1D Pyrite Oxidation with BYO(Build your own model files)¶
This tutorial reproduces the marine-sediment oxidation experiment of
Appelo et al. (1998): a column of pyrite-bearing sediment is first flushed
with a dilute MgCl\ :sub:2 solution and then with an oxidising solution,
driving pyrite oxidation and a cascade of secondary reactions (calcite
dissolution, cation/proton exchange, organic-matter oxidation, surface
complexation).
It uses the classic workflow (BYO): build the :class:~mf6rtm.mup3d.base.Mup3d
model first, then construct the MODFLOW 6 flow + per-component transport models
yourself. The classic workflow injects the inflow chemistry directly into the
well as per-period auxiliary concentrations, so the injected water can change
between stress periods (dilute in period 0, oxidising in period 1).
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¶
A 5.3 cm column in 16 cells, run in two stress periods: a dilute flush (period 0) followed by the oxidising flush (period 1). The injection well at the inlet runs at the same rate in both periods; only its chemistry changes.
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)]
# constant head at the outlet; injection well at the inlet in both periods
chdspd = [[(0, 0, ncol - 1), 1.0]]
wel_spd = {kper: [[(0, 0, 0), q]] for kper in range(nper)}
2. Geochemistry — defining the reaction network¶
mf6rtm mirrors PHREEQC’s chemistry blocks as mup3d classes. Every input
type follows the same pattern: load the data (here from CSV via a
utils helper), wrap it in the matching class, and place it with
.set_ic(...) — an integer zone number for uniform chemistry, or a
(nlay, nrow, ncol) array of zone numbers for spatially varying chemistry.
The objects are attached to the Mup3d model in the next section.
Solutions — the aqueous waters (pH, pe, element totals), one per column.
Column 1 is the initial pore water (applied everywhere); columns 2 and
3 are the dilute and oxidising inflow waters injected in periods 0 and 1.
solutionsdf = pd.read_csv(os.path.join(DATA, "tut02_solutions.csv"),
comment="#", index_col=0)
solutions = utils.solution_df_to_dict(solutionsdf)
solution = mup3d.Solutions(solutions)
solution.set_ic(np.ones((nlay, nrow, ncol), dtype=float))
solutionsdf
| cinit | cin_1 | cin_2 | |
|---|---|---|---|
| comp | |||
| Ca | 0.000386 | 1.000000e-06 | 1.000000e-07 |
| Cl | 0.020070 | 5.301000e-03 | 1.020000e-02 |
| Mg | 0.010000 | 2.650000e-03 | 5.100000e-03 |
| Fe(+2) | 0.000001 | 1.000000e-08 | 2.000000e-07 |
| Fe(+3) | 0.000000 | 0.000000e+00 | 0.000000e+00 |
| S(6) | 0.000010 | 1.000000e-08 | 2.000000e-07 |
| S(-2) | 0.000000 | 0.000000e+00 | 0.000000e+00 |
| C(+4) | 0.000586 | 1.000000e-06 | 1.000000e-07 |
| C(-4) | 0.000000 | 0.000000e+00 | 0.000000e+00 |
| Orgc_sed | 0.890000 | 0.000000e+00 | 0.000000e+00 |
| pH | 9.104000 | 7.000000e+00 | 7.000000e+00 |
| pe | -4.812000 | 1.587150e+01 | 1.450000e+01 |
Exchange phases — cation-exchange sites (PHREEQC EXCHANGE). The column
is split into four zones with different exchanger amounts; the set_ic array
maps cells 0–3 → zone 1, 4–7 → zone 2, and so on.
set_equilibrate_solutions pre-equilibrates each zone’s exchanger with the
given solution number before the run.
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 phases — rate-controlled reactions (PHREEQC KINETICS): pyrite
and organic-matter oxidation, the drivers of this experiment.
parse_kinetics_dataframe builds the per-phase parameter dict; set_ic(1)
applies the same kinetics to every cell.
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 — EquilibriumPhases are minerals kept at
equilibrium each step (PHREEQC EQUILIBRIUM_PHASES, here calcite);
Surfaces are surface-complexation sites (PHREEQC SURFACE). Both are
uniform, so set_ic(1).
