'H2(aq)':1e-6,
'O2(aq)':1e-4,
}
rate_scale=10e-8
thresh=0.0
reactions = [
# decomp_network.reaction(name='Aerobic decomposition',reactant_pools={'SOM':1.0},product_pools={'HCO3-':1.0},reactiontype='SOMDECOMP',
# rate_constant=1e-8,rate_units='1/sec',turnover_name='RATE_CONSTANT',
# # inhibition_terms=[decomp_network.inhibition(species='O2(aq)',k=6.25e-8,type='THRESHOLD 1.0d20')]),
# monod_terms=[decomp_network.monod(species='O2(aq)',k=conc_scales['O2(aq)'],threshold=thresh)]),
decomp_network.reaction(name='Hydrolysis',stoich='1.0 SOM -> 0.9 DOM1',reactiontype='SOMDECOMP',turnover_name='RATE_CONSTANT',
rate_constant=rate_scale,rate_units='1/sec', # Jianqiu Zheng et al., 2019: One third of fermented C is converted to CO2
inhibition_terms=[decomp_network.inhibition(species='DOM1',type='MONOD',k=conc_scales['DOM1']),
# decomp_network.inhibition(species='O2(aq)',type='MONOD',k=1e-11),
]),
# Calculating these as per unit carbon, so dividing by the 6 carbons in a glucose
# C6H12O6 + 4 H2O -> 2 CH3COO- + 2 HCO3- + 4 H+ + 4 H2
# Should it be inhibited by H2?
decomp_network.reaction(name='fermentation',reactant_pools={'DOM1':6/6},product_pools={'Acetate-':2/6,'HCO3-':2/6,'H+':4/6,'H2(aq)':4*2/6,'Tracer':2/6}, # balancing pH of FeIII release requires an extra 5.5 H+ to be released here
rate_constant=rate_scale,reactiontype='MICROBIAL', # Jianqiu Zheng et al., 2019: One third of fermented C is converted to CO2
inhibition_terms=[decomp_network.inhibition(species='O2(aq)',k=conc_scales['O2(aq)'],type='MONOD'),decomp_network.inhibition(species='Acetate-',k=conc_scales['Acetate-'],type='MONOD')],
monod_terms=[decomp_network.monod(species='DOM1',k=conc_scales['DOM1'],threshold=thresh)]),
# CH2O + H2O -> CO2 + 4H+ + 4 e-
# O2 + 4H+ + 4 e- -> 2H2O
decomp_network.reaction(name='DOM oxidation (O2)',stoich='1.0 DOM1 + 1.0 O2(aq) -> 1.0 HCO3- + 1.0 H+ + 1.0 Tracer',
monod_terms=[decomp_network.monod(species='O2(aq)',k=conc_scales['O2(aq)'],threshold=thresh),decomp_network.monod(species='DOM1',k=conc_scales['DOM1'],threshold=thresh)],
# Major issue so far is balancing pH: Fe(III) release from mineral sucks up a lot of H+, and I'm not sure whether it's being replenished from
# some reaction involving Fe++
# Beth: There should be a lot of solid OM functional groups, probably carboxylate/carboxylic acid that exchange protons and buffer pH in these soils
# Fe(II) is probably sorbing onto OM, or staying dissolved
# Fe(III) should precipitate in this system, so if it's dissolved it would be complexed with something
# Per Persson has papers on Fe partitioning in soils as a function of pH
# Derek Lovely has done a lot of Fe reduction lab work to look at reduction rates
# Kinetics of water-rock interaction (textbook) has lots of rate constants. Look for chapter by Eric Rodin
# Aaron Thompson does work on Fe oxides and redox fluctuations
hydrolysis = decomp_network.reaction(
name='Hydrolysis',
reactant_pools={'cellulose': 1.0},
product_pools={'DOM1': 1.0},
