1D Pyrite Oxidation with from_mf6¶
This is the same Appelo et al. (1998) pyrite-oxidation column as the
previous tutorial, solved with the transport-first
:meth:~mf6rtm.mup3d.base.Mup3d.from_mf6 workflow instead of the classic one.
Rather than building one transport model per component yourself, you build an
ordinary MODFLOW 6 flow model plus a single conservative tracer transport
model, then hand it to from_mf6, which clones that tracer model into one
reactive model per PHREEQC component. The inflow chemistry is switched per
stress period (dilute in period 0, oxidising in period 1) with a single
ChemStress('wel', type='aux').set_spd({0: [2], 1: [3]}) call.
import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import flopy
from mf6rtm import utils, mup3d
BASE = "." if os.path.isdir("data") else os.path.join("docs", "tutorials")
DATA = os.path.join(BASE, "data")
1. Discretization and flow¶
Identical column to the classic tutorial: 5.3 cm in 16 cells, two stress
periods (dilute then oxidising flush). The injection well carries a single
tracer auxiliary; from_mf6 replaces it with one aux column per
component at write_simulation().
length_units = "meters"
time_units = "days"
nlay, nrow, ncol = 1, 1, 16
Lx = 0.053
delr = Lx / ncol
delc = 1.0
top = 2.87433e-03
botm = np.linspace(top, 0.0, nlay + 1)[1:]
k11 = 1.0
prsity = 0.376
dispersivity = 0.00537
q = 2.4e-4 # injection rate (m3/d)
nper = 2
nstp = [64, 100]
perlen = [0.9333, 1.45833]
tdis_rc = [(pl, ns, 1.0) for pl, ns in zip(perlen, nstp)]
# WEL carries a single 'tracer' aux (placeholder 1.0) in both periods
wel_spd = {kper: [[(0, 0, 0), q, 1.0]] for kper in range(nper)}
chdspd = [[(0, 0, ncol - 1), 1.0]]
2. Build the flow + tracer transport model¶
A GWF flow model plus one conservative tracer GWT whose SSM sources the
well tracer auxiliary. This is the ordinary MODFLOW 6 model you would
build for conservative transport — from_mf6 takes it from here.
sim_ws = os.path.join(BASE, "_tutorial03_run")
sim = flopy.mf6.MFSimulation(sim_name="pyrite_from_mf6", sim_ws=sim_ws, exe_name="mf6")
flopy.mf6.ModflowTdis(sim, nper=nper, perioddata=tdis_rc, time_units=time_units)
# --- GWF ---
gwf = flopy.mf6.ModflowGwf(sim, modelname="gwf", save_flows=True)
imsgwf = flopy.mf6.ModflowIms(sim, complexity="complex", linear_acceleration="CG",
filename="gwf.ims")
sim.register_ims_package(imsgwf, ["gwf"])
flopy.mf6.ModflowGwfdis(gwf, length_units=length_units, nlay=nlay, nrow=nrow, ncol=ncol,
delr=delr, delc=delc, top=top, botm=botm, filename="gwf.dis")
flopy.mf6.ModflowGwfnpf(gwf, save_specific_discharge=True, save_saturation=True,
icelltype=1, k=k11, filename="gwf.npf")
flopy.mf6.ModflowGwfic(gwf, strt=1.0, filename="gwf.ic")
flopy.mf6.ModflowGwfwel(gwf, stress_period_data=wel_spd, auxiliary=["tracer"],
pname="wel", filename="gwf.wel")
flopy.mf6.ModflowGwfchd(gwf, stress_period_data=chdspd, pname="chd", filename="gwf.chd")
flopy.mf6.ModflowGwfoc(gwf, head_filerecord="gwf.hds", budget_filerecord="gwf.cbb",
saverecord=[("HEAD", "ALL"), ("BUDGET", "ALL")])
# --- single conservative tracer GWT (the from_mf6 template) ---
gwt = flopy.mf6.ModflowGwt(sim, modelname="tracer")
imsgwt = flopy.mf6.ModflowIms(sim, linear_acceleration="BICGSTAB", filename="tracer.ims")
sim.register_ims_package(imsgwt, ["tracer"])
flopy.mf6.ModflowGwtdis(gwt, length_units=length_units, nlay=nlay, nrow=nrow, ncol=ncol,
delr=delr, delc=delc, top=top, botm=botm, filename="tracer.dis")
flopy.mf6.ModflowGwtic(gwt, strt=0.0, filename="tracer.ic")
flopy.mf6.ModflowGwtssm(gwt, sources=[["wel", "aux", "tracer"]], filename="tracer.ssm")
flopy.mf6.ModflowGwtadv(gwt, scheme="tvd")
flopy.mf6.ModflowGwtdsp(gwt, xt3d_off=True, alh=dispersivity, ath1=dispersivity * 0.1,
filename="tracer.dsp")
flopy.mf6.ModflowGwtmst(gwt, porosity=prsity, filename="tracer.mst")
flopy.mf6.ModflowGwtoc(gwt, concentration_filerecord="tracer.ucn",
saverecord=[("CONCENTRATION", "ALL")])
flopy.mf6.ModflowGwfgwt(sim, exgtype="GWF6-GWT6", exgmnamea="gwf", exgmnameb="tracer",
filename="tracer.gwfgwt")
package_name = tracer.gwfgwt
filename = tracer.gwfgwt
package_type = gwfgwt
model_or_simulation_package = simulation
simulation_name = pyrite_from_mf6
3. Geochemistry — the pyrite reaction network¶
The chemistry is identical to the classic tutorial (the mup3d classes are
workflow-agnostic): initial pore water (Solutions), four-zone cation
ExchangePhases, kinetic pyrite + organic matter (KineticPhases),
calcite (EquilibriumPhases) and surface complexation (Surfaces).
