Sometimes regional models are required as an input for local models of flow and transport. This is an applied case of the groundwater modeling on the regional scale in the state of Guerrero, Mexico that will be the input for future local models of pit dewatering, and contaminant transport from the tailings dam and waste dump. The groundwater model is built with MODFLOW6 and mf6Voronoi on a series of Jupyter Notebooks and results are plotted with Paraview.

Tutorial

Input data

owncloud.hatarilabs.com/s/81eniQRXkWik142

Password to download: Hatarilabs

Code

This is the script for the second part of the tutorial related to the groundwater model construction and simulation.

Part 2a: generate disv properties

import sys, json, os ## Org
import rasterio, flopy ## Org
import numpy as np ## Org
import matplotlib.pyplot as plt ## Org
import geopandas as gpd ## Org
from mf6Voronoi.meshProperties import meshShape ## Org
from shapely.geometry import MultiLineString ## Org

C:\Users\saulm\anaconda3\Lib\site-packages\geopandas\_compat.py:7: DeprecationWarning: The 'shapely.geos' module is deprecated, and will be removed in a future version. All attributes of 'shapely.geos' are available directly from the top-level 'shapely' namespace (since shapely 2.0.0).
  import shapely.geos

# open the json file
with open('../json/disvDict.json') as file: ## Org
    gridProps = json.load(file) ## Org

cell2d = gridProps['cell2d']           #cellid, cell centroid xy, vertex number and vertex id list
vertices = gridProps['vertices']       #vertex id and xy coordinates
ncpl = gridProps['ncpl']               #number of cells per layer
nvert = gridProps['nvert']             #number of verts
centroids=gridProps['centroids']       #cell centroids xy

Part 2b: Model construction and simulation

#Extract dem values for each centroid of the voronois
src = rasterio.open('../rst/clipDem100m.tif')  ## Org
elevation=[x for x in src.sample(centroids)] ## Org

nlay = 5   ## Org

mtop=np.array([elev[0] for i,elev in enumerate(elevation)]) ## Org
zbot=np.zeros((nlay,ncpl)) ## Org


AcuifInf_Bottom = 100 ## Org
zbot[0,] = mtop - 20 ## Org
zbot[1,] = AcuifInf_Bottom + (0.85 * (mtop - AcuifInf_Bottom)) ## Org
zbot[2,] = AcuifInf_Bottom + (0.70 * (mtop - AcuifInf_Bottom)) ## Org
zbot[3,] = AcuifInf_Bottom + (0.50 * (mtop - AcuifInf_Bottom)) ## Org
zbot[4,] = AcuifInf_Bottom ## Org

Create simulation and model

# create simulation
simName = 'mf6Sim' ## Org
modelName = 'mf6Model' ## Org
modelWs = '../modelFiles' ## Org
sim = flopy.mf6.MFSimulation(sim_name=modelName, version='mf6', ## Org
                             exe_name='../bin/mf6.exe', ## Org
                             sim_ws=modelWs) ## Org

# create tdis package
tdis_rc = [(1000.0, 1, 1.0)] ## Org
tdis = flopy.mf6.ModflowTdis(sim, pname='tdis', time_units='SECONDS', ## Org
                             perioddata=tdis_rc) ## Org

# create gwf model
gwf = flopy.mf6.ModflowGwf(sim, ## Org
                           modelname=modelName, ## Org
                           save_flows=True, ## Org
                           newtonoptions="NEWTON UNDER_RELAXATION") ## Org

# create iterative model solution and register the gwf model with it
ims = flopy.mf6.ModflowIms(sim, ## Org
                           complexity='COMPLEX', ## Org
                           outer_maximum=50, ## Org
                           inner_maximum=30, ## Org
                           linear_acceleration='BICGSTAB') ## Org
sim.register_ims_package(ims,[modelName]) ## Org

# disv
disv = flopy.mf6.ModflowGwfdisv(gwf, nlay=nlay, ncpl=ncpl, ## Org
                                top=mtop, botm=zbot, ## Org
                                nvert=nvert, vertices=vertices, ## Org
                                cell2d=cell2d) ## Org

# initial conditions
ic = flopy.mf6.ModflowGwfic(gwf, strt=np.stack([mtop for i in range(nlay)])) ## Org

Kx =[4E-4,5E-6,1E-6,9E-7,5E-7] ## Org
icelltype = [1,1,0,0,0] ## Org

# node property flow
npf = flopy.mf6.ModflowGwfnpf(gwf, ## Org
                              save_specific_discharge=True, ## Org
                              icelltype=icelltype, ## Org
                              k=Kx) ## Org

## <==== inserted
crossSection = gpd.read_file('../shp/crossSection.shp') ## <==== inserted
sectionLine =list(crossSection.iloc[0].geometry.coords) ## <==== inserted

fig, ax = plt.subplots(figsize=(12,8)) ## <==== inserted
modelxsect = flopy.plot.PlotCrossSection(model=gwf, line={'Line': sectionLine}) ## <==== inserted
linecollection = modelxsect.plot_grid(lw=0.5) ## <==== inserted
modelxsect.plot_array(np.log(npf.k.array), alpha=0.5) ## <====== inserted
ax.grid() ## <==== inserted

