def pel_chem_eqns(pel_chem_parameters, environmental_parameters,
constant_parameters, temper, conc, flPTN6r):
""" calculates the non-living equations for DOM, POM, and nutrients """
# State variables
o2o = conc[0] # Dissolved oxygen (mg O_2 m^-3)
n3n = conc[2] # Nitrate (mmol N m^-3)
n4n = conc[3] # Ammonium (mmol N m^-3)
n6r = conc[6] # Reduction equivalents (mmol S m^-3)
r6s = conc[47] # Particulate organic silicate (mmol Si m^-3)
# Regulating factors
eo = max(constant_parameters["p_small"], o2o) / (
max(constant_parameters["p_small"], o2o) + pel_chem_parameters["h_o"])
er = n6r / (n6r + pel_chem_parameters["h_r"])
# Temperature regulating factors
fTn = eTq_vector(temper, environmental_parameters["basetemp"],
environmental_parameters["q10n"])
fTr6 = eTq_vector(temper, environmental_parameters["basetemp"],
environmental_parameters["q10n5"])
# Nitrification in the water [mmol N m^-3 s^-1]
dn4ndt_nit_n3n = max(0.0,
pel_chem_parameters["lambda_N4nit"] * n4n * fTn * eo)
# Denitrification flux [mmol N m^-3 s^-1] from PelChem.F90 line 134
rPAo = flPTN6r / constant_parameters["omega_r"]
dn3ndt_denit = max(
0.0, pel_chem_parameters["lambda_N3denit"] * fTn * er * rPAo /
pel_chem_parameters["m_o"] * n3n)
# Reoxidation of reduction equivalents [mmol S m^-3 s^-1]
dn6rdt_reox = pel_chem_parameters["lambda_N6reox"] * eo * n6r
# Dissolution of biogenic silicate [mmol Si m^-3 s^-1]
dr6sdt_rmn_n5s = pel_chem_parameters["lambda_srmn"] * fTr6 * r6s
return (dn4ndt_nit_n3n, dn3ndt_denit, dn6rdt_reox, dr6sdt_rmn_n5s)
def mesozoo_eqns(conc, mesozoo_parameters, constant_parameters, environmental_parameters, zc, zn, zp, i_c, i_n, i_p, temp):
""" Calculates the mesozooplankton (Z3 & Z4) terms needed for the zooplankton biological rate equations
Equations come from the BFM user manual and the fortran code MesoZoo.F90
"""
# Dissolved oxygen concentration (mg O_2 m^-3)
o2o = conc[0] # Dissolved oxygen (mg O_2 m^-3)
# Concentration ratios
zn_zc = get_concentration_ratio(zn, zc, constant_parameters["p_small"])
zp_zc = get_concentration_ratio(zp, zc, constant_parameters["p_small"])
# Temperature regulating factor
fTZ = eTq_vector(temp, environmental_parameters["basetemp"], environmental_parameters["q10z"])
# Oxygen dependent regulation factor
fZO = (max(constant_parameters["p_small"],o2o)**3)/(max(constant_parameters["p_small"],o2o)**3 + mesozoo_parameters["z_o2o"]**3)
# energy cost of ingestion
prI = 1.0 - mesozoo_parameters["etaZ"] - mesozoo_parameters["betaZ"]
# Zooplankton total repiration rate (from 'MesoZoo.F90' line 343)
dZcdt_rsp_o3c = prI*i_c + mesozoo_parameters["bZ"]*fTZ*zc
# Specific rates of low oxygen mortality and Density dependent mortality
# from fortran code MesoZoo.F90 lines 343-344
rdo_c = mesozoo_parameters["d_Zdns"]*(1.0 - fZO)*fTZ*zc
rd_c = mesozoo_parameters["d_Z"]*zc**mesozoo_parameters["gammaZ"]
# Total egestion including pellet production (from MesoZoo.F90 line 359 - 361)
dZcdt_rel_r6c = mesozoo_parameters["betaZ"]*i_c + rdo_c + rd_c
dZndt_rel_r6n = mesozoo_parameters["betaZ"]*i_n + zn_zc*(rdo_c + rd_c)
dZpdt_rel_r6p = mesozoo_parameters["betaZ"]*i_p + zp_zc*(rdo_c + rd_c)
# Check the assimilation rate for Carbon, Nitrogen and Phosphorus
# compute P:C and N:C ratios in the assimilation rate
# from MesoZoo.F90 lines 371-375
ru_c = mesozoo_parameters["etaZ"]*i_c
ru_n = (mesozoo_parameters["etaZ"] + prI)*i_n
ru_p = (mesozoo_parameters["etaZ"] + prI)*i_p
pu_e_n = ru_n/(constant_parameters["p_small"] + ru_c)
pu_e_p = ru_p/(constant_parameters["p_small"] + ru_c)
# Eliminate the excess of the non-limiting constituent
# Determine whether C, P or N is the limiting element and assign the value to variable limiting_nutrient
# from MesoZoo.F90 lines
limiting_nutrient = 'carbon'
temp_p = pu_e_p/(zp_zc + constant_parameters["p_small"])
temp_n = pu_e_n/(zn_zc + constant_parameters["p_small"])
if temp_p<temp_n or abs(temp_p - temp_n)<constant_parameters["p_small"]:
if pu_e_p<zp_zc:
limiting_nutrient = 'phosphorus'
else:
if pu_e_n<zn_zc:
limiting_nutrient = 'nitrogen'
# Compute the correction terms depending on the limiting constituent
if limiting_nutrient == 'carbon':
q_Zc = 0.0
q_Zp = max(0.0, (1.0 - mesozoo_parameters["betaZ"])*i_p - mesozoo_parameters["p_Zopt"]*ru_c)
q_Zn = max(0.0, (1.0 - mesozoo_parameters["betaZ"])*i_n - mesozoo_parameters["n_Zopt"]*ru_c)
elif limiting_nutrient == 'phosphorus':
q_Zp = 0.0
q_Zc = max(0.0, ru_c - (1.0 - mesozoo_parameters["betaZ"])*i_p/mesozoo_parameters["p_Zopt"])
q_Zn = max(0.0, (1.0 - mesozoo_parameters["betaZ"])*i_n - mesozoo_parameters["n_Zopt"]*(ru_c - q_Zc))
elif limiting_nutrient == 'nitrogen':
q_Zn = 0.0
q_Zc = max(0.0, ru_c - (1.0 - mesozoo_parameters["betaZ"])*i_n/mesozoo_parameters["n_Zopt"])
q_Zp = max(0.0, (1.0 - mesozoo_parameters["betaZ"])*i_p - mesozoo_parameters["p_Zopt"]*(ru_c - q_Zc))
# Nutrient remineralization basal metabolism + excess of non-limiting nutrients
dZpdt_rel_n1p = mesozoo_parameters["bZ"]*fZO*fTZ*zp + q_Zp
dZndt_rel_n4n = mesozoo_parameters["bZ"]*fZO*fTZ*zn + q_Zn
# Fluxes to particulate organic matter
# Add the correction term for organic carbon release based on the limiting constituent
dZcdt_rel_r6c += q_Zc
# mesozooplankton are assumed to have no dissolved products
dZcdt_rel_r1c = 0.0
dZndt_rel_r1n = 0.0
dZpdt_rel_r1p = 0.0
return dZcdt_rel_r1c, dZcdt_rel_r6c, dZcdt_rsp_o3c, dZndt_rel_r1n, dZndt_rel_r6n, dZpdt_rel_r1p, dZpdt_rel_r6p, dZpdt_rel_n1p, dZndt_rel_n4n
