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ex-gwt-mt3dsupp632.py.
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MT3DMS Supplemental Guide Problem 6.3.2
This example tests the capabilities of the GWT model to simulate 0-order production in a dual-domain system with & without sorption. Results from a GWT model are compared with results from an MT3DMS simulation that uses flows from a separate MODFLOW-2005 simulation. It is based on example problem 6.3.2 described in Zheng 2010. The problem consists of a one-dimensional model grid with inflow into the first cell and outflow through the last cell.
Initial setup
Import dependencies, define the example name and workspace, and read settings from environment variables.
[1]:
import os
import pathlib as pl
from pprint import pformat
import flopy
import git
import matplotlib.pyplot as plt
from flopy.plot.styles import styles
from modflow_devtools.misc import get_env, timed
# Example name and workspace paths. If this example is running
# in the git repository, use the folder structure described in
# the README. Otherwise just use the current working directory.
try:
root = pl.Path(git.Repo(".", search_parent_directories=True).working_dir)
except:
root = None
workspace = root / "examples" if root else pl.Path.cwd()
figs_path = root / "figures" if root else pl.Path.cwd()
# Settings from environment variables
write = get_env("WRITE", True)
run = get_env("RUN", True)
plot = get_env("PLOT", True)
plot_show = get_env("PLOT_SHOW", True)
plot_save = get_env("PLOT_SAVE", True)
Define parameters
Define model units, parameters and other settings.
[2]:
# Scenario-specific parameters - make sure there is at least one blank line before next item
parameters = {
"ex-gwt-mt3dsupp632a": {
"distribution_coefficient": 0.25,
"decay": 0.0,
"decay_sorbed": -1.0e-3,
},
"ex-gwt-mt3dsupp632b": {
"distribution_coefficient": 0.25,
"decay": -5.0e-4,
"decay_sorbed": -5.0e-4,
},
"ex-gwt-mt3dsupp632c": {
"distribution_coefficient": 0.0,
"decay": -1.0e-3,
"decay_sorbed": 0.0,
},
}
# Scenario parameter units - make sure there is at least one blank line before next item
# add parameter_units to add units to the scenario parameter table
parameter_units = {
"distribution_coefficient": "$mL g^{-1}$",
"decay": "$g/mL d^{-1}$",
"decay_sorbed": "$g/mL d^{-1}$",
}
# Model units
length_units = "meters"
time_units = "days"
# Model parameters
nper = 2 # Number of periods
nlay = 1 # Number of layers
nrow = 1 # Number of rows
ncol = 401 # Number of columns
delr = 2.5 # Column width ($m$)
delc = 1.0 # Row width ($m$)
top = 1.0 # Top of the model ($m$)
botm = 0 # Layer bottom elevation ($m$)
specific_discharge = 0.06 # Specific discharge ($md^{-1}$)
longitudinal_dispersivity = 10 # Longitudinal dispersivity ($m$)
volfrac = 0.2 # volume fraction that is immobile domain (unitless)
porosity = 0.2 # Porosity of mobile domain (unitless)
porosity_immobile = 0.05 # Porosity of immobile domain (unitless)
bulk_density = 4.0 # Bulk density ($gL^{-1})$
zeta_im = 1.0e-3 # First-order mass transfer rate between the mobile and immobile domains ($d^{-1}$)
f = 0.8 # Fraction of sorption sites in contact with mobile water (unitless)
source_duration = 1000 # Source duration ($d$)
total_time = 10000 # Simulation time ($t$)
obs_xloc = 200.0 # Observation x location ($m$)
# Flags that can be adjusted to change example configuration
zero_order_decay = True # Flag indicating whether decay is zero or first order
dual_domain = True # Flag indicating that dual domain is active
Model setup
Define functions to build models, write input files, and run the simulation.
