Local scale modeling of a 4 stage trench excavation on a coastal aquifer with mf6Voronoi. The main objective of this modeling work is assessing the impact of the excavation on the nearby groundwater flow regime.

Tutorial

Code

#!pip install -U mf6Voronoi

from mf6Voronoi.utils import listTemplates, copyTemplate

#listTemplates()

copyTemplate('generateVoronoi','trench')

copyTemplate('multilayeredTransient','trench')

copyTemplate('vtkGeneration','trench')

Mesh generation

Part 1 : Voronoi mesh generation

import warnings ## Org
warnings.filterwarnings('ignore') ## Org

import os, sys ## Org
import geopandas as gpd ## Org
from mf6Voronoi.geoVoronoi import createVoronoi ## Org
from mf6Voronoi.meshProperties import meshShape ## Org
from mf6Voronoi.utils import initiateOutputFolder, getVoronoiAsShp ## Org

#Create mesh object specifying the coarse mesh and the multiplier
vorMesh = createVoronoi(meshName='trenchExcavation',maxRef = 50, multiplier=2.5) ## Org

#Open limit layers and refinement definition layers
vorMesh.addLimit('basin','../shp/modelAoi.shp') ## <=== update
vorMesh.addLayer('trench','../shp/trenchExcavationDissolved.shp',1) ## <=== update
vorMesh.addLayer('ghb','../shp/compoundGhb.shp',10) ## <=== update
vorMesh.addLayer('wells','../shp/pumpingWells.shp',2) ## <=== update

#Generate point pair array
vorMesh.generateOrgDistVertices() ## Org

#Generate the point cloud and voronoi
vorMesh.createPointCloud() ## Org
vorMesh.generateVoronoi() ## Org

mf6Voronoi will have a web version in 2028

/--------Layer trench discretization-------/
Progressive cell size list: [1, 3.5, 9.75, 25.375] m.

/--------Layer ghb discretization-------/
Progressive cell size list: [10, 35.0] m.

/--------Layer wells discretization-------/
Progressive cell size list: [2, 7.0, 19.5] m.

/----Sumary of points for voronoi meshing----/
Distributed points from layers: 3
Points from layer buffers: 2427
Points from max refinement areas: 1121
Points from min refinement areas: 1011
Total points inside the limit: 5234
/--------------------------------------------/

Time required for point generation: 0.65 seconds 


/----Generation of the voronoi mesh----/

Time required for voronoi generation: 0.46 seconds

#Uncomment the next two cells if you have strong differences on discretization or you have encounter an FORTRAN error while running MODFLOW6

#vorMesh.checkVoronoiQuality(threshold=0.01)

#vorMesh.fixVoronoiShortSides()
#vorMesh.generateVoronoi()
#vorMesh.checkVoronoiQuality(threshold=0.01)

#Export generated voronoi mesh
initiateOutputFolder('../output') ## Org
getVoronoiAsShp(vorMesh.modelDis, shapePath='../output/'+vorMesh.modelDis['meshName']+'.shp') ## Org

The output folder ../output exists and has been cleared

/----Generation of the voronoi shapefile----/

Time required for voronoi shapefile: 1.33 seconds

# Show the resulting voronoi mesh

#open the mesh file
mesh=gpd.read_file('../output/'+vorMesh.modelDis['meshName']+'.shp') ## Org
#plot the mesh
mesh.plot(figsize=(35,25), fc='crimson', alpha=0.3, ec='teal') ## Org

Part 2 generate disv properties

# open the mesh file
mesh=meshShape('../output/'+vorMesh.modelDis['meshName']+'.shp') ## Org

# get the list of vertices and cell2d data
gridprops=mesh.get_gridprops_disv() ## Org

Creating a unique list of vertices [[x1,y1],[x2,y2],...]