rate_constant=1e-1,
rate_units=
'y', # Jianqiu Zheng et al., 2019: One third of fermented C is converted to CO2
inhibition_terms=[
decomp_network.inhibition(species='DOM1', type='MONOD', k=1e-5)
])
# Calculating these as per unit carbon, so dividing by the 6 carbons in a glucose
# C6H12O6 + 4 H2O -> 2 CH3COO- + 2 HCO3- + 4 H+ + 4 H2
fermentation = decomp_network.reaction(
name='fermentation',
reactant_pools={'DOM1': 6 / 6},
product_pools={
'Acetate-': 2 / 6,
'HCO3-': 2 / 6,
'H+': 4 / 6 + 4 * 2 / 6,
'Tracer': 2 / 6
def make_network(Mn_peroxidase_Mn3_leakage=1e-5,
leaf_Mn_mgkg=25.0,
change_constraints={},
Mn2_scale=1e-5,
Mn3_scale=1e-5,
NH4_scale=1e-2,
DOM_scale=1.0,
CEC=40.0,
change_rate={},
DOM_sorption_k=1.0):
Mn_molarmass = 54.94 #g/mol
C_molarmass = 12.01
leaf_Cfrac_mass = 0.4
# Converting from mol Mn/mol leaf C to mg Mn/kg leaf dry mass
leaf_Mn_frac = leaf_Mn_mgkg / ((Mn_molarmass * 1e3) /
(C_molarmass * 1e-3 / leaf_Cfrac_mass))
reactions = [
decomp_network.reaction(
name='Hydrolysis',
reactant_pools={'Cellulose': 1.0},
product_pools={'DOM1': 1.0},
rate_constant=2e-1,
rate_units='y',
# inhibition_terms=[decomp_network.inhibition(species='DOM1',type='MONOD',k=1e-1)],
reactiontype='SOMDECOMP'),
# Need a way to make a soluble reactive compound from lignin. Treating it like hydrolysis, but allowing only a small amount to be generated
# Model runs faster if Mn limitation is on this step (source limit) instead of limiting decomposition rate of DOM2 and building up inhibiting DOM2 concentrations
decomp_network.reaction(
name='Lignin exposure',
reactant_pools={'Lignin': 1.0},
product_pools={'DOM2': 1.0},
rate_constant=2e-1,
rate_units='y',
inhibition_terms=[
decomp_network.inhibition(species='DOM2', type='MONOD', k=1e0),
decomp_network.inhibition(
species='Cellulose', type='MONOD', k=40
), # Suggested by Sun et al 2019, which found that MnP activity only increased late in decomposition
decomp_network.inhibition(species='Mn++',
type='INVERSE_MONOD',
k=Mn2_scale),
decomp_network.inhibition(species='NH4+',
k=NH4_scale,
type='MONOD')
],
reactiontype='SOMDECOMP'),
# Direct depolymerization of lignin into DOM1. Basically to allow some decomposition to occur in absence of Mn++ so lignin doesn't build up indefinitely
# Still deciding whether to do this way or by DOM2 oxidation? Or leaching of DOM2? Or not at all?
decomp_network.reaction(name='Lignin depolymerization',
reactant_pools={'Lignin': 1.0},
product_pools={'DOM1': 1.0},
rate_constant=2e-1,
rate_units='y',
inhibition_terms=[
decomp_network.inhibition(species='Mn++',
type='MONOD',
k=Mn2_scale)
],
reactiontype='SOMDECOMP'),
# Mn reduction turns DOM2 (lignin-based) into DOM1 (odixized, decomposable)
# decomp_network.reaction(name='Lignin Mn reduction',reactant_pools={'DOM2':1.0,'Mn+++':1.0},product_pools={'Mn++':1.0,'H+':1.0,'DOM1':1.0},
# monod_terms=[decomp_network.monod(species='DOM2',k=2e-11,threshold=1.1e-20),decomp_network.monod(species='Mn+++',k=1.3e-18,threshold=1.1e-25)],
