ex-gwt-mt3dms-p06.py

# ## Concentration at an Injection/Extraction Well, Comparison of MODFLOW 6 transport with MT3DMS
#
# The purpose of this script is to (1) recreate the example problems that were first
# described in the 1999 MT3DMS report, and (2) compare MF6-GWT solutions to the
# established MT3DMS solutions.
#
# Ten example problems appear in the 1999 MT3DMS manual, starting on page 130.  This
# notebook demonstrates example 6 from the list below:
#
#   1. One-Dimensional Transport in a Uniform Flow Field
#   2. One-Dimensional Transport with Nonlinear or Nonequilibrium Sorption
#   3. Two-Dimensional Transport in a Uniform Flow Field
#   4. Two-Dimensional Transport in a Diagonal Flow Field
#   5. Two-Dimensional Transport in a Radial Flow Field
#   6. _Concentration at an Injection/Extraction Well_
#   7. Three-Dimensional Transport in a Uniform Flow Field
#   8. Two-Dimensional, Vertical Transport in a Heterogeneous Aquifer
#   9. Two-Dimensional Application Example
#   10. Three-Dimensional Field Case Study

# ### Initial setup
#
# Import dependencies, define the example name and workspace, and read settings from environment variables.

# +
import os
import pathlib as pl
from pprint import pformat

import flopy
import matplotlib.pyplot as plt
import numpy as np
from flopy.plot.styles import styles
from modflow_devtools.misc import get_env, timed

# Settings from environment variable
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)

# Example name and base workspace
workspace = pl.Path("../examples")
example_name = "ex-gwt-mt3dms-p06"
# -

# ### Define parameters
#
# Define model units, parameters and other settings.

# +
# Model units
length_units = "feet"
time_units = "days"

# Model parameters
nlay = 1  # Number of layers
nrow = 31  # Number of rows
ncol = 31  # Number of columns
delr = 900.0  # Column width ($ft$)
delc = 900.0  # Row width ($ft$)
delz = 20.0  # Layer thickness ($ft$)
top = 0.0  # Top of the model ($ft$)
prsity = 0.35  # Porosity
dum1 = 2.5  # Length of the injection period ($years$)
dum2 = 7.5  # Length of the extraction period ($years$)
k11 = 432.0  # Horizontal hydraulic conductivity ($ft/d$)
qwell = 1.0  # Volumetric injection rate ($ft^3/d$)
cwell = 100.0  # Relative concentration of injected water ($\%$)
al = 100.0  # Longitudinal dispersivity ($ft$)
trpt = 1.0  # Ratio of transverse to longitudinal dispersitivity

# Additional model input
perlen = [912.5, 2737.5]
nper = len(perlen)
nstp = [365, 1095]
tsmult = [1.0, 1.0]
k11 = 0.005 * 86400  # established above, but explicitly writing out its origin here
sconc = 0.0
c0 = 0.0
dt0 = 56.25
dmcoef = 0
ath1 = al * trpt
botm = [top - delz]  # Model geometry
k33 = k11  # Vertical hydraulic conductivity ($m/d$)
icelltype = 0
mixelm = -1
strt = np.zeros((nlay, nrow, ncol), dtype=float)

# Active model domain
ibound_mf2k5 = np.ones((nlay, nrow, ncol), dtype=int) * -1
ibound_mf2k5[:, 1 : nrow - 1, 1 : ncol - 1] = 1
idomain = np.ones((nlay, nrow, ncol), dtype=int)
icbund = 1

# Boundary conditions
# MF2K5 pumping info:
qwell = 86400.0
welspd = {
    0: [[0, 15, 15, qwell]],  # Well pumping info for MF2K5
    1: [[0, 15, 15, -qwell]],
}
cwell = 100.0
spd = {
    0: [0, 15, 15, cwell, 2],  # Well pupming info for MT3DMS
    1: [0, 15, 15, 0.0, 2],
}

# MF6 pumping information
#          (k,  i,  j),  flow,  conc
spd_mf6 = {0: [[(0, 15, 15), qwell, cwell]], 1: [[(0, 15, 15), -qwell, 0.0]]}

# MF6 constant head boundaries:
chdspd = []
# Loop through the left & right sides.
for i in np.arange(nrow):
    chdspd.append([(0, i, 0), strt[0, i, 0]])
    chdspd.append([(0, i, ncol - 1), strt[0, i, ncol - 1]])
# Loop through the top & bottom while omitting the corner cells
for j in np.arange(1, ncol - 1):
    chdspd.append([(0, 0, j), strt[0, 0, j]])
    chdspd.append([(0, nrow - 1, j), strt[0, nrow - 1, j]])

chdspd = {0: chdspd}

# Solver settings
nouter, ninner = 100, 300
hclose, rclose, relax = 1e-6, 1e-6, 1.0
percel = 1.0  # HMOC parameters
itrack = 3
wd = 0.5
dceps = 1.0e-5
nplane = 1
npl = 0
nph = 16
npmin = 2
npmax = 32
dchmoc = 1.0e-3
nlsink = nplane
npsink = nph

