ISH Journal of Hydraulic Engineering

ISSN: 0971-5010 (Print) 2164-3040 (Online) Journal homepage: http://www.tandfonline.com/loi/tish20

Application of genetic algorithm for the

groundwater management of a coastal aquifer

S. K. Pramada, S. Mohan & P. K. Sreejith

To cite this article: S. K. Pramada, S. Mohan & P. K. Sreejith (2017): Application of genetic
algorithm for the groundwater management of a coastal aquifer, ISH Journal of Hydraulic
Engineering, DOI: 10.1080/09715010.2017.1378597

To link to this article: http://dx.doi.org/10.1080/09715010.2017.1378597

Published online: 29 Sep 2017.

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 ISH Journal of Hydraulic Engineering, 2017
https://doi.org/10.1080/09715010.2017.1378597

Application of genetic algorithm for the groundwater management of a coastal

aquifer
S. K. Pramada#, S. Mohan and P. K. Sreejith
Department of Civil Engineering, IIT Madras, Chennai, India

ABSTRACT ARTICLE HISTORY

Drinking water wells close to coastal areas getting contaminated groundwater can be minimized Received 31 March 2017
by developing an optimal pumping strategy of pumping, both in space and time. Groundwater Accepted 8 September 2017
management problems are solved in a more efficient way by combining simulation and optimization KEYWORDS
in a single framework. Simulation–optimization-based development of the groundwater system Simulation–optimization;
is required, to reduce the risk of pumping contaminated water. This paper presents a study where coastal aquifer; SEAWAT;
a simulation–optimization model based on a 3D groundwater model and genetic algorithm was genetic algorithm;
developed and applied to a case study. A 3D groundwater model has been developed, for the case groundwater model
study system of South Chennai Aquifer System where significant amount of groundwater is being
Downloaded by [La Trobe University] at 02:19 30 September 2017

pumped for domestic consumption. The calibrated groundwater model was used as the simulation
component in the linked simulation–optimization model. The combined model was then used to
identify the optimum pumping strategy.

1. Introduction
In nature, physical processes are often represented by large sets of
nonlinear, partial differential equations. Unfortunately, this fact
limits the ability of many traditional optimization codes to solve
water resources management problems and leads to necessary
simplification of the actual problem. An alternative approach for
solving complex problems is to employ a combined simulation–
optimization approach. In combined simulation–optimization
approach, the output from the simulation model forms the input
to the optimization model. The significant advantage of inter-
facing a simulation model with an optimization algorithm is
that the solution requires no additional simplifying assump-
tions about the physics of the real system. The simulation model
can be combined with the optimization model either using the
governing equations as binding constraints in the optimiza-
tion model (embedding technique) or using a response matrix
method or by response surface method  (Bhattacharjya and
Datta 2005, Dhar and Datta 2009, Esfahani et al. 2016, Khosrow
and Hasan 1996, Pramada et al. 2014).
SEAWAT (Langevin et al. 2003), one of the widely used coastal
aquifer simulation models  (Holzbecher 1998, Mahesha and
Lakshmikant 2014, Motz and Sedighi 2013) could be combined
with heuristic optimization techniques such as genetic algo-
rithm to solve optimization-based groundwater management
problems. Owing to the complexity of the data files required by
the SEAWAT establishing an interface between the simulation
model and optimization models is not an easy procedure.
2. Simulation–optimization
A combined simulation–optimization approach coupling
groundwater simulation model with optimization routine based
on GA is proposed. This integration of optimization technique
into the computer simulation model process can provide sig-
nificant performance improvement over the results obtained
by traditional stand-alone simulation or optimization meth-
odology. For applying the simulation–optimization method-
ology, the first step is the development of a simulation model
to compute the head values at different locations for a given
pumping strategy. In second step, the simulation model needs to
be externally linked with the optimization model. Whenever the
optimization procedure requires the objective function and or
constraint evaluation, it calls the simulator and passes the modi-
fied input parameters to the simulator and the simulation model
executes and does the required evaluation. Genetic algorithm
module acts as a driver model where in it calls the simulation
model by passing the management decision variables and gets
back the corresponding objective function value. The genetic
algorithm then adjusts the management decision variables to get
a new objective function value and continue the process until
there is no further improvement in the objective function by
altering the decision variables. The genetic algorithm toolbox in
Matlab 7 (The MathWorks 2003) was used as the optimization
routine, in which, it calls the calibrated simulation model during
each iteration. A subroutine has been developed to interface
the genetic algorithm tool box with the calibrated model (to
communicate between both modules) using Matlab.
Usually interfacing a simulation and optimization model
means making a communication possible with each module.
That is whenever an optimization models requires a function
evaluation or constraint evaluation, it calls simulation model.
The batch run utility in the simulation model was used to cou-
ple the optimization model with the simulation model. Figure 1
shows the program execution sequence. The program of genetic
algorithm starts from an initial guess solution given by the
user. Pumping rates were generated randomly by the MATLAB
random number generator and GA performs generations of