# # inhibition_terms=[decomp_network.inhibition(species='O2(aq)',k=6.25e-8,type='MONOD')],
# rate_constant=2e-10,reactiontype='MICROBIAL'),
# Mn oxidation (Mn peroxidase?)
# decomp_network.reaction(name='Mn oxidation',reactant_pools={'O2(aq)':1.0,'H+':4.0,'Mn++':4.0},product_pools={'Mn+++':4.0},
# monod_terms=[decomp_network.monod(species='O2(aq)',k=1e-5,threshold=1.1e-15),decomp_network.monod(species='Mn++',k=1.3e-12,threshold=1.1e-15)],
# # inhibition_terms=[decomp_network.inhibition(species='O2(aq)',k=6.25e-8,type='MONOD')],
# rate_constant=8e-10,reactiontype='MICROBIAL'),
# Mn Peroxidase: Quasi-closed reaction loop for Mn2/3 with some leakage.
# 1 DOM2 + 1 Mn++ + x H+ -> 1 DOM1 + (1-x) Mn++ + x Mn+++
decomp_network.reaction(name='Mn Peroxidase',
reactant_pools={
'DOM2': 1.0,
'Mn++': Mn_peroxidase_Mn3_leakage,
'H+': Mn_peroxidase_Mn3_leakage
},
product_pools={
'DOM1': 1.0,
'Mn+++': Mn_peroxidase_Mn3_leakage
},
monod_terms=[
decomp_network.monod(species='DOM2',
k=1e-1,
threshold=1.1e-20),
decomp_network.monod(species='Mn++',
k=Mn2_scale * 1e1,
threshold=1.1e-20)
],
inhibition_terms=[
decomp_network.inhibition(species='NH4+',
k=NH4_scale,
type='MONOD')
],
rate_constant=5e-6,
reactiontype='MICROBIAL'),
# CH2O + H2O -> CO2 + 4H+ + 4 e-
# O2 + 4H+ + 4 e- -> 2H2O
decomp_network.reaction(name='DOM aerobic respiration',
reactant_pools={
'DOM1': 1.0,
'O2(aq)': 1.0
},
product_pools={
'HCO3-': 1.0,
'H+': 1.0,
'Tracer': 1.0,
'Mn++': leaf_Mn_frac
},
monod_terms=[
decomp_network.monod(species='O2(aq)',
k=1e-4,
threshold=1.1e-12),
decomp_network.monod(species='DOM1',
k=DOM_scale,
threshold=1.1e-14)
],
rate_constant=1.0e-5,
reactiontype='MICROBIAL'),
# CH2O + H2O -> CO2 + 4H+ + 4 e-
# O2 + 4H+ + 4 e- -> 2H2O
# Aerobic respiration of DOM2, to allow some lignin decomposition in absence of Mn. Assume it is very slow
decomp_network.reaction(name='DOM2 aerobic respiration',
reactant_pools={
'DOM2': 1.0,
'O2(aq)': 1.0
},
product_pools={
'HCO3-': 1.0,
'H+': 1.0,
'Tracer': 1.0,
'Mn++': leaf_Mn_frac
},
monod_terms=[
decomp_network.monod(species='O2(aq)',
k=1e-4,
threshold=1.1e-12),
decomp_network.monod(species='DOM2',
k=1e0,
threshold=1.1e-14)
],
inhibition_terms=[
decomp_network.inhibition(species='Mn++',
type='MONOD',
k=Mn2_scale)
],
rate_constant=1.0e-5,
reactiontype='MICROBIAL'),
# Manganese reduction reaction
# CH2O + 2 H2O -> HCO3- + 5 H+ + 4 e-
# 4 Mn+++ + 4 e- -> 4 Mn++
# Microbial-mediated manganese reduction, happens under anoxic conditions only
decomp_network.reaction(