def microzoo_eqns(conc, microzoo_parameters, constant_parameters,
environmental_parameters, zc, zn, zp, i_c, i_n, i_p, temp):
""" Calculates the micorzooplankton (Z5 & Z6) terms needed for the zooplankton biological rate equations
Equations come from the BFM user manual and the fortran code MicroZoo.F90
"""
# Dissolved oxygen concentration (mg O_2 m^-3)
o2o = conc[0]
# Concentration ratios
zn_zc = get_concentration_ratio(zn, zc, constant_parameters["p_small"])
zp_zc = get_concentration_ratio(zp, zc, constant_parameters["p_small"])
# Temperature regulating factor
fTZ = eTq_vector(temp, environmental_parameters["basetemp"],
environmental_parameters["q10z"])
# Oxygen dependent regulation factor
fZO = min(1.0, (o2o / (o2o + microzoo_parameters["z_o2o"])))
#---------------------- Microzooplankton Respiration ----------------------
# Zooplankton total repiration rate (eqn. 2.4.8, and matches fortran code)
rrac = i_c * (1.0 - microzoo_parameters["etaZ"] -
microzoo_parameters["betaZ"])
rrsc = microzoo_parameters["bZ"] * fTZ * zc
dZcdt_rsp_o3c = rrac + rrsc
#------------- Microzooplankton mortality and activity excretion ----------
# From fortran code MesoZoo.F90 lines 327-331
rdc = ((1.0 - fZO) * microzoo_parameters["d_ZO"] +
microzoo_parameters["d_Z"]) * zc
reac = i_c * (1.0 -
microzoo_parameters["etaZ"]) * microzoo_parameters["betaZ"]
rric = reac + rdc
dZcdt_rel_r1c = rric * constant_parameters["epsilon_c"]
dZcdt_rel_r6c = rric * (1.0 - constant_parameters["epsilon_c"])
#------------------- Microzooplankton nutrient dynamics -------------------
# Organic Nitrogen dynamics (from fortran code) [mmol N m^-3 s^-1]
rrin = i_n * microzoo_parameters["betaZ"] + rdc * zn_zc
dZndt_rel_r1n = rrin * constant_parameters["epsilon_n"]
dZndt_rel_r6n = rrin - dZndt_rel_r1n
# Organic Phosphorus dynamics (from fortran code) [mmol P m^-3 s^-1]
rrip = i_p * microzoo_parameters["betaZ"] + rdc * zp_zc
dZpdt_rel_r1p = rrip * constant_parameters["epsilon_p"]
dZpdt_rel_r6p = rrip - dZpdt_rel_r1p
#--------------- Microzooplankton Dissolved nutrient dynamics -------------
# Equations from fortran code (MicroZoo.F90 line 368-371)
runc = max(0.0, i_c * (1.0 - microzoo_parameters["betaZ"]) - rrac)
runn = max(0.0, i_n * (1.0 - microzoo_parameters["betaZ"]) + rrsc * zn_zc)
runp = max(0.0, i_p * (1.0 - microzoo_parameters["betaZ"]) + rrsc * zp_zc)
dZpdt_rel_n1p = max(
0.0, runp / (constant_parameters["p_small"] + runc) -
microzoo_parameters["p_Zopt"]) * runc
dZndt_rel_n4n = max(
0.0, runn / (constant_parameters["p_small"] + runc) -
microzoo_parameters["n_Zopt"]) * runc
return dZcdt_rel_r1c, dZcdt_rel_r6c, dZcdt_rsp_o3c, dZndt_rel_r1n, dZndt_rel_r6n, dZpdt_rel_r1p, dZpdt_rel_r6p, dZpdt_rel_n1p, dZndt_rel_n4n
def phyto_eqns(conc, phyto_parameters, env_parameters, constant_parameters,
group, pc, pn, pp, pl, qs, temp, time):
""" Calculates the terms needed for the phytoplnaktion biological rate equations
Equations come from the BFM user manual
"""
# Species concentrations
n1p = conc[1] # Phosphate (mmol P m^-3)
n3n = conc[2] # Nitrate (mmol N m^-3)
n4n = conc[3] # Ammonium (mmol N m^-3)
n5s = conc[5] # Silicate (mmol Si m^-3)
p1l = conc[13] # Diatoms chlorophyll (mg Chl-a m^-3)
p1s = conc[14] # Diatoms silicate (mmol Si m^-3)
p2l = conc[18] # NanoFlagellates chlorophyll (mg Chl-a m^-3)
p3l = conc[22] # Picophytoplankton chlorophyll (mg Chl-a m^-3)
p4l = conc[26] # Large phytoplankton chlorophyll (mg Chl-a m^-3)
r6c = conc[44] # Particulate organic carbon (mg C m^-3)
# Concentration ratios (constituents quota in phytoplankton)
pn_pc = get_concentration_ratio(pn, pc, constant_parameters["p_small"])
pp_pc = get_concentration_ratio(pp, pc, constant_parameters["p_small"])
pl_pc = get_concentration_ratio(pl, pc, constant_parameters["p_small"])
#--------------------------------------------------------------------------
# Temperature response of Phytoplankton Include cut-off at low temperature if p_temp>0
et = eTq_vector(temp, env_parameters["basetemp"], env_parameters["q10z"])
fTP = max(0.0, et - phyto_parameters["p_temp"])
#--------------------------------------------------------------------------
# Nutrient limitations (intracellular and extracellular) fpplim is the
# combined non-dimensional factor limiting photosynthesis
# from Phyto.F90 lines 268-308
in1p = min(
1.0,
max(constant_parameters["p_small"],
(pp_pc - phyto_parameters["phi_Pmin"]) /
(phyto_parameters["phi_Popt"] - phyto_parameters["phi_Pmin"])))
in1n = min(
1.0,
max(constant_parameters["p_small"],
(pn_pc - phyto_parameters["phi_Nmin"]) /
(phyto_parameters["phi_Nopt"] - phyto_parameters["phi_Nmin"])))
if group == 1:
fpplim = min(
1.0, n5s / (n5s + phyto_parameters["h_Ps"] +
(phyto_parameters["rho_Ps"] * p1s)))
else:
fpplim = 1.0
#--------------------------------------------------------------------------
# multiple nutrient limitation, Liebig rule (from Phyto.F90 line ~318, iN)
multiple_nut_lim = min(in1p, in1n)
#--------------------------------------------------------------------------
# Total extinction coef (m^-1)
suspended_sediments = 0.0
# from CalcVerticalExtinction.F90 line 82
xEPS = env_parameters["p_eps0"] + env_parameters[
"p_epsESS"] * suspended_sediments + env_parameters["p_epsR6"] * r6c
# from CalcVerticalExtinction.F90 line 101 (ChlAttenFlag=1, ChlDynamicsFlag=2)
xEPS = xEPS + p1l + p2l * 2 + p3l * 3 + p4l * 4
