consumed:
      bac1: [c,n,p]
    produced:
      microzoo1: [c,n,p]

  - type: grazing
    consumed:
      phyto1: [c,n,p,chl,si]
    produced:
      microzoo1: [c,n,p]
      pom1: [si]

  - type: grazing
    consumed:
      phyto2: [c,n,p,chl]
    produced:
      microzoo1: [c,n,p]

  - type: grazing
    consumed:
      phyto3: [c,n,p,chl]
    produced:
      microzoo1: [c,n,p]

  - type: grazing
    consumed:
      microzoo2: [c,n,p]
    produced:
      microzoo1: [c,n,p]

  - type: mortality
    consumed:
      microzoo1: [c,n,p]
    produced:
      dom1: [c,n,p]

  - type: mortality
    consumed:
      microzoo1: [c,n,p]
    produced:
      pom1: [c,n,p]

  - type: respiration
    consumed:
      microzoo1: [c]
      o2: [o]
    produced:
      co2: [c]

  # microzoo2 rates -------------------------------------------------------------------------------------------------
  - type: excretion
    consumed:
      microzoo2: [n]
    produced:
      nh4: [n]

  - type: excretion
    consumed:
      microzoo2: [p]
    produced:
      po4: [p]

  - type: egestion
    consumed: 
      microzoo2: [c,n,p]
    produced:
      dom1: [c,n,p]

  - type: egestion
    consumed: 
      microzoo2: [c,n,p]
    produced:
      pom1: [c,n,p]

  - type: grazing
    consumed:
      bac1: [c,n,p]
    produced:
      microzoo2: [c,n,p]

  - type: grazing
    consumed:
      phyto2: [c,n,p,chl]
    produced:
      microzoo2: [c,n,p]

  - type: grazing
    consumed:
      phyto3: [c,n,p,chl]
    produced:
      microzoo2: [c,n,p]

  - type: mortality
    consumed:
      microzoo2: [c,n,p]
    produced:
      dom1: [c,n,p]

  - type: mortality
    consumed:
      microzoo2: [c,n,p]
    produced:
      pom1: [c,n,p]

  - type: respiration
    consumed:
      microzoo2: [c]
      o2: [o]
    produced:
      co2: [c]

  # pom1 rates -------------------------------------------------------------------------------------------------
  - type: dissolution
    consumed:
      pom1: [si]
    produced:
      sio4: [si]