solutionsdf = pd.read_csv(os.path.join(DATA, "tut02_solutions.csv"),
comment="#", index_col=0)
solution = mup3d.Solutions(utils.solution_df_to_dict(solutionsdf))
solution.set_ic(np.ones((nlay, nrow, ncol), dtype=float))
# cation exchanger with four spatial zones
excdf = pd.read_csv(os.path.join(DATA, "tut02_exchange.csv"), comment="#", index_col=0)
excdf.columns = [0, 1, 2, 3]
exchanger_dict = excdf.to_dict()
for _z, subdict in exchanger_dict.items():
for key in subdict:
subdict[key] = {"m0": subdict[key]}
exchanger = mup3d.ExchangePhases(exchanger_dict)
exchanger_ic = np.ones((nlay, nrow, ncol), dtype=float)
exchanger_ic[0, 0, :4] = 1
exchanger_ic[0, 0, 4:8] = 2
exchanger_ic[0, 0, 8:12] = 3
exchanger_ic[0, 0, 12:] = 4
exchanger.set_ic(exchanger_ic)
exchanger.set_equilibrate_solutions([1, 1, 1, 1])
# kinetic pyrite + organic matter
kin_df = pd.read_csv(os.path.join(DATA, "tut02_kinetic_phases.csv"))
kin_phases = utils.parse_kinetics_dataframe(kin_df)
kin_phases[1]["Orgc_sed"]["formula"] = "Orgc_sed -1.0 C 1.0"
kinetics = mup3d.KineticPhases(kin_phases)
kinetics.set_ic(1)
# equilibrium phases + surfaces
eqp_df = pd.read_csv(os.path.join(DATA, "tut02_equilibrium_phases.csv"))
equilibriums = mup3d.EquilibriumPhases(utils.parse_equilibriums_dataframe(eqp_df))
equilibriums.set_ic(1)
surfaces = mup3d.Surfaces(utils.surfaces_csv_to_dict(
os.path.join(DATA, "tut02_surfaces.csv")))
surfaces.set_ic(1)
4. Couple with from_mf6 and set the per-period inflow¶
from_mf6 reads the grid from the GWF model and stores the tracer GWT as
the template to clone. The inflow well switches solution by stress period
via a dict: solution 2 (dilute) in period 0, solution 3 (oxidising) in period 1.
model = mup3d.Mup3d.from_mf6(sim, solution, name="pyrite_from_mf6", gwt_name="tracer")
model.set_wd(sim_ws)
model.set_database(os.path.join(DATA, "tut02_datab.dat"))
model.set_initial_temp([7.0, 7.0, 7.0])
model.set_postfix(os.path.join(DATA, "tut02_postfix.phqr"))
model.set_exchange_phases(exchanger)
model.set_phases(kinetics)
model.set_phases(equilibriums)
model.set_phases(surfaces)
model.initialize()
wellchem = mup3d.ChemStress("wel", type="aux")
wellchem.set_spd({0: [2], 1: [3]}) # period 0 -> solution 2, period 1 -> solution 3
model.set_chem_stress(wellchem)
Using temperatue of 7.0 from SOLUTION 1 for all cells
MF6RTM will run with the following configuration:
Reactive: True
Reaction timing: all
External files flag: False
Emulator flag: False
Min concentration: None (no clipping)
Reactions calculated at all time steps
Phreeqc initialized
Initializing ChemStress
ChemStress wel initialized
5. Write and run¶
model.write_simulation()
# Stage the platform's MODFLOW 6 binaries into the run directory (pixi fetches
# them into ``benchmark/bin``) so the solver finds libmf6 locally.
utils.prep_bins(model.wd, src_path=os.path.join(BASE, "..", "..", "benchmark", "bin"))
model.run()
writing simulation...
writing simulation name file...
writing simulation tdis package...
