def test_mflist_reference():
import os
import numpy as np
import shapefile
import flopy.modflow as fmf
# model_ws = os.path.join('..', 'data', 'freyberg')
# ml = fmf.Modflow.load('freyberg.nam', model_ws=model_ws)
# make the model
ml = fmf.Modflow()
assert isinstance(ml, fmf.Modflow)
perlen = np.arange(1, 20, 1)
nstp = np.flipud(perlen) + 3
tsmult = 1.2
nlay = 10
nrow, ncol = 50, 40
botm = np.arange(0, -100, -10)
hk = np.random.random((nrow, ncol))
dis = fmf.ModflowDis(ml,
delr=100.0,
delc=100.0,
nrow=nrow,
ncol=ncol,
nlay=nlay,
nper=perlen.shape[0],
perlen=perlen,
nstp=nstp,
tsmult=tsmult,
top=10,
botm=botm,
steady=False)
assert isinstance(dis, fmf.ModflowDis)
lpf = fmf.ModflowLpf(ml, hk=hk, vka=10.0, laytyp=1)
assert isinstance(lpf, fmf.ModflowLpf)
pcg = fmf.ModflowPcg(ml)
assert isinstance(pcg, fmf.ModflowPcg)
oc = fmf.ModflowOc(ml)
assert isinstance(oc, fmf.ModflowOc)
ibound = np.ones((nrow, ncol))
ibound[:, 0] = -1
ibound[25:30, 30:39] = 0
bas = fmf.ModflowBas(ml, strt=5.0, ibound=ibound)
assert isinstance(bas, fmf.ModflowBas)
rch = fmf.ModflowRch(ml, rech={0: 0.00001, 5: 0.0001, 6: 0.0})
assert isinstance(rch, fmf.ModflowRch)
wel_dict = {}
wel_data = [[9, 25, 20, -200], [0, 0, 0, -400], [5, 20, 32, 500]]
wel_dict[0] = wel_data
wel_data2 = [[45, 20, 200], [9, 49, 39, 400], [5, 20, 32, 500]]
wel_dict[10] = wel_data2
wel = fmf.ModflowWel(ml, stress_period_data={0: wel_data})
assert isinstance(wel, fmf.ModflowWel)
ghb_dict = {0: [1, 10, 10, 400, 300]}
ghb = fmf.ModflowGhb(ml, stress_period_data=ghb_dict)
assert isinstance(ghb, fmf.ModflowGhb)
test = os.path.join('temp', 'test3.shp')
ml.export(test, kper=0)
shp = shapefile.Reader(test)
assert shp.numRecords == nrow * ncol
def setup_class(cls):
"""Make a modflow model."""
print("setting up model...")
t0 = time.time()
size = 100
nlay = 10
nper = 10
nsfr = int((size**2) / 5)
cls.modelname = "junk"
cls.model_ws = "temp/t064"
external_path = "external/"
if not os.path.isdir(cls.model_ws):
os.makedirs(cls.model_ws)
if not os.path.isdir(os.path.join(cls.model_ws, external_path)):
os.makedirs(os.path.join(cls.model_ws, external_path))
m = fm.Modflow(cls.modelname,
model_ws=cls.model_ws,
external_path=external_path)
dis = fm.ModflowDis(
m,
nper=nper,
nlay=nlay,
nrow=size,
ncol=size,
top=nlay,
botm=list(range(nlay)),
)
rch = fm.ModflowRch(
m, rech={k: 0.001 - np.cos(k) * 0.001
for k in range(nper)})
ra = fm.ModflowWel.get_empty(size**2)
well_spd = {}
for kper in range(nper):
ra_per = ra.copy()
ra_per["k"] = 1
ra_per["i"] = ((np.ones((size, size)) *
np.arange(size)).transpose().ravel().astype(int))
ra_per["j"] = list(range(size)) * size
well_spd[kper] = ra
wel = fm.ModflowWel(m, stress_period_data=well_spd)
# SFR package
rd = fm.ModflowSfr2.get_empty_reach_data(nsfr)
rd["iseg"] = range(len(rd))
rd["ireach"] = 1
sd = fm.ModflowSfr2.get_empty_segment_data(nsfr)
sd["nseg"] = range(len(sd))
sfr = fm.ModflowSfr2(reach_data=rd, segment_data=sd, model=m)
cls.init_time = time.time() - t0
cls.m = m
def get_package(self, _mf):
content = self.merge()
return mf.ModflowRch(
_mf,
nrchop=content['nrchop'],
ipakcb=content['ipakcb'],
rech=content['stress_period_data'],
irch=content['irch'],
extension=content['extension'],
unitnumber=content['unitnumber']
)