CONTACT  S. K. Pramada  pramada@nitc.ac.in

#
Present Address: Department of Civil Engineering, NIT Calicut, Kozhikode, India
© 2017 Indian Society for Hydraulics
 2   S. K. PRAMADA ET AL.

Develop a Numerical Model

Input initial pumping rates

Model Calibration
and testing
Phase I
Numerical
model
Specify the direction of
time period to optimize

Numerical model
Run
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Run
Model.BAT

The numerical model will start

running from the initial time period
irrespective of the time period to
Modify the optimize and through this the Extract the Phase II
numerical model will take care of the
respective input head time relation ship required results
file for the Algorithm
numerical model development

Randomly Optimization Model

generating new - Evaluation of Objective
pumping rates function
- Checking for constraints

No Stop? Yes
Print RESULTS

Figure 1. The program execution sequence.

possible solutions. For every set of random pumping rates,
SEAWAT is executed once to update the hydraulic head dis-
tribution in response to those pumping rates. The output of
the simulation consists of the values of the hydraulic heads
at all model nodes/cells. The values of hydraulic heads for the
selected observation points are forwarded to the optimization
module. The optimization algorithm performs the evaluation
of the constraints and checks for termination, and if the con-
straints are not satisfied, then it computes new pumping rates
based on the GA model and passes the new rates to SEAWAT.
Based on the SEAWAT results, new set of pumping rates are
formed, and SEAWAT is called again to compute the head dis-
tribution. This process is continued until an optimal solution
is reached based on the objective function and the constraints.
The time period to optimize is given by the user. The numerical
model will start running from the initial time period irrespec-
tive of the time period to optimize and through this the numer-
ical model will take care of the time relationship. SEAWAT uses
many input files, but during pumping rate optimization, only
the pumping rate of individual well changes. All other param-
eters, for example hydraulic conductivity, specific storage, etc,
do not change, hence only the ‘well’ file is modified (contains
details pertaining to pumping) using the interfacing program
developed using Matlab during each iteration. The idea here is
to introduce new pumping rate through the ‘well’ file and then
run the batch file. Check the file containing the head obser-
vations and check whether the constraints are satisfied or not.
3.  Seawater intrusion model
SEAWAT-2000 (Langevin et al. 2003), which is based on dis-
perse interface approach has been used in the present study, in
order to simulate three dimensional, variable density, ground-
water flow and transport. SEAWAT-2000 was designed by com-
bining a modified version of MODFLOW-2000 (Harbaugh et al.
2000) and MT3DMS (Zheng and Wang 1999) into a single
 ISH JOURNAL OF HYDRAULIC ENGINEERING   3

