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tracers.json
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tracers.json
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{
"tracers":{
"bacterioplankton":{
"bac1":{
"long_name": "Aerobic/Anaerobic Bacteria",
"constituents": ["C", "N", "P"],
"units": ["mg C / m^3", "mmol N / m^3", "mmol P / m^3"]
}
},
"dissolved_organic_matter":{
"dom1":{
"long_name": "Labile Dissolved Organic Matter",
"constituents": ["C", "N", "P", "Fe"],
"units": ["mg C / m^3", "mmol N / m^3", "mmol P / m^3", "umol Fe / m^3"]
},
"dom2":{
"long_name": "Semi-Labile Dissolved Organic Matter",
"constituents": ["C"],
"units": ["mg C / m^3"]
},
"dom3":{
"long_name": "Semi-Refractory Dissolved Organic Matter",
"constituents": ["C"]
}
},
"inorganic":{
"CaCO3":{
"long_name": "Calcium Carbonate",
"units": "mg C / m^3"
},
"DIC":{
"long_name": "Dissolved Inorganic Carbon",
"units": "mg C / m^3"
},
"Fe":{
"long_name": "Iron",
"units": "umol Fe / m^3"
},
"N2":{
"long_name": "Nitrogen Sink",
"units": "mmol N / m^3"
},
"NH4":{
"long_name": "Ammonium",
"units": "mmol N / m^3"
},
"NO3":{
"long_name": "Nitrate",
"units": "mmol N / m^3"
},
"O2":{
"long_name": "Oxygen",
"units": "mmol O2 / m^3"
},
"PO4":{
"long_name": "Phosphate",
"units": "mmol P / m^3"
},
"HS":{
"long_name": "Bisulfide",
"units": "mmol S / m^3"
},
"SiO2":{
"long_name": "Silicate",
"units": "mmol Si / m^3"
},
"TALK":{
"long_name": "Total Alkalinity",
"units": "mmol Eq / m^3"
}
},
"particulate_organic_matter":{
"pom1":{
"long_name": "Particulate Organic Detritus",
"constituents": ["C", "N", "P", "Si", "Fe"],
"units": ["mg C / m^3", "mmol N / m^3", "mmol P / m^3", "mmol Si / m^3", "umol Fe / m^3"]
}
},
"phytoplankton":{
"phyto1":{
"long_name": "Diatoms",
"size_class": "Microphytoplankton",
"constituents": ["C", "N", "P", "Chl", "Si", "Fe"],
"units": ["mg C / m^3", "mmol N / m^3", "mmol P / m^3", "mg Chl-a / m^3", "mmol Si / m^3", "umol Fe / m^3"]
},
"phyto2":{
"long_name": "Phototrophic Nanoflagellates",
"size_class": "Nanophytoplankton",
"constituents": ["C", "N", "P", "Chl", "Fe"],
"units": ["mg C / m^3", "mmol N / m^3", "mmol P / m^3", "mg Chl-a / m^3", "umol Fe / m^3"]
},
"phyto3":{
"long_name": "Cyanobacteria",
"size_class": "Picophytoplankton",
"constituents": ["C", "N", "P", "Chl", "Fe"] ,
"units": ["mg C / m^3", "mmol N / m^3", "mmol P / m^3", "mg Chl-a / m^3", "umol Fe / m^3"]
},
"phyto4":{
"long_name": "Dinoflagellates",
"size_class": "Microphytoplankton",
"constituents": ["C", "N", "P", "Chl", "Fe"],
"units": ["mg C / m^3", "mmol N / m^3", "mmol P / m^3", "mg Chl-a / m^3", "umol Fe / m^3"]
}
},
"zooplankton":{
"zoo1":{
"long_name": "Carnivorous Mesozooplankton",
"size_class": "Mesozooplankton",
"constituents": ["C", "N", "P"],
"units": ["mg C / m^3", "mmol N / m^3", "mmol P / m^3"]
},
"zoo2":{
"long_name": "Copepods",
"size_class": "Mesozooplankton",
"constituents": ["C", "N", "P"],
"units": ["mg C / m^3", "mmol N / m^3", "mmol P / m^3"]
},
"zoo3":{
"long_name": "Ciliates",
"size_class": "Microzooplankton",
"constituents": ["C", "N", "P"],
"units": ["mg C / m^3", "mmol N / m^3", "mmol P / m^3"]