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INFORMATION: maxbound in ('gwf6', 'wel', 'dimensions') changed to 1 based on size of stress_period_data
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INFORMATION: maxbound in ('gwf6', 'chd', 'dimensions') changed to 1 based on size of stress_period_data
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MF6RTM will run with the following configuration:
Reactive: True
Reaction timing: all
External files flag: False
Emulator flag: False
Min concentration: None (no clipping)
Reactions calculated at all time steps
Simulation saved in /Users/portega/dev/code/mf6rtm/mf6rtm-main/docs/tutorials/_tutorial03_run
Running mf6rtm
Using libmf6 found in model directory: libmf6.dylib
Processing initial chemistry configuration
Starting Solution at 2026-07-20 15:57:09
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Reactions | Stress period: 2 | Time step: 10 | Completed in : 0 min 3.28e-04 sec
Transport | Stress period: 2 | Time step: 11 | Completed in : 0 min 1.40e-06 sec
Reactions | Stress period: 2 | Time step: 11 | Completed in : 0 min 3.33e-04 sec
Transport | Stress period: 2 | Time step: 12 | Completed in : 0 min 1.63e-06 sec
Reactions | Stress period: 2 | Time step: 12 | Completed in : 0 min 3.43e-04 sec
Transport | Stress period: 2 | Time step: 13 | Completed in : 0 min 1.52e-06 sec
Reactions | Stress period: 2 | Time step: 13 | Completed in : 0 min 3.35e-04 sec
Transport | Stress period: 2 | Time step: 14 | Completed in : 0 min 1.55e-06 sec
Reactions | Stress period: 2 | Time step: 14 | Completed in : 0 min 3.43e-04 sec
Transport | Stress period: 2 | Time step: 15 | Completed in : 0 min 1.55e-06 sec
Reactions | Stress period: 2 | Time step: 15 | Completed in : 0 min 3.49e-04 sec
Transport | Stress period: 2 | Time step: 16 | Completed in : 0 min 1.38e-06 sec
Reactions | Stress period: 2 | Time step: 16 | Completed in : 0 min 3.43e-04 sec
Transport | Stress period: 2 | Time step: 17 | Completed in : 0 min 1.53e-06 sec
Reactions | Stress period: 2 | Time step: 17 | Completed in : 0 min 3.54e-04 sec
Transport | Stress period: 2 | Time step: 18 | Completed in : 0 min 1.38e-06 sec
Reactions | Stress period: 2 | Time step: 18 | Completed in : 0 min 3.56e-04 sec
Transport | Stress period: 2 | Time step: 19 | Completed in : 0 min 1.43e-06 sec
Reactions | Stress period: 2 | Time step: 19 | Completed in : 0 min 3.62e-04 sec
Transport | Stress period: 2 | Time step: 20 | Completed in : 0 min 1.55e-06 sec
Reactions | Stress period: 2 | Time step: 20 | Completed in : 0 min 3.68e-04 sec
Transport | Stress period: 2 | Time step: 21 | Completed in : 0 min 1.58e-06 sec
Reactions | Stress period: 2 | Time step: 21 | Completed in : 0 min 3.75e-04 sec
Transport | Stress period: 2 | Time step: 22 | Completed in : 0 min 1.55e-06 sec
Reactions | Stress period: 2 | Time step: 22 | Completed in : 0 min 3.68e-04 sec
Transport | Stress period: 2 | Time step: 23 | Completed in : 0 min 1.60e-06 sec
Reactions | Stress period: 2 | Time step: 23 | Completed in : 0 min 3.82e-04 sec
Transport | Stress period: 2 | Time step: 24 | Completed in : 0 min 1.38e-06 sec
Reactions | Stress period: 2 | Time step: 24 | Completed in : 0 min 3.78e-04 sec
Transport | Stress period: 2 | Time step: 25 | Completed in : 0 min 1.57e-06 sec
Reactions | Stress period: 2 | Time step: 25 | Completed in : 0 min 3.80e-04 sec
Transport | Stress period: 2 | Time step: 26 | Completed in : 0 min 1.38e-06 sec
Reactions | Stress period: 2 | Time step: 26 | Completed in : 0 min 3.82e-04 sec
Transport | Stress period: 2 | Time step: 27 | Completed in : 0 min 1.53e-06 sec
Reactions | Stress period: 2 | Time step: 27 | Completed in : 0 min 3.95e-04 sec
Transport | Stress period: 2 | Time step: 28 | Completed in : 0 min 1.53e-06 sec
Reactions | Stress period: 2 | Time step: 28 | Completed in : 0 min 4.04e-04 sec
Transport | Stress period: 2 | Time step: 29 | Completed in : 0 min 1.53e-06 sec
Reactions | Stress period: 2 | Time step: 29 | Completed in : 0 min 3.77e-04 sec
Transport | Stress period: 2 | Time step: 30 | Completed in : 0 min 1.58e-06 sec
Reactions | Stress period: 2 | Time step: 30 | Completed in : 0 min 3.99e-04 sec
Transport | Stress period: 2 | Time step: 31 | Completed in : 0 min 1.45e-06 sec
WARNING: Negative moles in solution 0 for C, -6.066502e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.395885e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -2.248613e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -3.173225e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -4.178225e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -4.755068e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -5.094314e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -5.460239e-04. Recovering...