# [-1., 1., 1., ..., 1., 1., -1.], # [-1., -1., -1., ..., -1., -1., -1.]]]) # set center cell in upper layer to constant head (-1) ibound[0, Nhalf, Nhalf] = -1 # defining the start-values # in the calculation only the -1 cells will be considered # # all values are set to h1 start = h1 * np.ones((N, N)) # and the center value is set to h2 start[Nhalf, Nhalf] = h2 # instantiate the modflow-basic package with iBound and startvalues bas = mf.ModflowBas(ml, ibound=ibound, strt=start) # set the aquifer properties with the lpf-package lpf = mf.ModflowLpf(ml, hk=k) # instantiation of the solver with default values pcg = mf.ModflowPcg(ml) # instantiation of the output control with default values oc = mf.ModflowOc(ml) rch = mf.ModflowRch(ml) ml.write_input() ml.run_model()
def create_package(self, name, content):
if name == 'mf':
model_ws = os.path.realpath(os.path.join(self._data_folder, self._model_id, content['model_ws']))
if not os.path.exists(model_ws):
os.makedirs(model_ws)
self._mf = mf.Modflow(
modelname=content['modelname'],
exe_name=content['exe_name'],
version=content['version'],
model_ws=model_ws
)
if name == 'dis':
mf.ModflowDis(
self._mf,
nlay=content['nlay'],
nrow=content['nrow'],
ncol=content['ncol'],
nper=content['nper'],
delr=content['delr'],
delc=content['delc'],
laycbd=content['laycbd'],
top=content['top'],
botm=content['botm'],
perlen=content['perlen'],
nstp=content['nstp'],
tsmult=content['tsmult'],
steady=content['steady'],
itmuni=content['itmuni'],
lenuni=content['lenuni'],
extension=content['extension'],
unitnumber=content['unitnumber'],
xul=content['xul'],
yul=content['yul'],
rotation=content['rotation'],
proj4_str=content['proj4_str'],
start_datetime=content['start_datetime']
)
if name == 'bas':
mf.ModflowBas(
self._mf,
ibound=content['ibound'],
strt=content['strt'],
ifrefm=content['ifrefm'],
ixsec=content['ixsec'],
ichflg=content['ichflg'],
stoper=content['stoper'],
hnoflo=content['hnoflo'],
extension=content['extension'],
unitnumber=content['unitnumber']
)
if name == 'lpf':
mf.ModflowLpf(
self._mf,
laytyp=content['laytyp'],
layavg=content['layavg'],
chani=content['chani'],
layvka=content['layvka'],
laywet=content['laywet'],
ipakcb=content['ipakcb'],
hdry=content['hdry'],
iwdflg=content['iwdflg'],
wetfct=content['wetfct'],
iwetit=content['iwetit'],
ihdwet=content['ihdwet'],
hk=content['hk'],
hani=content['hani'],
vka=content['vka'],
ss=content['ss'],
sy=content['sy'],
vkcb=content['vkcb'],
wetdry=content['wetdry'],
storagecoefficient=content['storagecoefficient'],
constantcv=content['constantcv'],
thickstrt=content['thickstrt'],
nocvcorrection=content['nocvcorrection'],
novfc=content['novfc'],
extension=content['extension'],
unitnumber=content['unitnumber']
)
if name == 'pcg':
mf.ModflowPcg(
self._mf,
mxiter=content['mxiter'],
iter1=content['iter1'],
npcond=content['npcond'],
hclose=content['hclose'],
rclose=content['rclose'],
relax=content['relax'],
nbpol=content['nbpol'],
iprpcg=content['iprpcg'],
mutpcg=content['mutpcg'],
damp=content['damp'],
dampt=content['dampt'],
ihcofadd=content['ihcofadd'],
extension=content['extension'],
unitnumber=content['unitnumber']
)
if name == 'oc':
mf.ModflowOc(
self._mf,
ihedfm=content['ihedfm'],
iddnfm=content['iddnfm'],
chedfm=content['chedfm'],
cddnfm=content['cddnfm'],
cboufm=content['cboufm'],
compact=content['compact'],
stress_period_data=self.get_stress_period_data(content['stress_period_data']),
