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ARCSWAT

2005Advanced Workshop







R. Srinivasan (r-srinivasan@tamu.edu)

Ann van Griensven








2




Table of Contents

Table of Contents . 3
1. Introduction . 5
2. Introduction to Sensitivity and Uncertainty Analysis 7
3. Introduction to Automatic Model Calibration . 31
4. ArcSWAT Advanced Manual Sensitivity Analysis, Auto-calibration, and
Uncertainty .. ..57






4

5
1. Introduction

This book contains the material for the advanced course of the first European SWAT
summer school, which is jointly organized by the SWAT development team, the
Institute for Landscape Ecology and Resources Management of the J ustus-Liebig-
University Giessen and the collaborative research center 299 Land use options for
peripheral regions.

The Soil and Water Assessment Tool (SWAT) is a physically-based continuous-
event hydrologic model developed to predict the impact of land management
practices on water, sediment, and agricultural chemical yields in large, complex
watersheds with varying soils, land use, and management conditions over long
periods of time. For simulation, a watershed is subdivided into a number of
homogenous subbasins (hydrologic response units or HRUs) having unique soil and
land use properties. The input information for each subbasin is grouped into
categories of weather; unique areas of land cover, soil, and management within the
subbasin; ponds/reservoirs; groundwater; and the main channel or reach, draining
the subbasin. The loading and movement of runoff, sediment, nutrient and pesticide
loadings to the main channel in each subbasin is simulated considering the effect of
several physical processes that influence the hydrology. For a detailed description of
the capabilities of SWAT, refer to the Soil and Water Assessment Tool Users
Manual, Version 2000 (Neitsch et al., 2001), published by the Agricultural Research
Service and the Texas Agricultural Experiment Station, Temple, Texas. The manual
can be downloaded from the web site (www.brc.tamus.edu/swat/swatdoc.html#new).
In this course, we will use a beta-version of the latest SWAT2003 version. Besides all
the features included in SWAT2000, this version also includes modules for sensitivity
analysis, automatic model calibration and uncertainty analysis. The official release of
SWAT2003 including an update of the manuals is planned for the fall of 2004.

SWAT2003 can be installed on IBM-compatible personal computers with a minimum
166-Mhz Pentium processor, 620 MB of hard disk space, 64 Mb of RAM (plus 120
Mb of virtual memory swap space), quad speed compact disk reader, color monitor
configured for 16 colors and a Windows 95, 98, NT or XP operating system. ArcView
version 3.1 or 3.2 and Spatial Analyst version 1.1 or 2.0 are also required.

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2. Introduction to Sensitivity and Uncertainty Analysis





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References
Breuer, L., Eckhardt, K., and Frede, H-G. 2003. Plant parameter valued for models in
temperate climates. Ecological Modelling, 169, 237-293.

Christiaens, K., and Feyen, J . 2002. Use of sensitivity and uncertainty measures in
distributed hydrological modeling with an application to the MIKE SHE model. Water
Resources Research, 38(9), doi:10.1029/2001WR000478.

Lenhart, T., Eckhardt, K., Fohrer, N., and Frede, H-G. 2002. Comparison of two
different approaches of sensitivity analysis. Physics and Chemistry of the Earth, 27,
645-654.

Melching, C.S. 1995. Reliability estimation. In: Computer models of watershed
hydrology, edited by Singh, V.P.. Water resources publications, Highlands Ranch,
CO, USA, 69-118.

Vrugt, J .A., Diks, C.G.H., Gupta, H.V., Bouten, W., and Verstraten, J .M. 2004.
Improved treatment of uncertainty in hydrologic modeling: combining the strength of
global optimization and data assimilation. Submitted to Water Resources Research.

Vrugt, J .A., Gupta, H.V., Bouten, W., and Sorooshian, S. 2003. A shuffled complex
evolution metropolis algorithm for optimization and uncertainty assessment of
hydrological model parameters. Water Resources Research 39(8),
doi:10.1029/2002WR001642.



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4. Introduction to Automatic Model Calibration




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References
Duan, Q., Gupta, V.K., and Sorooshian, S. 1992. Effective and efficient global
minimalization for conceptual rainfall-runoff models. Water Resources Research, 28,
1015-1031.

Duan, Q., Sorooshian, S., and Gupta, V.K. 1994. Optimal use of the SCE-UA global
optimisation method for calibrating watershed models. J ournal of Hydrology, 158,
265-284.

Gupta, H.V., Sorooshian, S., and Yapo, P.O. 1998. Toward improved calibration of
hydrologic models: multiple and noncommensurable measures of information. Water
Resources Research, 34(4), 751-763.

Kuczera, G., and Parent, E. 1998. Monte Carlo assessment of parameter uncertainty
in conceptual catchment models: the Metropolis algorithm. J ournal of Hydrology, 211,
69-85.

Madsen, H. 2000. Automatic calibration of a conceptual rainfall-runoff model using
multiple objectives. J ournal of Hydrology, 235, 276-288.

Seibert, J ., and McDonell, J .J . 2002. On the dialog between experimentalist and
modeler in catchment hydrology: use of soft data for multicriteria model calibration.
Water Resources Research, 38(11), doi:10.1029/2001WR000978.

Van Griensven, A., and Bauwens, W. 2003. Multiobjective autocalibration for
semidistributed water quality models. Water Resources Research, 39(12),
doi:10.1029/2003WR002284.

Vrugt, J .A. 2004. Towards improved treatment of parameter uncertainty in hydrologic
modeling. PhD-thesis Universiteit van Amsterdam, The Netherlands, 253 pp.

Vrugt, J .A., Gupta, H.V., Bouten, W., and Sorooshian, S. 2003. A shuffled complex
evolution metropolis algorithm for optimization and uncertainty assessment of

56
hydrological model parameters. Water Resources Research, 39(8),
doi:10.1029/2002WR001642.

Yapo, P.O., Gupta, H.V, and Sorooshian, S. 1998. Multi-objective global optimization
for hydrologic models. J ournal of Hydrology, 204, 83-97.