Reactions | Stress period: 2 | Time step: 31 | Completed in : 0 min 4.04e-04 sec
Transport | Stress period: 2 | Time step: 32 | Completed in : 0 min 1.43e-06 sec
Reactions | Stress period: 2 | Time step: 32 | Completed in : 0 min 3.93e-04 sec
Transport | Stress period: 2 | Time step: 33 | Completed in : 0 min 1.42e-06 sec
Reactions | Stress period: 2 | Time step: 33 | Completed in : 0 min 3.93e-04 sec
Transport | Stress period: 2 | Time step: 34 | Completed in : 0 min 1.55e-06 sec
Reactions | Stress period: 2 | Time step: 34 | Completed in : 0 min 4.00e-04 sec
Transport | Stress period: 2 | Time step: 35 | Completed in : 0 min 1.18e-06 sec
Reactions | Stress period: 2 | Time step: 35 | Completed in : 0 min 4.09e-04 sec
Transport | Stress period: 2 | Time step: 36 | Completed in : 0 min 1.10e-06 sec
Reactions | Stress period: 2 | Time step: 36 | Completed in : 0 min 4.24e-04 sec
Transport | Stress period: 2 | Time step: 37 | Completed in : 0 min 1.15e-06 sec
Reactions | Stress period: 2 | Time step: 37 | Completed in : 0 min 4.35e-04 sec
Transport | Stress period: 2 | Time step: 38 | Completed in : 0 min 1.20e-06 sec
WARNING: Negative moles in solution 0 for C, -5.853989e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -6.275973e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -6.727258e-04. Recovering...
WARNING: Negative moles in solution 1 for C, -2.959380e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -7.208024e-04. Recovering...
WARNING: Negative moles in solution 1 for C, -9.737805e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -7.717981e-04. Recovering...
WARNING: Negative moles in solution 1 for C, -1.695636e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -8.256428e-04. Recovering...
WARNING: Negative moles in solution 1 for C, -2.466088e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -8.822197e-04. Recovering...
WARNING: Negative moles in solution 1 for C, -3.289608e-04. Recovering...
Reactions | Stress period: 2 | Time step: 38 | Completed in : 0 min 4.32e-04 sec
Transport | Stress period: 2 | Time step: 39 | Completed in : 0 min 1.05e-06 sec
Reactions | Stress period: 2 | Time step: 39 | Completed in : 0 min 4.03e-04 sec
Transport | Stress period: 2 | Time step: 40 | Completed in : 0 min 1.07e-06 sec
Reactions | Stress period: 2 | Time step: 40 | Completed in : 0 min 4.04e-04 sec
Transport | Stress period: 2 | Time step: 41 | Completed in : 0 min 1.18e-06 sec
Reactions | Stress period: 2 | Time step: 41 | Completed in : 0 min 4.17e-04 sec
Transport | Stress period: 2 | Time step: 42 | Completed in : 0 min 1.23e-06 sec
Reactions | Stress period: 2 | Time step: 42 | Completed in : 0 min 4.42e-04 sec
Transport | Stress period: 2 | Time step: 43 | Completed in : 0 min 1.32e-06 sec
Reactions | Stress period: 2 | Time step: 43 | Completed in : 0 min 4.30e-04 sec
Transport | Stress period: 2 | Time step: 44 | Completed in : 0 min 1.07e-06 sec
Reactions | Stress period: 2 | Time step: 44 | Completed in : 0 min 4.49e-04 sec
Transport | Stress period: 2 | Time step: 45 | Completed in : 0 min 1.20e-06 sec
WARNING: Negative moles in solution 0 for C, -9.413629e-04. Recovering...
WARNING: Negative moles in solution 1 for C, -3.981689e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.002855e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -4.231929e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.066335e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -4.496478e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.131843e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -4.774188e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.198682e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -5.067931e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.251013e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -5.374682e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.296184e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -5.693735e-04. Recovering...
WARNING: Negative moles in solution 2 for C, -7.767535e-06. Recovering...
WARNING: Negative moles in solution 0 for C, -1.341181e-03. Recovering...