[3]:
def build_mf6gwf(sim_folder):
print(f"Building mf6gwf model...{sim_folder}")
name = "flow"
sim_ws = os.path.join(workspace, sim_folder, "mf6gwf")
sim = flopy.mf6.MFSimulation(sim_name=name, sim_ws=sim_ws, exe_name="mf6")
tdis_ds = (
(source_duration, 1, 1.0),
(total_time - source_duration, 1, 1.0),
)
flopy.mf6.ModflowTdis(sim, nper=nper, perioddata=tdis_ds, time_units=time_units)
flopy.mf6.ModflowIms(sim)
gwf = flopy.mf6.ModflowGwf(sim, modelname=name, save_flows=True)
flopy.mf6.ModflowGwfdis(
gwf,
length_units=length_units,
nlay=nlay,
nrow=nrow,
ncol=ncol,
delr=delr,
delc=delc,
top=top,
botm=botm,
)
flopy.mf6.ModflowGwfnpf(
gwf,
save_specific_discharge=True,
save_saturation=True,
icelltype=0,
k=1.0,
)
flopy.mf6.ModflowGwfic(gwf, strt=1.0)
flopy.mf6.ModflowGwfchd(gwf, stress_period_data=[[(0, 0, ncol - 1), 1.0]])
wel_spd = {
0: [[(0, 0, 0), specific_discharge * delc * top]],
1: [[(0, 0, 0), specific_discharge * delc * top]],
}
flopy.mf6.ModflowGwfwel(gwf, stress_period_data=wel_spd, pname="WEL-1")
head_filerecord = f"{name}.hds"
budget_filerecord = f"{name}.bud"
flopy.mf6.ModflowGwfoc(
gwf,
head_filerecord=head_filerecord,
budget_filerecord=budget_filerecord,
saverecord=[("HEAD", "ALL"), ("BUDGET", "ALL")],
)
return sim
def build_mf6gwt(sim_folder, distribution_coefficient, decay, decay_sorbed):
print(f"Building mf6gwt model...{sim_folder}")
name = "trans"
sim_ws = os.path.join(workspace, sim_folder, "mf6gwt")
sim = flopy.mf6.MFSimulation(sim_name=name, sim_ws=sim_ws, exe_name="mf6")
pertim1 = source_duration
pertim2 = total_time - source_duration
tdis_ds = ((pertim1, 10, 1.0), (pertim2, 90, 1.0))
flopy.mf6.ModflowTdis(sim, nper=nper, perioddata=tdis_ds, time_units=time_units)
flopy.mf6.ModflowIms(sim, linear_acceleration="bicgstab")
gwt = flopy.mf6.ModflowGwt(sim, modelname=name, save_flows=True)
flopy.mf6.ModflowGwtdis(
gwt,
length_units=length_units,
nlay=nlay,
nrow=nrow,
ncol=ncol,
delr=delr,
delc=delc,
top=top,
botm=botm,
)
if zero_order_decay:
first_order_decay = False
else:
first_order_decay = True
if distribution_coefficient > 0:
sorption = "linear"
bd = bulk_density
kd = distribution_coefficient
else:
sorption = None
bd = None
kd = None
flopy.mf6.ModflowGwtic(gwt, strt=0)
flopy.mf6.ModflowGwtmst(
gwt,
zero_order_decay=zero_order_decay,
first_order_decay=first_order_decay,
sorption=sorption,
porosity=porosity / (1.0 - volfrac),
decay=decay,
decay_sorbed=decay_sorbed,
bulk_density=bd,
distcoef=kd,
)
istsorption = sorption is not None
if dual_domain:
flopy.mf6.ModflowGwtist(
gwt,
zero_order_decay=zero_order_decay,
first_order_decay=first_order_decay,
sorption=istsorption,
porosity=porosity_immobile / volfrac,
volfrac=volfrac,
zetaim=zeta_im,
decay=decay,
decay_sorbed=decay_sorbed,
bulk_density=bd,
distcoef=distribution_coefficient,
)
flopy.mf6.ModflowGwtadv(gwt)
flopy.mf6.ModflowGwtdsp(
gwt,
xt3d_off=True,
alh=longitudinal_dispersivity,
ath1=longitudinal_dispersivity,
)
pd = [
("GWFHEAD", "../mf6gwf/flow.hds", None),
("GWFBUDGET", "../mf6gwf/flow.bud", None),
]
flopy.mf6.ModflowGwtfmi(gwt, packagedata=pd)
cnc_spd = {
0: [[(0, 0, 0), 1.0]],
1: [[(0, 0, 0), 0.0]],
}
flopy.mf6.ModflowGwtcnc(gwt, stress_period_data=cnc_spd)
sourcerecarray = [[]]
flopy.mf6.ModflowGwtssm(gwt, sources=sourcerecarray)
obsj = int(obs_xloc / delr) + 1
obs_data = {
f"{name}.obs.csv": [
("myobs", "CONCENTRATION", (0, 0, obsj)),
],
}
obs_package = flopy.mf6.ModflowUtlobs(