ArcSWAT Advanced Manual
Sensitivity Analysis, Auto-calibration, and Uncertainty


















Ann van Griensven
ann@biomath.ugent.be

and

R. Srinivasan
r-srinivasan@tamu.edu
i
Notes



























ii
Table of Contents

ArcSWAT Advanced Manual


Chapter 1: Theory............................................................................................................................................1
The LH-OAT sensitivity analysis..................................................................................................................1
Parasol (Parameter Solutions method): optimization and uncertainty analysis in a single run ....................3
SUNGLASSES (Sources of UNcertainty GLobal Assessment using Split-SamlpES): Model evaluation ..8
Chapter 2: ArcSWAT Tutorial .....................................................................................................................13
Sensitivity Analysis.....................................................................................................................................13
Auto-calibration and Uncertainty Analysis.................................................................................................25
Chapter 3: SWAT statistical method formats for manual editing ............................................................29
General input file formats (valid for all methods).......................................................................................29
Running the MC-OAT Sensitivity Analysis ...............................................................................................38
Running PARASOL....................................................................................................................................40
Running in batch (Running the good parameter sets) .................................................................................43
Running SUNGLASSES.............................................................................................................................44
Appendix A: References ................................................................................................................................47


1
Chapter 1: Theory

The LH-OAT sensitivity analysis

A LH-OAT combines the OAT design and Latin Hypercube sampling by taking the Latin Hypercube
samples as initial points for an OAT design (Figure 1).

Latin-Hypercube simulations

Latin-Hypercube is a sophisticated way to perform random sampling such as Monte-Carlo sampling to allow
a robust analysis requiring not too many runs. Monte Carlo samples are in general robust, but may require a
high number of simulations and consequently a large amount of computational resources (time and disk
memory). The concept of the Latin-Hypercube Simulation (McKay et al., 1979; McKay, 1988) is based on
the Monte Carlo Simulation but uses a stratified sampling approach that allows efficient estimation of the
output statistics. It subdivides the distribution of each parameter into N ranges, each with a probability of
occurrence equal to 1/N. Random values of the parameters are generated such that each range is sampled
only once. The model is then run N times with the random combinations of the parameters. The model
results are typically analysed with multi-variate linear regression or correlation statistics methods. The Latin-
Hypercube sampling is commonly applied in water quality modeling due to its efficiency and robustness
(Weijers and Vanrolleghem, 1997; Vandenberghe et al., 2001). The main drawback is the assumptions on
linearity. If these are not fulfilled, the biased results can be obtained.

One-factor-At-a-Time (OAT) sampling

OAT (One-factor-At-a-Time) design as proposed by Morris (1991) is an example of an integration of a local
to a global sensitivity method. As in local methods, each run has only one parameter changed, so the changes
in the output in each model run can be unambiguously attributed to the input parameter changed. This
approach has the advantage of a lack of reliance on predefined (tacit or explicit) assumptions of relatively
few inputs having important effects, monotonicity of outputs with respect to inputs, or adequacy of low-
order polynomial models as an approximation to the computational model (Morris, 1991).The output
analysis is based on the study of the random sample of observed elementary effects, which are generated
from each considered input. The change in model outcome ) ,..., ,..., (
1 n i i
x x x x M + can then be
unambiguously attributed to such a modification by means of an elementary effect S
i
defined by Equation 1.
) ,..., ,..., (
1 n i i
x x x x M + is usually some lumped measure like total mass, SSQ or SAE.

Considering n parameters (i.e. i=1,,n), this means that this experiment involves performing n+1 model
runs to obtain one partial effect for each parameter according to Equation 1.

Ideally, the computational experiment should account for the whole set of input parameters {x
i
}. In this work
a simple design was used where the computational experiment varies each input parameter one by one
starting from an initial vector ) ,..., ,..., (
1 n i i
x x x .

The result is quantitative, elementary and exclusive for the parameter. However, this measure of sensitivity
is only relative: as the influence of x
i
may depend on the values chosen for the remaining parameters, this
2
result is only a sample of its sensitivity (i.e. a partial effect). Therefore, this experiment is repeated for
several sets of input parameters. The final effect will then be calculated as the average of a set of partial
effects, and the variance of such a set will provide a measure of how uniform the effects are (i.e. the
presence or absence of nonlinearities or crossed effects with other parameters).

The elementary effects obtained using this procedure allows the user to screen the entire set of input
parameters with a low computational requirement. In this way, local sensitivities get integrated to a global
sensitivity measure.

The OAT design appeared to be a very useful method for SWAT modeling (Francos et al., 2002; van
Griensven et al., 2001) as it is able to analyse sensitivity on high number of parameters.
The LH-OAT sensitivity analysis

The LH-OAT sensitivity analysis method combines thus the robustness of the Latin Hypercube sampling
that ensures that the full range of all parameters has been sampled with the precision of an OAT designs
assuring that the changes in the output in each model run can be unambiguously attributed to the input
changed in such a simulation leading to a robust and efficient sensitivity analysis method. The method is
also efficient, as for m intervals in the LH method, a total of m*(p+1) runs are required.


Figure 1: Illustration of MC-OAT sampling of values for a two parameters model where X represents the
Monte-Carlo points and represents the OAT points.
x
x
x
x
x
p1
p2
3
Parasol (Parameter Solutions method): optimization and uncertainty analysis
in a single run
Optimization method
The shuffled complex evolution algorithm

This is a global search algorithm for the minimization of a single function for up to 16 parameters [Duan et
al., 1992]. It combines the direct search method of the simplex procedure with the concept of a controlled
random search of Nelder and Mead (1965), a systematic evolution of points in the direction of global
improvement, competitive evolution (Holland, 1995) and the concept of complex shuffling. In a first step
(zero-loop), SCE-UA selects an initial population by random sampling throughout the feasible parameters
space for p parameters to be optimized (delineated by given parameter ranges). The population is portioned
in to several complexes that consist of 2p+1 points. Each complex evolves independently using the
simplex algorithm. The complexes are periodically shuffled to form new complexes in order to share the
gained information. It searches over the whole parameter space and finds the global optimum with a success
rate of 100% (Sorooshian et al. 1993).

SCE-UA has been widely used in watershed model calibration and other areas of hydrology such as soil
erosion, subsurface hydrology, remote sensing and land surface modeling (Duan, 2003). It was generally
found to be robust, effective and efficient (Duan, 2003).