extension=content['extension'],
unitnumber=content['unitnumber']
)
if name == 'risdlkfjlv':
mf.ModflowRiv(
self._mf,
ipakcb=content['ipakcb'],
stress_period_data=content['stress_period_data'],
dtype=content['dtype'],
extension=content['extension'],
unitnumber=content['unitnumber'],
options=content['options'],
naux=content['naux']
)
if name == 'wel':
mf.ModflowWel(
self._mf,
ipakcb=content['ipakcb'],
stress_period_data=content['stress_period_data'],
dtype=content['dtype'],
extension=content['extension'],
unitnumber=content['unitnumber'],
options=content['options']
)
if name == 'rch':
mf.ModflowRch(
self._mf,
ipakcb=content['ipakcb'],
nrchop=content['nrchop'],
rech=content['rech'],
extension=content['extension'],
unitnumber=content['unitnumber']
)
if name == 'chd':
mf.ModflowChd(
self._mf,
stress_period_data=content['stress_period_data'],
dtype=content['dtype'],
options=content['options'],
extension=content['extension'],
unitnumber=content['unitnumber']
)
if name == 'ghb':
mf.ModflowGhb(
self._mf,
ipakcb=content['ipakcb'],
stress_period_data=content['stress_period_data'],
dtype=content['dtype'],
options=content['options'],
extension=content['extension'],
unitnumber=content['unitnumber']
)
laycon = 1 # layer type, confined (0), unconfined (1), constant T, variable S (2), variable T, variable S (default is 3)
bcf = mf.ModflowBcf(m, hy=hy, sf1=sf, laycon=1)
# BAS package (Basic Package)
ibound = np.ones((nlay, nrow, ncol)) # # active cells
ibound[:, :, 0] = -1 # Set every first element of every column to -1
ibound[:, :, -1] = -1 # Set every last element of every column to -1
strt = 0 * np.ones(
(nrow, ncol)
) # in the calculation only the -1 cells will be considered (all values can be set to 0)
bas = mf.ModflowBas(m, ibound=ibound, strt=strt)
# setting up recharge data and recharge package
recharge_data = 0.250 # recharge flux mm/year (default is 1.e-3)
nrchop = 1 # optional code (1: to top grid layer only; 2: to layer defined in irch 3: to highest active cell)
rch = mf.ModflowRch(m, nrchop=nrchop, rech=recharge_data)
# setting up the well package with stress periods
pumping_rate = -4e+10 # m^3 / year
lrcq = {0: [[0, 5, 6, 0.]], 1: [[0, 5, 6, -4e+10]]}
wel = mf.ModflowWel(m, stress_period_data=lrcq)
# instantiation of the solver with default values
pcg = mf.ModflowPcg(m) # pre-conjugate gradient solver
# instantiation of the output control with default values
oc = mf.ModflowOc(m) # output control
timeStartWritingInput = datetime.now()
ml.write_input()
timeStartRunningModel = datetime.now()
def main():
'''
This is the main function.
'''
# Package all the required file paths into the Paths object
mfPaths = Paths()
# Package all the required framework specifications into the mfFrame object
mfFrame = Frame(Paths=mfPaths, dx_dy=dx_dy)
if build_from_gis:
# Build the model framework ASCII files from the GIS layers. Note that this
# requires a GDAL installation. If you don't want to get into that you
# can skip this step and simply build the model from the ASCII files that I've
# already created.
mfFrame.build_frame(Paths=mfPaths)
# ---------------------------------------------
# ---------------------------------------------
# Now use Flopy to build the MODFLOW model packages
# ---------------------------------------------
# ---------------------------------------------
start_dir = os.getcwd()