# Time discretization
tdis_rc = []
tdis_rc.append((perlen, nstp, 1.0))
# -

# ### Model setup
#
# Define functions to build models, write input files, and run the simulation.


# +
def build_models(sim_name, mixelm=0, silent=False):
    mt3d_ws = os.path.join(workspace, sim_name, "mt3d")
    modelname_mf = "p06-mf"

    # Instantiate the MODFLOW model
    mf = flopy.modflow.Modflow(
        modelname=modelname_mf, model_ws=mt3d_ws, exe_name="mf2005"
    )

    # Instantiate discretization package
    # units: itmuni=4 (days), lenuni=2 (m)
    flopy.modflow.ModflowDis(
        mf,
        nlay=nlay,
        nrow=nrow,
        ncol=ncol,
        delr=delr,
        delc=delc,
        top=top,
        botm=botm,
        nper=nper,
        nstp=nstp,
        perlen=perlen,
        itmuni=4,
        lenuni=1,
    )

    # Instantiate basic package
    flopy.modflow.ModflowBas(mf, ibound=ibound_mf2k5, strt=strt)

    # Instantiate layer property flow package
    flopy.modflow.ModflowLpf(mf, hk=k11, laytyp=icelltype)

    # Instantiate well package
    flopy.modflow.ModflowWel(mf, stress_period_data=welspd)

    # Instantiate solver package
    flopy.modflow.ModflowSip(mf)

    # Instantiate link mass transport package (for writing linker file)
    flopy.modflow.ModflowLmt(mf)

    # Transport
    modelname_mt = "p06-mt"
    mt = flopy.mt3d.Mt3dms(
        modelname=modelname_mt,
        model_ws=mt3d_ws,
        exe_name="mt3dusgs",
        modflowmodel=mf,
    )

    # Instantiate basic transport package
    flopy.mt3d.Mt3dBtn(
        mt,
        icbund=icbund,
        prsity=prsity,
        sconc=sconc,
        nper=nper,
        perlen=perlen,
        dt0=dt0,
        obs=[(0, 15, 15)],
    )

    # Instatiate the advection package
    flopy.mt3d.Mt3dAdv(
        mt,
        mixelm=mixelm,
        dceps=dceps,
        nplane=nplane,
        npl=npl,
        nph=nph,
        npmin=npmin,
        npmax=npmax,
        nlsink=nlsink,
        npsink=npsink,
        percel=percel,
        itrack=itrack,
        wd=wd,
    )

    # Instantiate the dispersion package
    flopy.mt3d.Mt3dDsp(mt, al=al, trpt=trpt, dmcoef=dmcoef)

    # Instantiate the source/sink mixing package
    flopy.mt3d.Mt3dSsm(mt, stress_period_data=spd)

    # Instantiate the GCG solver in MT3DMS
    flopy.mt3d.Mt3dGcg(mt)

    # MODFLOW 6
    name = "p06-mf6"
    gwfname = "gwf-" + name
    sim_ws = os.path.join(workspace, sim_name)
    sim = flopy.mf6.MFSimulation(sim_name=sim_name, sim_ws=sim_ws, exe_name="mf6")

    # Instantiating MODFLOW 6 time discretization
    tdis_rc = []
    for i in range(nper):
        tdis_rc.append((perlen[i], nstp[i], tsmult[i]))
    flopy.mf6.ModflowTdis(sim, nper=nper, perioddata=tdis_rc, time_units=time_units)

    # Instantiating MODFLOW 6 groundwater flow model
    gwf = flopy.mf6.ModflowGwf(
        sim,
        modelname=gwfname,
        save_flows=True,
        model_nam_file=f"{gwfname}.nam",
    )

    # Instantiating MODFLOW 6 solver for flow model
    imsgwf = flopy.mf6.ModflowIms(
        sim,
        print_option="SUMMARY",
        outer_dvclose=hclose,
        outer_maximum=nouter,
        under_relaxation="NONE",
        inner_maximum=ninner,
        inner_dvclose=hclose,
        rcloserecord=rclose,
        linear_acceleration="CG",
        scaling_method="NONE",
        reordering_method="NONE",
        relaxation_factor=relax,
        filename=f"{gwfname}.ims",
    )
    sim.register_ims_package(imsgwf, [gwf.name])

