MODFLOW Python Interface Examples¶
A way to access MODFLOW using Python and Jupyter Notebooks is avaliable at
FloPy: Python Package for Creating, Running, and Post-Processing MODFLOW-Based Models
The PDF link below shows the installation and an example run on the AWS server.
MODFLOW on a Jupyter Server - notes
Examples¶
The remainder of this section is worked examples using FLOPY and MODFLOW6 installed on a aarch-64 computer. x86-... architectures should use the ! get-modflow method to download (in near real time) current binaries
Unsteady Example¶
This example is adapted from the Obleo aquifer case, with modifications to make into an unsteady model.
import warnings
warnings.filterwarnings('ignore')
import os
import numpy as np
import matplotlib.pyplot as plt
import flopy
#dir(flopy.mf6)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# Workspace and Executibles
binary = "/home/sensei/ce-4363-webroot/ModflowExperimental/mf6-arm/mf6" # location on MY computer of the compiled modflow program
workarea = "/home/sensei/ce-4363-webroot/ModflowExperimental/mf6-arm/example_3" # location on MY computer to store files this example (directory must already exist)
# Set Simulation Name
name = "example_3"
#modelname=name
##### FLOPY Build simulation framework ####
sim = flopy.mf6.MFSimulation(
sim_name=name, exe_name=binary, version="mf6", sim_ws=workarea
)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# Set Time Structure
Time_Units="YEARS"
# Multiple stress periods
nper = 3 # how many periods
perlen = [1.0, 100.0, 100.0] # how long each one
nstp = [1, 100, 100] # how many steps in each
steady = [True, False, False] # which ones are steady
perioddata = [(1.0,1,1),(30.0,30,1),(30.0,30,1)]
##### FLOPY Build time framework ##########
tdis = flopy.mf6.ModflowTdis(
sim, pname="tdis", time_units=Time_Units, nper=3, perioddata=perioddata,
)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# Set Iterative Model Solution (choose solver parameters)
# about IMS see: https://water.usgs.gov/nrp/gwsoftware/ModelMuse/Help/sms_sparse_matrix_solution_pac.htm
# using defaults see: https://flopy.readthedocs.io/en/3.3.2/source/flopy.mf6.modflow.mfims.html
##### FLOPY Build IMS framework ###########
ims = flopy.mf6.ModflowIms(sim, pname="ims", complexity="SIMPLE")
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# Set Model Name (using same base name as the simulation)
model_nam_file = "{}.nam".format(name)
##### FLOPY Build Model Name framework ####
gwf = flopy.mf6.ModflowGwf(sim, modelname=name, model_nam_file=model_nam_file)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# Define The Grid
Nlay = 1 #number layers
Nrow = 11 #number rows
Ncol = 11 #number columns
# Define distances and elevations
delrow = 1000 # cell size along columns (how tall is a row)
delcol = 1000 # cell size along row (how wide is a column)
topelev = 100.0 # elevation of top of aquifer
thick = 1000.0 #aquifer thickness
bot = [topelev-thick] # bot is a list with Nlay entries
#print(bot)
##### FLOPY Build Model Grid framework #####
dis = flopy.mf6.ModflowGwfdis(gwf,nlay=Nlay,nrow=Nrow,ncol=Ncol,delr=delrow,delc=delcol,top=topelev,botm=bot,
)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# Define initial conditions
h1 = 0.0 #
start = h1 * np.ones((Nlay, Nrow, Ncol)) # start heads are h1 everywhere
##### FLOPY Build Initial Conditions framework ###
ic = flopy.mf6.ModflowGwfic(gwf, pname="ic", strt=start)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# Define hydraulic conductivity arrays
K = 3650.0
k = K * np.ones((Nlay, Nrow, Ncol)) # Hydraulic conductivity is K everywhere
# Use above to build layer-by-layer spatial varying K
# need to read: to deal with Kx!=Ky
##### FLOPY Build BCF framework ######
npf = flopy.mf6.ModflowGwfnpf(gwf, icelltype=1, k=k, save_flows=True)