name='DOM1 Mn+++ reduction',
stoich=
'1.0 DOM1 + 4.0 Mn+++ -> 1.0 HCO3- + 4.0 Mn++ + 5.0 H+ + 1.0 Tracer',
monod_terms=[
decomp_network.monod(species='DOM1', k=DOM_scale / 10),
decomp_network.monod(species='Mn+++', k=Mn3_scale)
],
inhibition_terms=[
decomp_network.inhibition(species='O2(aq)',
k=1e-8,
type='MONOD')
],
rate_constant=2e-10,
reactiontype='MICROBIAL'),
# Abiotic Mn reduction, happens under oxic conditions
decomp_network.reaction(
name='DOM1 Mn+++ abiotic reduction',
stoich=
'1.0 DOM1 + 4.0 Mn+++ -> 1.0 HCO3- + 4.0 Mn++ + 5.0 H+ + 1.0 Tracer',
rate_constant=2e-5,
reactiontype='GENERAL'),
# Microbial oxidation of Mn(II) under oxic conditions. See Tebo et al 2004. Mostly done by bacteria. Reduces O2 to water. Function unknown but might be chemoautotrophic
# Mn++ + 0.5 O2 + H2O -> Mn(+4)O2 + 2 H+ (but this includes an intermediate Mn3O4 step)
# or Mn++ + 0.25 O2 + 1.5 H2O -> Mn(+3)OOH + 2 H+
# or 3 Mn++ + 0.5 O2 + 3 H2O -> Mn(+3)3O4 + 6 H+
# Simplified version assuming further oxidation happens in Birnessite precipitation step:
# Mn++ + H+ + 0.25 O2 -> Mn+++ + 0.5 H2O
# then (implicitly) 7 Mn+++ + 1.25 O2 + 15.5 H2O -> Mn7O13*5H2O + 21 H+
decomp_network.reaction(
name='Bacterial Mn++ oxidation',
stoich='Mn++ + H+ + 0.25 O2(aq) -> Mn+++ + 0.5 H2O',
monod_terms=[
decomp_network.monod(species='Mn++', k=Mn2_scale),
decomp_network.monod(species='O2(aq)',
k=1e-4,
threshold=1.1e-12)
],
rate_constant=8e-8,
reactiontype='MICROBIAL'
), # Rate constant estimated from Fig 8 in Tebo et al 2004
# C2H3O2- + 2 H2O -> 2 CO2 + 7 H+ + 8 e-
# 2 O2 + 8 H+ + 8 e- -> 4 H2O
# decomp_network.reaction(name='Acetate aerobic respiration',reactant_pools={'Acetate-':1.0,'O2(aq)':2.0},product_pools={'HCO3-':2.0,'H+':2.0,'Tracer':2.0},
# monod_terms=[decomp_network.monod(species='O2(aq)',k=1e-5,threshold=1.1e-12),decomp_network.monod(species='Acetate-',k=1e-8,threshold=1.1e-14)],
# rate_constant=1.0e-9,reactiontype='MICROBIAL'),
#
# PFLOTRAN will not let you do isotherm sorption if there are any secondary species :-( - reaction_database.F90 line 3424
# decomp_network.sorption_isotherm(name='DOM sorption',mineral='Rock(s)',sorbed_species='DOM1',k=0.1,langmuir_b=1.0,sorbed_name='Sorbed DOM1'),
# Root uptake of Mn++. Does this need a charge balancing release of anions?
# According to Haynes (1990), imbalance in root anion vs cation uptake is usually balanced by H+ or OH- release. I guess in this case we need to assume that all other ions are balanced except for Mn?