#--------------------------------------------------------------------------
# Light limitation with Chl dynamics
# irradiance (uE m^-2 s^-1) from Phyto.F90 lines 353-355
irradiance = qs * env_parameters["epsilon_PAR"] / constant_parameters["e2w"]
r = xEPS * env_parameters["del_z"]
r = irradiance / xEPS / env_parameters["del_z"] * (1.0 - numpy.exp(-r))
irr = max(constant_parameters["p_small"], r)
# Compute exponent E_PAR/E_K = alpha0/PBmax (part of eqn. 2.2.4)
exponent = pl_pc * phyto_parameters["alpha_chl"] / phyto_parameters[
"rP0"] * irr
# light limitation factor (from Phyto.f90 line 374, eiPPY)
light_lim = (1.0 - numpy.exp(-exponent))
#--------------------------------------------------------------------------
# total photosynthesis (from Phyto.F90 line ~380, sum)
photosynthesis = phyto_parameters["rP0"] * fTP * light_lim * fpplim
#--------------------------------------------------------------------------
# Lysis nad excretion
# nutr. -stress lysis (from Phyto.F90 lines ~385-387, sdo)
nut_stress_lysis = (phyto_parameters["h_Pnp"] /
(multiple_nut_lim +
phyto_parameters["h_Pnp"])) * phyto_parameters["d_P0"]
nut_stress_lysis += phyto_parameters["p_seo"] * pc / (
pc + phyto_parameters["p_sheo"] + constant_parameters["p_small"])
# activity excretion (Phyto.F90 line 389)
activity_excretion = photosynthesis * phyto_parameters["betaP"]
# nutrient stress excretion from Phyto.F90 line 396
nut_stress_excretion = photosynthesis * (
1.0 - phyto_parameters["betaP"]) * (1.0 - multiple_nut_lim)
#--------------------------------------------------------------------------
# Apportioning over R1 and R6: Cell lysis generates both DOM and POM
pe_R6 = min(
phyto_parameters["phi_Pmin"] /
(pp_pc + constant_parameters["p_small"]),
phyto_parameters["phi_Nmin"] /
(pn_pc + constant_parameters["p_small"]))
pe_R6 = min(1.0, pe_R6)
rr6c = pe_R6 * nut_stress_lysis * pc
rr1c = (1.0 - pe_R6) * nut_stress_lysis * pc
#--------------------------------------------------------------------------
# Respiration rate
# activity (from Phyto.F90 line 416)
activity_rsp = phyto_parameters["gammaP"] * (
photosynthesis - activity_excretion - nut_stress_excretion)
# basal (from Phyto.F90 line 417)
basal_rsp = fTP * phyto_parameters["bP"]
# total (from Phyto.F90 line 418)
total_rsp = activity_rsp + basal_rsp
# total actual respiration
dPcdt_rsp_o3c = total_rsp * pc
#--------------------------------------------------------------------------
# Production, productivity and C flows
# Phytoplankton gross primary production [mg C m^-3 s^-1]
dPcdt_gpp_o3c = photosynthesis * pc
# specific loss terms (from Phyto.F90 line 428)
specific_loss_terms = activity_excretion + nut_stress_excretion + total_rsp + nut_stress_lysis
# All activity excretions are assigned to R1
# p_switchDOC=1 and P_netgrowth=FLASE: [mg C m^-3 s^-1]
rr1c += activity_excretion * pc + nut_stress_excretion * pc
dPcdt_exu_r2c = 0.0
# Phytoplankton DOM cell lysis- carbon lost to DOM [mg C m^-3 s^-1]
dPcdt_lys_r1c = rr1c
# Phytoplankton POM cell lysis- carbon lost to POM (eqn. 2.2.9) [mg C m^-3 s^-1]
dPcdt_lys_r6c = rr6c
#--------------------------------------------------------------------------
# Potential-Net primary production
# from Phyto.F90 line 455
sadap = fTP * phyto_parameters["rP0"]
# Net production (from Phyto.F90 line 457, 'run')
net_production = max(0.0, (photosynthesis - specific_loss_terms) * pc)
#--------------------------------------------------------------------------
# Nutrient Uptake: calculate maximum uptake of N, P based on affinity
cqun3 = phyto_parameters["h_Pn"] / (constant_parameters["p_small"] +
phyto_parameters["h_Pn"] + n4n)
# max potential uptake of N3 (from Phyto.F90 'rumn3')
max_upt_n3n = phyto_parameters["a_N"] * n3n * pc * cqun3
# max potential uptake of N4 (from Phyto.F90 'rumn4')
max_upt_n4n = phyto_parameters["a_N"] * n4n * pc
# max potential uptake of DIN (from Phyto.F90 'rumn')
max_upt_DIN = max_upt_n3n + max_upt_n4n
# max pot. uptake of PO4 (from Phyto.F90 line 468)
rump = phyto_parameters["a_P"] * n1p * pc
#--------------------------------------------------------------------------
# Nutrient dynamics: NITROGEN
# Intracellular missing amount of N (from Phyto.F90)
misn = sadap * (phyto_parameters["phi_Nmax"] * pc - pn)
# N uptake based on net assimilat. C (from Phyto.F90)
rupn = phyto_parameters["phi_Nmax"] * net_production
# actual uptake of NI (from Phyto.F90, 'runn')
dPndt_upt = min(max_upt_DIN, rupn + misn)
# if nitrogen uptake rate is positive, then uptake is divided between coming from the nitrate and ammonium reservoir
# if nitrogen uptake is negative, all nitrogen goes to the DOM pool
upt_switch_n = insw_vector(dPndt_upt)
# actual uptake of N3n (from Phyto.F90, 'runn3')
dPndt_upt_n3n = upt_switch_n * dPndt_upt * max_upt_n3n / (
constant_parameters["p_small"] + max_upt_DIN)
# actual uptake of N4n (from Phyto.F90, 'runn4')
dPndt_upt_n4n = upt_switch_n * dPndt_upt * max_upt_n4n / (
constant_parameters["p_small"] + max_upt_DIN)
extra_n = -dPndt_upt * (1.0 - upt_switch_n)
#--------------------------------------------------------------------------
# Nutrient dynamics: PHOSPHORUS
# intracellular missing amount of P (from Phyto.F90 line 514)
misp = sadap * (phyto_parameters["phi_Pmax"] * pc - pp)
# P uptake based on C uptake (from Phyto.F90 line 517)
rupp = phyto_parameters["phi_Pmax"] * net_production