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Extracting cell2d data and grid index


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#create folder
initiateOutputFolder('../json') ## Org

#export disv
mesh.save_properties('../json/disvDict.json') ## Org

The output folder ../json exists and has been cleared

Multilayer and transient model

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
from mf6Voronoi.tools.cellWork import getLayCellElevTupleFromRaster, getLayCellElevTupleFromElev
from mf6Voronoi.tools.graphs2d import generateRasterFromArray, generateContoursFromRaster

# 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/elevDem.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 = -20 ## Org
zbot[0,] = AcuifInf_Bottom + (0.8 * (mtop - AcuifInf_Bottom)) ## Org
zbot[1,] = AcuifInf_Bottom + (0.6 * (mtop - AcuifInf_Bottom)) ## Org
zbot[2,] = AcuifInf_Bottom + (0.4 * (mtop - AcuifInf_Bottom)) ## Org
zbot[3,] = AcuifInf_Bottom + (0.2 * (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 = [(1.0, 1, 1.0)] + [(86400, 1, 1.0) for level in range(4)] ## Org
print(tdis_rc[:3]) ## Org

tdis = flopy.mf6.ModflowTdis(sim, pname='tdis', time_units='SECONDS', ## Org
                             perioddata=tdis_rc, ## Org
                            nper=5) ## Org

[(1.0, 1, 1.0), (86400, 1, 1.0), (86400, 1, 1.0)]

# 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=150, ## Org
                           inner_maximum=50, ## Org
                           outer_dvclose=0.1, ## Org
                           inner_dvclose=0.0001, ## Org
                           backtracking_number=20, ## 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

disv.top.plot(figsize=(12,8), alpha=0.8) ## Org

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

fig, ax = plt.subplots(figsize=(12,8)) ## Org
modelxsect = flopy.plot.PlotCrossSection(model=gwf, line={'Line': sectionLine}) ## Org
linecollection = modelxsect.plot_grid(lw=0.5) ## Org
ax.grid() ## Org

# initial conditions

ic = flopy.mf6.ModflowGwfic(gwf, strt=np.stack([mtop for i in range(nlay)])) ## Org
#headsInitial = np.load('npy/headCalibInitial.npy')
#ic = flopy.mf6.ModflowGwfic(gwf, strt=headsInitial)

Kx =[7E-4 for x in range(5)] ## <=== updated
icelltype = [1, 1, 1, 0, 0] ## Org

# node property flow
npf = flopy.mf6.ModflowGwfnpf(gwf, ## Org
                              save_specific_discharge=True, ## Org
                              icelltype=icelltype, ## Org
                              k=Kx, ## Org
                              k33=np.array(Kx)/2) ## Org

# define storage and transient stress periods
sto = flopy.mf6.ModflowGwfsto(gwf, ## Org
                              iconvert=1, ## Org
                              steady_state={ ## Org
                                0:True, ## Org
                              },
                              transient={
                                  1:True, ## Org
                                  2:True, ## Org
                                  3:True, ## Org
                                  4:True, ## Org
                              },
                              ss=1e-06,
                              sy=0.001,
                              ) ## Org

Working with rechage, evapotranspiration

# rchr = 0.2/365/86400 ## 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

# regional flow as ghb ## <=== updated
layCellTupleList = getLayCellElevTupleFromElev(gwf,interIx,-1,'../shp/compoundGhb.shp') #elev of -1 to get all cells 
ghbSpd = {} ## <=== updated
ghbSpd[0] = [] ## <=== updated
for index, layCellTuple in enumerate(layCellTupleList): ## <=== updated
    ghbSpd[0].append([layCellTuple,0,0.01]) ## <=== updated
ghbSpd[0][:5] ## <=== updated

You have inserted a fixed elevation





[[(0, 4), 0, 0.01],
 [(0, 9), 0, 0.01],
 [(0, 10), 0, 0.01],
 [(0, 21), 0, 0.01],
 [(0, 26), 0, 0.01]]

ghb = flopy.mf6.ModflowGwfghb(gwf, stress_period_data=ghbSpd) ## <===== modified
#regional flow plot
ghb.plot(mflay=0, kper=0) ## <===== modified