decomp_network.reaction(name='Root uptake of Mn++',
stoich='1.0 Mn++ -> 1.0 Tracer2 + 2 H+',
monod_terms=[
decomp_network.monod(species='Mn++',
k=1e-7,
threshold=1.1e-20)
],
biomass='Root_biomass',
biomass_yield=0.0,
rate_constant=1.0e-5,
reactiontype='MICROBIAL'),
# Cation exchange
decomp_network.ion_exchange(name='Cation exchange',
cations={
'Mn++': 5.0,
'Mn+++': 0.6,
'Al+++': 10.0,
'Mg++': 1.1,
'Ca++': 1.0,
'Na+': 0.5,
'K+': 0.1,
'H+': 1.1
},
CEC=CEC,
mineral=None),
# sorption rate is microbial DOM1 -> DOM3 (d/dt = V1*sorption_capacity*DOM1/(DOM1+k))
# Desorption rate is general DOM3 -> DOM1 (d/dt = V2*DOM3)
# Equilibrium sorption = V1/V2*sorption_capacity*DOM/(k+DOM) so actual maximum sorption is V1/V2*sorption_capacity
decomp_network.reaction(name='DOM sorption',
stoich='DOM1 -> DOM3',
monod_terms=[
decomp_network.monod(species='DOM1',
k=DOM_sorption_k)
],
biomass='Sorption_capacity',
biomass_yield=0.0,
rate_constant=1.0e-10,
reactiontype='MICROBIAL'),
decomp_network.reaction(name='DOM desorption',
stoich='DOM3 -> DOM1',
reactiontype='GENERAL',
rate_constant=1.0e-10),
] # End of reactions list
import copy
pools_copy = copy.deepcopy(pools)
for n, p in enumerate(pools_copy):
if p['name'] in change_rate:
pools_copy[n]['rate'] = change_rate[p['name']]
return decomp_network.decomp_network(
pools=decomp_network.change_constraints(pools_copy,
change_constraints),
reactions=reactions)
import decomp_network
import plot_pf_output
pflotran_exe = '../pflotran-interface/src/pflotran/pflotran'
# Simple decomposition network 1: 1 POM pool, one DOM pool, first order
POM = decomp_network.decomp_pool(name='POM', CN=15, initval=1e3)
DOM = decomp_network.decomp_pool(name='DOM1',
CN=15,
initval=1e-3,
immobile=False)
CO2 = decomp_network.decomp_pool(name='CO2(aq)', immobile=False, initval=1e-15)
POM_dissolve = decomp_network.reaction(name='POM dissolution (no inhibition)',
reactant_pools={'POM': 1.0},
product_pools={'DOM1': 1.0},
rate_constant=0.1,
reactiontype='SOMDECOMP')
simple_network_DOM1 = decomp_network.decomp_network(pools=[POM, DOM, CO2],
reactions=[POM_dissolve])
DOM1_result, DOM1_units = decomp_network.PF_network_writer(
simple_network_DOM1).run_simulation('SOMdecomp_template.txt', 'DOM1',
pflotran_exe)
# Simple decomposition network 2: 1 POM pool, one DOM pool, inhibited by DOM
POM = decomp_network.decomp_pool(name='POM', CN=15, initval=1e3)
DOM = decomp_network.decomp_pool(name='DOM1',
CN=15,
initval=1e-3,
immobile=False)
POM_dissolve_inhib = decomp_network.reaction(
def make_reactions(conc_scales=conc_scales,anox_inhib_conc=anox_inhib_conc,Fe_inhibit_CH4=True,rate_scale=1e-8):
# Turn off inhibition of methanogenesis by Fe+++ by setting inhibition constant very high
if Fe_inhibit_CH4:
Fe_CH4_inhib=1.0
else:
Fe_CH4_inhib=1e10
reactions = [
# decomp_network.reaction(name='Aerobic decomposition',reactant_pools={'cellulose':1.0},product_pools={'HCO3-':1.0},reactiontype='SOMDECOMP',
# rate_constant=0.0,rate_units='1/d',turnover_name='RATE_DECOMPOSITION',
# # inhibition_terms=[decomp_network.inhibition(species='O2(aq)',k=6.25e-8,type='THRESHOLD 1.0d20')]),
# monod_terms=[decomp_network.monod(species='O2(aq)',k=conc_scales['O2(aq)'],threshold=1.1e-9)]),
# From Dave Graham: SOM-C + H2O -> DOM-C
decomp_network.reaction(name='Hydrolysis',stoich='1.0 cellulose -> 1.0 DOM1',reactiontype='SOMDECOMP',
rate_constant=rate_scale,rate_units='y', # Jianqiu Zheng et al., 2019: One third of fermented C is converted to CO2
inhibition_terms=[decomp_network.inhibition(species='DOM1',type='MONOD',k=conc_scales['DOM1']),