# setting icelltype > 0 is unconfined
# https://flopy.readthedocs.io/en/3.3.5/source/flopy.mf6.modflow.mfgwfnpf.html?highlight=icelltype#flopy.mf6.modflow.mfgwfnpf.ModflowGwfnpf.icelltype
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# Define the storativity arrays
Sy = 0.25 # specific yield
Ss = 2.5e-4 # specific storage
sto = flopy.mf6.ModflowGwfsto(gwf, sy=Sy)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# Define constant head boundary conditions - these need to be supplied for each stress period
chd_rec = []
#h2 = 90 # Just a different value
#chd_rec.append(((0, 5, 5), h2))
# L,R,T,B constant head boundaries
for layer in range(0, Nlay):
for row in range(0, Nrow):
chd_rec.append(((layer, row, 0), h1)) #left column held at h1
chd_rec.append(((layer, row, Ncol-1), h1)) #right column held at h1
# for col in range(1,Ncol-1):
# chd_rec.append(((layer, 0, col), h1)) # top row held at h1
# chd_rec.append(((layer, Nrow-1 , col), h1)) # bottom row held at h1
stress_period_data = {0: chd_rec, 1: chd_rec, 2: chd_rec} # dictionary same BC each stress period
##### FLOPY Build CHD framework #####
chd = flopy.mf6.ModflowGwfchd(gwf,maxbound=len(chd_rec),stress_period_data=stress_period_data,save_flows=True,
)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# Define wellfields
#wel_rec = []
# wel_rec.append((0, 5, 5, -0e6)) # 0 Mm3/yr - use to examine recharge only
#wel_rec.append((0, 5, 5, -2114e6)) # 2,114 Mm3/yr
# Multiple Stress Periods
pumping_rate = -1000e6
wel_sp1 = [[0, 5, 5, 0.0]]
wel_sp2 = [[0, 5, 5, 1*pumping_rate]]
wel_sp3 = [[0, 5, 5, 2.115*pumping_rate]]
stress_period_data = {0: wel_sp1, 1: wel_sp2, 2: wel_sp3}
#wel = flopy.modflow.ModflowWel(mf, stress_period_data=stress_period_data)
##### FLOPY Build Wellfields framework #####
wel = flopy.mf6.ModflowGwfwel(gwf,maxbound=1,stress_period_data=stress_period_data,)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# Define recharge
rech_val = 0.25 # rate as depth/year
rech_rec = rech_val * np.ones((1, Nrow, Ncol)) # set recharge top layer only
rec_sp1 = rech_rec
rec_sp2 = rech_rec
rec_sp3 = rech_rec
stress_period_data = {0: rec_sp1, 1: rec_sp2, 2: rec_sp3}
rch = flopy.mf6.ModflowGwfrcha(gwf, maxbound=len(rech_rec),recharge=stress_period_data,)
#rch = flopy.mf6.ModflowGwfrcha(gwf, recharge=rech_val) # default entry format
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# something to do with stress periods
iper = 0
ra = chd.stress_period_data.get_data(key=iper)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# Create the output control (`OC`) Package
headfile = "{}.hds".format(name)
head_filerecord = [headfile]
budgetfile = "{}.cbb".format(name)
budget_filerecord = [budgetfile]
saverecord = [("HEAD", "ALL"), ("BUDGET", "ALL")]
printrecord = [("HEAD", "LAST")]
##### FLOPY Build OC framework
oc = flopy.mf6.ModflowGwfoc(
gwf,
saverecord=saverecord,
head_filerecord=head_filerecord,
budget_filerecord=budget_filerecord,
printrecord=printrecord,
)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# Write files to the directory
sim.write_simulation()
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
writing simulation...
writing simulation name file...
writing simulation tdis package...
writing ims package ims...
writing model example_3...
writing model name file...
writing package dis...
writing package ic...
writing package npf...
writing package sto...
writing package chd_0...
writing package wel_0...
writing package rcha_0...
writing package oc...
# Attempt to run MODFLOW this model
success, buff = sim.run_simulation()
if not success:
raise Exception("MODFLOW 6 did not terminate normally.")