},
"zoo4":{
"long_name": "Heterotrophic Nanoflagellates",
"size_class": "Nanozooplankton",
"constituents": ["C", "N", "P"],
"units": ["mg C / m^3", "mmol N / m^3", "mmol P / m^3"]
}
}
},
"parameters":{
"bac1":{
"bac_version": 3,
"spec_growth_rate": 8.38,
"spec_mort_rate": 0.1,
"dens_mort_rate": 0.0,
"spec_resp_rate": 0.01,
"anoxic_resp_frac": 0.2,
"activity_resp_frac": 0.6,
"half_sat_oxy": 30.0,
"spec_aff_nit": 0.0,
"min_nit_quota": 0.0167,
"opt_nit_quota": 0.0167,
"half_sat_nit": 5.0,
"relax_time_nit": 1.0,
"spec_aff_phos": 0.0,
"min_phos_quota": 0.00185,
"opt_phos_quota": 0.00185,
"half_sat_phos": 1.0,
"relax_time_phos": 1.0,
"spec_upt_poor_lab_dom": 0.0,
"spec_upt_rich_lab_dom": 0.3,
"spec_upt_semilab_dom": 0.0,
"spec_upt_semiref_dom": 0.01,
"excr_semiref_dom": 0.0,
"relax_time_semilab_dom": 1.0
},
"phyto1":{
"chl_light_absorp": 0.03,
"chl_relax_rate": 0.25,
"chl_switch": 3,
"max_chl_quota": 0.035,
"max_light_util": 1.1e-05,
"max_photo_rate": 2.5,
"spec_aff_nit": 0.025,
"nit_mult_factor": 2.0,
"max_nit_quota": 0.0126,
"min_nit_quota": 6.87e-03,
"opt_nit_quota": 0.0126,
"half_sat_amm": 1.0,
"spec_aff_phos": 2.5e-03,
"phos_mult_factor": 2.0,
"max_phos_quota": 0.001572,
"min_phos_quota": 4.29e-04,
"opt_phos_quota": 0.000786,
"spec_aff_iron": 2.3148148148148148e-09,
"iron_mult_factor": 0.0,
"min_iron_quota": 0.0,
"opt_iron_quota": 0.0,
"spec_aff_si": 0.0,
"half_sat_si": 1.0,
"half_sat_si_contois": 0.0,
"si_switch": 1,
"min_si_quota": 0.0,
"opt_si_quota": 0.01,
"extra_lysis_rate": 0.0,
"half_sat_lysis": 0.1,
"half_sat_extra_lysis": 0.0,
"max_spec_lysis_rate": 0.01,
"opt_par_irrad_ratio": 3.0,
"spec_resp_rate": 0.05,
"excr_prim_prod": 0.01,
"activity_resp_frac": 0.1,
"cuttof_temp_threshold": 0.0,
"nut_stress_threshold": 0.70,
"background_sink_rate": 0.0,
"bot_burial_vel": 0.0,
"max_sedi_rate": 5.0
},
"phyto2":{
"chl_light_absorp": 0.03,
"chl_relax_rate": 0.0,
"chl_switch": 3,
"max_chl_quota": 0.016,
"max_photo_rate": 1.6,
"max_light_util": 1.52e-05,
"spec_aff_nit": 0.025,
"nit_mult_factor": 1.0,
"max_nit_quota": 0.0126,
"min_nit_quota": 6.87e-03,
"opt_nit_quota": 0.0126,
"half_sat_amm": 1.5,
"spec_aff_phos": 2.5e-03,
"phos_mult_factor": 1.0,
"max_phos_quota": 7.86e-04,
"min_phos_quota": 4.29e-04,
"opt_phos_quota": 0.000786,
"spec_aff_iron": 2.3148148148148148e-09,
"iron_mult_factor": 0.0,
"min_iron_quota": 0.0,
"opt_iron_quota": 0.0,
"extra_lysis_rate": 0.0,
"half_sat_lysis": 0.1,
"half_sat_extra_lysis": 0.0,
"max_spec_lysis_rate": 0.05,
"opt_par_irrad_ratio": 0.0,
"spec_resp_rate": 0.05,
"excr_prim_prod": 0.05,
"activity_resp_frac": 0.05,
"cuttof_temp_threshold": 0.0,
"nut_stress_threshold": 0.75,
"background_sink_rate": 0.0,
"bot_burial_vel": 0.0,
"max_sedi_rate": 0.5
},
"phyto3":{
"chl_light_absorp": 0.03,
"chl_relax_rate": 0.25,
"chl_switch": 3,
"max_chl_quota": 0.02,
"max_photo_rate": 1.02,
"max_light_util": 0.7e-05,
"spec_aff_nit": 0.025,
"nit_mult_factor": 2.0,
"max_nit_quota": 0.0126,
"min_nit_quota": 6.87e-03,
"opt_nit_quota": 0.0126,
"half_sat_amm": 0.1,
"spec_aff_phos": 2.5e-03,
"phos_mult_factor": 2.0,
"max_phos_quota": 0.001572,