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)
3. Build the Mup3d model and assign inflow chemistry¶
Create the model, attach every phase type, and initialize PhreeqcRM. Then map
the inflow solutions to the well per stress period with set_spd([2, 3])
(solution 2 in period 0, solution 3 in period 1). set_chem_stress stores
the per-period component concentrations in model.wel.data.
sim_ws = os.path.join(BASE, "_tutorial02_run")
model = mup3d.Mup3d("pyrite_oxidation", solution, nlay, nrow, ncol)
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()
# inflow chemistry: solution 2 (dilute) in period 0, solution 3 (oxidising) in period 1
wellchem = mup3d.ChemStress("wel")
wellchem.set_spd([2, 3])
model.set_chem_stress(wellchem)
# append the per-period component concentrations to the well stress period data
for kper in wel_spd:
for i in range(len(wel_spd[kper])):
wel_spd[kper][i].extend(model.wel.data[kper])
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
4. Build the flow + per-component transport models¶
The well injects the components as auxiliary variables (per period); one GWT model is then built per chemical component, each sourcing the well auxiliary.
def build_model(model):
sim = flopy.mf6.MFSimulation(sim_name=model.name, sim_ws=model.wd, exe_name="mf6")
flopy.mf6.ModflowTdis(sim, nper=nper, perioddata=tdis_rc, time_units=time_units)
# --- GWF flow model ---
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.name])
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.ModflowGwfchd(gwf, stress_period_data=chdspd, pname="chd",
filename="gwf.chd")
flopy.mf6.ModflowGwfwel(gwf, stress_period_data=wel_spd, auxiliary=model.components,
pname="wel", filename="gwf.wel")
flopy.mf6.ModflowGwfoc(gwf, head_filerecord="gwf.hds", budget_filerecord="gwf.cbb",
saverecord=[("HEAD", "ALL"), ("BUDGET", "ALL")])
# --- one GWT model per component ---
for c in model.components:
gwt = flopy.mf6.MFModel(sim, model_type="gwt6", modelname=c,
model_nam_file=f"{c}.nam")
imsgwt = flopy.mf6.ModflowIms(sim, linear_acceleration="BICGSTAB",
filename=f"{c}.ims")
sim.register_ims_package(imsgwt, [gwt.name])
flopy.mf6.ModflowGwtdis(gwt, length_units=length_units, nlay=nlay, nrow=nrow,
ncol=ncol, delr=delr, delc=delc, top=top, botm=botm,
filename=f"{c}.dis")
flopy.mf6.ModflowGwtic(gwt, strt=model.sconc[c], filename=f"{c}.ic")
flopy.mf6.ModflowGwtssm(gwt, sources=[["wel", "aux", c]], filename=f"{c}.ssm")
flopy.mf6.ModflowGwtadv(gwt, scheme="tvd")
flopy.mf6.ModflowGwtdsp(gwt, xt3d_off=True, alh=dispersivity,
ath1=dispersivity * 0.1, filename=f"{c}.dsp")
flopy.mf6.ModflowGwtmst(gwt, porosity=prsity, filename=f"{c}.mst")
flopy.mf6.ModflowGwtoc(gwt, concentration_filerecord=f"{c}.ucn",
saverecord=[("CONCENTRATION", "ALL")])
flopy.mf6.ModflowGwfgwt(sim, exgtype="GWF6-GWT6", exgmnamea="gwf",
exgmnameb=c, filename=f"{c}.gwfgwt")
sim.write_simulation()
return sim
sim = build_model(model)
writing simulation...