# Actual uptake
runp = min(rump, rupp + misp)
upt_switch_p = insw_vector(runp)
dPpdt_upt_n1p = runp * upt_switch_p
# is uptake is negative flux goes to DIP (R1P) pool
dPpdt_upt_r1p = -runp * (1.0 - upt_switch_p)
#--------------------------------------------------------------------------
# Excretion of N and P to PON and POP
dPndt_lys_r6n = pe_R6 * nut_stress_lysis * pn
dPndt_lys_r1n = nut_stress_lysis * pn - dPndt_lys_r6n
dPpdt_lys_r6p = pe_R6 * nut_stress_lysis * pp
dPpdt_lys_r1p = nut_stress_lysis * pp - dPpdt_lys_r6p
#--------------------------------------------------------------------------
# Nutrient dynamics: SILICATE
if group == 1:
# Gross uptake of silicate excluding respiratory costs (from Phyto.F90, 'runs')
dPsdt_upt_n5s = max(
0.0,
phyto_parameters["phi_Sopt"] * pc * (photosynthesis - basal_rsp))
# losses of Si (from Phyto.F90)
dPsdt_lys_r6s = nut_stress_lysis * p1s
else:
dPsdt_upt_n5s = 0.0
dPsdt_lys_r6s = 0.0
#--------------------------------------------------------------------------
# Chl-a synthesis and photoacclimation
if phyto_parameters["chl_switch"] == 1:
# dynamical chl:c ratio from Fortran code Phyto.F90
rho_chl = phyto_parameters["theta_chl0"] * min(
1.0, phyto_parameters["rP0"] * light_lim * pc /
(phyto_parameters["alpha_chl"] *
(pl + constant_parameters["p_small"]) * irr))
# Chlorophyll synthesis from Fortran code Phyto.F90, rate_chl
dPldt_syn = rho_chl * (photosynthesis - nut_stress_excretion -
activity_excretion -
activity_rsp) * pc - nut_stress_lysis * pl
else:
sys.exit(
"Warning: This code does not support other chl systhesis parameterizations"
)
#--------------------------------------------------------------------------
return (dPcdt_gpp_o3c, dPcdt_rsp_o3c, dPcdt_lys_r1c, dPcdt_lys_r6c,
dPcdt_exu_r2c, dPndt_upt_n3n, dPndt_upt_n4n, extra_n,
dPndt_lys_r1n, dPndt_lys_r6n, dPpdt_upt_n1p, dPpdt_upt_r1p,
dPpdt_lys_r1p, dPpdt_lys_r6p, dPldt_syn, dPsdt_upt_n5s,
dPsdt_lys_r6s)
def get_mesozoo_predation_terms(conc, mesozoo3_parameters, mesozoo4_parameters,
zoo_availability_parameters,
environmental_parameters, constant_parameters,
temp):
""" Calculates the predation terms for mesozooplankton """
# Species concentrations
p1c = conc[10] # Diatoms carbon (mg C m^-3)
p1n = conc[11] # Diatoms nitrogen (mmol N m^-3)
p1p = conc[12] # Diatoms phosphate (mmol P m^-3)
p1l = conc[13] # Diatoms chlorophyll (mg Chl-a m^-3)
p1s = conc[14] # Diatoms silicate (mmol Si m^-3)
p2c = conc[15] # NanoFlagellates carbon (mg C m^-3)
p2n = conc[16] # NanoFlagellates nitrogen (mmol N m^-3)
p2p = conc[17] # NanoFlagellates phosphate (mmol P m^-3)
p2l = conc[18] # NanoFlagellates chlorophyll (mg Chl-a m^-3)
p3c = conc[19] # Picophytoplankton carbon (mg C m^-3)
p3n = conc[20] # Picophytoplankton nitrogen (mmol N m^-3)
p3p = conc[21] # Picophytoplankton phosphate (mmol P m^-3)
p3l = conc[22] # Picophytoplankton chlorophyll (mg Chl-a m^-3)
p4c = conc[23] # Large phytoplankton carbon (mg C m^-3)
p4n = conc[24] # Large phytoplankton nitrogen (mmol N m^-3)
p4p = conc[25] # Large phytoplankton phosphate (mmol P m^-3)
p4l = conc[26] # Large phytoplankton chlorophyll (mg Chl-a m^-3)
z3c = conc[27] # Carnivorous mesozooplankton carbon (mg C m^-3)
z3n = conc[28] # Carnivorous mesozooplankton nitrogen (mmol N m^-3)
z3p = conc[29] # Carnivorous mesozooplankton phosphate (mmol P m^-3)
z4c = conc[30] # Omnivorous mesozooplankton carbon (mg C m^-3)
z4n = conc[31] # Omnivorous mesozooplankton nitrogen (mmol N m^-3)
z4p = conc[32] # Omnivorous mesozooplankton phosphate (mmol P m^-3)
z5c = conc[33] # Microzooplankton carbon (mg C m^-3)
z5n = conc[34] # Microzooplankton nitrogen (mmol N m^-3)
z5p = conc[35] # Microzooplankton phosphate (mmol P m^-3)
z6c = conc[36] # Heterotrophic flagellates carbon (mg C m^-3)
z6n = conc[37] # Heterotrophic flagellates nitrogen (mmol N m^-3)
z6p = conc[38] # Heterotrophic flagellates phosphate (mmol P m^-3)
# concentration ratios
conc_ratio_n = {
"p1": get_concentration_ratio(p1n, p1c,
constant_parameters["p_small"]),
"p2": get_concentration_ratio(p2n, p2c,
constant_parameters["p_small"]),
"p3": get_concentration_ratio(p3n, p3c,
constant_parameters["p_small"]),
"p4": get_concentration_ratio(p4n, p4c,
constant_parameters["p_small"]),
"z3": get_concentration_ratio(z3n, z3c,
constant_parameters["p_small"]),
"z4": get_concentration_ratio(z4n, z4c,
constant_parameters["p_small"]),
"z5": get_concentration_ratio(z5n, z5c,
constant_parameters["p_small"]),
"z6": get_concentration_ratio(z6n, z6c, constant_parameters["p_small"])
}
conc_ratio_p = {
"p1": get_concentration_ratio(p1p, p1c,
constant_parameters["p_small"]),
"p2": get_concentration_ratio(p2p, p2c,
constant_parameters["p_small"]),
"p3": get_concentration_ratio(p3p, p3c,
constant_parameters["p_small"]),
"p4": get_concentration_ratio(p4p, p4c,
constant_parameters["p_small"]),
"z3": get_concentration_ratio(z3p, z3c,
constant_parameters["p_small"]),
"z4": get_concentration_ratio(z4p, z4c,
constant_parameters["p_small"]),
"z5": get_concentration_ratio(z5p, z5c,
constant_parameters["p_small"]),
"z6": get_concentration_ratio(z6p, z6c, constant_parameters["p_small"])
}
# Zooplankton temperature regulating factor
fTZ = eTq_vector(temp, environmental_parameters["basetemp"],
environmental_parameters["q10z"])