The SCE-UA has also been applied with success on SWAT for the hydrologic parameters (Eckardt and
Arnold, 2001) and hydrologic and water quality parameters (van Griensven et al., 2002).
Objective functions

Sum of the squares of the residuals (SSQ): similar to the Mean Square Error method (MSE) it aims at
matching a simulated series to a measured time series.

(1)
with n the number of pairs of measured (x
measured
) and simulated (x
simulated
) variables.

Sum of the squares of the difference of the measured and simulated values after ranking (SSQR): The
SSQR method aims at the fitting of the frequency distributions of the observed and the simulated series. As
opposed to the SSQ method, the time of occurrence of a given value of the variable is not accounted for in
the SSQR method (van Griensven and Bauwens, 2001).

After independent ranking of the measured and the simulated values, new pairs are formed and the SSQR is
calculated as:

(2)

[ ]

=
=
n j
simulated j measured j
x x SSQR
, 1
2
, ,
[ ]

=
=
n i
simulated i measured i
x x SSQ
, 1
2
, ,
4
where j represents the rank.
Multi-objective optimization
This following is based on the Bayesian theory (1763), assuming normal distribution of the residuals (Box
and Tiao, 1973). Residual can be assumed to have a normal distribution N (0,
2
), whereby the variance is
estimated by the residuals correspond to random errors:
(3)
with SSQ
MIN
the sum of the squares at the optimum and nobs the number of observations. The probability of
a residual can then be calculated as:



(4)


or

( )



2
2
, ,
,
2
exp ) | (

obs t sim t
obs t
y y
y p (5)

for a time series (1..T) this gives:

( )
( )

=
T
t
obs t sim t
T
obs
y y
Y p
1
2
2
, ,
2 2
exp
2
1
) | (

(6)
or


( )



=
2
2
, ,
1
2
exp ) | (

obs t sim t
T
t
obs
y y
Y p (7)

For a certain time series Y
obs
the probability of the parameter set p(|Y
obs
) is thus proportional to:


2
1
1
* 2
exp ) | (

SSQ
Y p
obs
(8)
where SSQ
1
are the sum of the squares of the residuals with corresponding variance
1
for a certain time
series. For 2 objectives, a Bayesian multiplication gives:

=
2
2
2
2
1
1
* 2
exp *
* 2
exp * 1 ) | (

SSQ SSQ
C Y p
obs
(9)
nobs
SSQ
MIN
=
2

( )

=
2
2
, ,
2
,
2
exp
2
1
) | (

obs t sim t
obs t
y y
y p
5
Applying Equation 3, Equation 9 can be written as:

=
min , 2
2 2
min , 1
1 1
*
exp *
*
exp * 2 ) | (
SSQ
nobs SSQ
SSQ
nobs SSQ
C Y p
obs

(10)
In accordance with Equation 10, it is true that:

[ ]
min , 2
2 2
min 2
2 2
* *
3 ) | ( ln
SSQ
nobs SSQ
SSQ
nobs SSQ
C Y p
obs
+ + =
(11)
We can thus optimize or maximize the probability of Equation 11 by minimizing a Global Optimization
Criterion (GOC) that is set to the equation:


min , 2
2 2
min , 1
1 1
* *
SSQ
nobs SSQ
SSQ
nobs SSQ
GOC + =
(12)
while according to equation (11) the probability can is related to the GOC according to:

[ ] GOC Y p
obs
exp ) | (
(13)
The sum of the squares of the residuals thus gets weights that are equal to the number of observations
divided by the minimum. This equation allows also for the uncertainty analysis as described below.
Parameter change options

Parameters affecting hydrology or pollution can be changed either in a lumped way (over the entire
catchment), or in a distributed way (for selected subbasins or HRUs). They can be modified by replacement,
by addition of an absolute change or by a multiplication of a relative change. It is never allowed to go
beyond the predefined parameter ranges. A relative change allows for a lumped calibration of distributed
parameters while they keep there relative physical meaning (soil conductivity of sand will be higher than soil
conductivity of clay).
Parameter change options for SWAT

In the ParaSol algorithm as implemented with SWAT2005 parameters affecting hydrology or pollution can
be changed either in a lumped way (over the entire catchment), or in a distributed way (for selected sub-
basins or HRUs). They can be modified by replacement, by addition of an absolute change or by a
multiplication of a relative change. A relative change means that the parameters, or several distributed
parameters simultaneously, are changed by a certain percentage. However, a parameter is never allowed to
go beyond the predefined parameter ranges. For instance, all soil conductivities for all HRUs can be changed
simultaneously over a range of -50 to +50 % of their initial values which are different for the HRUs
according to their soil type. This mechanism allows for a lumped calibration of distributed parameters while
they keep their relative physical meaning (soil conductivity of sand will be higher than soil conductivity of
clay).
6
Uncertainty analysis method

The uncertainty analysis divides the simulations that have been performed by the SCE-UA optimization into
good simulations and not good simulations. The simulations gathered by SCE-UA are very valuable as
the algorithm samples over the entire parameter space with a focus of solutions near the optimum/optima.

There are two separation techniques; both are based on a threshold value for the objective function (or global
optimization criterion) to select the good simulations by considering all the simulations that give an
objective function below this threshold. The threshold value can be defined by
2
-statistics where the
selected simulations correspond to the confidence region (CR) or Bayesian statistics that are able point out
the high probability density region (HPD) for the parameters or the model outputs (Figure 2).

2
-method

For a single objective calibration for the SSQ, the SCE-UA will find a parameter set * consisting of the p
free parameters (*
1
, *
2
, *
p
), that corresponds to the minimum of the sum the square SSQ. According to

2
statistics, we can define a threshold c for good parameter set using equation:


) 1 ( * *) (
95 . 0 ,
2
p n
OF c
p

+ =

(14)
whereby the
2
p,0.95
gets a higher value for more free parameters p.
For multi-objective calibration, the selections are made using the GOC of equation (11) that normalizes the
sum of the squares for n, equal to the sum of nobs1 and nobs2, observation. A threshold for the GOC

is the
calculated by:


)
2 1
1 ( * *) (
95 . 0 ,
2
p nobs nobs
GOC c
p
+
+ =

(15)
Bayesian method

According to the Bayesian theorem, the probability p(|Y
obs
) of a parameter set is proportional to equation
(11).