Reactions | Stress period: 2 | Time step: 45 | Completed in : 0 min 4.56e-04 sec
Transport | Stress period: 2 | Time step: 46 | Completed in : 0 min 1.20e-06 sec
Reactions | Stress period: 2 | Time step: 46 | Completed in : 0 min 4.40e-04 sec
Transport | Stress period: 2 | Time step: 47 | Completed in : 0 min 1.17e-06 sec
Reactions | Stress period: 2 | Time step: 47 | Completed in : 0 min 4.63e-04 sec
Transport | Stress period: 2 | Time step: 48 | Completed in : 0 min 1.20e-06 sec
Reactions | Stress period: 2 | Time step: 48 | Completed in : 0 min 4.73e-04 sec
Transport | Stress period: 2 | Time step: 49 | Completed in : 0 min 1.22e-06 sec
Reactions | Stress period: 2 | Time step: 49 | Completed in : 0 min 4.90e-04 sec
Transport | Stress period: 2 | Time step: 50 | Completed in : 0 min 1.15e-06 sec
Reactions | Stress period: 2 | Time step: 50 | Completed in : 0 min 4.67e-04 sec
Transport | Stress period: 2 | Time step: 51 | Completed in : 0 min 1.07e-06 sec
Reactions | Stress period: 2 | Time step: 51 | Completed in : 0 min 4.86e-04 sec
Transport | Stress period: 2 | Time step: 52 | Completed in : 0 min 1.07e-06 sec
WARNING: Negative moles in solution 1 for C, -6.024443e-04. Recovering...
WARNING: Negative moles in solution 2 for C, -6.243593e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.385677e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -6.365850e-04. Recovering...
WARNING: Negative moles in solution 2 for C, -1.190085e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.429382e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -6.716911e-04. Recovering...
WARNING: Negative moles in solution 2 for C, -1.775235e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.472024e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -7.076298e-04. Recovering...
WARNING: Negative moles in solution 2 for C, -2.379699e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.513359e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -7.442710e-04. Recovering...
WARNING: Negative moles in solution 2 for C, -3.002754e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.553170e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -7.814825e-04. Recovering...
WARNING: Negative moles in solution 2 for C, -3.383371e-04. Recovering...
Reactions | Stress period: 2 | Time step: 52 | Completed in : 0 min 4.90e-04 sec
Transport | Stress period: 2 | Time step: 53 | Completed in : 0 min 1.07e-06 sec
Reactions | Stress period: 2 | Time step: 53 | Completed in : 0 min 4.93e-04 sec
Transport | Stress period: 2 | Time step: 54 | Completed in : 0 min 1.18e-06 sec
Reactions | Stress period: 2 | Time step: 54 | Completed in : 0 min 4.95e-04 sec
Transport | Stress period: 2 | Time step: 55 | Completed in : 0 min 1.07e-06 sec
Reactions | Stress period: 2 | Time step: 55 | Completed in : 0 min 5.10e-04 sec
Transport | Stress period: 2 | Time step: 56 | Completed in : 0 min 1.07e-06 sec
Reactions | Stress period: 2 | Time step: 56 | Completed in : 0 min 5.13e-04 sec
Transport | Stress period: 2 | Time step: 57 | Completed in : 0 min 1.20e-06 sec
Reactions | Stress period: 2 | Time step: 57 | Completed in : 0 min 5.16e-04 sec
Transport | Stress period: 2 | Time step: 58 | Completed in : 0 min 1.22e-06 sec
WARNING: Negative moles in solution 0 for C, -1.591256e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -8.191042e-04. Recovering...
WARNING: Negative moles in solution 2 for C, -3.532809e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.627459e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -8.569765e-04. Recovering...
WARNING: Negative moles in solution 2 for C, -3.681708e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.661674e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -8.949940e-04. Recovering...
WARNING: Negative moles in solution 2 for C, -3.829498e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.693797e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -9.330035e-04. Recovering...
WARNING: Negative moles in solution 2 for C, -3.975217e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.723755e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -9.708490e-04. Recovering...
WARNING: Negative moles in solution 2 for C, -4.117902e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -7.917385e-07. Recovering...
WARNING: Negative moles in solution 0 for C, -1.751501e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.008375e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -4.256649e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -4.349669e-05. Recovering...