# Calculate total potential food given the non-dim prey availability
# There is no parameter for capture efficiency in mesozooplankton
# From MesoZoo.F90 lines 247-259
# Phytoplankton LFG: Food availability of prey Phytoplankton for predator Z3 and Z4
available_phyto_c3 = (zoo_availability_parameters["del_z3p1"] * p1c) + (
zoo_availability_parameters["del_z3p2"] *
p2c) + (zoo_availability_parameters["del_z3p3"] *
p3c) + (zoo_availability_parameters["del_z3p4"] * p4c)
available_phyto_c4 = (zoo_availability_parameters["del_z4p1"] * p1c) + (
zoo_availability_parameters["del_z4p2"] *
p2c) + (zoo_availability_parameters["del_z4p3"] *
p3c) + (zoo_availability_parameters["del_z4p4"] * p4c)
# Mesozooplankton LFG
available_mesozoo_c3 = (zoo_availability_parameters["del_z3z3"] * z3c) + (
zoo_availability_parameters["del_z3z4"] * z4c)
available_mesozoo_c4 = (zoo_availability_parameters["del_z4z3"] * z3c) + (
zoo_availability_parameters["del_z4z4"] * z4c)
# Microzooplankton LFG
available_microzoo_c3 = (zoo_availability_parameters["del_z3z5"] * z5c) + (
zoo_availability_parameters["del_z3z6"] * z6c)
available_microzoo_c4 = (zoo_availability_parameters["del_z4z5"] * z5c) + (
zoo_availability_parameters["del_z4z6"] * z6c)
# sys.exit(available_microzoo_c4)
# Total potential food (from Meso.F90 'rumc')
f_c3 = available_phyto_c3 + available_mesozoo_c3 + available_microzoo_c3
f_c4 = available_phyto_c4 + available_mesozoo_c4 + available_microzoo_c4
# Calculate total food uptake rate (from Meso.F90 'rugc')
total_uptake_rate_z3 = fTZ * mesozoo3_parameters["r_Z0"] * (
mesozoo3_parameters["nu_z"] * f_c3 /
((mesozoo3_parameters["nu_z"] * f_c3) +
mesozoo3_parameters["r_Z0"])) * z3c
total_uptake_rate_z4 = fTZ * mesozoo4_parameters["r_Z0"] * (
mesozoo4_parameters["nu_z"] * f_c4 /
((mesozoo4_parameters["nu_z"] * f_c4) +
mesozoo4_parameters["r_Z0"])) * z4c
# Calculate specific uptake rate considering potentially available food (from Meso.F90 'sut')
specific_uptake_rate_z3 = total_uptake_rate_z3 / (
constant_parameters["p_small"] + f_c3)
specific_uptake_rate_z4 = total_uptake_rate_z4 / (
constant_parameters["p_small"] + f_c4)
# Total Gross Uptakes from every LFG
dZ3cdt_prd = {
"p1":
specific_uptake_rate_z3 * zoo_availability_parameters["del_z3p1"] *
p1c,
"p2":
specific_uptake_rate_z3 * zoo_availability_parameters["del_z3p2"] *
p2c,
"p3":
specific_uptake_rate_z3 * zoo_availability_parameters["del_z3p3"] *
p3c,
"p4":
specific_uptake_rate_z3 * zoo_availability_parameters["del_z3p4"] *
p4c,
"z3":
specific_uptake_rate_z3 * zoo_availability_parameters["del_z3z3"] *
z3c,
"z4":
specific_uptake_rate_z3 * zoo_availability_parameters["del_z3z4"] *
z4c,
"z5":
specific_uptake_rate_z3 * zoo_availability_parameters["del_z3z5"] *
z5c,
"z6":
specific_uptake_rate_z3 * zoo_availability_parameters["del_z3z6"] * z6c
}
dZ4cdt_prd = {
"p1":
specific_uptake_rate_z4 * zoo_availability_parameters["del_z4p1"] *
p1c,
"p2":
specific_uptake_rate_z4 * zoo_availability_parameters["del_z4p2"] *
p2c,
"p3":
specific_uptake_rate_z4 * zoo_availability_parameters["del_z4p3"] *
p3c,
"p4":
specific_uptake_rate_z4 * zoo_availability_parameters["del_z4p4"] *
p4c,
"z3":
specific_uptake_rate_z4 * zoo_availability_parameters["del_z4z3"] *
z3c,
"z4":
specific_uptake_rate_z4 * zoo_availability_parameters["del_z4z4"] *
z4c,
"z5":
specific_uptake_rate_z4 * zoo_availability_parameters["del_z4z5"] *
z5c,
"z6":
specific_uptake_rate_z4 * zoo_availability_parameters["del_z4z6"] * z6c
}
# Total ingestion rate
ic3 = 0.0
in3 = 0.0
ip3 = 0.0
for key in dZ3cdt_prd:
ic3 += dZ3cdt_prd[key]
in3 += dZ3cdt_prd[key] * conc_ratio_n[key]
ip3 += dZ3cdt_prd[key] * conc_ratio_p[key]
ic4 = 0.0
in4 = 0.0
ip4 = 0.0
for key in dZ4cdt_prd:
ic4 += dZ4cdt_prd[key]
in4 += dZ4cdt_prd[key] * conc_ratio_n[key]
ip4 += dZ4cdt_prd[key] * conc_ratio_p[key]
return dZ3cdt_prd, dZ4cdt_prd, ic3, in3, ip3, ic4, in4, ip4
def get_microzoo_predation_terms(conc, microzoo5_parameters,
microzoo6_parameters,
zoo_availability_parameters,
environmental_parameters, constant_parameters,
temp):
""" Calculates the predation terms for microzooplankton """
# Species concentrations
b1c = conc[7] # Pelagic bacteria carbon (mg C m^-3)
b1n = conc[8] # Pelagic bacteria nitrogen (mmol N m^-3)
b1p = conc[9] # Pelagic bacteria phosphate (mmol P m^-3)
p1c = conc[10] # Diatoms carbon (mg C m^-3)
p1n = conc[11] # Diatoms nitrogen (mmol N m^-3)
p1p = conc[12] # Diatoms phosphate (mmol P m^-3)
p1l = conc[13] # Diatoms chlorophyll (mg Chl-a m^-3)
p1s = conc[14] # Diatoms silicate (mmol Si m^-3)
p2c = conc[15] # NanoFlagellates carbon (mg C m^-3)
p2n = conc[16] # NanoFlagellates nitrogen (mmol N m^-3)
p2p = conc[17] # NanoFlagellates phosphate (mmol P m^-3)
p2l = conc[18] # NanoFlagellates chlorophyll (mg Chl-a m^-3)
p3c = conc[19] # Picophytoplankton carbon (mg C m^-3)
p3n = conc[20] # Picophytoplankton nitrogen (mmol N m^-3)
p3p = conc[21] # Picophytoplankton phosphate (mmol P m^-3)
p3l = conc[22] # Picophytoplankton chlorophyll (mg Chl-a m^-3)
p4c = conc[23] # Large phytoplankton carbon (mg C m^-3)
p4n = conc[24] # Large phytoplankton nitrogen (mmol N m^-3)
p4p = conc[25] # Large phytoplankton phosphate (mmol P m^-3)
p4l = conc[26] # Large phytoplankton chlorophyll (mg Chl-a m^-3)
z3c = conc[27] # Carnivorous mesozooplankton carbon (mg C m^-3)
z3n = conc[28] # Carnivorous mesozooplankton nitrogen (mmol N m^-3)
z3p = conc[29] # Carnivorous mesozooplankton phosphate (mmol P m^-3)