After normalizing the probabilities (to ensure that the integral over the entire parameter space is equal to 1) a
cumulative distribution can be made thereby defining a 95% confidence region. As the parameter sets were
not sampled randomly but were more densely sampled near the optimum during SCE-UA optimisation, it is
necessary to avoid having the densely sampled regions dominate the results. This problem is prevented by
determining a weight for each parameter set
i
by using the following calculations:

1. Dividing the p parameter range into m intervals
2. For each interval k of the parameter j, the sampling density nsamp(k,j) is calculated by summing the
times that the interval was sampled for a parameter j.

7
A weight for a parameter set
i
is then estimated by:

1. Determining the interval k of the parameter j,i
2. Considering the number of samples within that interval = nsamp(k,j)

The weight is then calculated as:

P
p
i j
i
j k nsamp
W
/ 1
1
) , (
1
) (

(16)
The c threshold is determined by the following process:
1. Sort parameter sets and GOC values according to decreasing probabilities
2. Multiply probabilities by weights.
3. Normalize the weighted probabilities by division by PT with:


) | ( * ) (
1
obs I
T
i
i
Y p W PT

=
=
(17)
4. Sum normalized weighted probabilities starting from rank 1 until the sum is higher than the
cumulative probability limit (95% or 97.5%). The GOC corresponding to the latest probability
defines then the c threshold.

0
50
100
150
200
0.0 0.2 0.4 0.6 0.8 1.0
k
S
m
a
x
sce sampling Xi-squared CR Bayesian HPD

Figure 2: Confidence region CR for the
2
-statistics and high probability density (HPD) region for the
Bayesian statistics for a 2-parameter test model.
8
SUNGLASSES (Sources of UNcertainty GLobal Assessment using Split-
SamlpES): Model evaluation

Introduction

Model uncertainty analysis aims to quantitatively assess the reliability of model outputs. Many water quality
modeling applications used to support policy and land management decisions lack this information and
thereby lose credibility (Beck, 1987). Several sources of modeling unknowns and uncertainties result in the
fact that model predictions are not a certain value, but should be represented with a confidence range of
values (Gupta et al., 1998; Vrugt et al. 2003; Kuczera, 1983a; Kuczera 1983b; Beven, 1993). These sources
of uncertainty are often categorized as input uncertainties (such as errors in rainfall or pollutant sources
inputs), model structure/model hypothesis uncertainties (uncertainties caused by inappropriateness of the
model to reflect reality or the inability to identify the model parameters) and uncertainties in the
observations used to calibrate/validate the model outputs (Figure 3).

Over the last decade model uncertainty analysis has been investigated by several research groups from a
variety of perspectives. These methods have typically focused on methodologies that focus on model
parametric uncertainty but investigators have had a more difficult time assessing model structural and data
errors and properly accounting for these sources of model prediction error (e.g. see commentaries in Beven
and Young, 2003; Gupta et al., 2003). The focus on parametric uncertainty in model calibration and
uncertainty methodologies does not address overall model predictive uncertainty which encompasses
uncertainty introduced by data errors (in input and output observations), model structural errors and
uncertainties introduced by the likelihood measure or objective function used to develop a model and its
particular application to a single location (Gupta et al., 2003; Thiemann et al., 2001; Kuczera and
Mroczkowski, 1998). It is important to note that proper assessment of model prediction uncertainty is
somewhat of an unattainable goal and that questions about the informativeness of data and model structural
error are typically best assessed in a comparison mode such as one model structure is superior in a specific
situation as opposed a wholesale accounting of the size of model structural error (e.g. Gupta et al., 1998).
This problem of not being able to quantitatively account for model structural error and errors introduced
during the model calibration process has been a continuing source of problems and has generally prohibited
the use of robust statistical methods for assessing uncertainty since these methods typically assume that the
structural form of the model is correct and that only model parameters need to be adjusted to properly match
a computational model to the observations (Beven and Young, 2003; Gupta et al., 2003). It is well known
that hydrologic models, particularly those of the rainfall-runoff process and even more so for models of
water quality, are not perfect models and thus the assumption that the model being used in the calibration
process is correct does not hold for the application of hydrologic models (for examples see Mroczkowski et
al., 1997; Boyle et al., 2001; Meixner et al., 2002; Beven, 1993).

The traditional way in which hydrologists assess how good their model is and whether the calibration
process they went through was valuable and meaningful, is to conduct an evaluation of the model via some
methodology. Model calibration and evaluation in hydrology has a long history. A fundamental necessity
noted by many is that the model must be evaluated using data not used for model calibration [Klemes,
1986]. This concept typically goes under the name split sample methodology. Typically this split sample
approach is conducted using one half of a data set to calibrate the model and the second half of the time
9
series to evaluate the calibration data set. This approach represents the minimum bar over which a model
must pass to be considered suitable for further application (Mroczkowski et al., 1997). More robust
methodologies exist for assessing the suitability of a calibrated model including calibration before a change
in land use and evaluation of the model after that change (Mroczkowski et al., 1997), the use of so-called
soft data that represent the in-depth knowledge of field hydrologists (Seibert and McDonnell, 2003), or the
use of observations at the same time or different times that were not used during the model calibration
process (Mroczkowski et al., 1997; Meixner et al., 2003). Still the split sample in time methodology remains
the dominant form of assessing model and model calibration performance due to its simplicity and the
general lack of robust multi-flux data sets of a long duration.

The split sample methodology is not without its flaws. It is well-known that a model typically performs
worse during an evaluation time period than during the calibration period and if a model performs almost as
well during the evaluation period it is generally accepted that this means the model is at least an acceptable
representation of the natural system it represents (e.g. Meixner et al., 2000).

Singh (1988) discusses the problem of model calibration at length and particularly notes that the model
calibration problem has several fundamental attributes. First, model calibration starts with the problem that
the data the model is being calibrated to has some error associated with it. Next, Singh (1988) notes that
model calibration typically over-compensates for the data error and that the standard error of the estimate
ends up being smaller than it should be. When the calibrated model is then taken to another time period for
evaluation the standard error of prediction is generally larger than the original standard error of the data
since the model was overly tuned to the observations for the calibration period. Singh notes that, while the
standard error of the data and of the estimate can be quantified using standard methods, the standard error of
the prediction, which we are most interested in, has no formalized methodology for estimation. This problem
remains to this day. These properties of standard error of the data, estimate and prediction extend to most of
the uncertainty methods used in hydrology since they share many similarities to the model calibration
problem.