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
FloPy is using the following executable to run the model: /home/sensei/ce-4363-webroot/ModflowExperimental/mf6-arm/mf6
MODFLOW 6
U.S. GEOLOGICAL SURVEY MODULAR HYDROLOGIC MODEL
VERSION 6.4.1 Release 12/09/2022
MODFLOW 6 compiled Apr 16 2023 18:27:14 with GCC version 9.4.0
This software has been approved for release by the U.S. Geological
Survey (USGS). Although the software has been subjected to rigorous
review, the USGS reserves the right to update the software as needed
pursuant to further analysis and review. No warranty, expressed or
implied, is made by the USGS or the U.S. Government as to the
functionality of the software and related material nor shall the
fact of release constitute any such warranty. Furthermore, the
software is released on condition that neither the USGS nor the U.S.
Government shall be held liable for any damages resulting from its
authorized or unauthorized use. Also refer to the USGS Water
Resources Software User Rights Notice for complete use, copyright,
and distribution information.
Run start date and time (yyyy/mm/dd hh:mm:ss): 2024/02/01 17:44:22
Writing simulation list file: mfsim.lst
Using Simulation name file: mfsim.nam
Solving: Stress period: 1 Time step: 1
Solving: Stress period: 2 Time step: 1
Solving: Stress period: 2 Time step: 2
Solving: Stress period: 2 Time step: 3
Solving: Stress period: 2 Time step: 4
Solving: Stress period: 2 Time step: 5
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Solving: Stress period: 2 Time step: 30
Solving: Stress period: 3 Time step: 1
Solving: Stress period: 3 Time step: 2
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Solving: Stress period: 3 Time step: 4
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Solving: Stress period: 3 Time step: 20
Solving: Stress period: 3 Time step: 21
Solving: Stress period: 3 Time step: 22
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Solving: Stress period: 3 Time step: 24
Solving: Stress period: 3 Time step: 25
Solving: Stress period: 3 Time step: 26
Solving: Stress period: 3 Time step: 27
Solving: Stress period: 3 Time step: 28
Solving: Stress period: 3 Time step: 29
Solving: Stress period: 3 Time step: 30
Run end date and time (yyyy/mm/dd hh:mm:ss): 2024/02/01 17:44:22
Elapsed run time: 0.137 Seconds
Normal termination of simulation.
# now attempt to postprocess
h = gwf.output.head().get_data(kstpkper=(0, 0))
print(h[0].max())
x = np.linspace(0, delrow*Ncol, Ncol)
y = np.linspace(0, delrow*Nrow, Nrow)
y = y[::-1]
vmin, vmax = -200., 100.0
contour_intervals = np.arange(-10., 1.0, 0.1)
# ### Plot a Map of Layer 1
fig = plt.figure(figsize=(9, 9))
ax = fig.add_subplot(1, 1, 1, aspect="equal")
c = ax.contour(x, y, h[0], contour_intervals, colors="black")
plt.title("Obleo Aquifer Example 2 Head Map at Time = PreDevelopment ")
plt.xlabel("Easting (meters)")
plt.ylabel("Northing (meters)")
plt.clabel(c, fmt="%2.1f");
0.9213486227356542
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# ### Use the FloPy `PlotMapView()` capabilities for MODFLOW 6
fig = plt.figure(figsize=(9, 9))
ax = fig.add_subplot(1, 1, 1, aspect="equal")
ax.set_title("Obleo Aquifer Example 2 \n Head Map")
ax.set_xlabel("Easting (meters)")
ax.set_ylabel("Northing (meters)")
modelmap = flopy.plot.PlotMapView(model=gwf, ax=ax)
pa = modelmap.plot_array(h, vmin=-900, vmax=100)
quadmesh = modelmap.plot_bc("CHD")
linecollection = modelmap.plot_grid(lw=0.5, color="0.5")
contours = modelmap.contour_array(
h,
levels=contour_intervals,
colors="black",
)
ax.clabel(contours, fmt="%2.1f")
cb = plt.colorbar(pa, shrink=0.5, ax=ax)
