GMDGeoscientific Model DevelopmentGMDGeosci. Model Dev.1991-9603Copernicus PublicationsGöttingen, Germany10.5194/gmd-12-167-2019Particle swarm optimization for the estimation of surface complexation
constants with the geochemical model PHREEQC-3.1.2Particle swarm optimization for the estimation of surface complexation constantsAbdelazizRamadanramawaad@gmail.comramadan.abdelaziz@asu.edu.omhttps://orcid.org/0000-0002-8394-9486MerkelBroder J.Zambrano-BigiariniMauriciohttps://orcid.org/0000-0002-9536-643XNairSreejeshCollege Of Engineering, A'Sharqiyah University, Ibra, OmanTU Bergakademie Freiberg, Freiberg, GermanyDepartment of Civil Engineering, Universidad de La Frontera, Temuco, ChileInstitute of Environmental Physics, University of Bremen, Bremen, GermanyRamadan Abdelaziz (ramawaad@gmail.com, ramadan.abdelaziz@asu.edu.om)8January201912116717716March201717July201724August201814September2018This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this licence, visit https://creativecommons.org/licenses/by/3.0/This article is available from https://gmd.copernicus.org/articles/12/167/2019/gmd-12-167-2019.htmlThe full text article is available as a PDF file from https://gmd.copernicus.org/articles/12/167/2019/gmd-12-167-2019.pdf
Sorption of metals on minerals is a key process in treatment
water, natural aquatic environments, and other water-related technologies.
Sorption processes are usually simulated with surface complexation models;
however, identifying numeric values for the thermodynamic constants from
batch experiments requires a robust parameter estimation technique that does
not get trapped in local minima. Recently, particle swarm optimization
(PSO) techniques have attracted many researchers as an efficient and
effective optimization technique to find (near-)optimum model parameters in
several fields of research. In this work, uranium at low concentrations was
sorbed on quartz at different pH, and the hydroPSO R optimization package was
used – the first time – to calibrate the PHREEQC geochemical model,
version 3.1.2. Results show that thermodynamic parameter values identified
with hydroPSO are more reliable than those identified with the well-known
parameter estimation (PEST) software, when both parameter estimation software
are coupled to PHREEQC using the same thermodynamic input data. In addition,
post-processing tools included in hydroPSO were helpful for the correct
interpretation of uncertainty in the obtained model parameters and simulated
values. Thus, hydroPSO proved to be an efficient and versatile optimization
tool for identifying reliable thermodynamic parameter values of the PHREEQC
geochemical model.
Introduction and scope
Particle swarm optimization technique (PSO) is an evolutionary optimization
technique proposed by Eberhart and Kennedy (1995) and was influenced by the
activities of flocks of birds in search of corn (Kennedy and Eberhart, 1995;
Eberhart and Kennedy, 1995). Both PSO and genetic algorithms (GAs) share a
few similarities (Eberhart and Shi, 1998). GAs have evolutionary operators
like crossover or selection, while PSO does not have it (Eberhart and Shi,
1998). Recently, PSO has been implemented in a wide range of applications,
e.g., in the water resources (e.g., Bisselink et al. 2016; Zambrano-Bigiarini
and Rojas, 2013; Abdelaziz and Zambrano-Bigiarini, 2014; Formetta et al.,
2014), geothermal resources (Ma et al., 2013; Beck et al., 2010), finance and
economics (Das, 2012), structural design (Kaveh and Talatahari, 2009;
Schutte and Groenwold, 2003), and applications of video and image analysis (Donelli and Massa, 2005;
Huang and Mohan, 2007; Abdelaziz et al., 2018). For example, the groundwater
model MODFLOW2000/2005 was linked with PSO to estimate permeability
coefficients (Sedki and Ouazar, 2010) and a multi-objective PSO code was used
to derive rainfall–runoff model parameters by introducing the Pareto rank
concept (Gill et al., 2006). Notwithstanding recent popularity, PSO has never
been used to calculate the parameters of a surface complexation model (SCM)
simulating sorption behavior of metal and metalloids on mineral surfaces.
Hence, this paper attempts to examine the efficiency and effectiveness of PSO
for parameter estimation of a surface complexation model as the PHREEQC
(Parkhurst and Appelo, 1999).