    # Instantiating MODFLOW 6 discretization package
    flopy.mf6.ModflowGwfdis(
        gwf,
        length_units=length_units,
        nlay=nlay,
        nrow=nrow,
        ncol=ncol,
        delr=delr,
        delc=delc,
        top=top,
        botm=botm,
        idomain=idomain,
        filename=f"{gwfname}.dis",
    )

    # Instantiating MODFLOW 6 node-property flow package
    flopy.mf6.ModflowGwfnpf(
        gwf,
        save_flows=False,
        icelltype=icelltype,
        k=k11,
        k33=k33,
        save_specific_discharge=True,
        filename=f"{gwfname}.npf",
    )

    # Instantiating MODFLOW 6 storage package (steady flow conditions, so no actual storage, using to print values in .lst file)
    flopy.mf6.ModflowGwfsto(gwf, ss=0, sy=0, filename=f"{gwfname}.sto")

    # Instantiating MODFLOW 6 initial conditions package for flow model
    flopy.mf6.ModflowGwfic(gwf, strt=strt, filename=f"{gwfname}.ic")

    # Instantiating MODFLOW 6 constant head package
    flopy.mf6.ModflowGwfchd(
        gwf,
        maxbound=len(chdspd),
        stress_period_data=chdspd,
        save_flows=False,
        pname="CHD-1",
        filename=f"{gwfname}.chd",
    )

    # Instantiate the wel package
    flopy.mf6.ModflowGwfwel(
        gwf,
        print_input=True,
        print_flows=True,
        stress_period_data=spd_mf6,
        save_flows=False,
        auxiliary="CONCENTRATION",
        pname="WEL-1",
        filename=f"{gwfname}.wel",
    )

    # Instantiating MODFLOW 6 output control package for flow model
    flopy.mf6.ModflowGwfoc(
        gwf,
        head_filerecord=f"{gwfname}.hds",
        budget_filerecord=f"{gwfname}.bud",
        headprintrecord=[("COLUMNS", 10, "WIDTH", 15, "DIGITS", 6, "GENERAL")],
        saverecord=[("HEAD", "LAST"), ("BUDGET", "LAST")],
        printrecord=[("HEAD", "LAST"), ("BUDGET", "LAST")],
    )

    # Instantiating MODFLOW 6 groundwater transport package
    gwtname = "gwt_" + name
    gwt = flopy.mf6.MFModel(
        sim,
        model_type="gwt6",
        modelname=gwtname,
        model_nam_file=f"{gwtname}.nam",
    )
    gwt.name_file.save_flows = True

    # create iterative model solution and register the gwt model with it
    imsgwt = flopy.mf6.ModflowIms(
        sim,
        print_option="SUMMARY",
        outer_dvclose=hclose,
        outer_maximum=nouter,
        under_relaxation="NONE",
        inner_maximum=ninner,
        inner_dvclose=hclose,
        rcloserecord=rclose,
        linear_acceleration="BICGSTAB",
        scaling_method="NONE",
        reordering_method="NONE",
        relaxation_factor=relax,
        filename=f"{gwtname}.ims",
    )
    sim.register_ims_package(imsgwt, [gwt.name])

    # Instantiating MODFLOW 6 transport discretization package
    flopy.mf6.ModflowGwtdis(
        gwt,
        nlay=nlay,
        nrow=nrow,
        ncol=ncol,
        delr=delr,
        delc=delc,
        top=top,
        botm=botm,
        idomain=idomain,
        filename=f"{gwtname}.dis",
    )

    # Instantiating MODFLOW 6 transport initial concentrations
    flopy.mf6.ModflowGwtic(gwt, strt=sconc, filename=f"{gwtname}.ic")

    # Instantiating MODFLOW 6 transport advection package
    if mixelm >= 0:
        scheme = "UPSTREAM"
    elif mixelm == -1:
        scheme = "TVD"
    else:
        raise Exception()
    flopy.mf6.ModflowGwtadv(gwt, scheme=scheme, filename=f"{gwtname}.adv")

    # Instantiating MODFLOW 6 transport dispersion package
    if al != 0:
        flopy.mf6.ModflowGwtdsp(
            gwt,
            xt3d_off=True,
            alh=al,
            ath1=ath1,
            filename=f"{gwtname}.dsp",
        )

    # Instantiating MODFLOW 6 transport mass storage package (formerly "reaction" package in MT3DMS)
    flopy.mf6.ModflowGwtmst(
        gwt,
        porosity=prsity,
        first_order_decay=False,
        decay=None,
        decay_sorbed=None,
        sorption=None,
        bulk_density=None,
        distcoef=None,
        filename=f"{gwtname}.mst",
    )

    # Instantiating MODFLOW 6 transport source-sink mixing package
    sourcerecarray = [("WEL-1", "AUX", "CONCENTRATION")]
    flopy.mf6.ModflowGwtssm(gwt, sources=sourcerecarray, filename=f"{gwtname}.ssm")