The framework established by Singh (1988) proves useful as we think about the problem of estimating
model predictive uncertainty. Since most methods estimate the standard error of the estimate they are stuck
at the reduced uncertainty level indicated by Singh (1988). Given the fundamental interest in knowing the
uncertainty of model predictions as opposed to estimates during the calibration period it should prove useful
to investigate methods that can assess the uncertainty of predictions. The discussion above would indicate
that using the split sample approach and an assessment of model performance during the evaluation period
would be useful for estimating overall model predictive uncertainty.

Many researchers noted the problem that parameter uncertainty was much smaller than expected for the level
of trust we should have in model predictions (Thiemann et al., 2001; Beven and Freer, 2001; Freer et al.,
2003). Here we develop a methodology that utilizes a split sample approach to estimate overall model
predictive uncertainty and we compare these results to those garnered using our previously developed
parametric uncertainty method based on statistical approaches ParaSol (Parameter Solutions).
SUNGLASSES and ParaSol are then compared using the commonly used river basin water quality model,
the Soil Water Assessment Tool (SWAT).


10

Figure 3: Scheme of sources of errors in distributed water quality modeling.
Description

ParaSol is an optimization and statistical uncertainty method that assesses model parameter uncertainty. On
top of ParaSol, SUNGLASSES uses all parameter sets and simulations. Additional sources of uncertainty are
detected using an evaluation period, in addition to the calibration period.

In order to get a stronger evaluation of model prediction power, the Sources of Uncertainty Global
Assessment using Split SamplES (SUNGLASSES) is designed to assess predictive uncertainty that is not
captured by parameter uncertainty. The method accounts for strong increases in model prediction errors
when simulations are done outside the calibration period by using a split sample strategy whereby the
evaluation period is used to define the model output uncertainties. The assessment during the evaluation
period should depend on a criterion related to the sort of decision the model is being used for.

These uncertainty ranges depend on the GOC, representing the objective functions, at one side to calibrate
the model and develop an initial estimate of model parameter sets, and an evaluation criterion (to be used in
decision making) at the other that is used to estimate uncertainty bounds. The GOC is used to assess the
degree of error on the process dynamics, while the evaluation criteria define a threshold on the GOC. This
threshold should be as small as possible, but the uncertainty ranges on the criterion should include the true
value for both the calibration and the validation period. For example when model bias is used as the
criterion, these true values are then a model bias equal to zero. Thus, the threshold for the GOC would be
Environmental
Observations
Real world values
On a spatial / temporal
Sources of Mode

Forcing Inputs
Recording errors of forcing inputs
Spatial/temporal discretization
Observed spatial resolution
Observed temporal
resolution
Observed forcing data

Landuse
Soil
Topography
Spatial Inputs
Spatial discretization of landuse,
soil, and topography
Errors on parameters for landuse,
soil, and topography
Landuse Map
Soil Map
Topographic map
NO
3

NO
2
-
NH
4
+
SOM
Model
Structure
Model scale discretization
Model hypothesis
Model spatial structure
Simplified processes
Uncertain parameters
Point Sources
Diffuse
Sources
Pollution
Observation and temporal errors
for point-source pollution
Errors on land use practices
Temporal discretization for diffuse
Model diffuse pollution
sources
Model point pollution sources
Uncertain model
output
Environmental
Errors on observed values
RESIDUAL Observations Model
11
increased until the uncertainty ranges on the total mass flux include zero bias. SUNGLASSES operates by
ranking the GOCs (Figure 4). Statistical methods can be used to define a threshold considering parameter
uncertainty. In this case, ParaSol was used to define such a threshold. However, when we look at the
predictions, it is possible that unbiased simulations are not within the ParaSol uncertainty range other than
parameter uncertainty. This result means that there are additional uncertainties acting on the model outputs
(Figure 5). Thus, a new, higher threshold is needed in order to have unbiased simulations included within the
uncertainty bounds (Figures 4 and 5). This methodology is flexible in the sense that different combinations
of objective functions can be used within the GOC. Also alternatives for the bias as the criterion for the
model evaluation period are possible depending on the model outputs to be used for decision making.
Examples of alternative criteria are the percentage of time a certain output variable is higher or lower than a
certain threshold (being common for water quality policy) or the maximum value or the value of a certain
model prediction percentile (often important for flood control).











Figure 4: Selection of good parameter sets using a threshold imposed by ParaSol or by SUNGLASSES

Ranked GOCs for all SCE-UA simulations
1.E+02
1.E+03
1.E+04
1.E+05
1.E+06
1 5001 10001 15001 20001 25001 30001
Rank
G
O
C

(
l
o
g
-
s
c
a
l
e
)
ParaSol threshold
SUNGLASSES
12
Model bias for the sediment loads (%)
-80.00
-40.00
0.00
40.00
80.00
120.00
160.00
200.00
1998-1999 2000-2001 1998-1999 2000-2001
ParaSol SUNGLASSES

Figure 5: Confidence regions for the sediment loads calculations according to ParaSol and SUNGLASSES

13
Chapter 2: ArcSWAT Tutorial
Sensitivity Analysis
1. Open the Yellow River project (run3).

2. To use the sensitivity analysis tool, click on the SWAT Simulation tab on the ArcSWAT toolbar. A
dropdown menu will allow you to choose between several options. Choose Sensitivity Analysis
(Figure 6).


Figure 6: SWAT Simulation Tools Sensitivity Analysis.

3. A new dialog box will open (Figure 7). This dialog box allows you to select between Sensitivity
Analysis Inputs and Outputs. Click on the Sensitivity Analysis Input tab, which allows you to select
the simulation and subbasin you want to use as the outlet for the analysis.

4. Select firsttry for the simulation and Subbasin 3. If there are more simulations available, you can
click on each one to see a summary of the main properties in the right panel of this dialog box.

5. You are also offered three options under Sensitivity Parameters: 1) flow, 2) sediment and 3) water
quality. Further, you can choose to perform this analysis on observed data or average flow values (by
unchecking the observed data box).