Reactions | Stress period: 2 | Time step: 58 | Completed in : 0 min 5.53e-04 sec
Transport | Stress period: 2 | Time step: 59 | Completed in : 0 min 1.08e-06 sec
Reactions | Stress period: 2 | Time step: 59 | Completed in : 0 min 5.43e-04 sec
Transport | Stress period: 2 | Time step: 60 | Completed in : 0 min 1.20e-06 sec
Reactions | Stress period: 2 | Time step: 60 | Completed in : 0 min 5.48e-04 sec
Transport | Stress period: 2 | Time step: 61 | Completed in : 0 min 1.15e-06 sec
Reactions | Stress period: 2 | Time step: 61 | Completed in : 0 min 5.36e-04 sec
Transport | Stress period: 2 | Time step: 62 | Completed in : 0 min 1.07e-06 sec
Reactions | Stress period: 2 | Time step: 62 | Completed in : 0 min 5.33e-04 sec
Transport | Stress period: 2 | Time step: 63 | Completed in : 0 min 1.20e-06 sec
Reactions | Stress period: 2 | Time step: 63 | Completed in : 0 min 5.39e-04 sec
Transport | Stress period: 2 | Time step: 64 | Completed in : 0 min 1.23e-06 sec
WARNING: Negative moles in solution 0 for C, -1.777012e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.045425e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -4.390627e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -8.651190e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.800288e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.081847e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -4.519149e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.296530e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.821348e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.117496e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -4.641610e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.726836e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.840229e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.152230e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -4.757788e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.153082e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.856981e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.185914e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -4.867375e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.571838e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.871666e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.218442e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -4.970439e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.838065e-04. Recovering...
Reactions | Stress period: 2 | Time step: 64 | Completed in : 0 min 5.38e-04 sec
Transport | Stress period: 2 | Time step: 65 | Completed in : 0 min 1.07e-06 sec
Reactions | Stress period: 2 | Time step: 65 | Completed in : 0 min 5.64e-04 sec
Transport | Stress period: 2 | Time step: 66 | Completed in : 0 min 1.20e-06 sec
Reactions | Stress period: 2 | Time step: 66 | Completed in : 0 min 5.50e-04 sec
Transport | Stress period: 2 | Time step: 67 | Completed in : 0 min 1.20e-06 sec
Reactions | Stress period: 2 | Time step: 67 | Completed in : 0 min 5.59e-04 sec
Transport | Stress period: 2 | Time step: 68 | Completed in : 0 min 1.22e-06 sec
Reactions | Stress period: 2 | Time step: 68 | Completed in : 0 min 5.65e-04 sec
Transport | Stress period: 2 | Time step: 69 | Completed in : 0 min 1.07e-06 sec
Reactions | Stress period: 2 | Time step: 69 | Completed in : 0 min 5.61e-04 sec
Transport | Stress period: 2 | Time step: 70 | Completed in : 0 min 1.25e-06 sec
WARNING: Negative moles in solution 0 for C, -1.884353e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.249678e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.066971e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.900178e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.895127e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.279544e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.157477e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.953044e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.904078e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.307972e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.242745e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.995702e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.911295e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.332549e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.323620e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -3.027038e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.916871e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.345627e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.400727e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -3.046027e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.781302e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.920895e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.357542e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.474631e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -3.051752e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -6.277435e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.923455e-03. Recovering...
Reactions | Stress period: 2 | Time step: 70 | Completed in : 0 min 5.75e-04 sec
Transport | Stress period: 2 | Time step: 71 | Completed in : 0 min 1.18e-06 sec
Reactions | Stress period: 2 | Time step: 71 | Completed in : 0 min 5.96e-04 sec
Transport | Stress period: 2 | Time step: 72 | Completed in : 0 min 1.22e-06 sec
Reactions | Stress period: 2 | Time step: 72 | Completed in : 0 min 5.88e-04 sec
Transport | Stress period: 2 | Time step: 73 | Completed in : 0 min 1.37e-06 sec
Reactions | Stress period: 2 | Time step: 73 | Completed in : 0 min 5.80e-04 sec
Transport | Stress period: 2 | Time step: 74 | Completed in : 0 min 1.07e-06 sec
Reactions | Stress period: 2 | Time step: 74 | Completed in : 0 min 5.77e-04 sec
Transport | Stress period: 2 | Time step: 75 | Completed in : 0 min 8.17e-07 sec
Reactions | Stress period: 2 | Time step: 75 | Completed in : 0 min 5.97e-04 sec
Transport | Stress period: 2 | Time step: 76 | Completed in : 0 min 8.33e-07 sec
WARNING: Negative moles in solution 1 for C, -1.368279e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.545419e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -3.043289e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -9.714935e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.924645e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.377856e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.615227e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -3.020644e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -1.306676e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.924548e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.386268e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.684006e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.983388e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -1.629756e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.923252e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.393531e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.752340e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.931602e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -1.936797e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.920839e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.399666e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.820730e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.865668e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.223507e-04. Recovering...