Nowadays, a number of PSO software codes exist, such as MADS (Harp and
Vesselinov, 2011; Vesselinov and Harp, 2012) and OSTRICH (Matott, 2005), with
most of the codes using the basic PSO formulation developed in 1995. However,
in this paper, we use the latest standard particle swarm optimization proposed
in literature (Clerc, 2012; Zambrano-Bigiarini et al., 2013), named SPSO2011,
as implemented in the hydroPSO R package (R Core team, 2016) version 0.3-3
(Zambrano-Bigiarini and Rojas, 2013, 2014). hydroPSO is an independent R
package that includes the newest standard PSO (SPSO-2011), which was
specifically developed to calibrate a wide range of environmental models. In
addition, the plotting functions in hydroPSO are user-friendly and aid the
numeric and visual interpretation of the optimization results. The source
code, installation files, tutorial (vignette), and manual are available on
https://cran.r-project.org/web/package=hydroPSO (last access: 12 June 2018).
hydroPSO is used in this article, for the first time, to estimate the
parameters of a surface complexation for uranium(VI)–quartz system, to properly
capture the non-linear interactions between the model parameters. The aim of
this article is to examine the suitability of hydroPSO as a global
optimization tool for parameter estimation of geochemical models, in
particular PHREEQC v3.1.2. To this end, surface/sorption reaction constants
(logK) of the SCM obtained with hydroPSO
will be compared to those previously obtained with parameter estimation (PEST) software (Doherty, 2010) by
Nair et al. (2014).
PEST and PSO are both model-independent parameter optimizers; i.e., they do
not require making any change to the model code. PEST uses the
Gauss–Marquardt–Levenberg method to minimize, in the weighted least squares
sense, the differences between observations and the corresponding
model-simulated values (Abdelaziz and Bakr, 2012; Edet et al., 2014). PEST is
a gradient-based algorithm that initially calculates the Jacobian matrix and
is then used to build and upgrade parameter set, to enhance the searching
ability to obtain a better objective function value (Doherty, 2010). The
model then iterates adjusting the model parameters on the basis of a new
Marquardt lambda value (Doherty, 2010), which drives the objective function
for faster convergence. As a local optimizer, PEST is sensitive to the
initial condition (see a complete description in Doherty, 2010). In contrast,
PSO is global optimizer which randomly initializes a population of particles
within the D-dimensional parameter space. PSO allows initializing the
position of each particle using a random uniform distribution or Latin
hypercube sampling (LHS), while velocities can be initialized at zero, with
two different random distributions, or with two different LHS strategies (see
Zambrano-Bigiarini and Rojas, 2013). Velocity and position of each particle
in the parameter space are updated in successive iterations following
equations specific to the selected PSO version (see a complete description in
Zambrano-Bigiarini and Rojas, 2013, and Abdelaziz and Zambrano-Bigiarini,
2014). As a state-of-the-art global optimizer, PSO is less subject get
trapped in local minima compared to PEST.
Model description
PHREEQC version 3.1.2 (Parkhurst and Appelo, 1999) and the database of Nuclear
Energy Agency thermodynamic (NEA_2007) (Grenthe et al., 2007), as well as the
LLNL database (Lawrence Livermore National Laboratory) are used to model
sorption of metal species. Both databases were modified by setting constant
values for MUO2(CO3)32- and
M2UO2(CO3)30 species (M equals Ca, Mg, Sr) obtained
from Geipel et al. (2008) and Dong and Brooks (2006, 2008). PHREEQC is a
geochemical software which is able to simulate sorption, surface
complexation, and other types of reactions. SCMs are considered to be able to
describe the processes at liquid–solid interfaces (Huber and
Lützenkirchen, 2009), and have been widely used to simulate the sorption
of metal species from aqueous solution depending on its concentration, pH
value, ionic strength, and redox conditions (Davis et al., 2004; Štamberg
et al., 2003; Zheng et al., 2003). A different group of reactions has taken
place between aqueous species in the bulk solution and the surface of the
sorbent leads to the formation of surface complexes (Nair et al., 2014). The
surface complexation constants for these reactions are indispensable and
independent of changes in solution condition or solution complex (Dzombak and
Morel, 1990; Hayes et al., 1991;
Volesky, 2003).