computer program. The governing equation for variable den- 3.1.  Spatial and temporal discretization
sity flow in terms of freshwater head as used in SEAWAT is
A regularly spaced, finite-difference model grid was developed
(Guo and Langevin 2002).
to study the seawater–freshwater interface. The model grid is
[ ( 𝜌−𝜌 )] [ ( )] depicted in Figure 2. Each cell represents 100 × 100 m. The
𝜕hf 𝜕hf 𝜌 − 𝜌f 𝜕Z
𝜕
𝜌Kx +
f 𝜕Z
+
𝜕
𝜌Ky + grid consists of 92 rows and 53 columns. The top and bottom
𝜕x 𝜕x 𝜌f 𝜕x 𝜕y 𝜕y 𝜌f 𝜕y of the single layer model is based on borehole details from nine
boreholes. The top elevation varies from 0 to 9 m above MSL
[ ( )]
𝜕 𝜕hf 𝜌 − 𝜌f 𝜕Z 𝜕hf 𝜕𝜌 𝜕C
+ 𝜌Kz + = 𝜌Sf +𝜃 − 𝜌 s qs
(1) and bottom elevation varies from 1 to 16 m below MSL. Figure
𝜕z 𝜕z 𝜌f 𝜕z 𝜕z 𝜕C 𝜕t
3 shows the east–west section through Besant Nagar.
Temporal discretization was done by dividing the simula-
where x, y, z are orthogonal coordinate axes, aligned with
tion time into 72 monthly stress periods from January 2000 to
the principal directions of permeability; K is hydraulic con-
December 2005. The stress period is again divided into trans-
ductivity [LT−1]; S is specific storage [L−1]; t is time [T]; θ is
port steps. The transport step is automatically selected by the
effective porosity [dimensionless]; C is solute concentration
program to meet various stability constraints that are solution
[ML−3]; 〉s is fluid density source or sink water [ML−3]; 〉 is the
dependent.
density of the native aquifer water [ML−3]; 〉f is the density
of freshwater[ML−3], Z is the elevation at the measurement
point [L]. and qs is the volumetric flow rate of sources and 3.2.  Initial and boundary conditions
sinks per unit volume of aquifer [T−1]. hf the equivalent fresh-
Boundary conditions were established to represent as closely as
water head.
possible the conceptual model of the flow system. The bound-
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In addition to the flow equation (Equation 1), a second par-

