pools = [
decomp_network.decomp_pool(name='SOM',initCN=25,constraints={'initial':1e1},kind='immobile'),
# decomp_network.decomp_pool(name='Lignin',CN=50,constraints={'initial':1e2},kind='immobile'),
decomp_network.decomp_pool(name='HRimm',constraints={'initial':1e-20},kind='immobile'),
decomp_network.decomp_pool(name='DOM1',CN=25,constraints={'initial':1e-15},kind='primary'),
# decomp_network.decomp_pool(name='DOM2',CN=50,constraints={'initial':1e-30},kind='primary'),
decomp_network.decomp_pool(name='H+',kind='primary',constraints={'initial':'6.0 P'}),
decomp_network.decomp_pool(name='O2(aq)',kind='primary',constraints={'initial':'0.2 G O2(g)'}),
decomp_network.decomp_pool(name='HCO3-',kind='primary',constraints={'initial':'400e-6 G CO2(g)'}),
# decomp_network.decomp_pool(name='Mn+++',kind='primary',constraints={'initial':'1.0e-30 M Manganite'}),
# decomp_network.decomp_pool(name='Mn++',kind='primary',constraints={'initial':'1.0e-30'}),
decomp_network.decomp_pool(name='Fe+++',kind='primary',constraints={'initial':'.37e-10 M Fe(OH)3'}),
decomp_network.decomp_pool(name='Fe++',kind='primary',constraints={'initial':'0.37e-15'}),
decomp_network.decomp_pool(name='NH4+',kind='primary',constraints={'initial':1e-5}), # SOMDecomp sandbox requires this
decomp_network.decomp_pool(name='NO3-',kind='primary',constraints={'initial':1e-5}),
decomp_network.decomp_pool(name='SO4--',kind='primary',constraints={'initial':1e-5}),
decomp_network.decomp_pool(name='Tracer',kind='primary',constraints={'initial':1e-15}), # Just to accumulate CO2 loss
decomp_network.decomp_pool(name='CH4(aq)',kind='primary',constraints={'initial':1e-15}),
decomp_network.decomp_pool(name='H2S(aq)',kind='secondary',constraints={'initial':1e-15}),
decomp_network.decomp_pool(name='Acetate-',kind='primary',constraints={'initial':1e-15}),
decomp_network.decomp_pool(name='H2(aq)',kind='primary',constraints={'initial':1e-15}),
decomp_network.decomp_pool(name='N2(aq)',kind='primary',constraints={'initial':1e-15}),
decomp_network.decomp_pool(name='Na+',kind='primary',constraints={'initial':1e-15}),
decomp_network.decomp_pool(name='Cl-',kind='primary',constraints={'initial':1e-15}),
decomp_network.decomp_pool(name='Ca++',kind='primary',constraints={'initial':1e-15}),
decomp_network.decomp_pool(name='HS-',kind='primary',constraints={'initial':1e-15}),
decomp_network.decomp_pool(name='N2O(aq)',kind='primary',constraints={'initial':1e-15}),
decomp_network.decomp_pool(name='CO2(g)',kind='gas'),
decomp_network.decomp_pool(name='O2(g)',kind='gas'),
decomp_network.decomp_pool(name='N2(g)*',kind='gas'),
# decomp_network.decomp_pool(name='N2O(g)',kind='gas'),
decomp_network.decomp_pool(name='CO2(aq)',kind='secondary'),
decomp_network.decomp_pool(name='OH-',kind='secondary'),
# decomp_network.decomp_pool(name='MnO4--',kind='secondary'),
decomp_network.decomp_pool(name='Acetic_acid(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='MnIIIDOM2(aq)',kind='secondary'),
decomp_network.decomp_pool(name='FeIIIDOM1(aq)',kind='secondary'),
decomp_network.decomp_pool(name='FeIIIAcetate(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='NH3(aq)',kind='secondary'),
decomp_network.decomp_pool(name='CO3--',kind='secondary'),
# decomp_network.decomp_pool(name='NH4SO4-',kind='secondary'),
# decomp_network.decomp_pool(name='Urea(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='HSO4-',kind='secondary'),
# decomp_network.decomp_pool(name='H2SO4(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='HNO3(aq) ',kind='secondary'),
# decomp_network.decomp_pool(name='NaNO3(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='NaCl(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='NaSO4-',kind='secondary'),
# decomp_network.decomp_pool(name='NaCO3-',kind='secondary'),
# decomp_network.decomp_pool(name='NaHCO3(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='HCl(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='CaCO3(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='CaCl+',kind='secondary'),
# decomp_network.decomp_pool(name='CaCl2(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='CaHCO3+',kind='secondary'),
# decomp_network.decomp_pool(name='CaSO4(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='CO(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='CO2(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='Acetic_acid(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='S--',kind='secondary'),