Complexation reactions with their respective logK range values.
There are different type of SCMs, such as the generalized two-layer model (GTLM),
non-electrostatic model (NEM), constant capacitance model (CCM), diffuse-layer
model (DLM), and modified triple-layer model (modified TLM). Here, a GTLM (Dzombak and Morel, 1990) was used to simulate the
sorption behavior of U(VI) on quartz. The GTLM was used instead of other
models because it is relatively simple and can be used in a wide range of
chemical conditions. A comprehensive review of the GTLM is presented in Dzombak
and Morel (1990). Quartz is a non-porous and non-layered mineral, and
therefore the actual area of surface is supposed to be equal to the specific
surface area. In this study, the surface of quartz is considered as a single
binding site which takes the charge for every surface reaction. The sorption
reactions and logK values are related to the aqueous species and thus
depend on the thermodynamic database used. Uranyl carbonate complexes
((UO2)2CO3(OH)3-, UO2(CO3)22-, and
UO2(CO3)34-) are the dominant species under our
experimental conditions. Therefore, the surface complexation reactions for
quartz were calculated with respect to these species.
The sorption of U(VI) on quartz was investigated and discussed by Huber and
Lützenkirchen (2009) without considering the formation of alkaline metal
uranyl carbonates. The formation of Mg-, Ca-, and Sr–uranyl-carbonato
complexes shows a significant impact on the sorption of uranium on quartz.
This was studied by Nair and Merkel (2011) in batch experiments adding 10 g
of powdered quartz to 0.1 L of water containing rather low U(VI)
concentrations (0.126×10-6 M) in the absence and presence of Mg,
Sr, and Ca (1 mM) at a pH value between 9 and 6.5 in steps of 0.5.
NaHCO3 (1×10-3 M) and NaCl (1.5×10-3 M)
were used as ionic strength buffers. The low U concentrations were used to
avoid precipitation of Ca–U carbonates. In the absence of alkaline earth
elements, the percentage of uranium was sorbed on quartz approximately
90 % independent from pH. In the existence of Mg, Sr, and Ca, the
percentage of sorption of uranium on quartz decreased to 50 %, 30 %,
and 10 % respectively (Nair and Merkel, 2011). In this paper, the
surface was the generalized
two-layer model and was taken from Dzombak and Morel (1990) with no explicit
calculation of the diffuse-layer composition.
Table 1 displays the parameter ranges used to optimize the six parameters
selected to calibrate PHREEQC, based on Nair et al. (2014).
Flow chart used to couple (a) PHREEQC with hydroPSO and
(b) PHREEQC with PEST for inverse modeling of surface complexation
constants for uranium carbonate (U(VI)) species on quartz using the PHREEQC
geochemical model.
Computational implementation
Inverse modeling is a complex issue for modelers as a result of the numerous
uncertainties in model parameters and observations (e.g., Carrera et al.,
2005; Beven, 2006). PSO is an evolutionary optimization algorithm originally
developed by Kennedy and Eberhart (1995), which has proven to be highly
efficient when solving a large collection of case studies from different
disciplines (see, e.g., Poli, 2008). In PSO, each individual of the
population searches for the global optimum in a multi-dimensional parameter
space, considering the individual and collective past experiences. The
canonical PSO algorithm starts with a random initialization of the particles'
positions and velocities within the parameter space. Velocity and position of
each particle in the parameter space are updated in successive iterations
following equations specific to the selected PSO version, in order to find
the minimum or (maximum) value of a user-defined objective function (see a
complete description in Zambrano-Bigiarini and Rojas, 2013). In the last
decades, several improvements have been proposed to the canonical PSO
algorithm, and the selected optimization tool implements several of them in a
single piece of software. The hydroPSO R package v0.3-3 (Rojas and
Zambrano-Bigiarini, 2012; Zambrano-Bigiarini and Rojas, 2013, 2014) is a
model-independent optimization package, which implements a state-of-the-art
PSO algorithm to carry out a global parameter optimization, and it has been
successfully applied as calibration tool for both hydrogeological and
hydrological models (Zambrano-Bigiarini and Rojas, 2013; Thiemig et al.,
2013; Abdelaziz and Zambrano-Bigiarini, 2014; Bisselink et al., 2016). In
particular, hydroPSO implements six PSO variants (equations used to update
particles' position and velocities), four topologies (ways in which particles
are linked during each iteration), two initialization of particles' positions
(random uniform distribution or Latin hypercube sampling), and five
alternatives for initializing particles' velocities, among other fine-tuning
options (see Zambrano-Bigiarini and Rojas, 2013). In the application of
hydroPSO to PHREEQC, the following configuration was used: a swarm with
10 particles, 200 iterations, LH initialization of particle positions and
velocities, random topology with five informants, acceleration coefficients
c1 and c2 equal to 2.05, linearly decreasing clamping factor for
Vmax in the range [1.0, 0.5], and use of Clerc's constriction factor
instead of the inertia weight. hydroPSO requires no instruction or template
files as UCODE (Poeter et al., 2005; Abdelaziz and Merkel, 2015) and PEST
software (Doherty, 2010, 2013) do. In order to couple hydroPSO with the
PHREEQC geochemical model, three text files have to be prepared by the user
to handle data transfer between the model code and the optimization engine.