6. Select Flow and check the Use Observed Data box. The measured flow data are provided in the file
observations9394.txt.
14

Figure 7: Sensitivity Analysis Input Simulation dialog box.

7. Click on the Sensitivity Analysis Output tab (Figure 8), which provides options to further refine the
output parameters for the analysis. The Output Parameter Sensitivity (responsemet.dat) section can
be used to define additional output parameters that can be evaluated through average or threshold
criteria. In addition, when using observed data, you can choose to evaluate those output parameters
that are in the observed data based on various objective functions.

15

Figure 8: Sensitivity Analysis Output Simulation dialog box.

8. Click on Write Input Files. A message box will notify you that the input files have been written.
Click OK and then click the Run Sensitivity Analysis button.

9. A DOS window will open and SWAT2005 will begin running. This analysis may take several
minutes or even hours or days in the case of large SWAT projects. It will take N+1 * 10 runs to
complete this analysis, where N is the number of parameters that are analyzed for sensitivity. In this
case it will take 270 model runs to complete the sensitivity analysis for the hydrologic parameters.
16
10. Once the SWAT run is complete you can read the sensitivity reports by clicking on the SWAT
Simulation tab on the ArcSWAT toolbar and then choose Sensitivity/Calibration Reports (Figure
9).



Figure 9: SWAT Simulation Tools Sensitivity/Calibration Reports.

11. A new dialogue box will open that gives you the option to choose the simulation and analysis youre
interested in. Choose firsttry and Sensitivity Analysis. You can then choose the report of interest
under the Select Report section (Figure 10).


Figure 10: SWAT Run Reports Sensitivity Analysis.

The model parameters included in the sensitivity analysis can be controlled outside of the ArcSWAT
interface. In the following, the text-based input files required for the sensitivity analysis will be discussed in
detail. These input files are located in the directory \run3\Scenarios\firsttry\TxtInOut\Sensitivity.

Input file 1: Sensin.dat

The first three lines of sensin.dat (Figure 11) specify three control variables of the LH-OAT sensitivity
analysis:
17
1. Number of intervals m within Latin Hypercube sampling
2. Fraction of parameter range defined by minimum and maximum bounds that is varied in the OAT
part of the sensitivity analysis (see Figure 1)
3. Random seed required for random sampling within the m intervals.


Figure 11: Sensin.dat
Input file 2: changepar.dat

The changepar.dat file (Figure 12) specifies the model parameters included in the sensitivity analysis. These
lines consist of five columns:
1. Lower bound of parameter value
2. Upper bound of parameter value
3. Number specifying the model parameter (Table 1)
4. Variation method (imet, see Table 2)
5. Number of HRU

If you specify the number of HRU as larger than 2000, the parameter is changed for all HRU. If the number
of HRU is lower than 2000, the parameter is changed for a selected number of HRU. In this case, the HRU
numbers must be provided in the next line in sets of 50*5i. Please note that the number of HRU is only
required for the subbasin type variables (sub) given in Table 1.

18

Figure 12: changepar.dat

Table 1: Parameter codes for sensitivity analysis, automatic model calibration and uncertainty analysis.
Par Name Type Description Location
1 ALPHA_BF Sub Baseflow alpha factor [days] *.gw
2 GW_DELAY Sub Groundwater delay [days] *.gw
3 GW_REVAP Sub Groundwater "revap" coefficient *.gw
4 RCHRG_DP Sub Deep aquifer percolation fraction *.gw
5 REVAPMN Sub Threshold water depth in the shallow aquifer for "revap" [mm] *.gw
6 QWQMN Sub Threshold water depth in the shallow aquifer for flow [mm] *.gw
7 CANMX Sub Maximum canopy storage [mm] *.hru
8 GWNO3 Sub Concentration of nitrate in groundwater contribution [mg N/l] *.gw
10 CN2 Sub Initial SCS CN II value *.mgt
15 SOL_K Sub Saturated hydraulic conductivity [mm/hr] *.sol
16 SOL_Z Sub Soil depth [mm] *.sol
17 SOL_AWC Sub Available water capacity [mm H20/mm soil] *.sol
18 SOL_LABP Sub Initial labile P concentration [mg/kg] *.chm
19 SOL_ORGN Sub Initial organic N concentration [mg/kg] *.chm
20 SOL_ORGP Sub Initial organic P concentration [mg/kg] *.chm
21 SOL_NO3 Sub Initial N0
3
concentration [mg/kg] *.chm
19
22 SOL_ALB Sub Moist soil albedo *.sol
23 SLOPE Sub Average slope steepness [m/m] *.hru
24 SLSUBBSN Sub Average slope length [m] *.hru
25 BIOMIX Sub Biological mixing efficiency *.mgt
26 USLE_P Sub USLE support practice factor *.mgt
27 ESCO Sub Soil evaporation compensation factor *.hru
28 EPCO Sub Plant uptake compensation factor *.hru
30 SPCON Bas Lin. re-entrainment parameter for channel sediment routing *.bsn
31 SPEXP Bas Exp. re-entrainment parameter for channel sediment routing *.bsn
33 SURLAG Bas Surface runoff lag time [days] *.bsn
34 SMFMX Bas Melt factor for snow on J une 21 [mm H2O/C-day] *.bsn
35 SMFMN Bas Melt factor for snow on December 21 [mm H2O/C-day] *.bsn
36 SFTMP Bas Snowfall temperature [C] *.bsn
37 SMTMP Bas Snow melt base temperature [C] *.bsn
38 TIMP Bas Snow pack temperature lag factor *.bsn
41 NPERCO Bas Nitrogen percolation coefficient *.bsn
42 PPERCO Bas Phosphorus percolation coefficient *.bsn
43 PHOSKD Bas Phosphorus soil partitioning coefficient *.bsn
50 CH_EROD Sub Channel erodibility factor *.rte
51 CH_N Sub Manning's nvalue for main channel *.rte
52 TLAPS Sub Temperature lapse rate [C/km] *.sub
53 CH_COV Sub Channel cover factor *.rte
54 CH_K2 Sub Channel effective hydraulic conductivity [mm/hr] *.rte
60 USLE_C Sub Minimum USLE cover factor crop.dat
61 BLAI Sub Maximum potential leaf area index crop.dat

The sensitivity analysis provides three methods for varying the parameters. The first option allows you to
replace the value directly (option 1). For example, the parameter ALPHA_BF is varied between 0 and 1 and
the randomly drawn value is substituted directly into all *.gw files. The second method allows you to add
values to the initial values. The third method allows you to multiply the initial value with the drawn
parameter value. For example, the specified settings for the parameter CN2 in figure II.4 allow this
parameter to vary between 0.5 to 1.5 (-50% to +50%) times the value currently specified in each *.mgt files.