# decomp_network.inhibition(species='O2(aq)',k=6.25e-11,type='THRESHOLD -1.0d10')
# decomp_network.inhibition(species='O2(aq)',type='MONOD',k=1e-11),
]),
# Calculating these as per unit carbon, so dividing by the 6 carbons in a glucose
# C6H12O6 + 4 H2O -> 2 CH3COO- + 2 HCO3- + 4 H+ + 4 H2
# Dave Graham: DOM-C + 0.67 H2O -> 0.33 CH3COO- + 0.33 HCO3- + 0.67 H+ + 0.67 H2
# Should it be inhibited by H2?
decomp_network.reaction(name='fermentation',reactant_pools={'DOM1':1/6,'H2O':2/3},product_pools={'Acetate-':1/3,'HCO3-':1/3,'H+':2/3,'H2(aq)':2/3,'Tracer':1/3}, # balancing pH of FeIII release requires an extra 5.5 H+ to be released here
rate_constant=rate_scale*40,reactiontype='MICROBIAL', # Jianqiu Zheng et al., 2019: One third of fermented C is converted to CO2
inhibition_terms=[decomp_network.inhibition(species='O2(aq)',k=anox_inhib_conc,type='MONOD'),decomp_network.inhibition(species='Acetate-',k=conc_scales['Acetate-'],type='MONOD')],
monod_terms=[decomp_network.monod(species='DOM1',k=conc_scales['DOM1'],threshold=1.1e-15)]),
# CH2O + H2O -> CO2 + 4H+ + 4 e-
# O2 + 4H+ + 4 e- -> 2H2O
decomp_network.reaction(name='DOM aerobic respiration',stoich='1.0 DOM1 + 1.0 O2(aq) + 1.0 H2O -> 1.0 HCO3- + 1.0 H+ + 1.0 Tracer',
monod_terms=[decomp_network.monod(species='O2(aq)',k=conc_scales['O2(aq)'],threshold=0.0),decomp_network.monod(species='DOM1',k=conc_scales['DOM1'],threshold=1.1e-16)],
rate_constant=rate_scale*50,reactiontype='MICROBIAL'),
# C2H3O2- + 2 H2O -> 2 CO2 + 7 H+ + 8 e-
# 2 O2 + 8 H+ + 8 e- -> 4 H2O
decomp_network.reaction(name='Acetate aerobic respiration',stoich='1.0 Acetate- + 2.0 O2(aq) -> 2.0 HCO3- + 2.0 H+ + 2.0 Tracer ',
monod_terms=[decomp_network.monod(species='O2(aq)',k=conc_scales['O2(aq)'],threshold=0.0),decomp_network.monod(species='Acetate-',k=conc_scales['Acetate-'],threshold=1.1e-16)],
rate_constant=rate_scale*50,reactiontype='MICROBIAL'),
# C2H3O2- + 2 H2O -> 2 CO2 + 7 H+ + 8 e-
# 8 Fe+++ + 8 e- -> 8 Fe++
decomp_network.reaction(name='Fe(III) reduction',stoich='1.0 Acetate- + 8.0 Fe+++ + 4.0 H2O -> 2.0 HCO3- + 8.0 Fe++ + 9.0 H+ + 2.0 Tracer',
monod_terms=[decomp_network.monod(species='Acetate-',k=conc_scales['Acetate-'],threshold=1.1e-15),decomp_network.monod(species='Fe+++',k=conc_scales['Fe+++'],threshold=1.1e-15)],
inhibition_terms=[decomp_network.inhibition(species='O2(aq)',k=anox_inhib_conc,type='MONOD')],
rate_constant=rate_scale*3,reactiontype='MICROBIAL'),
# Oxidation of Fe++
# Currently assuming backward reaction rate is zero
decomp_network.reaction(name='Fe(II) abiotic oxidation',stoich='1.0 Fe++ + 0.25 O2(aq) + 1.0 H+ <-> 1.0 Fe+++ + 0.5 H2O',
rate_constant=0.0,backward_rate_constant=0.0,reactiontype='GENERAL'),
decomp_network.reaction(name='Fe(II) microbial oxidation',stoich='1.0 Fe++ + 0.25 O2(aq) + 1.0 H+ -> 1.0 Fe+++ + 0.5 H2O',