gwt, digits=10, print_input=True, continuous=obs_data
)
return sim
def build_mf2005(sim_folder):
print(f"Building mf2005 model...{sim_folder}")
name = "flow"
sim_ws = os.path.join(workspace, sim_folder, "mf2005")
mf = flopy.modflow.Modflow(modelname=name, model_ws=sim_ws, exe_name="mf2005")
pertim1 = source_duration
pertim2 = total_time - source_duration
perlen = [pertim1, pertim2]
dis = flopy.modflow.ModflowDis(
mf,
nlay=nlay,
nrow=nrow,
ncol=ncol,
delr=delr,
delc=delc,
top=top,
botm=botm,
nper=nper,
perlen=perlen,
)
bas = flopy.modflow.ModflowBas(mf)
lpf = flopy.modflow.ModflowLpf(mf)
pcg = flopy.modflow.ModflowPcg(mf)
lmt = flopy.modflow.ModflowLmt(mf)
chd = flopy.modflow.ModflowChd(mf, stress_period_data=[[0, 0, ncol - 1, 1.0, 1.0]])
wel_spd = {
0: [[0, 0, 0, specific_discharge * delc * top]],
1: [[0, 0, 0, specific_discharge * delc * top]],
}
wel = flopy.modflow.ModflowWel(mf, stress_period_data=wel_spd)
return mf
def build_mt3dms(
sim_folder, distribution_coefficient, decay, decay_sorbed, modflowmodel
):
print(f"Building mt3dms model...{sim_folder}")
name = "trans"
sim_ws = os.path.join(workspace, sim_folder, "mt3d")
mt = flopy.mt3d.Mt3dms(
modelname=name,
model_ws=sim_ws,
exe_name="mt3dms",
modflowmodel=modflowmodel,
ftlfilename="../mf2005/mt3d_link.ftl",
)
dt0 = source_duration / 10.0
btn = flopy.mt3d.Mt3dBtn(
mt, laycon=0, prsity=porosity, obs=[(0, 0, 81)], dt0=dt0, ifmtcn=1
)
adv = flopy.mt3d.Mt3dAdv(mt, mixelm=0)
dsp = flopy.mt3d.Mt3dDsp(mt, al=longitudinal_dispersivity)
sp1 = distribution_coefficient
sp2 = 0.0
rc1 = decay
rc2 = decay_sorbed
prsity2 = 0.0
if dual_domain:
prsity2 = porosity_immobile
if distribution_coefficient > 0:
isothm = 6 # dual domain with sorption
sp2 = zeta_im
else:
isothm = 5 # dual domain without sorption
sp2 = zeta_im
rc2 = 0.0
else:
isothm = 1
if distribution_coefficient > 0:
rc2 = decay_sorbed
else:
rc2 = 0
if zero_order_decay:
ireact = 100 # zero order decay
else:
ireact = 1 # first order decay
rct = flopy.mt3d.Mt3dRct(
mt,
isothm=isothm,
ireact=ireact,
igetsc=0,
rhob=bulk_density,
sp1=sp1,
sp2=sp2,
prsity2=prsity2,
rc1=rc1,
rc2=rc2,
)
ssm_spd = {0: [0, 0, 0, 1.0, -1], 1: [0, 0, 0, 0.0, -1]}
ssm = flopy.mt3d.Mt3dSsm(mt, stress_period_data=ssm_spd)
gcg = flopy.mt3d.Mt3dGcg(mt)
return mt
def build_models(sim_name, distribution_coefficient, decay, decay_sorbed):
sim_mf6gwf = build_mf6gwf(sim_name)
sim_mf6gwt = build_mf6gwt(sim_name, distribution_coefficient, decay, decay_sorbed)
sim_mf2005 = build_mf2005(sim_name)
sim_mt3dms = build_mt3dms(
sim_name, distribution_coefficient, decay, decay_sorbed, sim_mf2005
)
return sim_mf6gwf, sim_mf6gwt, sim_mf2005, sim_mt3dms
def write_models(sims, silent=True):
sim_mf6gwf, sim_mf6gwt, sim_mf2005, sim_mt3dms = sims
sim_mf6gwf.write_simulation(silent=silent)
sim_mf6gwt.write_simulation(silent=silent)
sim_mf2005.write_input()
sim_mt3dms.write_input()
@timed
def run_models(sims, silent=True):
sim_mf6gwf, sim_mf6gwt, sim_mf2005, sim_mt3dms = sims
success, buff = sim_mf6gwf.run_simulation(silent=silent, report=True)
assert success, pformat(buff)
success, buff = sim_mf6gwt.run_simulation(silent=silent, report=True)
assert success, pformat(buff)
success, buff = sim_mf2005.run_model(silent=silent, report=True)
assert success, pformat(buff)
success, buff = sim_mt3dms.run_model(
silent=silent, normal_msg="Program completed", report=True
)
assert success, pformat(buff)
Plotting results
Define functions to plot model results.