os.chdir(mfPaths.modflow_dir
) # This is simplest if done inside the MODFLOW directory
# Initialize a Flopy model object. This is the base class around which the model
# packages are built.
Modflow = mf.Modflow(mfFrame.model_name,
external_path='./',
version=mfPaths.mf_version)
# The .oc ('output control') package specifies how the model output is written.
# This model includes a single steady state stress period. Save the
# distribution of heads as well as the flow budget/mass balance to binaries.
# These can be plotted or converted to rasters (the current version of the script
# doesn't do any post-processing.)
oc = mf.ModflowOc(Modflow,
stress_period_data={
(0, 0): ['SAVE HEAD', 'SAVE BUDGET']
})
# The .dis and .bas packages define the model framework. I've already defined
# the framework attributes using the mfFrame object and simply pass those
# attributes to the constructor.
dis = mf.ModflowDis(Modflow,mfFrame.nlay,mfFrame.nrow,mfFrame.ncol,\
delr=mfFrame.delr,delc=mfFrame.delc,\
top=mfFrame.top,botm=mfFrame.bottom)
bas = mf.ModflowBas(Modflow,
ibound=mfFrame.ibound,
strt=mfFrame.top,
hnoflo=mfFrame.hnoflo)
# The .upw package describes the system properties (e.g., transmissivity/conductivity).
# For this model I simply give it a constant hydraulic conductivity field. This model
# converges but I have no idea how physically realistic it is. If you would
# like to make it more physically realistic (e.g., try to fit head or discharge
# data) you would need to estimate the hydraulic conductivity field via
# calibration/inverse modeling
hk = np.ones(np.shape(mfFrame.ibound))
upw = mf.ModflowUpw(Modflow, laytyp=mfFrame.laytyp, hk=hk, ipakcb=53)
# The .nwt package defines the solver specs. Just use the defaults.
nwt = mf.ModflowNwt(Modflow)
# RECHARGE INPUTS TO THE SYSTEM
# -----------------------------
# The .rch packages specifies recharge/precipitation inputs to the water table.
# Remember that I have already generated an array from the GIS layer and attached
# it to the mfFrame object.
rch = mf.ModflowRch(Modflow, nrchop=3, rech={0: mfFrame.rch}, ipakcb=53)
# BASEFLOW DISCHARGE FROM THE SYSTEM
# ----------------------------------
# The .drn package is one method of simulating the discharge of groundwater as
# base-flow in streams in rivers. Define every landsurface cell as a drain
# in order to allow the discharge network to emerge from topography.
drn_stages = mfFrame.top
drn_stages[mfFrame.ibound.squeeze() <= 0] = np.nan
drn_input = build_drain_input(mfFrame=mfFrame, stages=drn_stages)
drn = mf.ModflowDrn(Modflow, stress_period_data=drn_input, ipakcb=53)