# define storage and transient stress periods
sto = flopy.mf6.ModflowGwfsto(gwf, ## Org
                              iconvert=1, ## Org
                              steady_state={ ## Org
                                0:True, ## Org
                              } ## Org
                              ) ## Org

Working with rechage, evapotranspiration

rchr = 0.15/365/86400 ## Org
rch = flopy.mf6.ModflowGwfrcha(gwf, recharge=rchr) ## Org
evtr = 1.2/365/86400 ## Org
evt = flopy.mf6.ModflowGwfevta(gwf,ievt=1,surface=mtop,rate=evtr,depth=1.0) ## Org

Definition of the intersect object

For the manipulation of spatial data to determine hydraulic parameters or boundary conditions

# Define intersection object
interIx = flopy.utils.gridintersect.GridIntersect(gwf.modelgrid) ## Org

#open the river shapefile
rivers =gpd.read_file('../hatariUtils/river_basin.shp') ## Org
list_rivers=[] ## Org
for i in range(rivers.shape[0]): ## Org
    list_rivers.append(rivers['geometry'].loc[i]) ## Org
    
riverMls = MultiLineString(lines=list_rivers) ## Org

#intersec rivers with our grid
riverCells=interIx.intersect(riverMls).cellids ## Org
riverCells[:10] ## Org

array([252, 275, 291, 321, 336, 344, 370, 434, 441, 446], dtype=object)

#river package
riverSpd = {} ## Org
riverSpd[0] = [] ## Org
for cell in riverCells: ## Org
    riverSpd[0].append([(0,cell),mtop[cell],0.01]) ## Org
riv = flopy.mf6.ModflowGwfdrn(gwf, stress_period_data=riverSpd) ## Org

#river plot
riv.plot(mflay=0) ## Org

[<Axes: title={'center': ' drn_0 location stress period 1 layer 1'}>]

Set the Output Control and run simulation

#oc
head_filerecord = f"{gwf.name}.hds" ## Org
budget_filerecord = f"{gwf.name}.cbc" ## Org
oc = flopy.mf6.ModflowGwfoc(gwf, ## Org
                            head_filerecord=head_filerecord, ## Org
                            budget_filerecord = budget_filerecord, ## Org
                            saverecord=[("HEAD", "LAST"),("BUDGET","LAST")]) ## Org

# Run the simulation
sim.write_simulation() ## Org
success, buff = sim.run_simulation() ## Org

writing simulation...
  writing simulation name file...
  writing simulation tdis package...
  writing solution package ims_-1...
  writing model mf6Model...
    writing model name file...
    writing package disv...
    writing package ic...
    writing package npf...
    writing package sto...
    writing package rcha_0...
    writing package evta_0...
    writing package drn_0...
INFORMATION: maxbound in ('gwf6', 'drn', 'dimensions') changed to 929 based on size of stress_period_data
    writing package oc...
FloPy is using the following executable to run the model: ..\bin\mf6.exe
                                   MODFLOW 6
                U.S. GEOLOGICAL SURVEY MODULAR HYDROLOGIC MODEL
                            VERSION 6.6.0 12/20/2024

   MODFLOW 6 compiled Dec 31 2024 17:10:16 with Intel(R) Fortran Intel(R) 64
   Compiler Classic for applications running on Intel(R) 64, Version 2021.7.0
                             Build 20220726_000000

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.

 
 MODFLOW runs in SEQUENTIAL mode
 
 Run start date and time (yyyy/mm/dd hh:mm:ss): 2025/07/11 16:14:46
 
 Writing simulation list file: mfsim.lst
 Using Simulation name file: mfsim.nam
 
    Solving:  Stress period:     1    Time step:     1
 
 Run end date and time (yyyy/mm/dd hh:mm:ss): 2025/07/11 16:14:53
 Elapsed run time:  6.815 Seconds
 
 Normal termination of simulation.

Model output visualization

headObj = gwf.output.head() ## Org
headObj.get_kstpkper() ## Org

[(0, 0)]

heads = headObj.get_data() ## Org
heads[2,0,:5] ## Org

array([1016.74658849, 1003.30308189, 1016.19148927, 1015.36206045,
       1017.46065387])

# Plot the heads for a defined layer and boundary conditions
fig = plt.figure(figsize=(12,8)) ## Org
ax = fig.add_subplot(1, 1, 1, aspect='equal') ## Org
modelmap = flopy.plot.PlotMapView(model=gwf) ## Org

####
levels = np.linspace(heads[heads>-1e+30].min(),heads[heads>-1e+30].max(),num=50) ## Org
contour = modelmap.contour_array(heads[3],ax=ax,levels=levels,cmap='PuBu') ## Org
ax.clabel(contour) ## Org


quadmesh = modelmap.plot_bc('DRN') ## Org
cellhead = modelmap.plot_array(heads[3],ax=ax, cmap='Blues', alpha=0.8) ## Org

linecollection = modelmap.plot_grid(linewidth=0.3, alpha=0.5, color='cyan', ax=ax) ## Org

plt.colorbar(cellhead, shrink=0.75) ## Org

plt.show() ## Org