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5. Run¶
# 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()
Running mf6rtm
Using libmf6 found in model directory: libmf6.dylib
Processing initial chemistry configuration
Starting Solution at 2026-07-20 15:57:02
Transport | Stress period: 1 | Time step: 1 | Completed in : 0 min 1.03e-06 sec
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Transport | Stress period: 1 | Time step: 63 | Completed in : 0 min 8.83e-07 sec
Reactions | Stress period: 1 | Time step: 63 | Completed in : 0 min 2.86e-04 sec
Transport | Stress period: 1 | Time step: 64 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 1 | Time step: 64 | Completed in : 0 min 2.86e-04 sec
Transport | Stress period: 2 | Time step: 1 | Completed in : 0 min 1.00e-06 sec
Reactions | Stress period: 2 | Time step: 1 | Completed in : 0 min 2.94e-04 sec
Transport | Stress period: 2 | Time step: 2 | Completed in : 0 min 1.30e-06 sec
Reactions | Stress period: 2 | Time step: 2 | Completed in : 0 min 2.94e-04 sec
Transport | Stress period: 2 | Time step: 3 | Completed in : 0 min 1.28e-06 sec
Reactions | Stress period: 2 | Time step: 3 | Completed in : 0 min 2.97e-04 sec
Transport | Stress period: 2 | Time step: 4 | Completed in : 0 min 1.23e-06 sec
Reactions | Stress period: 2 | Time step: 4 | Completed in : 0 min 2.99e-04 sec
Transport | Stress period: 2 | Time step: 5 | Completed in : 0 min 1.40e-06 sec
Reactions | Stress period: 2 | Time step: 5 | Completed in : 0 min 3.11e-04 sec
Transport | Stress period: 2 | Time step: 6 | Completed in : 0 min 1.23e-06 sec
Reactions | Stress period: 2 | Time step: 6 | Completed in : 0 min 3.16e-04 sec
Transport | Stress period: 2 | Time step: 7 | Completed in : 0 min 1.28e-06 sec
Reactions | Stress period: 2 | Time step: 7 | Completed in : 0 min 3.19e-04 sec
Transport | Stress period: 2 | Time step: 8 | Completed in : 0 min 1.32e-06 sec
Reactions | Stress period: 2 | Time step: 8 | Completed in : 0 min 3.31e-04 sec
Transport | Stress period: 2 | Time step: 9 | Completed in : 0 min 1.27e-06 sec
Reactions | Stress period: 2 | Time step: 9 | Completed in : 0 min 3.48e-04 sec
Transport | Stress period: 2 | Time step: 10 | Completed in : 0 min 1.35e-06 sec
Reactions | Stress period: 2 | Time step: 10 | Completed in : 0 min 3.41e-04 sec
Transport | Stress period: 2 | Time step: 11 | Completed in : 0 min 1.22e-06 sec
Reactions | Stress period: 2 | Time step: 11 | Completed in : 0 min 3.28e-04 sec
Transport | Stress period: 2 | Time step: 12 | Completed in : 0 min 1.58e-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 1.25e-06 sec
Reactions | Stress period: 2 | Time step: 13 | Completed in : 0 min 3.52e-04 sec
Transport | Stress period: 2 | Time step: 14 | Completed in : 0 min 1.43e-06 sec
Reactions | Stress period: 2 | Time step: 14 | Completed in : 0 min 3.39e-04 sec
Transport | Stress period: 2 | Time step: 15 | Completed in : 0 min 1.22e-06 sec
Reactions | Stress period: 2 | Time step: 15 | Completed in : 0 min 3.47e-04 sec
Transport | Stress period: 2 | Time step: 16 | Completed in : 0 min 1.43e-06 sec
Reactions | Stress period: 2 | Time step: 16 | Completed in : 0 min 3.50e-04 sec
Transport | Stress period: 2 | Time step: 17 | Completed in : 0 min 1.28e-06 sec
Reactions | Stress period: 2 | Time step: 17 | Completed in : 0 min 3.48e-04 sec
Transport | Stress period: 2 | Time step: 18 | Completed in : 0 min 1.22e-06 sec
Reactions | Stress period: 2 | Time step: 18 | Completed in : 0 min 3.59e-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 3.90e-04 sec
Transport | Stress period: 2 | Time step: 20 | Completed in : 0 min 1.38e-06 sec
Reactions | Stress period: 2 | Time step: 20 | Completed in : 0 min 3.78e-04 sec
Transport | Stress period: 2 | Time step: 21 | Completed in : 0 min 2.97e-06 sec
Reactions | Stress period: 2 | Time step: 21 | Completed in : 0 min 4.01e-04 sec
Transport | Stress period: 2 | Time step: 22 | Completed in : 0 min 1.38e-06 sec
Reactions | Stress period: 2 | Time step: 22 | Completed in : 0 min 4.10e-04 sec
Transport | Stress period: 2 | Time step: 23 | Completed in : 0 min 1.25e-06 sec
Reactions | Stress period: 2 | Time step: 23 | Completed in : 0 min 4.81e-04 sec
Transport | Stress period: 2 | Time step: 24 | Completed in : 0 min 1.43e-06 sec
Reactions | Stress period: 2 | Time step: 24 | Completed in : 0 min 4.22e-04 sec