# trench as drain package from stress period 1 flow as ghb ## <=== updated

drainSpd = {} ## Org
drainSpd[0] = [] ## Org

drainDf = gpd.read_file('../shp/trenchExcavationDissolved.shp')

tempTrench = drainDf.iloc[1].geometry
tempTrench
i = 1
for index, row in drainDf.iterrows():
    tempTrench = row.geometry
    tempLayCellTupleList = getLayCellElevTupleFromElev(gwf,interIx,-4.5,tempTrench) #elev of -1 to get all cells 
    drainSpd[i] = [] # start a new list for a given stress period
    for layCellTuple in tempLayCellTupleList:
        drainSpd[i].append([layCellTuple,-4.5,0.01])
    i+=1

drn = flopy.mf6.ModflowGwfdrn(gwf, stress_period_data=drainSpd) ## Org

You have inserted a fixed elevation
You have inserted a fixed elevation
You have inserted a fixed elevation
You have inserted a fixed elevation

#trench plot
drn.plot(mflay=1, kper=2) ## Org

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

fig, ax = plt.subplots(figsize=(12,8)) ## Org
xsect = flopy.plot.PlotCrossSection(model=gwf, line={'Line': sectionLine}) ## Org
lc = xsect.plot_grid(lw=0.5, alpha=0.3) ## Org
xsect.plot_bc('DRN',kper=3) ## <== updated
ax.grid(alpha=0.2) ## Org

#river package
#layCellTupleList, cellElevList = getLayCellElevTupleFromRaster(gwf,interIx,'rst/elevWgs18S.tif','shp/riversSpart.shp') ## Org
#riverSpd = {} ## Org
#riverSpd[0] = [] ## Org
#for index, layCellTuple in enumerate(layCellTupleList): ## Org
#    riverSpd[0].append([layCellTuple,cellElevList[index],0.01]) ## Org

#riv = flopy.mf6.ModflowGwfdrn(gwf, stress_period_data=riverSpd) ## Org

#river plot
#riv.plot(mflay=0, kper=1) ## Org

#crossSection = gpd.read_file('shp/crossSection.shp') ## Org
#sectionLine =list(crossSection.iloc[0].geometry.coords) ## Org
#fig, ax = plt.subplots(figsize=(12,8)) ## Org
#xsect = flopy.plot.PlotCrossSection(model=gwf, line={'Line': sectionLine}) ## Org
#lc = xsect.plot_grid(lw=0.5) ## Org
#xsect.plot_bc('DRN',kper=4) ## Org
#ax.grid() ## Org

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_0...
  writing model mf6Model...
    writing model name file...
    writing package disv...
    writing package ic...
    writing package npf...
    writing package sto...
    writing package ghb_0...
INFORMATION: maxbound in ('gwf6', 'ghb', 'dimensions') changed to 1486 based on size of stress_period_data
    writing package drn_0...
INFORMATION: maxbound in ('gwf6', 'drn', 'dimensions') changed to 102 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 6.6.2 05/12/2025

   MODFLOW 6 compiled May 12 2025 12:42:18 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): 2025/09/12  9:50:17
 
 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:     3    Time step:     1
    Solving:  Stress period:     4    Time step:     1
    Solving:  Stress period:     5    Time step:     1
 
 Run end date and time (yyyy/mm/dd hh:mm:ss): 2025/09/12  9:50:25
 Elapsed run time:  7.248 Seconds
 
 Normal termination of simulation.