# Hui/Beth say pyrolusite probably not precipitating in soils. Look for delta-MnO2? Maybe try 'Mn(OH)2(am)'?
# See Roberts Earth Sci Rev article for some discussion of minerals? More Fe focused though
# decomp_network.decomp_pool(name='Birnessite',rate='0.d-16 mol/m^2-sec',constraints={'initial':'0.0d-5 1.d2 m^2/m^3'},kind='mineral'),
# decomp_network.decomp_pool(name='Mn(OH)2(am)',rate='0.d-16 mol/m^2-sec',constraints={'initial':'0.0d-5 1.d2 m^2/m^3'},kind='mineral'),
# decomp_network.decomp_pool(name='Manganite',rate='1.d-12 mol/m^2-sec',constraints={'initial':'0.0d-5 1.d2 m^2/m^3'},kind='mineral'),
decomp_network.decomp_pool(name='Fe(OH)3',rate='0.d-3 mol/m^2-sec',constraints={'initial':'0.1d-3 1.d2 m^2/m^3'},kind='mineral'),
decomp_network.decomp_pool(name='Pyrite',rate='0.d-3 mol/m^2-sec',constraints={'initial':'0.0d-3 1.d2 m^2/m^3'},kind='mineral'),
decomp_network.decomp_pool(name='Calcite',rate='0.d-3 mol/m^2-sec',constraints={'initial':'0.875d-3 1.d2 m^2/m^3'},kind='mineral'),
decomp_network.decomp_pool(name='Pyrrhotite',rate='0.d-3 mol/m^2-sec',constraints={'initial':'0.0d-3 1.d2 m^2/m^3'},kind='mineral'),
# This is a workaround to allow pH buffering associated with solid substrate (Rock is a placeholder)
# decomp_network.decomp_pool(name='Rock(s)',rate='0.0 mol/m^2-sec',constraints={'initial':'0.5 5.0e3 m^2/m^3'},kind='mineral'),
# decomp_network.decomp_pool(name='>Carboxylate-',kind='surf_complex',mineral='Rock(s)',site_density=0.0e4,complexes=['>Carboxylic_acid']),
decomp_network.decomp_pool(name='H2O',kind='implicit'),
]
import decomp_network
import plot_pf_output
pflotran_exe = '../pflotran-interface/src/pflotran/pflotran'
simlength = 365
pools = [
decomp_network.decomp_pool(name='cellulose',
CN=50,
constraints={'initial': 1e2},
kind='immobile'),
decomp_network.decomp_pool(name='HRimm',
constraints={'initial': 1e-20},
kind='immobile'),
decomp_network.decomp_pool(name='DOM1',
CN=50,
constraints={'initial': 1e-30},
kind='primary'),
decomp_network.decomp_pool(name='H+',
kind='primary',
constraints={'initial': '4.0 P'}),
decomp_network.decomp_pool(name='O2(aq)',
kind='primary',
constraints={'initial': 1e-12}),
decomp_network.decomp_pool(name='HCO3-',
kind='primary',
constraints={'initial': '400e-6 G CO2(g)'}),
decomp_network.decomp_pool(name='Fe+++',
kind='primary',
constraints={'initial': '.37e-3 M Fe(OH)3'}),
import run_alquimia
#I'm not sure why but if you import run_alquimia after decomp_network it gets messed up with some compiler library
import decomp_network
# Importing matplotlib fails if you don't module load anaconda3 first
from matplotlib import pyplot
import numpy
pools = [
decomp_network.decomp_pool(name='SOM',
CN=50,
constraints={'initial': 1e1},
kind='immobile'),
# decomp_network.decomp_pool(name='Lignin',CN=50,constraints={'initial':1e2},kind='immobile'),
decomp_network.decomp_pool(name='HRimm',
constraints={'initial': 1e-20},
kind='immobile'),
decomp_network.decomp_pool(name='DOM1',
CN=50,
constraints={'initial': 1e-15},
kind='primary'),
# decomp_network.decomp_pool(name='DOM2',CN=50,constraints={'initial':1e-30},kind='primary'),
decomp_network.decomp_pool(name='H+',
kind='primary',
constraints={'initial': '6.0 P'}),
decomp_network.decomp_pool(name='O2(aq)',
kind='primary',
constraints={'initial': '0.2 G O2(g)'}),
decomp_network.decomp_pool(name='HCO3-',
kind='primary',
constraints={'initial': '400e-6 G CO2(g)'}),
# decomp_network.decomp_pool(name='Mn+++',kind='primary',constraints={'initial':'1.0e-30 M Manganite'}),
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(
import decomp_network, plot_pf_output
from numpy import *
from matplotlib import pyplot
import matplotlib
pools = [
decomp_network.decomp_pool(name='Cellulose',
CN=50,
constraints={'initial': 5e3 * 0.6},
kind='immobile'),
decomp_network.decomp_pool(name='Lignin',
CN=50,
constraints={'initial': 5e3 * 0.4},
kind='immobile'),
decomp_network.decomp_pool(name='HRimm',
constraints={'initial': 1e-20},
kind='immobile'),
decomp_network.decomp_pool(name='Root_biomass',
constraints={'initial': 1e-20},
kind='immobile'),
decomp_network.decomp_pool(name='DOM1',