ary conditions are shown in Figure 4. The seaside is repre-
tial differential equation is required to describe solute transport
sented with constant head of zero meter and constant TDS
in the aquifer system. Solute mass is transported in porous
concentration of 35,000 mg/lit. The large water body nearby
media by the flow of groundwater (advection), molecular
Velachery is represented with a flux boundary. The Adyar river
diffusion, and mechanical dispersion. The transport of solute
is represented as the river boundary condition and the top
mass in groundwater can be described by the following partial
boundary is represented as a recharge boundary. The recharge
differential equation:
rate was taken as 10% of the rainfall based on an earlier study
𝜕(𝜃C)
( ) ( ) ( ) (Mohan 2003) and evapotranspiration is negligible since not
𝜕 𝜕C 𝜕 𝜕C 𝜕 𝜕C
= 𝜃Dx + Dy + Dz much vegetation and the groundwater level is well below the
𝜕t 𝜕x 𝜕x 𝜕y 𝜕y 𝜕z 𝜕z
(2) ground level. The groundwater extraction for different years
𝜕 ( ) 𝜕( 𝜕(
)
𝜃vz C + qs C s was obtained from PWD, Taramani, Chennai and the ground-
)
− 𝜃vx C − 𝜃vy C −
𝜕x 𝜕y 𝜕z water extraction during the year 2005 is shown in Table 2.
The western and southern boundaries are represented as time
where; D is the hydrodynamic dispersion coefficient [L2T−1];
v is seepage or linear pore water velocity [LT−1]; Cs is concen-
tration of the source or sink flux [ML−3]
Groundwater flow causes the redistribution of solute con-
centration, and the redistribution of solute concentration
alters the density field, thus, affecting groundwater movement.
Therefore, the movement of groundwater and the transport
of solutes in the aquifer are coupled processes, and the two
equations (Equations 1 and 2) must be solved jointly.
The following empirical relation between the density of salt-
water and concentration was developed by Baxter and Wallace
as reported by Guo and Langevin (Guo and Langevin 2002).
𝜌 = 𝜌f + EC (3)
where E is an empirical, dimensionless constant with an approx-
imate value of 0.7143 for salts commonly found in seawater.
The aquifer of interest in this study is the Besant Nagar–
Injambakkam aquifer, which is a part of the South Chennai
aquifer system adjacent to the city of Chennai. The Besant
Nagar–Injambakkam aquifer system covers an areal extent of
about 55.2  km2. The ever-increasing population of Chennai
and rapid urbanization has lead to indiscriminate exploitation
of water. Water levels are dropping at an alarming rate due to
this large-scale extraction coupled with increase in high rise
buildings, poor recharge, and destruction of traditional water
harvesting systems like tanks and ponds. The area has been
severely affected by seawater intrusion because of the large-
scale groundwater depletion. To quantify seawater movement
into the Besant Nagar–Injambakkam aquifer SEAWAT was
used and TDS is taken as the indicator of seawater intrusion. Figure 2. Areal discretization of Besant Nagar–Injambakkam aquifer.
 4   S. K. PRAMADA ET AL.
Figure 3. East–west section through Besant Nagar.
Flux boundary
River
Boundary
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Constant Head and
Constant concentration
Y in meters
X in meters
Time varying head
Figure 4. Boundary conditions.
varying head boundaries based on the observed head values.
The water level and TDS concentration data for January 2000
was specified as the initial head and initial concentration.
3.3.  Aquifer parameters and model calibration
The initial aquifer parameters for modeling were obtained from
the earlier study (Mohan 2003). During calibration, the aqui-
fer parameters were slightly modified to match the observed
head and concentration to that of simulated values. SEAWAT
simulation model was run for 72 monthly stress periods from
January 2000 to December 2005. Specifications on observa-
tion wells were given in the control points specified, and used
for calibration. The hydraulic heads and concentration values
calculated at nine control points (Figure 5) were compared
with the respective monthly head and concentration values
for years 2000 to 2005. The model was calibrated to observed
field conditions by adjusting the hydraulic conductivity and
dispersivity parameters. Dispersivity was varied to match the
simulated and observed TDS values. The calibrated longitudi-
nal dispersivity was found to be 35 m. Figure 6 shows the com-
parison between observed and computed heads for a typical
control point. Figure 7 shows the comparison of observed and
computed TDS concentration at a control well at Besant Nagar.
Figure 8 shows the observed and computed TDS concentration
during August 2004. It can be seen that there is reasonable
agreement between the observed and computed values of head
and concentration values. The hydraulic conductivity varies
from 50.2 to 65 m/day for this aquifer. The initially and final
calibrated values of aquifer parameters in the model are given
in Table 1. The longitudinal dispersivity varies from 50 to 35 m
and tranverse dispersivity is assumed as 1/10 of longitudinal
dispersivity.
4.  Use of genetic algorithm in simulation–
optimization
The genetic algorithm is a search technique based on the prin-
ciple of natural evolution. GA is most appropriate for complex
nonlinear models in which getting the global optimum is a dif-
ficult task. After the initial population is randomly generated,
GA applies a sequence of operations to the population, guided
by the relative fitness of the individuals, and allows the popu-
lation to evolve over a number of generations. There are many
parameters required to run genetic algorithm namely popula-
tion size, the mutation probability, and crossover probability.
Usual way to get these parameters is to do lot of experimen-
tation to find a set of values which solves a particular prob-
lem. A broad rule of thumb to start with, is to use a mutation
probability of 0.05, a crossover rate of 0.6, and a population
size of about 50 (Sastry et al. 2005). To make use of the GA
application, the basic steps are
(1) Description of the problem
(2) Generate an initial population
(3) Evaluation of the solution set
(4) Select solutions
(5) Apply crossover operator
(6) Apply the mutation operator
(7) Repeat evaluation
A brief account of each of these steps are given below
4.1.  Description of the problem
The decision variables of the groundwater management prob-
lem are the pumping rates of each well in each management
period.