"min_phos_quota": 4.29e-04,
"opt_phos_quota": 0.000786,
"spec_aff_iron": 2.3148148148148148e-09,
"iron_mult_factor": 0.0,
"min_iron_quota": 0.0,
"opt_iron_quota": 0.0,
"extra_lysis_rate": 0.0,
"half_sat_lysis": 0.1,
"half_sat_extra_lysis": 0.0,
"max_spec_lysis_rate": 0.01,
"opt_par_irrad_ratio": 3.0,
"spec_resp_rate": 0.05,
"excr_prim_prod": 0.1,
"activity_resp_frac": 0.2,
"cuttof_temp_threshold": 0.0,
"nut_stress_threshold": 0.75,
"background_sink_rate": 0.0,
"bot_burial_vel": 0,
"max_sedi_rate": 0.5
},
"phyto4":{
"chl_light_absorp": 0.03,
"chl_relax_rate": 0.25,
"chl_switch": 3,
"max_chl_quota": 0.035,
"max_photo_rate": 0.83,
"max_light_util": 6.8e-06,
"spec_aff_nit": 0.025,
"nit_mult_factor": 2.0,
"max_nit_quota": 0.0126,
"min_nit_quota": 6.87e-03,
"opt_nit_quota": 0.0126,
"half_sat_amm": 1.0,
"spec_aff_phos": 2.5e-03,
"phos_mult_factor": 2.0,
"max_phos_quota": 0.001572,
"min_phos_quota": 4.29e-04,
"opt_phos_quota": 0.000786,
"spec_aff_iron": 2.3148148148148148e-09,
"iron_mult_factor": 0.0,
"min_iron_quota": 0.0,
"opt_iron_quota": 0.0,
"extra_lysis_rate": 0.5,
"half_sat_lysis": 0.5,
"half_sat_extra_lysis": 100.0,
"max_spec_lysis_rate": 0.2,
"opt_par_irrad_ratio": 3.0,
"spec_resp_rate": 0.1,
"excr_prim_prod": 0.15,
"activity_resp_frac": 0.1,
"cuttof_temp_threshold": 0,
"nut_stress_threshold": 0.75,
"background_sink_rate": 0.0,
"bot_burial_vel": 0.0,
"max_sedi_rate": 5.0
},
"zoo1":{
"max_nit_quota": 0.01258,
"opt_nit_quota": 0.015,
"max_phos_quota": 7.862e-04,
"opt_phos_quota": 0.00167,
"half_sat_oxy": 30.0,
"assim_eff": 0.6,
"excr_uptake": 0.3,
"nut_excr_rate": 2.5e-03,
"dens_mort_rate": 0.01,
"dens_mort_rate_exp": 2.0,
"spec_growth_rate": 2.0,
"spec_mort_rate": 0.02,
"spec_resp_rate": 0.01
},
"zoo2":{
"max_nit_quota": 0.01258,
"opt_nit_quota": 0.015,
"max_phos_quota": 7.862e-04,
"opt_phos_quota": 0.00167,
"half_sat_oxy": 30.0,
"assim_eff": 0.6,
"excr_uptake": 0.35,
"nut_excr_rate": 0.025,
"dens_mort_rate": 0.01,
"dens_mort_rate_exp": 2.0,
"spec_growth_rate": 2.0,
"spec_mort_rate": 0.02,
"spec_resp_rate": 0.02
},
"zoo3":{
"max_nit_quota": 1.67e-2,
"opt_nit_quota": 0.0128,
"max_phos_quota": 1.85e-3,
"opt_phos_quota": 0.00185,
"half_sat_oxy": 0.5,
"mort_rate_oxy": 0.25,
"assim_eff": 0.5,
"feeding_threshold": 50.0,
"excr_uptake": 0.25,
"michaelis_constant": 200.0,
"spec_growth_rate": 2.0,
"spec_mort_rate": 1.0e-06,
"spec_resp_rate": 0.02
},
"zoo4":{
"max_nit_quota": 1.67e-2,
"opt_nit_quota": 0.0128,
"max_phos_quota": 1.85e-3,
"opt_phos_quota": 0.00185,
"half_sat_oxy": 0.5,
"mort_rate_oxy": 0.25,
"assim_eff": 0.3,
"feeding_threshold": 50.0,
"excr_uptake": 0.35,
"michaelis_constant": 200.0,
"spec_growth_rate": 5.0,
"spec_mort_rate": 1.0e-06,
"spec_resp_rate": 0.02
}
},
"reactions":[
{
"type": "lysis",
"consumed": "bac1",
"produced": "dom1",
"parameters": {
}
},
{
"type": "uptake",
"consumed": "dom1",
"produced": "bac1",
"parameters": {
}
},
{
"type": "release",
"consumed": "bac1",
"produced": "dom2",
"parameters": {
}
},
{
"type": "uptake",
"consumed": "dom2",
"produced": "bac1",
"parameters": {
}
},
{
"type": "release",
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