Transport | Stress period: 2 | Time step: 25 | Completed in : 0 min 1.43e-06 sec
Reactions | Stress period: 2 | Time step: 25 | Completed in : 0 min 4.27e-04 sec
Transport | Stress period: 2 | Time step: 26 | Completed in : 0 min 1.43e-06 sec
Reactions | Stress period: 2 | Time step: 26 | Completed in : 0 min 4.08e-04 sec
Transport | Stress period: 2 | Time step: 27 | Completed in : 0 min 1.28e-06 sec
Reactions | Stress period: 2 | Time step: 27 | Completed in : 0 min 3.93e-04 sec
Transport | Stress period: 2 | Time step: 28 | Completed in : 0 min 1.27e-06 sec
Reactions | Stress period: 2 | Time step: 28 | Completed in : 0 min 4.05e-04 sec
Transport | Stress period: 2 | Time step: 29 | Completed in : 0 min 1.23e-06 sec
Reactions | Stress period: 2 | Time step: 29 | Completed in : 0 min 3.87e-04 sec
Transport | Stress period: 2 | Time step: 30 | Completed in : 0 min 1.22e-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: 30 | Completed in : 0 min 3.90e-04 sec
Transport | Stress period: 2 | Time step: 31 | Completed in : 0 min 1.43e-06 sec
Reactions | Stress period: 2 | Time step: 31 | Completed in : 0 min 3.86e-04 sec
Transport | Stress period: 2 | Time step: 32 | Completed in : 0 min 1.32e-06 sec
Reactions | Stress period: 2 | Time step: 32 | Completed in : 0 min 3.89e-04 sec
Transport | Stress period: 2 | Time step: 33 | Completed in : 0 min 1.37e-06 sec
Reactions | Stress period: 2 | Time step: 33 | Completed in : 0 min 3.82e-04 sec
Transport | Stress period: 2 | Time step: 34 | Completed in : 0 min 1.37e-06 sec
Reactions | Stress period: 2 | Time step: 34 | Completed in : 0 min 3.95e-04 sec
Transport | Stress period: 2 | Time step: 35 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 35 | Completed in : 0 min 4.06e-04 sec
Transport | Stress period: 2 | Time step: 36 | Completed in : 0 min 1.00e-06 sec
Reactions | Stress period: 2 | Time step: 36 | Completed in : 0 min 4.19e-04 sec
Transport | Stress period: 2 | Time step: 37 | Completed in : 0 min 1.07e-06 sec
Reactions | Stress period: 2 | Time step: 37 | Completed in : 0 min 4.37e-04 sec
Transport | Stress period: 2 | Time step: 38 | Completed in : 0 min 1.07e-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 4.33e-04 sec
Transport | Stress period: 2 | Time step: 39 | Completed in : 0 min 1.00e-06 sec
Reactions | Stress period: 2 | Time step: 39 | Completed in : 0 min 4.17e-04 sec
Transport | Stress period: 2 | Time step: 40 | Completed in : 0 min 1.02e-06 sec
Reactions | Stress period: 2 | Time step: 40 | Completed in : 0 min 4.18e-04 sec
Transport | Stress period: 2 | Time step: 41 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 41 | Completed in : 0 min 4.30e-04 sec
Transport | Stress period: 2 | Time step: 42 | Completed in : 0 min 9.17e-07 sec
Reactions | Stress period: 2 | Time step: 42 | Completed in : 0 min 4.40e-04 sec
Transport | Stress period: 2 | Time step: 43 | Completed in : 0 min 9.33e-07 sec
Reactions | Stress period: 2 | Time step: 43 | Completed in : 0 min 4.42e-04 sec
Transport | Stress period: 2 | Time step: 44 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 44 | Completed in : 0 min 4.30e-04 sec
Transport | Stress period: 2 | Time step: 45 | Completed in : 0 min 9.83e-07 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, -7.767534e-06. Recovering...
Reactions | Stress period: 2 | Time step: 45 | Completed in : 0 min 4.38e-04 sec
Transport | Stress period: 2 | Time step: 46 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 46 | Completed in : 0 min 4.36e-04 sec
Transport | Stress period: 2 | Time step: 47 | Completed in : 0 min 8.83e-07 sec
Reactions | Stress period: 2 | Time step: 47 | Completed in : 0 min 4.59e-04 sec
Transport | Stress period: 2 | Time step: 48 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 48 | Completed in : 0 min 4.75e-04 sec
Transport | Stress period: 2 | Time step: 49 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 49 | Completed in : 0 min 4.81e-04 sec
Transport | Stress period: 2 | Time step: 50 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 50 | Completed in : 0 min 4.84e-04 sec
Transport | Stress period: 2 | Time step: 51 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 51 | Completed in : 0 min 4.96e-04 sec
Transport | Stress period: 2 | Time step: 52 | Completed in : 0 min 9.17e-07 sec
WARNING: Negative moles in solution 0 for C, -1.341181e-03. Recovering...