z4c = conc[30] # Omnivorous mesozooplankton carbon (mg C m^-3)
z4n = conc[31] # Omnivorous mesozooplankton nitrogen (mmol N m^-3)
z4p = conc[32] # Omnivorous mesozooplankton phosphate (mmol P m^-3)
z5c = conc[33] # Microzooplankton carbon (mg C m^-3)
z5n = conc[34] # Microzooplankton nitrogen (mmol N m^-3)
z5p = conc[35] # Microzooplankton phosphate (mmol P m^-3)
z6c = conc[36] # Heterotrophic flagellates carbon (mg C m^-3)
z6n = conc[37] # Heterotrophic flagellates nitrogen (mmol N m^-3)
z6p = conc[38] # Heterotrophic flagellates phosphate (mmol P m^-3)
# concentration ratios
conc_ratio_n = {
"b1": get_concentration_ratio(b1n, b1c,
constant_parameters["p_small"]),
"p1": get_concentration_ratio(p1n, p1c,
constant_parameters["p_small"]),
"p2": get_concentration_ratio(p2n, p2c,
constant_parameters["p_small"]),
"p3": get_concentration_ratio(p3n, p3c,
constant_parameters["p_small"]),
"p4": get_concentration_ratio(p4n, p4c,
constant_parameters["p_small"]),
"z5": get_concentration_ratio(z5n, z5c,
constant_parameters["p_small"]),
"z6": get_concentration_ratio(z6n, z6c, constant_parameters["p_small"])
}
conc_ratio_p = {
"b1": get_concentration_ratio(b1p, b1c,
constant_parameters["p_small"]),
"p1": get_concentration_ratio(p1p, p1c,
constant_parameters["p_small"]),
"p2": get_concentration_ratio(p2p, p2c,
constant_parameters["p_small"]),
"p3": get_concentration_ratio(p3p, p3c,
constant_parameters["p_small"]),
"p4": get_concentration_ratio(p4p, p4c,
constant_parameters["p_small"]),
"z5": get_concentration_ratio(z5p, z5c,
constant_parameters["p_small"]),
"z6": get_concentration_ratio(z6p, z6c, constant_parameters["p_small"])
}
# Zooplankton temperature regulating factor
fTZ = eTq_vector(temp, environmental_parameters["basetemp"],
environmental_parameters["q10z"])
# Capture efficiencies
capture_efficiencies_z5 = {
"b1": b1c / (b1c + microzoo5_parameters["mu_z"]),
"p1": p1c / (p1c + microzoo5_parameters["mu_z"]),
"p2": p2c / (p2c + microzoo5_parameters["mu_z"]),
"p3": p3c / (p3c + microzoo5_parameters["mu_z"]),
"p4": p4c / (p4c + microzoo5_parameters["mu_z"]),
"z5": z5c / (z5c + microzoo5_parameters["mu_z"]),
"z6": z6c / (z6c + microzoo5_parameters["mu_z"])
}
capture_efficiencies_z6 = {
"b1": b1c / (b1c + microzoo6_parameters["mu_z"]),
"p1": p1c / (p1c + microzoo6_parameters["mu_z"]),
"p2": p2c / (p2c + microzoo6_parameters["mu_z"]),
"p3": p3c / (p3c + microzoo6_parameters["mu_z"]),
"p4": p4c / (p4c + microzoo6_parameters["mu_z"]),
"z5": z5c / (z5c + microzoo6_parameters["mu_z"]),
"z6": z6c / (z6c + microzoo6_parameters["mu_z"])
}
# Calculate total potential food given the non-dim prey availability and capture efficiency
# From MicroZoo.F90 lines 209-237
# Bacteria LFG: Food availability of prey Bacteria for predator Z5 and Z6
available_bact_c5 = zoo_availability_parameters[
"del_z5b1"] * b1c * capture_efficiencies_z5["b1"]
available_bact_n5 = zoo_availability_parameters[
"del_z5b1"] * b1c * capture_efficiencies_z5["b1"] * conc_ratio_n["b1"]
available_bact_p5 = zoo_availability_parameters[
"del_z5b1"] * b1c * capture_efficiencies_z5["b1"] * conc_ratio_p["b1"]
available_bact_c6 = zoo_availability_parameters[
"del_z6b1"] * b1c * capture_efficiencies_z6["b1"]
available_bact_n6 = zoo_availability_parameters[
"del_z6b1"] * b1c * capture_efficiencies_z6["b1"] * conc_ratio_n["b1"]
available_bact_p6 = zoo_availability_parameters[
"del_z6b1"] * b1c * capture_efficiencies_z6["b1"] * conc_ratio_p["b1"]
# Phytoplankton LFG: Food availability of prey Phytoplankton for predator Z5 and Z6
available_phyto_c5 = ((zoo_availability_parameters["del_z5p1"] * p1c *
capture_efficiencies_z5["p1"]) +
(zoo_availability_parameters["del_z3p2"] * p2c *
capture_efficiencies_z5["p2"]) +
(zoo_availability_parameters["del_z3p3"] * p3c *
capture_efficiencies_z5["p3"]) +
(zoo_availability_parameters["del_z3p4"] * p4c *
capture_efficiencies_z5["p4"]))
available_phyto_n5 = (
(zoo_availability_parameters["del_z5p1"] * p1c *
capture_efficiencies_z5["p1"] * conc_ratio_n["p1"]) +
(zoo_availability_parameters["del_z3p2"] * p2c *
capture_efficiencies_z5["p2"] * conc_ratio_n["p2"]) +
(zoo_availability_parameters["del_z3p3"] * p3c *
capture_efficiencies_z5["p3"] * conc_ratio_n["p3"]) +
(zoo_availability_parameters["del_z3p4"] * p4c *
capture_efficiencies_z5["p4"] * conc_ratio_n["p4"]))
available_phyto_p5 = (
(zoo_availability_parameters["del_z5p1"] * p1c *
capture_efficiencies_z5["p1"] * conc_ratio_p["p1"]) +
(zoo_availability_parameters["del_z3p2"] * p2c *
capture_efficiencies_z5["p2"] * conc_ratio_p["p2"]) +
(zoo_availability_parameters["del_z3p3"] * p3c *
capture_efficiencies_z5["p3"] * conc_ratio_p["p3"]) +
(zoo_availability_parameters["del_z3p4"] * p4c *
capture_efficiencies_z5["p4"] * conc_ratio_p["p4"]))
available_phyto_c6 = ((zoo_availability_parameters["del_z6p1"] * p1c *
capture_efficiencies_z6["p1"]) +
(zoo_availability_parameters["del_z6p2"] * p2c *
capture_efficiencies_z6["p2"]) +
(zoo_availability_parameters["del_z6p3"] * p3c *
capture_efficiencies_z6["p3"]) +
(zoo_availability_parameters["del_z6p4"] * p4c *
capture_efficiencies_z6["p4"]))
available_phyto_n6 = (
(zoo_availability_parameters["del_z6p1"] * p1c *
capture_efficiencies_z6["p1"] * conc_ratio_n["p1"]) +
(zoo_availability_parameters["del_z6p2"] * p2c *
capture_efficiencies_z6["p2"] * conc_ratio_n["p2"]) +
