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MT3DMS Supplemental Guide Problem 6.3.1
This example is for zero-order production in a uniform flow field. It is based on example problem 6.3.1 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. This example is simulated with a GWT model in, which receives flow information from a GWF model. Results from the GWT model are compared with the results from a MT3DMS simulation that uses flows from a MODFLOW-2005 simulation.
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.
example_name = "ex-gwt-mt3dsupp631"
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]:
# 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 = 101 # Number of columns
delr = 0.16 # 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 = 0.1 # Specific discharge ($md^{-1}$)
longitudinal_dispersivity = 1.0 # Longitudinal dispersivity ($m$)
porosity = 0.37 # Porosity of mobile domain (unitless)
zero_order_decay = -2.0e-3 # Zero-order production rate ($mg/L d^{-1}$)
source_duration = 160.0 # Source duration ($d$)
total_time = 840.0 # Simulation time ($t$)
obs_xloc = 8.0 # Observation x location ($m$)
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]],
1: [[(0, 0, 0), specific_discharge * delc * top, 0.0]],
}
flopy.mf6.ModflowGwfwel(
gwf,
stress_period_data=wel_spd,
pname="WEL-1",
auxiliary=["CONCENTRATION"],
)
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):
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, 16, 1.0), (pertim2, 84, 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,
)
flopy.mf6.ModflowGwtic(gwt, strt=0)
flopy.mf6.ModflowGwtmst(
gwt, zero_order_decay=True, porosity=porosity, decay=zero_order_decay
)
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)
sourcerecarray = [["WEL-1", "AUX", "CONCENTRATION"]]
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, 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 = 10.0
obsj = int(obs_xloc / delr) + 1
btn = flopy.mt3d.Mt3dBtn(
mt, laycon=0, prsity=porosity, obs=[(0, 0, obsj)], dt0=dt0, ifmtcn=1
)
adv = flopy.mt3d.Mt3dAdv(mt, mixelm=0)
dsp = flopy.mt3d.Mt3dDsp(mt, al=longitudinal_dispersivity)
rc1 = zero_order_decay
ireact = 100 # zero order decay
rct = flopy.mt3d.Mt3dRct(mt, igetsc=0, ireact=ireact, rc1=rc1)
ssm_spd = {0: [0, 0, 0, 1.0, 2], 1: [0, 0, 0, 0.0, 2]}
ssm = flopy.mt3d.Mt3dSsm(mt, mxss=3, stress_period_data=ssm_spd)
gcg = flopy.mt3d.Mt3dGcg(mt)
return mt
def build_models(sim_name):
sim_mf6gwf = build_mf6gwf(sim_name)
sim_mf6gwt = build_mf6gwt(sim_name)
sim_mf2005 = build_mf2005(sim_name)
sim_mt3dms = build_mt3dms(sim_name, 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 = (5, 3)
def plot_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"],
marker="o",
ls="none",
mec="blue",
mfc="none",
markersize="4",
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)
colname = mt3dms_ra.dtype.names[2]
axs.plot(
mt3dms_ra["time"],
mt3dms_ra[colname],
linestyle="-",
color="k",
label="MT3DMS",
)
axs.set_xlabel("Time (days)")
axs.set_ylabel("Normalized Concentration (unitless)")
axs.legend()
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):
sim = build_models(example_name)
if write:
write_models(sim, silent=silent)
if run:
run_models(sim, silent=silent)
if plot:
plot_results(sim, idx)
scenario(0)
Building mf6gwf model...ex-gwt-mt3dsupp631
Building mf6gwt model...ex-gwt-mt3dsupp631
Building mf2005 model...ex-gwt-mt3dsupp631
Building mt3dms model...ex-gwt-mt3dsupp631
run_models took 68.94 ms