# Now write the files. Flopy can also run the model if you tell it where the
# binary is, but if I understood your method correctly you will be invoking something
# from hydroshare. For convenience I am writing a windows .bat file that
# can be used to run the model.
Modflow.write_input()
os.chdir(start_dir)
with open(mfPaths.mf_bat_file, 'w') as fout:
fout.write('%s %s' % (binary_path, os.path.basename(mfPaths.nam_file)))
folder = mfPaths.scratch_dir
for the_file in os.listdir(folder):
file_path = os.path.join(folder, the_file)
try:
if os.path.isfile(file_path):
os.unlink(file_path)
except Exception as e:
print(e)
folder = mfPaths.model_frame_dir
for the_file in os.listdir(folder):
file_path = os.path.join(folder, the_file)
try:
if os.path.isfile(file_path):
os.unlink(file_path)
except Exception as e:
print(e)
folder = mfPaths.data_dir
for the_file in os.listdir(folder):
file_path = os.path.join(folder, the_file)
try:
if os.path.isfile(file_path):
os.unlink(file_path)
except Exception as e:
print(e)
return
def get_package(self, _mf):
content = self.merge()
return mf.ModflowRch(_mf, **content)
def calculate_model(z1_hk, z2_hk, z3_hk):
# Z1_hk = 15 # 3<Z1_hk<15
# Z2_hk = 15 # 3<Z2_hk<15
# Z3_hk = 3 # 3<Z3_hk<15
hobs = [
[0, 20, 10, 69.52],
[0, 40, 10, 71.44],
[0, 60, 10, 72.99],
[0, 80, 10, 73.86],
[0, 20, 45, 58.73],
[0, 40, 45, 50.57],
[0, 60, 45, 54.31],
[0, 80, 45, 58.06],
[0, 20, 80, 56.31],
[0, 40, 80, 52.32],
[0, 60, 80, 46.35],
[0, 80, 80, 29.01],
[0, 20, 100, 57.24],
[0, 40, 100, 54.24],
[0, 60, 100, 39.48],
[0, 80, 100, 48.47],
]
model_path = os.path.join('_model')
if os.path.exists(model_path):
shutil.rmtree(model_path)
modelname = 'parEstMod'
version = 'mf2005'
exe_name = 'mf2005'
if platform.system() == 'Windows':
exe_name = 'mf2005.exe'
ml = mf.Modflow(modelname=modelname,
exe_name=exe_name,
version=version,
model_ws=model_path)
nlay = 1
nrow = 90
ncol = 120
area_width_y = 9000
area_width_x = 12000
delc = area_width_x / ncol
delr = area_width_y / nrow
nper = 1
top = 100
botm = 0
dis = mf.ModflowDis(ml,
nlay=nlay,
nrow=nrow,
ncol=ncol,
delr=delr,
delc=delc,
top=top,
botm=botm,
nper=nper,
steady=True)
ibound = 1
strt = 100
bas = mf.ModflowBas(ml, ibound=ibound, strt=strt)
mask_arr = np.zeros((nlay, nrow, ncol))
mask_arr[:, :, 0] = 80
mask_arr[:, :, -1] = 60
ghb_spd = {0: []}
for layer_id in range(nlay):
for row_id in range(nrow):
for col_id in range(ncol):
if mask_arr[layer_id][row_id][col_id] > 0:
ghb_spd[0].append([
layer_id, row_id, col_id,
mask_arr[layer_id][row_id][col_id], 200
])
ghb = mf.ModflowGhb(ml, stress_period_data=ghb_spd)
rch = 0.0002
rech = {}
rech[0] = rch
rch = mf.ModflowRch(ml, rech=rech, nrchop=3)
welSp = {}
welSp[0] = [
[0, 20, 20, -20000],
[0, 40, 40, -20000],
[0, 60, 60, -20000],
[0, 80, 80, -20000],
[0, 60, 100, -20000],
]
wel = mf.ModflowWel(ml, stress_period_data=welSp)
hk = np.zeros((nlay, nrow, ncol))
hk[:, :, 0:40] = z1_hk
hk[:, :, 40:80] = z2_hk
hk[:, :, 80:120] = z3_hk
lpf = mf.ModflowLpf(ml, hk=hk, layavg=0, layvka=0, sy=0.3, ipakcb=53)
pcg = mf.ModflowPcg(ml, rclose=1e-1)
oc = mf.ModflowOc(ml)
ml.write_input()
ml.run_model(silent=True)
hds = fu.HeadFile(os.path.join(model_path, modelname + '.hds'))
times = hds.get_times()
response = []
for hob in hobs:
observed = hob[3]
calculated = hds.get_data(totim=times[-1])[hob[0]][hob[1]][hob[2]]
response.append(observed - calculated)
return json.dumps(response)
nrow=nrow,
ncol=ncol,
laycbd=0,
delr=delr,
delc=delc,
top=botm[0],
botm=botm[1:],
nper=nper,