Table 2: Variation methods (imet) available in sensing.dat
imet Description
1 Replacement of initial parameter by value
2 Adding value to initial parameter
3 Multiplying initial parameter by value (in percentage)

Input file 3: responsmet.dat

This file contains the output variables and methods that will be used for the sensitivity analysis (Figure 13).
Each line represents an output variable (with a maximum of 100) and has five columns that indicate:
20
1. Output variable number (see Table 3)
2. Parameter that allows you to either use the average of the output variable specified in column 1
(setting 1) or the percentage of time that the output variable is below the threshold defined in column
5 (setting 2)
3. When the output variable is a solute, you can either perform the sensitivity analysis on the
concentrations (setting 0) or the loads (setting 1)
4. Code number for the autocal file in fig.fig. This is required when the sensitivity analysis is
performed for more than one subbasin.
5. Threshold value corresponding to column 2, setting 2.

In the case of the example file shown in figure 3.6, the sensitivity analysis is performed on the average flow,
average sediment load, average organic N load, average organic P load and the average nitrate load.


Figure 13: Responsmet.dat.

Table 3: Output variable number.
Nr. Variable
1 Flow [m3/s]
2 Sediment concentration [g/l]
3 Organic N concentration [mg N/l]
4 Organic P concentration [mg P/l]
5 Nitrate concentration [mg N/l]
6 Ammonia concentration [mg N/l]
7 Nitrite concentration [mg N/l]
8 CBOD concentration [mg/l]
9 Dissolved oxygen concentration [mg/l]
10 Mineral P concentration [mg P/l]
11 Chlorophyll-a concentration [g/l]
21
12 Soluble pesticide concentration [mg/l]
13 Sorbed pesticide concentration [mg/l]
14 Temperature [C]
20 Kjeldahl nitrogen concentration [mg N/l]
21 Total nitrogen concentration [mg N/l]
22 Total phosporus concentration [mg P/l]

Input file 4: objmet.dat

This file contains the output variables and methods that will be used when the sensitivity analysis is applied
to an error measure instead of an output variable (Figure 14). Each line stands for an output variable (with a
maximum of 100) and has five columns that indicate:
1. Output variable number (see Table 3)
2. Parameter that allows you to use different error measures (1=SSQ, 5=SSQR). The error measures are
discussed in more detail in the automatic calibration sections.
3. When the output variable is a solute, you can either perform the sensitivity analysis on the
concentrations (setting 0) or the loads (setting 1)
4. Code number for the autocal file in fig.fig. This is required when the sensitivity analysis is
performed for more than one subbasin.
5. Weight for the objective function in the case of a multi-objective calibration.


Figure 14: Objmet.dat

These three files allow you to customize the sensitivity analysis to your needs. If you make changes to one
of these three input files, you cannot run the sensitivity analysis from the SWAT interface anymore. Instead,
you have to copy swat2005.exe from the \arcswat directory into the directory of the sensitivity analysis
and run this executable from a DOS interface.

22
After completing the sensitivity analysis, SWAT2005 will produce a set of output files. A short description
of these input files is provided in Table 4. The files that you will mostly use are sensresult.out and
sensout.out. Since the file sensresult.out only contains the final ranking of each parameter in the analysis, we
will only discuss the file sensout.out here (Figure 15). In the first lines of sensout.out, the settings of the
sensitivity analysis are summarized (not shown here). Then, the results of the sensitivity analysis are shown
for each objective function and for each model output variable selected in either responsmet.dat or
objmet.dat.

Table 4: Output files of the sensitivity analysis.
File name Description
sensresult.out List of parameter ranks
sensout.out Detailed output with mean, variance and partial sensitivities
senspar.out Parameter values of each run
sensobjf.out Value of objective function for each run
sensrespons.out Model output values for each run
lathyppar.out Normalized Latin-Hypercube sampling points
oatpar.out Normalized OAT sampling points

Figure 15 shows part of the results for one model output variable. In the first lines shown, each column
represents a model parameter. Each of the 10 lines represents the results of the AOT sensitivity analysis for
each LH sampling point. In the following lines, the maximum, variance, mean and ranking for each model
parameter (column) are provided. Finally, a summary with mean and ranking for each model parameter is
given.


EXERCISE 3.1
The results of the standard sensitivity analysis are provided in the directory
\run3\sensitivity. We have performed a sensitivity analysis for the period 1993-1994.
Study the sensitivity ranking of each of the model parameters.



23

Figure 15: sensout.out details.


EXERCISE 3.2
You can also compare the ranking of the model parameters between the sensitivity analysis
performed on the mean daily flow and the sensitivity analysis performed on the sum of
squared residuals between measured and modeled flow. There is a large difference in
ranking for the surface runoff lag time (SURLAG). Do you have an explanation for this
large difference?

24

EXERCISE 3.3
To practice setting up your own sensitivity analysis, create the appropriate input files to
perform a sensitivity analysis on the average flow for the model parameters: CN2, SOL_K,
SOL_AWC and CANMX. The base simulation for the sensitivity analysis should run from
1.1.1993 to 31.12.1993. Make relative changes from 10 to 10% for CN2, relative changes
from 25 to 25% for SOL_AWC, relative changes from 50 to 50% for SOL_K and use
actual values between 0 and 5 for CANMX. Which of these four parameters is the most
sensitive? How do you rate the variances of the mean partial sensitivities in sensout.out?

EXERCISE 3.4
The results of the sensitivity analysis also depend on the bounds selected for each parameter.
To test this, increase the bounds from CN2 to 25% to 25%. Did the ranking of the model
parameters change?




















25
Auto-calibration and Uncertainty Analysis

1. To use the Auto Calibration and Uncertainly Analysis tool, click on the SWAT Simulation tab on
the ArcSWAT toolbar. A dropdown menu will allow you to choose between several options. Choose
Auto Calibration and Uncertainly Analysis (Figure 16).