Reactions | Stress period: 2 | Time step: 76 | Completed in : 0 min 6.08e-04 sec
Transport | Stress period: 2 | Time step: 77 | Completed in : 0 min 7.33e-07 sec
Reactions | Stress period: 2 | Time step: 77 | Completed in : 0 min 6.09e-04 sec
Transport | Stress period: 2 | Time step: 78 | Completed in : 0 min 7.33e-07 sec
Reactions | Stress period: 2 | Time step: 78 | Completed in : 0 min 6.34e-04 sec
Transport | Stress period: 2 | Time step: 79 | Completed in : 0 min 8.33e-07 sec
Reactions | Stress period: 2 | Time step: 79 | Completed in : 0 min 6.21e-04 sec
Transport | Stress period: 2 | Time step: 80 | Completed in : 0 min 8.17e-07 sec
Reactions | Stress period: 2 | Time step: 80 | Completed in : 0 min 6.31e-04 sec
Transport | Stress period: 2 | Time step: 81 | Completed in : 0 min 7.33e-07 sec
WARNING: Negative moles in solution 0 for C, -1.917391e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.404704e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.889441e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.786339e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.485168e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.912982e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.408669e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.958766e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.694334e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.506400e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.907689e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.411608e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.028729e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.591073e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.507099e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.901588e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.413565e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.099419e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.478333e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.493873e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.537755e-06. Recovering...
WARNING: Negative moles in solution 0 for C, -1.894745e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.414583e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.170657e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.357656e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.465849e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -3.102858e-05. Recovering...
Reactions | Stress period: 2 | Time step: 81 | Completed in : 0 min 6.32e-04 sec
Transport | Stress period: 2 | Time step: 82 | Completed in : 0 min 7.50e-07 sec
Reactions | Stress period: 2 | Time step: 82 | Completed in : 0 min 6.48e-04 sec
Transport | Stress period: 2 | Time step: 83 | Completed in : 0 min 8.50e-07 sec
Reactions | Stress period: 2 | Time step: 83 | Completed in : 0 min 6.60e-04 sec
Transport | Stress period: 2 | Time step: 84 | Completed in : 0 min 8.33e-07 sec
Reactions | Stress period: 2 | Time step: 84 | Completed in : 0 min 6.37e-04 sec
Transport | Stress period: 2 | Time step: 85 | Completed in : 0 min 9.33e-07 sec
Reactions | Stress period: 2 | Time step: 85 | Completed in : 0 min 6.30e-04 sec
Transport | Stress period: 2 | Time step: 86 | Completed in : 0 min 8.00e-07 sec
WARNING: Negative moles in solution 0 for C, -1.887223e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.414709e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.242193e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.230997e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.421899e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -5.969475e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.879061e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.413923e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.313462e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.100569e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.361514e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -8.725795e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.870324e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.412324e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.384676e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.967483e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.283840e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.134055e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.861072e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.409968e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.455436e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.833901e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.188325e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.377782e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.851356e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.406888e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.525114e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.701671e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.075008e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.599823e-04. Recovering...
Reactions | Stress period: 2 | Time step: 86 | Completed in : 0 min 6.47e-04 sec
Transport | Stress period: 2 | Time step: 87 | Completed in : 0 min 8.00e-07 sec
Reactions | Stress period: 2 | Time step: 87 | Completed in : 0 min 6.34e-04 sec
Transport | Stress period: 2 | Time step: 88 | Completed in : 0 min 8.83e-07 sec
Reactions | Stress period: 2 | Time step: 88 | Completed in : 0 min 6.37e-04 sec
Transport | Stress period: 2 | Time step: 89 | Completed in : 0 min 8.50e-07 sec
Reactions | Stress period: 2 | Time step: 89 | Completed in : 0 min 6.49e-04 sec
Transport | Stress period: 2 | Time step: 90 | Completed in : 0 min 7.33e-07 sec
Reactions | Stress period: 2 | Time step: 90 | Completed in : 0 min 6.53e-04 sec
Transport | Stress period: 2 | Time step: 91 | Completed in : 0 min 8.33e-07 sec
WARNING: Negative moles in solution 0 for C, -1.841223e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.403126e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.593512e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.572555e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -1.944132e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.795794e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.830723e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.398741e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.660185e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.448025e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -1.796217e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.960986e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.819900e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.393779e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.724548e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.329529e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -1.632153e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -2.090524e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.808793e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.388281e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.786651e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.218284e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -1.453076e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -2.153088e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.797439e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.382288e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.845962e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.115014e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -9.767394e-05. Recovering...
WARNING: Negative moles in solution 5 for C, -2.109213e-04. Recovering...
WARNING: Negative moles in solution 6 for C, -2.544422e-06. Recovering...
Reactions | Stress period: 2 | Time step: 91 | Completed in : 0 min 6.80e-04 sec
Transport | Stress period: 2 | Time step: 92 | Completed in : 0 min 7.67e-07 sec
Reactions | Stress period: 2 | Time step: 92 | Completed in : 0 min 6.75e-04 sec
Transport | Stress period: 2 | Time step: 93 | Completed in : 0 min 7.67e-07 sec
Reactions | Stress period: 2 | Time step: 93 | Completed in : 0 min 6.74e-04 sec
Transport | Stress period: 2 | Time step: 94 | Completed in : 0 min 8.67e-07 sec
Reactions | Stress period: 2 | Time step: 94 | Completed in : 0 min 6.56e-04 sec
Transport | Stress period: 2 | Time step: 95 | Completed in : 0 min 7.33e-07 sec
Reactions | Stress period: 2 | Time step: 95 | Completed in : 0 min 6.56e-04 sec
Transport | Stress period: 2 | Time step: 96 | Completed in : 0 min 7.50e-07 sec
WARNING: Negative moles in solution 0 for C, -1.785876e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.375845e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.902336e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -8.318861e-05. Recovering...