Model output visualization

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

[(np.int32(0), np.int32(0)),
 (np.int32(0), np.int32(1)),
 (np.int32(0), np.int32(2)),
 (np.int32(0), np.int32(3)),
 (np.int32(0), np.int32(4))]

kper = 3 ## Org
lay = 0 ## Org

heads = headObj.get_data(kstpkper=(0,kper)) 
#heads[lay,0,:5] 
#heads = headObj.get_data(kstpkper=(0,0)) 
#np.save('npy/headCalibInitial', heads)

### 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[lay],ax=ax,levels=levels,cmap='PuBu') 
ax.clabel(contour) ## Org


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

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

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

waterTable = flopy.utils.postprocessing.get_water_table(heads)

fig, ax = plt.subplots(figsize=(12,8))
xsect = flopy.plot.PlotCrossSection(model=gwf, line={'Line': sectionLine})
lc = modelxsect.plot_grid(lw=0.5)
xsect.plot_array(heads, alpha=0.5)
xsect.plot_surface(waterTable)
xsect.plot_bc('drn', kper=kper, facecolor='none', edgecolor='teal')
plt.show()

generateRasterFromArray(gwf, 
                        waterTable, 
                        meshLayer=None, 
                        rasterRes=2, 
                        epsg=crossSection.crs.to_epsg(), 
                        outputPath='../output/waterTable.tif', 
                        limitLayer=None)

Raster X Dim: 2220.00, Raster Y Dim: 1350.00
Number of cols:  1111, Number of rows: 676

generateContoursFromRaster('../output/waterTable.tif',
                           interval = 1,
                           outputPath = '../output/waterTable_0_5_m.tif')

3d geometry generation on Vtk format

#Vtk generation
import flopy ## Org
from mf6Voronoi.tools.vtkGen import Mf6VtkGenerator ## Org
from mf6Voronoi.utils import initiateOutputFolder ## Org

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

loading simulation...
  loading simulation name file...
  loading tdis package...
  loading model gwf6...
    loading package disv...
    loading package ic...
    loading package npf...
    loading package sto...
    loading package ghb...
    loading package drn...
    loading package oc...
  loading solution package mf6model...

vtkDir = '../vtk' ## Org
initiateOutputFolder(vtkDir) ## Org

mf6Vtk = Mf6VtkGenerator(sim, vtkDir) ## Org

The output folder ../vtk exists and has been cleared

mf6Voronoi will have a web version in 2028

/--------GHB_0 vtk generation-------/
Working for GHB_0 package, creating the datasets: ('bhead', 'cond')
[WARNING] There is no data for the required stress period
Vtk file took 0.0549 seconds to be generated.
/--------GHB_0 vtk generated-------/


/--------DRN_0 vtk generation-------/
Working for DRN_0 package, creating the datasets: ('elev', 'cond')
Vtk file took 0.2655 seconds to be generated.
/--------DRN_0 vtk generated-------/

mf6Vtk.generateHeadVtk(nper=1, crop=True) ## Org

mf6Vtk.generateWaterTableVtk(nper=1) ## Org

Input data

You can download the input data from this link:

owncloud.hatarilabs.com/s/KIJP2EC3SKuFMF3

Password: Hatarilabs

Blog

Transient simulation of the trench excavation impact on a coastal aquifer with mf6Voronoi - Tutorial

Tutorial

Code

Mesh generation

Part 1 : Voronoi mesh generation

Follow us:

Part 2 generate disv properties

Multilayer and transient model

Part 2a: generate disv properties

Part 2b: Model construction and simulation

Create simulation and model

Working with rechage, evapotranspiration

Definition of the intersect object

Set the Output Control and run simulation

Model output visualization

3d geometry generation on Vtk format

Follow us:

Input data

Hatari Labs

Our courses:

Blog

Tutorial

Code

Mesh generation

Part 1 : Voronoi mesh generation

Follow us:

Part 2 generate disv properties

Multilayer and transient model

Part 2a: generate disv properties

Part 2b: Model construction and simulation

Create simulation and model

Working with rechage, evapotranspiration

Definition of the intersect object

Set the Output Control and run simulation

Model output visualization

3d geometry generation on Vtk format

Follow us:

Input data

Hatari Labs

Our courses:

Follow Us

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