(zoo_availability_parameters["del_z6p3"] * p3c *
capture_efficiencies_z6["p3"] * conc_ratio_n["p3"]) +
(zoo_availability_parameters["del_z6p4"] * p4c *
capture_efficiencies_z6["p4"] * conc_ratio_n["p4"]))
available_phyto_p6 = (
(zoo_availability_parameters["del_z6p1"] * p1c *
capture_efficiencies_z6["p1"] * conc_ratio_p["p1"]) +
(zoo_availability_parameters["del_z6p2"] * p2c *
capture_efficiencies_z6["p2"] * conc_ratio_p["p2"]) +
(zoo_availability_parameters["del_z6p3"] * p3c *
capture_efficiencies_z6["p3"] * conc_ratio_p["p3"]) +
(zoo_availability_parameters["del_z6p4"] * p4c *
capture_efficiencies_z6["p4"] * conc_ratio_p["p4"]))
# Phytoplankton LFG: Food availability of prey Microzooplankton for predator Z5 and Z6
available_microzoo_c5 = (zoo_availability_parameters["del_z5z5"] * z5c *
capture_efficiencies_z5["z5"]) + (
zoo_availability_parameters["del_z5z6"] *
z6c * capture_efficiencies_z5["z6"])
available_microzoo_n5 = (zoo_availability_parameters["del_z5z5"] * z5c *
capture_efficiencies_z5["z5"] * conc_ratio_n["z5"]
) + (zoo_availability_parameters["del_z5z6"] *
z6c * capture_efficiencies_z5["z6"] *
conc_ratio_n["z6"])
available_microzoo_p5 = (zoo_availability_parameters["del_z5z5"] * z5c *
capture_efficiencies_z5["z5"] * conc_ratio_p["z5"]
) + (zoo_availability_parameters["del_z5z6"] *
z6c * capture_efficiencies_z5["z6"] *
conc_ratio_p["z6"])
available_microzoo_c6 = (zoo_availability_parameters["del_z6z5"] * z5c *
capture_efficiencies_z6["z5"]) + (
zoo_availability_parameters["del_z6z6"] *
z6c * capture_efficiencies_z6["z6"])
available_microzoo_n6 = (
zoo_availability_parameters["del_z6z5"] * z5c *
capture_efficiencies_z6["z5"]**conc_ratio_n["z5"]) + (
zoo_availability_parameters["del_z6z6"] * z6c *
capture_efficiencies_z6["z6"]**conc_ratio_n["z6"])
available_microzoo_p6 = (
zoo_availability_parameters["del_z6z5"] * z5c *
capture_efficiencies_z6["z5"]**conc_ratio_p["z5"]) + (
zoo_availability_parameters["del_z6z6"] * z6c *
capture_efficiencies_z6["z6"]**conc_ratio_p["z6"])
# Total potential food (from MicroZoo.F90 'rumc', 'rumn', 'rump')
f_c5 = available_bact_c5 + available_phyto_c5 + available_microzoo_c5
f_n5 = available_bact_n5 + available_phyto_n5 + available_microzoo_n5
f_p5 = available_bact_p5 + available_phyto_p5 + available_microzoo_p5
f_c6 = available_bact_c6 + available_phyto_c6 + available_microzoo_c6
f_n6 = available_bact_n6 + available_phyto_n6 + available_microzoo_n6
f_p6 = available_bact_p6 + available_phyto_p6 + available_microzoo_p6
# Calculate total food uptake rate (from MicroZoo.F90 line 243 'rugc')
total_uptake_rate_z5 = fTZ * microzoo5_parameters["r_Z0"] * (
f_c5 / (f_c5 + microzoo5_parameters["h_Z_F"])) * z5c
total_uptake_rate_z6 = fTZ * microzoo6_parameters["r_Z0"] * (
f_c6 / (f_c6 + microzoo6_parameters["h_Z_F"])) * z6c
# Calculate specific uptake rate considering potentially available food (from MicroZoo.F90 line 244 'sut')
specific_uptake_rate_z5 = total_uptake_rate_z5 / (
f_c5 + constant_parameters["p_small"])
specific_uptake_rate_z6 = total_uptake_rate_z6 / (
f_c6 + constant_parameters["p_small"])
# Total Gross Uptakes from every LFG
dZ5cdt_prd = {
"b1":
specific_uptake_rate_z5 * zoo_availability_parameters["del_z5b1"] *
b1c * capture_efficiencies_z5["b1"],
"p1":
specific_uptake_rate_z5 * zoo_availability_parameters["del_z5p1"] *
p1c * capture_efficiencies_z5["p1"],
"p2":
specific_uptake_rate_z5 * zoo_availability_parameters["del_z5p2"] *
p2c * capture_efficiencies_z5["p2"],
"p3":
specific_uptake_rate_z5 * zoo_availability_parameters["del_z5p3"] *
p3c * capture_efficiencies_z5["p3"],
"p4":
specific_uptake_rate_z5 * zoo_availability_parameters["del_z5p4"] *
p4c * capture_efficiencies_z5["p4"],
"z5":
specific_uptake_rate_z5 * zoo_availability_parameters["del_z5z5"] *
z5c * capture_efficiencies_z5["z5"],
"z6":
specific_uptake_rate_z5 * zoo_availability_parameters["del_z5z6"] *
z6c * capture_efficiencies_z5["z6"]
}
dZ6cdt_prd = {
"b1":
specific_uptake_rate_z6 * zoo_availability_parameters["del_z6b1"] *
b1c * capture_efficiencies_z6["b1"],
"p1":
specific_uptake_rate_z6 * zoo_availability_parameters["del_z6p1"] *
p1c * capture_efficiencies_z6["p1"],
"p2":
specific_uptake_rate_z6 * zoo_availability_parameters["del_z6p2"] *
p2c * capture_efficiencies_z6["p2"],
"p3":
specific_uptake_rate_z6 * zoo_availability_parameters["del_z6p3"] *
p3c * capture_efficiencies_z6["p3"],
"p4":
specific_uptake_rate_z6 * zoo_availability_parameters["del_z6p4"] *
p4c * capture_efficiencies_z6["p4"],
"z5":
specific_uptake_rate_z6 * zoo_availability_parameters["del_z6z5"] *
z5c * capture_efficiencies_z6["z5"],
"z6":
specific_uptake_rate_z6 * zoo_availability_parameters["del_z6z6"] *
z6c * capture_efficiencies_z6["z6"]
}
# Total ingestion rate
ic5 = 0.0
in5 = 0.0
ip5 = 0.0
for key in dZ5cdt_prd:
ic5 += dZ5cdt_prd[key]
in5 += dZ5cdt_prd[key] * conc_ratio_n[key]
ip5 += dZ5cdt_prd[key] * conc_ratio_p[key]
ic6 = 0.0
in6 = 0.0
ip6 = 0.0
for key in dZ6cdt_prd:
ic6 += dZ6cdt_prd[key]
in6 += dZ6cdt_prd[key] * conc_ratio_n[key]
ip6 += dZ6cdt_prd[key] * conc_ratio_p[key]
return dZ5cdt_prd, dZ6cdt_prd, ic5, in5, ip5, ic6, in6, ip6
def bacteria_eqns(conc, bacteria_parameters, constant_parameters, environmental_parameters, temper):
""" Calculates the terms needed for the bacteria biological rate equations
Equations come from the BFM user manual
"""