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Figure 5. Location of control wells for calibration.
Figure 6. Comparison of observed and computed heads of observation well at
Besant Nagar.
Figure 7.  The comparison of observed and computed TDS concentration of
observation well at Besant Nagar.
ISH JOURNAL OF HYDRAULIC ENGINEERING   5
4.2.  Generate an initial population
The first step is to generate a certain number of inputs. In the GA
terminology, each input is called chromosome. The set of chro-
mosomes is designated as a population. Computation is done
over generations. GA toolbox in MATLAB is used as the opti-
mization module for the current problem, in which MATLAB
random number generator is used to generate initial population.
For the current problem, population size is fixed as 100.
4.3.  Evaluation of the solution set
To each chromosome, a value is assigned depending on how
close it actually to the optimum. Stronger individuals, that is
those chromosomes with fitness values closer to the optimal
will have greater chance to survive across generations. Fitness
could be determined by an objective function. The objective
function and constraints for the problem are
( ) ∑N
Maximize Z qt = qi,t (4)
i=1
ST
qit = f (ht−1
j ) From the simulation model (5)
htj − h∗tj ≥ 0.5 j = 1............, m (6)
∗
0 < qi,t < qi,t i = 1.................., n (7)
where Z(qt): the objective function for a given time period
t; htj: computed hydraulic head at the observation well j; h∗tj:
minimum allowed hydraulic head (MSL) at the observation
well j; qi,t: pumping rate from well i; qi∗ t: maximum allowed
pumping rate from well i; m: number of observation wells; n:
number of pumping wells.
The problem is formulated as an optimization problem to
maximize pumping considering the constraints on water levels
and pumping. The quantity of water being pumped from each
well during the year 2005 was calculated based on the given
rates and that was given as upper limit in the optimization
and the lower limit is set to zero. The constraint on hydraulic
head is given a safe value of 0.5 i.e. the hydraulic head in the
aquifer should be above 0.5 m of mean sea level so that there is
no danger of saltwater intrusion. The primary objective of the
model is to maximize freshwater withdrawal to meet drinking
water needs from the aquifer, while maintaining hydraulic head
under permissible limit.
Application of genetic algorithm to constrained optimiza-
tion problems is often a challenging effort. There are several
approaches proposed in GA to handle constrained optimi-
zation problems. Among these methods, the most common
method in genetic algorithm to handle constraints is to use
penalty functions (Yeniay 2005). For the current study, the
optimization problem is transformed into an unconstrained
one by incorporating a penalty to the objective function. The
constraints are checked in the objective function evaluation
stage and the constraints for each management period are han-
dled by adding a penalty to the objective function if they are
not met. Penalty will be calculated based on the deviation of
the simulated head from the target head. Greater the violation,
higher will be the penalty assessed.
 6   S. K. PRAMADA ET AL.
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Figure 8.  Comparison of observed and computed TDS concentration during

August 2004. Figure 9. Predicted water level after pumping at optimum rate for 18 months.

Table 1. The initial and finally adopted parameter values. to prefer better solutions to worse ones. There are many selec-
tion procedures, including roulette wheel selection, stochastic
Sl.No Parameter Initial value Final calibrated value
universal selection, ranking selection, and tournament selec-
1 Hydraulic conductivity 65 50.2–65
(K in m/day) tion. These different selection procedures were tried for the
2 Specific yield 0.15 0.15 current problem. Stochastic selection was taking lot of time in
3 Effective porosity (θ) 0.2 0.2 terms of number of days to get the optimum, whereas roulette
4 Longitudinal dispersion 50 35
(αL in m) wheel selection was taking only 8 h. Thus, roulette wheel selec-
5 Transverse dispersion 5 3.5 tion was adopted in this selection process. The parent strings
(αT in m) of a string that will exist on the next generation are picked by
6 Density of freshwater(ρf 1000 1000
in kg/m3) a roulette wheel selection algorithm. This means that higher
7 Density of source(ρs in 1025 1025 fitness strings represent bigger parts of the wheel so they have
kg/m3) more chances to be picked.
8 Concentration of source 35,000 35,000
(Csmg/l)
4.5.  Crossover operator
Table 2. Optimum pumping for each zone. After selection, individuals from the population are recom-
bined (or crossed over) to create new offspring. Recombining
Actual Pumping Optimal rate of
Number of during the Year pumping Year good individuals likely to create better individuals. Crossover
Zone wells 2005 (m3/day) (2006) m3/day exchanges portions of a pair of chromosomes at a randomly
Besant Nagar 4 8686.74 0 chosen point called the crossover point. The split position is
Thiruvanmiyur 2 2570.736 0 determined randomly. There are different crossover methods
Kottivakkam 3 1079.075 1070.6
Palavakkam 7 344.3517 317.8 available, namely single point, two point, n point, uniform,
Neelangarai 11 3570.467 3560.6 etc., Crossover does not occur always. Those chromosomes
Injambakkam 2 272.4218 270.3 with a higher fitness value are more likely to reproduce off-
spring. Crossover takes place based on a set probability, called
crossover probability. Two-point cross over is applied for the
4.4.  Select solutions problem. Crossover probability was determined by conduct-
Selection allocates more copies of those solutions with higher ing sensitivity analysis. The crossover probability was varied
fitness values and thus imposes the survival of the fittest mech- from 0.6 to 1. For the current problem, crossover probability
anism of the candidate solutions. The main idea of selection is is fixed as 0.9.