These files include (i) ParamFiles.txt, which describes the names of
a set of parameters to be estimated and locations in the model input files to
be utilized in the inverse modeling, (ii) ParamRanges.txt, which
defines the minimum and maximum values that each selected parameter might
have during the optimization, and (iii) PSO_OBS.txt, which contains
the observations that will be compared against its simulated counterparts. In
addition, a user-defined R script file (Read_output.R) should
define the instructions to read model outputs. Finally, for coupling hydroPSO
with PHREEQC, an R script template provided by hydroPSO developers was
slightly modified by the user in order to carry out the optimization.
Figure 1a shows a flow chart that depicts how hydroPSO is coupled with
PHREEQC to calibrate its parameters. Run-phreeqc.bat is a batch file to run
PHREEQC-3.1.2 in the DOS environment, which reads
*.phrq files to produce *.prn files as output (simulated data);
*.ins files are instructions to read model outputs, by using the
Read_output.R script. At each iteration, hydroPSO modifies model
parameter values to minimize the value of the user-defined objective
function. Finally, the new parameter values are updated following the
locations provided in the “ParamFiles.txt” file. In contrast, to couple
PEST with PHREEQC, four files are required. These include (i) template files
(*.tpl), (ii) instruction files (*.ins), (iii) a main control file (*.pst),
and (iv) a batch file to execute PHREEQC and PEST(*.bat). Template files are
built to modify the input files for PHREEQC with other values while an
instruction file is used to extract the simulated values from the output file
for PHREEQC. The main control file includes the model application to be run,
the observations, parameters to be estimated, control data keywords, and
others. Further information about PEST can be found in its manual
(Doherty, 2010). Figure 1a, b show the key files used to couple PHREEQC with
hydroPSO and explain the flowchart and files involved in the inverse
modeling of the surface complexation constants for the U(VI) sorption model.
For numerical optimization, the residual sum of squares (RSS or SSR; see
Eq. 1) was utilized to compute the goodness of fit (GoF) between the
corresponding model outputs (Cjs) and observed U-carbonate
concentration values (Cjo) at different pH values for every
iteration step i; n is the number of observation points (measured sorption
U(VI) onto quartz). Minimizing the residual sum of squares was chosen as the
method for estimating the surface/sorption reaction constants in calibrations
by Nair et al. (2014) when PEST was combined with PHREEQC. It was decided for
consistency to select SSR as the criterion for goodness of fit when applying
hydroPSO with PHREEQC. After some initial trials, the number of maximum
iterations (T) was set to 200 and the number of particles used to search for
the minimum RSS in the parameter space was fixed at 10 (i.e., 2000 model
runs). All the input files required for running PHREEQC and hydroPSO can be
found at Zenodo
(https://zenodo.org/record/1044951#.WgVTbVuCzIU, last access: 10 November 2017), including all the optimization results.