    # Instantiating MODFLOW 6 transport output control package
    flopy.mf6.ModflowGwtoc(
        gwt,
        budget_filerecord=f"{gwtname}.cbc",
        concentration_filerecord=f"{gwtname}.ucn",
        concentrationprintrecord=[("COLUMNS", 10, "WIDTH", 15, "DIGITS", 6, "GENERAL")],
        saverecord=[("CONCENTRATION", "LAST"), ("BUDGET", "LAST")],
        printrecord=[("CONCENTRATION", "LAST"), ("BUDGET", "LAST")],
    )

    # Instantiate observation package (for transport)
    obslist = [["bckgrnd_cn", "concentration", (0, 15, 15)]]
    obsdict = {f"{gwtname}.obs.csv": obslist}
    obs = flopy.mf6.ModflowUtlobs(gwt, print_input=False, continuous=obsdict)

    # Instantiating MODFLOW 6 flow-transport exchange mechanism
    flopy.mf6.ModflowGwfgwt(
        sim,
        exgtype="GWF6-GWT6",
        exgmnamea=gwfname,
        exgmnameb=gwtname,
        filename=f"{name}.gwfgwt",
    )
    return mf, mt, sim


def write_models(mf2k5, mt3d, sim, silent=True):
    mf2k5.write_input()
    mt3d.write_input()
    sim.write_simulation(silent=silent)


@timed
def run_models(mf2k5, mt3d, sim, silent=True):
    success, buff = mf2k5.run_model(silent=silent, report=True)
    assert success, pformat(buff)
    success, buff = mt3d.run_model(
        silent=silent, normal_msg="Program completed", report=True
    )
    assert success, pformat(buff)
    success, buff = sim.run_simulation(silent=silent, report=True)
    assert success, pformat(buff)


# -

# ### Plotting results
#
# Define functions to plot model results.

# +
# Figure properties
figure_size = (6, 4.5)


def plot_results(mt3d, mf6, idx, ax=None):
    mt3d_out_path = mt3d.model_ws
    mf6_out_path = mf6.simulation_data.mfpath.get_sim_path()
    mf6.simulation_data.mfpath.get_sim_path()

    # Get the MT3DMS observation output file
    fname = os.path.join(mt3d_out_path, "MT3D001.OBS")
    cvt = mt3d.load_obs(fname) if os.path.isfile(fname) else None

    # Get the MODFLOW 6 concentration observation output file
    fname = os.path.join(mf6_out_path, list(mf6.model_names)[1] + ".obs.csv")
    mf6cobs = flopy.utils.Mf6Obs(fname).data

    # Create figure for scenario
    with styles.USGSPlot():
        sim_name = mf6.name
        plt.rcParams["lines.dashed_pattern"] = [5.0, 5.0]
        if ax is None:
            fig = plt.figure(figsize=figure_size, dpi=300, tight_layout=True)
            ax = fig.add_subplot(1, 1, 1)

        x = cvt["time"] / 365.0
        y = cvt["(1, 16, 16)"]
        # Pare down the list length to clean plot
        x_pare = x[::20]
        y_pare = y[::20]
        ax.plot(x_pare, y_pare, label="Upstream FD", marker="^")

        # Add MF6 output
        x_mf6 = mf6cobs["totim"] / 365.0
        y_mf6 = mf6cobs["BCKGRND_CN"]
        x_mf6_pare = x_mf6[::20]
        y_mf6_pare = y_mf6[::20]
        ax.plot(
            x_mf6_pare,
            y_mf6_pare,
            label="MODFLOW 6",
            marker="x",
            linestyle=":",
        )

        plt.xlim(0, 10)
        plt.ylim(0, 100.0)
        plt.xlabel("Time, in years")
        plt.ylabel("Normalized Concentration, in percent")
        plt.legend()
        title = "Calculated Concentration at an Injection/Pumping Well"

        letter = chr(ord("@") + idx + 1)
        styles.heading(letter=letter, heading=title)

        if plot_show:
            plt.show()
        if plot_save:
            fpth = os.path.join(
                "..",
                "figures",
                f"{sim_name}.png",
            )
            fig.savefig(fpth)


# -

# ### Running the example
#
# Define and invoke a function to run the example scenario, then plot results.


# +
def scenario(idx, silent=True):
    mf2k5, mt3d, sim = build_models(example_name, mixelm=mixelm)
    if write:
        write_models(mf2k5, mt3d, sim, silent=silent)
    if run:
        run_models(mf2k5, mt3d, sim, silent=silent)
    if plot:
        plot_results(mt3d, sim, idx)


# Compares the standard finite difference solutions between MT3D and MF6
scenario(0)
# -