4.6.  Mutation operator
Mutation generates an offspring by randomly changing the val-
ues of genes at one or more gene positions of a selected chro-
mosome. The main purpose of mutation is to maintain diversity
within the population and also to inhibit premature conver-
gence. Mutation occurs with some low probability called muta-
tion probability. The mutation probability was varied from 0.01
to 0.08 for a constant value of crossover probability of 0.9. For
the current problem, the mutation probability is fixed as 0.05.
4.7.  Repeat evaluation
The steps of selection, crossover, and mutation have to be
repeated over different generations. The algorithm stops when
a specified criterion providing an estimate of convergence is
reached. GA toolbox uses four different criteria to stop the
solver, and the most simple among these is to just stop after
some predetermined number of generations is over. GA also
detects if there is no change in the best fitness value for some
time given in seconds (stall time limit), or for some number
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of generations (stall generation limit). Another criterion is the
maximum time limit in seconds. In this study, the maximum
number of generations is taken as 30.
4.8.  Optimum pumping
Simulation–optimization method can be used to derive optimal
and efficient management strategies for controlling saltwater
intrusion in coastal aquifers. For determining optimal with-
drawal, the seawater intrusion model needs to be incorporated
in an optimization model. The linked simulation optimization
model is applied to the case study. Considering all other param-
eters same, the linked simulation–optimization model was run
for a one-year period to get the optimum pumping rate. Table
2 shows the optimal pumping from different locations. From
this result, it can be concluded that the high rate of pumping
over the past years (considering up to the end of year 2005) the
optimization models suggests that pumping from the first two
zones should be curtailed completely and reduced pumping
rates from other zones. With the optimum pumping strategy,
it was not possible to obtain the desired water level at the first
two zones. A trial run was made with the optimum pumping
to find out how long the same rate needs to be maintained to
achieve the desired level. Figure 9 shows the result for this
run. It is found that the optimal pumping strategy needs to be
continued at least for further 18 months.
5. Conclusions
Because of close proximity to sea and over exploitation of
groundwater, the equilibrium condition that once existed
between fresh and saline water in Besant Nagar–Injambakkam
aquifer, which is a part of South Chennai aquifer, has been
disturbed. The aquifer has been overexploited and this has
resulted in seawater flow toward the major pumping centers
in this aquifer. It is concluded that there is an increasing
trend of rapid movement of interface in the Besant Nagar
and Thiruvanmiyur. The developed model coupling SEAWAT
with GA when applied to examine how far inland the seawater
ISH JOURNAL OF HYDRAULIC ENGINEERING   7
transition zone has moved in Besant Nagar–Injambakkam
aquifer, it was found that the maximum length of intrusion is
about 750 m. The optimal pumping for the six different zones
in the Besant Nagar–Injambakkam aquifer are found to be 0.0,
0.0, 1070.6, 317.8, 3560.6, 270.3 m3/day, which implied that
the pumping from Besant Nagar and Thiruvanmiyur should
be curtailed completely. It is also concluded that the reduced
pumping as stipulated above need to be followed in the other
zones a period of at least 18 months in order to protect the
aquifer from seawater intrusion.
Disclosure statement
No potential conflict of interest was reported by the authors.
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