# State variables
o2o = conc[0] # Dissolved oxygen (mg O_2 m^-3)
n1p = conc[1] # Phosphate (mmol P m^-3)
n4n = conc[3] # Ammonium (mmol N m^-3)
b1c = conc[7] # Pelagic bacteria carbon (mg C m^-3)
b1n = conc[8] # Pelagic bacteria nitrogen (mmol N m^-3)
b1p = conc[9] # Pelagic bacteria phosphate (mmol P m^-3)
r1c = conc[39] # Labile dissolved organic carbon (mg C m^-3)
r1n = conc[40] # Labile dissolved organic nitrogen (mmol N m^-3)
r1p = conc[41] # Labile dissolved organic phosphate (mmol P m^-3)
r2c = conc[42] # Semi-labile dissolved organic carbon (mg C m^-3)
r3c = conc[43] # Semi-refractory Dissolved Organic Carbon (mg C m^-3)
r6c = conc[44] # Particulate organic carbon (mg C m^-3)
r6n = conc[45] # Particulate organic nitrogen (mmol N m^-3)
r6p = conc[46] # Particulate organic phosphate (mmol P m^-3)
# concentration ratios
bp_bc = get_concentration_ratio(b1p, b1c, constant_parameters["p_small"])
bn_bc = get_concentration_ratio(b1n, b1c, constant_parameters["p_small"])
r1p_r1c = get_concentration_ratio(r1p, r1c, constant_parameters["p_small"])
r6p_r6c = get_concentration_ratio(r6p, r6c, constant_parameters["p_small"])
r1n_r1c = get_concentration_ratio(r1n, r1c, constant_parameters["p_small"])
r6n_r6c = get_concentration_ratio(r6n, r6c, constant_parameters["p_small"])
# Temperature effect on pelagic bacteria
fTB = eTq_vector(temper, environmental_parameters["basetemp"], environmental_parameters["q10b"])
# oxygen non-dimensional regulation factor[-]
# Oxygen environment: bacteria are both aerobic and anaerobic
f_B_O = max(constant_parameters["p_small"],o2o)**3/(max(constant_parameters["p_small"],o2o)**3 + bacteria_parameters["h_B_O"]**3)
# external nutrient limitation
f_B_n = n4n/(n4n + bacteria_parameters["h_B_n"])
f_B_p = n1p/(n1p + bacteria_parameters["h_B_p"])
# Bacteria mortality (lysis) process [mg C m^-3 s^-1]
dBcdt_lys = (bacteria_parameters["d_0B"]*fTB + bacteria_parameters["d_B_d"]*b1c)*b1c
dBcdt_lys_r1c = dBcdt_lys*constant_parameters["epsilon_c"]
dBcdt_lys_r1n = dBcdt_lys*bn_bc*constant_parameters["epsilon_n"]
dBcdt_lys_r1p = dBcdt_lys*bp_bc*constant_parameters["epsilon_p"]
dBcdt_lys_r6c = dBcdt_lys*(1.0 - constant_parameters["epsilon_c"])
dBcdt_lys_r6n = dBcdt_lys*bn_bc*(1.0 - constant_parameters["epsilon_n"])
dBcdt_lys_r6p = dBcdt_lys*bp_bc*(1.0 - constant_parameters["epsilon_p"])
# Substrate availability
if bacteria_parameters["bact_version"]==1 or bacteria_parameters["bact_version"]==2:
# nutrient limitation (intracellular)
nut_lim_n = min(1.0, max(0.0, bn_bc/bacteria_parameters["n_B_opt"])) # Nitrogen
nut_lim_p = min(1.0, max(0.0, bp_bc/bacteria_parameters["p_B_opt"])) # Phosphorus
f_B_n_P = min(nut_lim_n, nut_lim_p)
# Potential uptake by bacteria
potential_upt = f_B_n_P*fTB*bacteria_parameters["r_0B"]*b1c
# correction of substrate quality depending on nutrient content
f_r1_n_P = min(1.0, r1p_r1c/bacteria_parameters["p_B_opt"], r1n_r1c/bacteria_parameters["n_B_opt"])
f_r6_n_P = min(1.0, r6p_r6c/bacteria_parameters["p_B_opt"], r6n_r6c/bacteria_parameters["n_B_opt"])
else:
sys.exit('This code does not support this parameterization option, only bact_version=1')
# Calculate the realized substrate uptake rate depending on the type of detritus and quality
upt_R1c = (bacteria_parameters["v_B_r1"]*f_r1_n_P + bacteria_parameters["v_0B_r1"]*(1.0 - f_r1_n_P))*r1c
upt_R2c = bacteria_parameters["v_B_r2"]*r2c
upt_R3c = bacteria_parameters["v_B_r3"]*r3c
upt_R6c = bacteria_parameters["v_B_r6"]*f_r6_n_P*r6c
realized_upt = constant_parameters["p_small"] + upt_R1c + upt_R2c + upt_R3c + upt_R6c
# Actual uptake by bacteria
actual_upt = min(potential_upt, realized_upt)
# Carbon fluxes into bacteria
dBcdt_upt_r1c = actual_upt*upt_R1c/realized_upt
dBcdt_upt_r2c = actual_upt*upt_R2c/realized_upt
dBcdt_upt_r3c = actual_upt*upt_R3c/realized_upt
dBcdt_upt_r6c = actual_upt*upt_R6c/realized_upt
# Organic Nitrogen and Phosphrous uptake
dBcdt_upt_r1n = r1n_r1c*dBcdt_upt_r1c
dBcdt_upt_r6n = r6n_r6c*dBcdt_upt_r6c
dBcdt_upt_r1p = r1p_r1c*dBcdt_upt_r1c
dBcdt_upt_r6p = r6p_r6c*dBcdt_upt_r6c
# Bacteria respiration [mc C m^-3 s^-1]
dBcdt_rsp_o3c = (bacteria_parameters["gamma_B_a"] + bacteria_parameters["gamma_B_O"]*(1.0 - f_B_O))*actual_upt + bacteria_parameters["b_B"]*b1c*fTB
# Fluxes from bacteria
if bacteria_parameters["bact_version"]==1:
# There is no Carbon excretion
dBcdt_rel_r2c = 0.0
dBcdt_rel_r3c = 0.0
# Dissolved Nitrogen dynamics
dBndt_upt_rel_n4n = (bn_bc - bacteria_parameters["n_B_opt"])*b1c*bacteria_parameters["v_B_n"]
# Dissolved Phosphorus dynamics
dBpdt_upt_rel_n1p = (bp_bc - bacteria_parameters["p_B_opt"])*b1c*bacteria_parameters["v_B_p"]
# BACT2 parameterization
if bacteria_parameters["bact_version"]==2:
print('This code does not support this parameterization option, only bact_version=1')
# BACT3 parameterization
if bacteria_parameters["bact_version"]==3:
print('This code does not support this parameterization option, only bact_version=1')
# Term needed for denitrification flux (dn3ndt_denit) (from PelBac.F90 line 352)
flPTN6r = (1.0 - f_B_O)*dBcdt_rsp_o3c*constant_parameters["omega_c"]*constant_parameters["omega_r"]
return (dBcdt_lys_r1c, dBcdt_lys_r1n, dBcdt_lys_r1p, dBcdt_lys_r6c, dBcdt_lys_r6n, dBcdt_lys_r6p,
dBcdt_upt_r1c, dBcdt_upt_r6c, dBpdt_upt_rel_n1p, dBndt_upt_rel_n4n, dBcdt_upt_r2c, dBcdt_upt_r3c,
dBcdt_rel_r2c, dBcdt_rel_r3c, dBcdt_rsp_o3c, flPTN6r, f_B_O, f_B_n, f_B_p)