CN=50,
constraints={'initial': 1e-30},
kind='primary'),
decomp_network.decomp_pool(name='DOM2',
CN=50,
constraints={'initial': 1e-30},
kind='primary'),
decomp_network.decomp_pool(name='H+',
kind='primary',
constraints={'initial': '5.0 P'}),
pools = [
decomp_network.decomp_pool(name='cellulose',CN=50,constraints={'initial':8e3},kind='immobile'),
decomp_network.decomp_pool(name='HRimm',constraints={'initial':1e-20},kind='immobile'),
decomp_network.decomp_pool(name='DOM1',CN=50,constraints={'initial':0.5e-1},kind='primary'),
decomp_network.decomp_pool(name='H+',kind='primary',constraints={'initial':'5.0 P'}),
decomp_network.decomp_pool(name='O2(aq)',kind='primary',constraints={'initial':'0.2 G O2(g)'}),
decomp_network.decomp_pool(name='HCO3-',kind='primary',constraints={'initial':'400e-6 G CO2(g)'}),
decomp_network.decomp_pool(name='Fe+++',kind='primary',constraints={'initial':'.37e-10 M Fe(OH)3'}),
decomp_network.decomp_pool(name='Fe++',kind='primary',constraints={'initial':'0.37e-3'}),
decomp_network.decomp_pool(name='NH4+',kind='primary',constraints={'initial':1e-15}), # SOMDecomp sandbox requires this
decomp_network.decomp_pool(name='Tracer',kind='primary',constraints={'initial':1e-15}), # Just to accumulate CO2 loss
decomp_network.decomp_pool(name='CH4(aq)',kind='primary',constraints={'initial':1e-15}),
decomp_network.decomp_pool(name='Acetate-',kind='primary',constraints={'initial':1e-15}),
decomp_network.decomp_pool(name='H2(aq)',kind='primary',constraints={'initial':1e-15}),
decomp_network.decomp_pool(name='Mg++',kind='primary',constraints={'initial':0.5e-3}),
decomp_network.decomp_pool(name='Ca++',kind='primary',constraints={'initial':0.5e-3}),
decomp_network.decomp_pool(name='Na+',kind='primary',constraints={'initial':2e-3}),
decomp_network.decomp_pool(name='K+',kind='primary',constraints={'initial':2e-5}),
decomp_network.decomp_pool(name='CO2(g)',kind='gas'),
decomp_network.decomp_pool(name='O2(g)',kind='gas'),
decomp_network.decomp_pool(name='CO2(aq)',kind='secondary'),
decomp_network.decomp_pool(name='OH-',kind='secondary'),
decomp_network.decomp_pool(name='FeCO3+',kind='secondary'),
decomp_network.decomp_pool(name='Fe(OH)4-',kind='secondary'),
decomp_network.decomp_pool(name='Acetic_acid(aq)',kind='secondary'),
decomp_network.decomp_pool(name='FeCH3COO+',kind='secondary'),
decomp_network.decomp_pool(name='FeIIIDOM1(aq)',kind='secondary'),
decomp_network.decomp_pool(name='FeIIDOM1(aq)',kind='secondary'),
decomp_network.decomp_pool(name='FeIIIAcetate(aq)',kind='secondary'),
decomp_network.decomp_pool(name='Fe(OH)2(aq)',kind='secondary'),
# decomp_network.decomp_pool(name='Fe(OH)2+',kind='secondary'),
decomp_network.decomp_pool(name='FeCO3(aq)',kind='secondary'),
decomp_network.decomp_pool(name='CO3--',kind='secondary'),
decomp_network.decomp_pool(name='CaHCO3+',kind='secondary'),
# See Roberts Earth Sci Rev article for discussion of iron minerals, including some time scales
decomp_network.decomp_pool(name='Fe(OH)3',rate='1.d-6 mol/m^2-sec',constraints={'initial':'0.875d-3 1.d2 m^2/m^3'},kind='mineral'),
# decomp_network.decomp_pool(name='Goethite',rate='1.d-5 mol/m^2-sec',constraints={'initial':'1.75d-2 1.d1 m^2/m^3'},kind='mineral'),
# decomp_network.decomp_pool(name='Fe',rate='1.d-7 mol/m^2-sec',constraints={'initial':'1.0e-6 1. m^2/m^3'},kind='mineral'),
decomp_network.decomp_pool(name='Fe(OH)2',rate='1.d-7 mol/m^2-sec',constraints={'initial':'0.0e-20 1.d2 m^2/m^3'},kind='mineral'),
decomp_network.decomp_pool(name='Rock(s)',rate='0.0 mol/m^2-sec',constraints={'initial':'0.5 5.0e3 m^2/m^3'},kind='mineral'),
# decomp_network.decomp_pool(name='Calcite',rate='1.d-3 mol/m^2-sec',constraints={'initial':'0.0d-3 1.d2 m^2/m^3'},kind='mineral'),
# Maybe this should be a cation exchange reaction instead?
# Probably makes sense to include both
# There should be some Fe(II) sorption or complexation with OM
decomp_network.decomp_pool(name='>Carboxylate-',kind='surf_complex',mineral='Rock(s)',site_density=2000.0*5.0,complexes=['>Carboxylic_acid']), # site density in mol/m3
decomp_network.decomp_pool(name='H2O',kind='implicit'),
]