WARNING: Negative moles in solution 4 for C, -4.155214e-05. Recovering...
WARNING: Negative moles in solution 5 for C, -2.049568e-04. Recovering...
WARNING: Negative moles in solution 6 for C, -2.694925e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.774138e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.368992e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.955539e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -5.704391e-05. Recovering...
WARNING: Negative moles in solution 5 for C, -1.973241e-04. Recovering...
WARNING: Negative moles in solution 6 for C, -5.028380e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.762247e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.361768e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -7.005413e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -3.385372e-05. Recovering...
WARNING: Negative moles in solution 5 for C, -1.879481e-04. Recovering...
WARNING: Negative moles in solution 6 for C, -7.231573e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.750241e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.354209e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -7.051847e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.363668e-05. Recovering...
WARNING: Negative moles in solution 5 for C, -1.767783e-04. Recovering...
WARNING: Negative moles in solution 6 for C, -9.271123e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.738141e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.346341e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -7.094925e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.591886e-04. Recovering...
WARNING: Negative moles in solution 6 for C, -1.111777e-04. Recovering...
Reactions | Stress period: 2 | Time step: 96 | Completed in : 0 min 6.80e-04 sec
Transport | Stress period: 2 | Time step: 97 | Completed in : 0 min 8.50e-07 sec
Reactions | Stress period: 2 | Time step: 97 | Completed in : 0 min 6.73e-04 sec
Transport | Stress period: 2 | Time step: 98 | Completed in : 0 min 7.50e-07 sec
Reactions | Stress period: 2 | Time step: 98 | Completed in : 0 min 6.47e-04 sec
Transport | Stress period: 2 | Time step: 99 | Completed in : 0 min 7.50e-07 sec
Reactions | Stress period: 2 | Time step: 99 | Completed in : 0 min 6.85e-04 sec
Transport | Stress period: 2 | Time step: 100 | Completed in : 0 min 7.50e-07 sec
Reactions | Stress period: 2 | Time step: 100 | Completed in : 0 min 7.12e-04 sec
MODFLOW 6 converged successfully without any fails
MODEL RUN FINISHED BUT CHECK THE RESULTS
Solution finished at 2026-07-20 15:57:14. Running time: 0.085165 mins
WARNING: Negative moles in solution 0 for C, -1.725972e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.338204e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -7.134284e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.271992e-04. Recovering...
WARNING: Negative moles in solution 6 for C, -1.273273e-04. Recovering...
True
6. Results: effluent breakthrough curves¶
Outlet-cell concentrations versus cumulative effluent volume, compared with the measured effluent data of Appelo et al. (1998). This is the same result as the classic tutorial, reached through the transport-first workflow.
sout = pd.read_csv(os.path.join(model.wd, "sout.csv"))
qml = q * 1.0e6 # m3/d -> mL/d, so time (d) * qml = effluent volume (mL)
outlet = sout[sout["col"] == sout["col"].max()].copy()
outlet["vol"] = outlet["time_d"] * qml
# Measured effluent data (real experiment, not a model benchmark).
obs = pd.read_csv(os.path.join(DATA, "tut02_obs.txt"), sep="\t", skipinitialspace=True)
obs.replace(-9999, np.nan, inplace=True)
obs.dropna(axis=0, how="all", inplace=True)
obs.columns = ["vol", "Mg", "Ca", "Alk", "Cl", "S(6)", "pH"]
obs.set_index("vol", inplace=True)
obs = obs.iloc[3:, :]
plot_vars = [v for v in ["Mg", "Ca", "Alk", "S(6)", "pH"] if v in outlet.columns]
fig, axs = plt.subplots(len(plot_vars), 1, figsize=(7, 2.0 * len(plot_vars)),
sharex=True)
for ax, var in zip(np.atleast_1d(axs), plot_vars):
ax.plot(outlet["vol"], outlet[var], color="tab:blue", zorder=10, label="mf6rtm (from_mf6)")
if var in obs.columns:
ax.scatter(obs.index, obs[var], s=18, facecolors="none",
edgecolors="green", label="Appelo (1998), observed")
ax.set_ylabel(var)
ax.grid(alpha=0.3)
ax.legend(fontsize=8)
np.atleast_1d(axs)[-1].set_xlabel("effluent volume (mL)")
fig.suptitle("Pyrite oxidation column (from_mf6): outlet breakthrough")
fig.tight_layout()