SSR=∑j=1nCjs-Cjo2
Results and discussion
One approach to evaluate model performance is by plotting the simulation
against observed values (i.e., visualizing model outputs), as shown in
Fig. 1. The coefficient of determination (R2) for the relation between
calculated and observed values is 0.89, indicating that the simulated values
obtained with the best parameter set found by hydroPSO are able to explain a
good portion of the variability of the response data (Fig. 2).
Scatter plot with the experimentally observed and calculated values
of uranium carbonate (sorption percentage).
In hydroPSO, there are two types of criteria for convergence:
“absolute”, when the global optimum found in a given iteration
is below/above a user-defined threshold (useful for
minimization/maximization problems where the true minimum/maximum is known);
and
“relative”, when the absolute difference between the model
performance in the current iteration and the model performance in the
previous iteration for the best performing particle is less than or equal to a
user-defined threshold (useful to prevent too many model runs without any
improvement in the optimum found by the algorithm).
If none of the two previous criteria are met, then the algorithm stops when
the user-defined number of iterations is finally achieved. Figure 3 shows the
evolution of the best model performance (i.e., smallest RSS) found by all the
particles in a given iteration, and the normalized swarm radius
(δnorm, a measure of the spread of the population in the range
of search-space) versus the iterations number. One may observe that both
δnorm and the best model performance become smaller with an
increasing iteration number, which indicates that the main particles are
“flying” around a small region within the parameter space. Only 100
iterations (i.e., 100×10=1000 model runs) were enough to reach the
region of the global optimum (i.e., RSS ca. 2.52), and the remaining
iterations were just used to refine the search, as shown in Fig. 3.
Evolution of the normalized swarm radius (δ norm) and the
global optimum (SSR) over 200 iterations.
The boxplots in Fig. 4 are graphical representations of the values sampled
during optimization. The bottom and top of the box show the first and third
quartiles of the distribution of each one of the surface/sorption reaction
constants (logK) sampled during the optimization, respectively. The
horizontal line within the box denotes the median of the distribution. Points
outside the whiskers are considered to be outliers, where notches are within
±1.58IQR/(n), IQR represents the interquartile range and
n the total number of parameter sets used in the optimization. The
horizontal red lines in Fig. 4 point out the optimum value found during
optimization for each parameter.
Boxplots for the optimized parameters. The horizontal red lines
indicate the optimum value for each parameter. Parameter names are defined in
Table 1.
Quasi-three-dimensional dotty plots.
Quasi-three-dimensional dotty plots in Fig. 5 depict the goodness-of-fit values
achieved by different parameter sets. They are suitable for identifying
ranges where different sets of parameters lead to the same model performance
(equifinality, Beven, 2006). So, Fig. 5 also shows the model performance as
function of the interaction of different parameter ranges. The (quasi-)three-dimensional dotty plot shown in Fig. 5 is a projection of the values of
pairs of parameters onto the RSS response surface. Parameter values where the
model presents high performance are shown in light blue (points density),
whilst the parameter values where the model shows low performance are shown
in dark red (points density). Figure 5 was used to identify regions of the
solution space with good and bad model performance.
Empirical cumulative density functions for each calibrated
parameter.
Histograms of calibrated parameter values. Horizontal axis shows the
sampled range for each parameter, and the vertical axis represents the amount of
parameter sets in each of the classes used to divide the horizontal axis.
Visual inspection of Fig. 5 shows a good exploratory capability of PSO
because the particles are well spread over the entire range space. It is
clearly visible that the parameter samples are denser around the optimum
value (lowest SSR), showing a small uncertainty range around the optimum
value.
Correlation matrix between model performance (SSR) and calibrated
parameters. Red lines represent lowest smoothing, using locally weighted
polynomial regression, and numbers in the upper panel represents the
Pearson-moment correlation coefficient between each pair of parameters.
Vertical and horizontal axes illustrate the physical range utilized for
parameter optimization. *** stands for a p<0.001; ** stands for
p<0.01, according to level of statistical significance
Figures 6 and 7 give a graphical summary for optimized parameters. Empirical
cumulative density functions (ECDFs) in Fig. 6 show the sampled frequencies
for the six calibrated parameters. The horizontal gray dotted lines show the
median of the distribution (cumulative probability equal to 0.5), while the
vertical gray dotted lines depict the corresponding parameter value displayed
at the top of every panel in Fig. 6. The thin vertical red line in Fig. 7 points out
the optimum value achieved for each parameter. Histograms in Fig. 7 show
near-normal distributions for K1 and K2, while K4 and K5 follow a
skewed distribution with sampled values concentrated near the upper boundary
of each parameter.