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 4.97e-04 sec
Transport | Stress period: 2 | Time step: 53 | Completed in : 0 min 1.00e-06 sec
Reactions | Stress period: 2 | Time step: 53 | Completed in : 0 min 5.10e-04 sec
Transport | Stress period: 2 | Time step: 54 | Completed in : 0 min 9.17e-07 sec
Reactions | Stress period: 2 | Time step: 54 | Completed in : 0 min 4.96e-04 sec
Transport | Stress period: 2 | Time step: 55 | Completed in : 0 min 9.67e-07 sec
Reactions | Stress period: 2 | Time step: 55 | Completed in : 0 min 5.15e-04 sec
Transport | Stress period: 2 | Time step: 56 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 56 | Completed in : 0 min 5.28e-04 sec
Transport | Stress period: 2 | Time step: 57 | Completed in : 0 min 1.02e-06 sec
Reactions | Stress period: 2 | Time step: 57 | Completed in : 0 min 5.22e-04 sec
Transport | Stress period: 2 | Time step: 58 | Completed in : 0 min 1.07e-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 5.17e-04 sec
Transport | Stress period: 2 | Time step: 59 | Completed in : 0 min 9.17e-07 sec
Reactions | Stress period: 2 | Time step: 59 | Completed in : 0 min 5.29e-04 sec
Transport | Stress period: 2 | Time step: 60 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 60 | Completed in : 0 min 5.35e-04 sec
Transport | Stress period: 2 | Time step: 61 | Completed in : 0 min 1.00e-06 sec
Reactions | Stress period: 2 | Time step: 61 | Completed in : 0 min 5.19e-04 sec
Transport | Stress period: 2 | Time step: 62 | Completed in : 0 min 9.67e-07 sec
Reactions | Stress period: 2 | Time step: 62 | Completed in : 0 min 5.31e-04 sec
Transport | Stress period: 2 | Time step: 63 | Completed in : 0 min 1.02e-06 sec
Reactions | Stress period: 2 | Time step: 63 | Completed in : 0 min 5.30e-04 sec
Transport | Stress period: 2 | Time step: 64 | Completed in : 0 min 9.00e-07 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...
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...
Reactions | Stress period: 2 | Time step: 64 | Completed in : 0 min 5.36e-04 sec
Transport | Stress period: 2 | Time step: 65 | Completed in : 0 min 1.03e-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 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 66 | Completed in : 0 min 5.52e-04 sec
Transport | Stress period: 2 | Time step: 67 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 67 | Completed in : 0 min 5.51e-04 sec
Transport | Stress period: 2 | Time step: 68 | Completed in : 0 min 9.17e-07 sec
Reactions | Stress period: 2 | Time step: 68 | Completed in : 0 min 5.54e-04 sec
Transport | Stress period: 2 | Time step: 69 | Completed in : 0 min 1.00e-06 sec
Reactions | Stress period: 2 | Time step: 69 | Completed in : 0 min 5.77e-04 sec
Transport | Stress period: 2 | Time step: 70 | Completed in : 0 min 9.33e-07 sec
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...
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...