monod_terms=[decomp_network.monod(species='O2(aq)',k=conc_scales['O2(aq)'],threshold=0.0),decomp_network.monod(species='Fe++',k=conc_scales['Fe++'],threshold=1.1e-15)],
rate_constant=rate_scale*200,reactiontype='MICROBIAL'),
# Acetoclastic methanogenesis
# C2H3O2- + H+ -> CH4 + HCO3- + H+
# pH dependence: Dunfield et al 1992 has some bell curves. Kotsyurbenko et al 2007 has info on different pathways at different pH. Le Mer and Roger 2001 is a big review with a bit on pH thresholds
# See methane_ph.py: Optimization against Kotsyurbenko data yields K_M=5.54 and K_I=5.54 for acetaclastic, and k_M=6.75 for hydrogenotrophic
# Also gives rate constant of hydro = 0.415 that of acetaclastic
decomp_network.reaction(name='Acetaclastic methanogenesis',stoich='1.0 Acetate- + H2O -> 1.0 CH4(aq) + 1.0 HCO3- + 1.0 Tracer',
monod_terms=[decomp_network.monod(species='Acetate-',k=conc_scales['Acetate-'],threshold=1.1e-15),
],
inhibition_terms=[decomp_network.inhibition(species='O2(aq)',k=anox_inhib_conc,type='MONOD'),
decomp_network.inhibition(species='Fe+++',k=conc_scales['Fe+++']*Fe_CH4_inhib,type='MONOD'),
decomp_network.inhibition(species='H+',k=10**-5.54,type='MONOD'),
decomp_network.inhibition(species='H+',k=10**-5.54,type='INVERSE_MONOD')],
rate_constant=rate_scale*2,reactiontype='MICROBIAL'),
# Hydrogenotrophic methanogenesis
decomp_network.reaction(name='Hydrogenotrophic methanogenesis',stoich='4.0 H2(aq) + 1.0 HCO3- + 1.0 H+ -> 1.0 CH4(aq) + 3.0 H2O',
monod_terms=[decomp_network.monod(species='H2(aq)',k=conc_scales['H2(aq)'],threshold=1.1e-15),decomp_network.monod(species='HCO3-',k=conc_scales['HCO3-'],threshold=1.1e-15)],
# inhibition_terms=[decomp_network.inhibition(species='O2(aq)',k=conc_scales['O2(aq)'],type='MONOD'),decomp_network.inhibition(species='Fe+++',k=conc_scales['Fe+++'],type='MONOD')],
inhibition_terms=[decomp_network.inhibition(species='O2(aq)',k=anox_inhib_conc,type='MONOD'),
decomp_network.inhibition(species='Fe+++',k=conc_scales['Fe+++']*Fe_CH4_inhib,type='MONOD'),
decomp_network.inhibition(species='H+',k=10**-6.75,type='MONOD'),
# decomp_network.inhibition(species='NO3-',k=conc_scales['NO3-'],type='MONOD'),
# decomp_network.inhibition(species='SO4--',k=conc_scales['SO4--'],type='MONOD')
],
rate_constant=rate_scale*3*0.32,reactiontype='MICROBIAL'),
# H2 oxidation if oxygen available
decomp_network.reaction(name='Hydrogen oxidation',stoich='2.0 H2(aq) + 1.0 O2(aq) -> 2.0 H2O',
monod_terms=[decomp_network.monod(species='H2(aq)',k=conc_scales['H2(aq)'],threshold=1.1e-15),
decomp_network.monod(species='O2(aq)',k=conc_scales['O2(aq)'],threshold=0.0)],
rate_constant=rate_scale*200,reactiontype='MICROBIAL'),
# Cation exchange
decomp_network.ion_exchange(name='Cation exchange',cations={'Fe++':0.1,'Fe+++':0.3,'Mg++':1.1,'Ca++':4.1,'Na+':1.0,'K+':0.9,'H+':1.1},CEC=2000.0,mineral=None)
]
return reactions