Observed and simulated sorption of uranium in quartz vs. pH with
both PEST and hydroPSO calibrated logK values.
Figure 8 illustrates the correlation matrix among K values and model
performance (SSR), with horizontal and vertical axes displaying the ranges
used for the calibration of each parameter. The figure shows that
the highest correlation coefficient occurred among the measure of model
performance (SSR) and K4, K6, and K3. In addition, a higher
correlation coefficient was observed between K4 and K5, K3 and
K4, and K1 and K6.
Figure 9 shows the model output using hydroPSO fitted logK values and the
monitored sorption ratio.
It is worthwhile to mention that the surface complexation constants for
Eqs. (1), (2), and (5) (Table 1) are more important, and the equations that
are less important are Eqs. (3), (4), and (6) in optimizing the logK
values. It proves that UO2(CO3)34-,
UO2(CO3)22-, and (UO2)CO3(OH)3- are the
most dominant species for sorption on quartz. The surface complexation
constants for Eqs. (2) and (4) were 21.18 and 3.229, respectively (Nair et
al., 2014), which is higher than the electrostatic (ES) and non-electrostatic
(NES) models, while the optimized value for Eq. (1) is 25.156, which is
higher than the NES model and almost the same as the ES model (Nair et al.,
2014).
The experimental conditions used to calibrate PHREEQC with hydroPSO were the
same as during the PEST optimization carried out by Nair et al. (2014). In
other words, PEST was applied for the same experiment and the same data, and
Fig. 9 shows that the logK values obtained with hydroPSO are better than
those obtained by PEST, except for pH = 7. The main reason is that PSO is
a global optimization technique, which searches for optimum values in the whole
parameter space using the parameter ranges given in Table 1, while PEST
searches in a neighborhood of the initial solution. In particular, local
optimization carried out by PEST minimize a weighted least squares objective
function via the Gauss–Marquardt–Levenberg non-linear regression method
(Marquardt, 1963). Actually, a major drawback of PEST, as of all
gradient-based techniques, is the dependency of the quality of the
optimization results upon the initial point used for the optimization, which
might lead to a local optimum rather than the global one. Thus, PSO
techniques offer promising possibilities for similar surface complexation and
reactive transport applications in hydrogeology and hydrochemistry.
Conclusions
The coupling of hydroPSO and PHREEQC was successfully carried to estimate
surface complexation constants for uranium (VI) species on quartz, based on a
data set published by Nair and Merkel (2011), and Nair et al. (2014). The
open-source hydroPSO R package proved to be a useful tool for inverse
modeling of surface complexation models with PHREEQC and allowed a prompt
evaluation of the calibration results. Furthermore, thermodynamic values
obtained with hydroPSO provided a better match to observation
sorption rates in comparison to those obtained with PEST, using the same
input data and experimental setup.
PHREEQC is available at
http://www.hydrochemistry.eu/ph3/index.html (Parkhurst and Appelo,
2016). Source code, tutorials, and the reference manual of hydroPSO can be
obtained from https://CRAN.R-project.org/package=hydroPSO
(Zambrano-Bigiarini and Rojas, 2012). The PHREEQC model input files along
with the R scripts used for coupling it with hydroPSO and the model outputs
can be obtained from the Zenodo repository
(https://zenodo.org/record/1044951#.WgVTbVuCzIU, last access:
10 November 2017; Abdelaziz, 2017).
All authors contributed to the writing of the paper. RA
developed the coupling of PHREEQC and hydroPSO, carried out all simulations,
and prepared the manuscript. MZB, BJM, and SN were involved in visualizing and writing some
chapters. RA and co-authors contributed in reviewing and editing.
The authors declare that they have no conflict of
interest.
Acknowledgements
The authors thank the topical editor Claire Levy and the anonymous reviewers
whose helped us to improve the original manuscript
significantly. The authors would also like to thank Autumn Dinkelman for proofreading this paper.
Edited by: Claire Levy
Reviewed by: two anonymous referees
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