[4]:
# Figure properties
figure_size = (3, 3)
def plot_results():
with styles.USGSPlot():
fig, axs = plt.subplots(1, 1, figsize=figure_size, dpi=300, tight_layout=True)
case_colors = ["blue", "green", "red"]
for icase, sim_name in enumerate(parameters.keys()):
sim_ws = os.path.join(workspace, sim_name)
fname = os.path.join(sim_ws, "mf6gwt", "trans.obs.csv")
mf6gwt_ra = flopy.utils.Mf6Obs(fname).data
axs.plot(
mf6gwt_ra["totim"],
mf6gwt_ra["MYOBS"],
markerfacecolor="None",
markeredgecolor="k",
marker="o",
markersize="4",
linestyle="None",
)
fname = os.path.join(sim_ws, "mt3d", "MT3D001.OBS")
mt3dms_ra = flopy.mt3d.Mt3dms.load_obs(fname)
axs.plot(
mt3dms_ra["time"],
mt3dms_ra["(1, 1, 82)"],
color=case_colors[icase],
label=f"Scenario {icase + 1}",
)
axs.set_ylim(0, 16)
axs.set_xlabel("Time (days)")
axs.set_ylabel("Normalized Concentration (unitless)")
axs.legend()
if plot_show:
plt.show()
if plot_save:
fname = "{}{}".format("ex-gwt-mt3dsupp632", ".png")
fpth = figs_path / fname
fig.savefig(fpth)
def plot_scenario_results(sims, idx):
_, sim_mf6gwt, _, sim_mt3dms = sims
with styles.USGSPlot():
mf6gwt_ra = sim_mf6gwt.get_model("trans").obs.output.obs().data
fig, axs = plt.subplots(1, 1, figsize=figure_size, dpi=300, tight_layout=True)
axs.plot(
mf6gwt_ra["totim"],
mf6gwt_ra["MYOBS"],
markerfacecolor="None",
markeredgecolor="b",
marker="o",
markersize="4",
linestyle="None",
label="MODFLOW 6 GWT",
)
sim_ws = sim_mt3dms.model_ws
fname = os.path.join(sim_ws, "MT3D001.OBS")
mt3dms_ra = sim_mt3dms.load_obs(fname)
axs.plot(
mt3dms_ra["time"],
mt3dms_ra["(1, 1, 82)"],
linestyle="-",
color="k",
label="MT3DMS",
)
axs.legend()
title = f"Case {idx + 1} "
letter = chr(ord("@") + idx + 1)
styles.heading(letter=letter, heading=title)
if plot_show:
plt.show()
if plot_save:
sim_folder = os.path.split(sim_ws)[0]
sim_folder = os.path.basename(sim_folder)
fname = f"{sim_folder}.png"
fpth = figs_path / fname
fig.savefig(fpth)
Running the example
Define and invoke a function to run the example scenario, then plot results.
[5]:
def scenario(idx, silent=True):
key = list(parameters.keys())[idx]
parameter_dict = parameters[key]
sims = build_models(key, **parameter_dict)
if write:
write_models(sims, silent=silent)
if run:
run_models(sims, silent=silent)
if plot:
plot_scenario_results(sims, idx)
# ### Case 1
#
# ex-gwt-mt3dsupp632a
# * distribution_coefficient = 0.25
# * decay = 0.0
# * decay_sorbed = -1.0e-3
scenario(0)
# ### Case 2
#
# ex-gwt-mt3dsupp632a
# * distribution_coefficient = 0.25
# * decay = -5.e-4
# * decay_sorbed = -5.e-4
scenario(1)
# ### Case 3
#
# ex-gwt-mt3dsupp632a
# * distribution_coefficient = 0.
# * decay = -1.0e-3
# * decay_sorbed = 0.
scenario(2)
# Plot the results for all 3 scenarios in one plot.
if plot:
plot_results()
Building mf6gwf model...ex-gwt-mt3dsupp632a
Building mf6gwt model...ex-gwt-mt3dsupp632a
Building mf2005 model...ex-gwt-mt3dsupp632a
Building mt3dms model...ex-gwt-mt3dsupp632a
run_models took 112.58 ms
Building mf6gwf model...ex-gwt-mt3dsupp632b
Building mf6gwt model...ex-gwt-mt3dsupp632b
Building mf2005 model...ex-gwt-mt3dsupp632b
Building mt3dms model...ex-gwt-mt3dsupp632b
run_models took 112.94 ms
Building mf6gwf model...ex-gwt-mt3dsupp632c
Building mf6gwt model...ex-gwt-mt3dsupp632c
Building mf2005 model...ex-gwt-mt3dsupp632c
Building mt3dms model...ex-gwt-mt3dsupp632c
run_models took 105.95 ms