Reactions | Stress period: 2 | Time step: 70 | Completed in : 0 min 5.83e-04 sec
Transport | Stress period: 2 | Time step: 71 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 71 | Completed in : 0 min 5.87e-04 sec
Transport | Stress period: 2 | Time step: 72 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 72 | Completed in : 0 min 5.91e-04 sec
Transport | Stress period: 2 | Time step: 73 | Completed in : 0 min 1.02e-06 sec
Reactions | Stress period: 2 | Time step: 73 | Completed in : 0 min 5.90e-04 sec
Transport | Stress period: 2 | Time step: 74 | Completed in : 0 min 9.00e-07 sec
Reactions | Stress period: 2 | Time step: 74 | Completed in : 0 min 5.79e-04 sec
Transport | Stress period: 2 | Time step: 75 | Completed in : 0 min 6.00e-07 sec
Reactions | Stress period: 2 | Time step: 75 | Completed in : 0 min 5.84e-04 sec
Transport | Stress period: 2 | Time step: 76 | Completed in : 0 min 5.67e-07 sec
Reactions | Stress period: 2 | Time step: 76 | Completed in : 0 min 5.99e-04 sec
Transport | Stress period: 2 | Time step: 77 | Completed in : 0 min 5.83e-07 sec
Reactions | Stress period: 2 | Time step: 77 | Completed in : 0 min 6.11e-04 sec
Transport | Stress period: 2 | Time step: 78 | Completed in : 0 min 5.83e-07 sec
Reactions | Stress period: 2 | Time step: 78 | Completed in : 0 min 6.06e-04 sec
Transport | Stress period: 2 | Time step: 79 | Completed in : 0 min 6.00e-07 sec
Reactions | Stress period: 2 | Time step: 79 | Completed in : 0 min 6.25e-04 sec
Transport | Stress period: 2 | Time step: 80 | Completed in : 0 min 5.67e-07 sec
Reactions | Stress period: 2 | Time step: 80 | Completed in : 0 min 6.19e-04 sec
Transport | Stress period: 2 | Time step: 81 | Completed in : 0 min 6.33e-07 sec
Reactions | Stress period: 2 | Time step: 81 | Completed in : 0 min 6.29e-04 sec
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...
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, -1.408670e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -5.958772e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.694337e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.506400e-04. Recovering...
Transport | Stress period: 2 | Time step: 82 | Completed in : 0 min 5.83e-07 sec
Reactions | Stress period: 2 | Time step: 82 | Completed in : 0 min 6.36e-04 sec
Transport | Stress period: 2 | Time step: 83 | Completed in : 0 min 7.00e-07 sec
Reactions | Stress period: 2 | Time step: 83 | Completed in : 0 min 6.28e-04 sec
Transport | Stress period: 2 | Time step: 84 | Completed in : 0 min 6.17e-07 sec
Reactions | Stress period: 2 | Time step: 84 | Completed in : 0 min 6.39e-04 sec
Transport | Stress period: 2 | Time step: 85 | Completed in : 0 min 7.17e-07 sec
Reactions | Stress period: 2 | Time step: 85 | Completed in : 0 min 6.58e-04 sec
Transport | Stress period: 2 | Time step: 86 | Completed in : 0 min 6.83e-07 sec
WARNING: Negative moles in solution 0 for C, -1.907690e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.411608e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.028733e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.591076e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.507100e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.901589e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.413566e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.099421e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.478335e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.493874e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.537825e-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, -6.170659e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.357657e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.465850e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -3.102866e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.887224e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.414709e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.242195e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.230997e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.421900e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -5.969485e-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, -6.313463e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -2.100569e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.361515e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -8.725807e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.870324e-03. Recovering...
Reactions | Stress period: 2 | Time step: 86 | Completed in : 0 min 6.69e-04 sec
Transport | Stress period: 2 | Time step: 87 | Completed in : 0 min 6.50e-07 sec
Reactions | Stress period: 2 | Time step: 87 | Completed in : 0 min 7.13e-04 sec
Transport | Stress period: 2 | Time step: 88 | Completed in : 0 min 6.00e-07 sec
Reactions | Stress period: 2 | Time step: 88 | Completed in : 0 min 6.56e-04 sec
Transport | Stress period: 2 | Time step: 89 | Completed in : 0 min 6.83e-07 sec
Reactions | Stress period: 2 | Time step: 89 | Completed in : 0 min 6.61e-04 sec
Transport | Stress period: 2 | Time step: 90 | Completed in : 0 min 6.50e-07 sec
Reactions | Stress period: 2 | Time step: 90 | Completed in : 0 min 6.47e-04 sec
Transport | Stress period: 2 | Time step: 91 | Completed in : 0 min 5.83e-07 sec
WARNING: Negative moles in solution 1 for C, -1.412324e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.384677e-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, -1.134056e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.861073e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.409969e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.455436e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.833900e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.188325e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.377783e-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, -1.701670e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -2.075008e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.599824e-04. Recovering...
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, -1.572554e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -1.944132e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.795796e-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, -6.660184e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.448024e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -1.796217e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.960987e-04. Recovering...