cb.set_label(' Head (meters) ', rotation=90)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# now attempt to postprocess
h = gwf.output.head().get_data(kstpkper=(0, 1))
#print(h[0].min())
x = np.linspace(0, delrow*Ncol, Ncol)
y = np.linspace(0, delrow*Nrow, Nrow)
y = y[::-1]
vmin, vmax = -200., 100.0
contour_intervals = np.arange(-200., 1.0, 10)
# ### Plot a Map of Layer 1
fig = plt.figure(figsize=(9, 9))
ax = fig.add_subplot(1, 1, 1, aspect="equal")
c = ax.contour(x, y, h[0], contour_intervals, colors="black")
plt.title("Obleo Aquifer Example 2 Head Map at Time = 30 years ")
plt.xlabel("Easting (meters)")
plt.ylabel("Northing (meters)")
plt.clabel(c, fmt="%2.1f");
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# ### Use the FloPy `PlotMapView()` capabilities for MODFLOW 6
fig = plt.figure(figsize=(9, 9))
ax = fig.add_subplot(1, 1, 1, aspect="equal")
ax.set_title("Obleo Aquifer Example 2 \n Head Map at Time = 30 years ")
ax.set_xlabel("Easting (meters)")
ax.set_ylabel("Northing (meters)")
modelmap = flopy.plot.PlotMapView(model=gwf, ax=ax)
pa = modelmap.plot_array(h, vmin=-900, vmax=100)
quadmesh = modelmap.plot_bc("CHD")
linecollection = modelmap.plot_grid(lw=0.5, color="0.5")
contours = modelmap.contour_array(
h,
levels=contour_intervals,
colors="black",
)
ax.clabel(contours, fmt="%2.1f")
cb = plt.colorbar(pa, shrink=0.5, ax=ax)
cb.set_label(' Head (meters) ', rotation=90)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
# now attempt to postprocess
h = gwf.output.head().get_data(kstpkper=(0, 2))
print(h[0].max())
x = np.linspace(0, delrow*Ncol, Ncol)
y = np.linspace(0, delrow*Nrow, Nrow)
y = y[::-1]
vmin, vmax = -200., 100.0
contour_intervals = np.arange(-200., 1.0, 10)
# ### Plot a Map of Layer 1
fig = plt.figure(figsize=(9, 9))
ax = fig.add_subplot(1, 1, 1, aspect="equal")
c = ax.contour(x, y, h[0], contour_intervals, colors="black")
plt.title("Obleo Aquifer Example 2 Head Map at Time = 60 years ")
plt.xlabel("Easting (meters)")
plt.ylabel("Northing (meters)")
plt.clabel(c, fmt="%2.1f");
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
0.0
# ### Use the FloPy `PlotMapView()` capabilities for MODFLOW 6
fig = plt.figure(figsize=(9, 9))
ax = fig.add_subplot(1, 1, 1, aspect="equal")
ax.set_title("Obleo Aquifer Example 2 \n Head Map at Time = 60 years ")
ax.set_xlabel("Easting (meters)")
ax.set_ylabel("Northing (meters)")
modelmap = flopy.plot.PlotMapView(model=gwf, ax=ax)
pa = modelmap.plot_array(h, vmin=-900, vmax=100)
quadmesh = modelmap.plot_bc("CHD")
linecollection = modelmap.plot_grid(lw=0.5, color="0.5")
contours = modelmap.contour_array(
h,
levels=contour_intervals,
colors="black",
)
ax.clabel(contours, fmt="%2.1f")
cb = plt.colorbar(pa, shrink=0.5, ax=ax)
cb.set_label(' Head (meters) ', rotation=90)
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
Now for pretty mapping!
So this is the working model, so now we can assess effect of pumping and decide if we can increase the pumping any We already have this information contained in the output object.
print("Minimum allowed is -650.0 meters")
#print("Pumping at P-1 is:",wel_rec[0][3]/1e6," Mm^3/yr")
print("Minimum Head is:",round(h[0].min(),1)," meters")
if h[0].min() < -650.0:
print("Computed head is below allowed value - reduce pumpage and rerun simulation")
Minimum allowed is -650.0 meters
Minimum Head is: -552.3 meters
/opt/jupyterhub/lib/python3.8/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
and should_run_async(code)
References¶
MODFLOW Notes (Cleveland circa 1992) The Obleo Aquifer simulation in the MODFLOW88 video is described in these notes.
MODFLOW Manual (US EPA) An EPA training document on the use of MODFLOW