perlen=perlen,
nstp=nstp,
steady=steady)
bas = mf.ModflowBas(ml, ibound=ibound, strt=ihead)
lpf = mf.ModflowLpf(ml, laytyp=laytyp, hk=hk, vka=vka)
wel = mf.ModflowWel(ml, stress_period_data=base_well_data)
ghb = mf.ModflowGhb(ml, stress_period_data=ghb_data)
rch = mf.ModflowRch(ml, rech=rch_data)
swi = mf.ModflowSwi2(ml,
nsrf=1,
istrat=1,
toeslope=toeslope,
tipslope=tipslope,
nu=nu,
zeta=z,
ssz=ssz,
isource=iso,
nsolver=1,
adaptive=adaptive,
nadptmx=nadptmx,
nadptmn=nadptmn,
nobs=nobs,
iswiobs=iswiobs,
Ny,
Nx,
delr=dx,
delc=dy,
top=zTop,
botm=zBot,
laycbd=LAYCBD,
nper=NPER,
perlen=PERLEN,
nstp=NSTP,
steady=STEADY)
bas = fm.ModflowBas(mf, ibound=IBOUND, strt=STRTHD)
lpf = fm.ModflowLpf(mf, hk=HK, vka=VKA, sy=SY, ss=SS, laytyp=LAYTYP, vkcb=VKCB)
ghb = fm.ModflowGhb(mf, stress_period_data=GHB)
wel = fm.ModflowWel(mf, stress_period_data=WEL)
rch = fm.ModflowRch(mf, nrchop=3, rech=RECH)
evt = fm.ModflowEvt(mf, nevtop=3, evtr=EVTR)
oc = fm.ModflowOc(mf, stress_period_data=OC, compact=True)
pcg = fm.ModflowPcg(mf)
#%% Write the model input files and running MODFLOW
mf.write_input()
success, mfoutput = mf.run_model(silent=False, pause=False)
print('Running success = {}'.format(success))
if not success:
raise Exception('MODFLOW did not terminate normally.')
#%% SHOWING RESULTS
steady=STEADY)
bas = fm.ModflowBas(mf, ibound=IBOUND, strt=STRTHD)
lpf = fm.ModflowLpf(mf,
hk=HK,
vka=VKA,
chani=[1.e-20, 1.e-20],
sy=SY,
ss=SS,
laytyp=LAYTYP,
vkcb=VKCB,
ipakcb=53)
ghb = fm.ModflowGhb(mf, stress_period_data=GHB, ipakcb=53)
riv = fm.ModflowRiv(mf, stress_period_data=RIV, ipakcb=53)
drn = fm.ModflowDrn(mf, stress_period_data=DRN, ipakcb=53)
wel = fm.ModflowWel(mf, stress_period_data=SEEP, ipakcb=53)
rch = fm.ModflowRch(mf, nrchop=3, rech=RECH, ipakcb=53)
evt = fm.ModflowEvt(mf, nevtop=3, evtr=EVTR, ipakcb=53)
oc = fm.ModflowOc(mf, stress_period_data=OC, compact=True)
#pcg = fm.ModflowPcg(mf, mxiter=200, iter1=200, hclose=0.001, rclose=0.001)
sms = fm.ModflowSms(mf) #, mxiter=200, iter1=200, hclose=0.001, rclose=0.001)
#%% Write the model input files and run MODFLOW
mf.write_input()
success, mfoutput = mf.run_model(silent=False, pause=False)
print('Running success = {}'.format(success))
if not success:
raise Exception('MODFLOW did not terminate normally.')
#%% SHOWING RESULTS
#to 1m (delc = 1). The latter requires specification
#of the layer, row, column, and injection rate of the
#well for each stress period. The layers, rows, columns,
#and the stress period are numbered (consistent with
#Python's zero-based numbering convention) starting at
#0. The required data are stored in a Python dictionary
#(lrcQ in the code below), which is used in FloPy to
#store data that can vary by stress period. The lrcQ
#dictionary specifies that two wells (one in cell 1, 1,
#51 and one in cell 1, 1, 151), each with a rate of
#-1 m3/d, will be active for the first stress period.
#Because this is a steady-state model, there is only
#one stress period and therefore only one entry in the
#dictionary.
fpm.ModflowRch(model, rech=0.001)
lrcQ = {0: [[0, 0, 50, -1], [0, 0, 150, -1]]}
fpm.ModflowWel(model, stress_period_data=lrcQ)
#5. The preconditioned conjugate-gradient (PCG) solver,
#using the default settings, is specified to solve the
#model.
fpm.ModflowPcg(model)
#6. The frequency and type of output that MODFLOW
#writes to an output file is specified with the output
#control (OC) package. In this case, the budget is printed
#and heads are saved (the default), so no arguments are
#needed.