Reactions | Stress period: 2 | Time step: 91 | Completed in : 0 min 6.97e-04 sec
Transport | Stress period: 2 | Time step: 92 | Completed in : 0 min 6.17e-07 sec
Reactions | Stress period: 2 | Time step: 92 | Completed in : 0 min 6.77e-04 sec
Transport | Stress period: 2 | Time step: 93 | Completed in : 0 min 6.00e-07 sec
Reactions | Stress period: 2 | Time step: 93 | Completed in : 0 min 6.86e-04 sec
Transport | Stress period: 2 | Time step: 94 | Completed in : 0 min 6.67e-07 sec
Reactions | Stress period: 2 | Time step: 94 | Completed in : 0 min 6.65e-04 sec
Transport | Stress period: 2 | Time step: 95 | Completed in : 0 min 6.00e-07 sec
Reactions | Stress period: 2 | Time step: 95 | Completed in : 0 min 6.51e-04 sec
Transport | Stress period: 2 | Time step: 96 | Completed in : 0 min 5.83e-07 sec
WARNING: Negative moles in solution 0 for C, -1.819901e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.393779e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.724554e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.329530e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -1.632153e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -2.090525e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.808794e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.388281e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.786660e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.218286e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -1.453078e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -2.153089e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.797440e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.382288e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -6.845967e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.115015e-04. Recovering...
WARNING: Negative moles in solution 4 for C, -9.767438e-05. Recovering...
WARNING: Negative moles in solution 5 for C, -2.109214e-04. Recovering...
WARNING: Negative moles in solution 6 for C, -2.544583e-06. Recovering...
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, -6.902339e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -8.318858e-05. Recovering...
WARNING: Negative moles in solution 4 for C, -4.155235e-05. Recovering...
WARNING: Negative moles in solution 5 for C, -2.049569e-04. Recovering...
WARNING: Negative moles in solution 6 for C, -2.694943e-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, -6.955540e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -5.704349e-05. Recovering...
WARNING: Negative moles in solution 5 for C, -1.973242e-04. Recovering...
WARNING: Negative moles in solution 6 for C, -5.028400e-05. Recovering...
Reactions | Stress period: 2 | Time step: 96 | Completed in : 0 min 6.69e-04 sec
Transport | Stress period: 2 | Time step: 97 | Completed in : 0 min 6.67e-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 6.50e-07 sec
Reactions | Stress period: 2 | Time step: 98 | Completed in : 0 min 6.33e-04 sec
Transport | Stress period: 2 | Time step: 99 | Completed in : 0 min 6.00e-07 sec
Reactions | Stress period: 2 | Time step: 99 | Completed in : 0 min 6.77e-04 sec
Transport | Stress period: 2 | Time step: 100 | Completed in : 0 min 5.83e-07 sec
Reactions | Stress period: 2 | Time step: 100 | Completed in : 0 min 7.06e-04 sec
MODFLOW 6 converged successfully without any fails
MODEL RUN FINISHED BUT CHECK THE RESULTS
Solution finished at 2026-07-20 15:57:07. Running time: 0.085496 mins
WARNING: Negative moles in solution 0 for C, -1.762248e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.361769e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -7.005413e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -3.385307e-05. Recovering...
WARNING: Negative moles in solution 5 for C, -1.879482e-04. Recovering...
WARNING: Negative moles in solution 6 for C, -7.231593e-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, -7.051848e-04. Recovering...
WARNING: Negative moles in solution 3 for C, -1.363587e-05. Recovering...
WARNING: Negative moles in solution 5 for C, -1.767783e-04. Recovering...
WARNING: Negative moles in solution 6 for C, -9.271144e-05. Recovering...
WARNING: Negative moles in solution 0 for C, -1.738142e-03. Recovering...
WARNING: Negative moles in solution 1 for C, -1.346342e-03. Recovering...
WARNING: Negative moles in solution 2 for C, -7.094925e-04. Recovering...
WARNING: Negative moles in solution 5 for C, -1.591888e-04. Recovering...
WARNING: Negative moles in solution 6 for C, -1.111780e-04. Recovering...
WARNING: Negative moles in solution 0 for C, -1.725973e-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, -1.273275e-04. Recovering...
True
6. Results: effluent breakthrough curves¶
Concentrations at the outlet cell over the experiment, plotted against cumulative effluent volume and compared with the measured effluent data of Appelo et al. (1998). (These are real laboratory measurements, not another model.)
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:red", zorder=10, label="mf6rtm")
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: outlet breakthrough")
fig.tight_layout()