Figure 16: SWAT Simulation Tools Auto Calibration and Uncertainly Analysis.

2. A new dialog box will open (Figure 17). This dialog box allows you to select between Auto-
Calibration Inputs and Outputs. Click the Auto-Calibration Input tab, which allows you to select
the simulation and subbasin you want to use as the outlet for the automatic model calibration. Select
firsttry and Subbasin 3. If there are more simulations available, you can click on the simulation of
interest to perform auto-calibration.

3. You are also able to modify various input settings, add observed data, and select the calibration
method and you can choose between three variation methods: 1) replace by value, 2) add to value
and 3) multiply by value (%). In addition, you can calibrate parameters in specific HRUs, landuses,
soil types, and slopes if necessary, by clicking on the Select HRUs/LU button. Choose the
PARASOL calibration method and add the observed data provided in the file observations9394.txt.

26

Figure 17: Auto-Calibration Input dialog box.



4. Click on the Auto-Calibration Output tab (Figure 18), which provides options to further refine the
output parameters for the analysis. When using observed data, you can choose to evaluate only those
output parameters based on various objective functions in the Calibration Output Evaluations
(objmet.dat) section. The Model Output Evaluations (responsemet.dat) section can be used to define
additional output parameters that can be evaluated through average or threshold criteria.

27


Figure 18: Auto-calibration Output dialog box.


12. Click on Write Input Files. A message box will notify you that the input files have been written.
Click OK and then click the Run Auto-Calibration button.

13. A DOS window will open and SWAT2005 will begin running. This analysis may take several hours
or even days in the case of large SWAT projects.


28
14. Once the SWAT run is complete you can read the sensitivity reports by clicking on the SWAT
Simulation tab on the ArcSWAT toolbar and then choose Sensitivity/Calibration Reports (Figure
19).

15. A new dialogue box will open that gives you the option to choose the simulation and analysis youre
interested in. Choose firsttry and Auto-Calibration. You can then choose the report of interest
under the Select Report section (Figure 19).



Figure 19: Output reports dialog box.


The Objective functions values for each optimization run (sceobjf.out) report provides the objective
function values for all parameter sets considered in the automatic calibration.
The Parameter values for all simulation runs (scepar.out) report provides the parameter sets considered in
the automatic calibration.
The Detailed output for each optimization loop (parasolout.out) report provides a detailed summary of the
input and the results of the automatic calibration.
The Good parameter values (goodpar.out) report provides the parameter sets that had acceptable values for
the objective function.
The Best parameter values (bestpar.out) report provides the parameter set that had the lowest value for the
objective function.
The derivation and interpretation of these parameter sets are discussed further in Chapter 3.

The only settings that cannot be controlled from the auto-calibration interface are the control parameters of
the SCE-UA optimization algorithm. These settings are listed in the file parasolin.dat. The first 8 lines of this
file are the SCE-UA control parameters. Generally, these parameters do not have to be changed. If you still
want to change them, for example to reduce the number of simulations, we advise that you study the
meaning of each of the parameters in Duan et al. (1992) and Duan et al. (1994).

29
Chapter 3: SWAT statistical formats for manual editing
General input file formats (valid for all methods)
File.cio
ICLB The flag for autocalibration in the *.COD file has to be activated

0 ! I CLB: aut o- cal i br at i on opt i on: 0=nor mal r un , >1 st at i st i cal r uns

ICLB VALUES AND MEANING:

Table 5: Options for ICLB in File.cio
0 no autocalibration
1 Sensitivity analysis
2 Opimization using PARASOL
3 Opimization and uncertainty using PARASOL
4 Rerun model with best parameter set
5 Rerun the model with good parameter sets (to obtain uncertainty bounds on output time
series)
6 (re)calculate uncertainty results (e.g. when optimization was abrupted manually)
8 Run sunglasses

Some other adaptations are always required while others depend on the method that is indicated in the
File.cio (Figure 20).













Figure 20: File.cio.
1: sensitivity analysis
2: auto-calibration (ParaSol)
4: rerun best parameter set
5: rerun good parameter set
9: auto-calibration
(SUNGLASSES)
1: sensitivity analysis
2: auto-calibration (ParaSol)
4: rerun best parameter set
5: rerun good parameter set
9: auto-calibration
(SUNGLASSES)
30
FIG file

In the *.fig file (Figure 21), a line has to be added that indicates the node where calibration has to take place
and the variable that will be optimised.

Autocal command (16)

This command allows the user to print the SWAT output to an output file "autocal.out" for one variable to
generate a calibration time series. This output file can then be read by the autocalibration. Variables required
on the save command line are listed in Table 6.

Table 6: inputs in the autocal command in *.fig file
Variable name Definition
COMMAND The command code =16 for autocalibration
HYD_STOR Number of one of the previous hydrograph storage location numbers to be used
for autocalibration
INUM1S

Number of autocalibration file (up to 10)
INUM2S

Subdaily, daily or monthly
0: daily registration
1: hourly registration (Only when ievent =1)
3: monthly registration
AUTO_IN Name of the file with the measurements

The format of the autocal command line is shown in Table 7.

Table 7: Format for autocal command in *.fig file
Variable name Line # Position Format
COMMAND 1 space 11-16 6-digit integer
HYD_STOR 1 space 17-22 6-digit integer
INUM1S 1 space 23-28 6-digit integer
INUM2S 1 space 29-34 6-digit integer
AUTO_IN 2 Space 11-23 13 characters

31
observation filename
file number (cfr. objmet/responsmet)
Time resolution: 0: daily 1: hourly
3: monthly
observation filename
file number (cfr. objmet/responsmet)
Time resolution: 0: daily 1: hourly
3: monthly

Figure 21: Fig file.
Data file with observations

This file (Figure 21) has the measurements of the variable that has to be optimized by calibration.

This file is a list with following columns:

Hourly observations:
year (1X5i) day (2x3i) [hour/zero (1x2i)] measured values (1X10F.3)

Daily observations:
year (1X5i) day (2x,3i), 3x, measured values (1X11F.3)

Measured values are in columns with:

1. FLOWm^3/ s
2. SED mg/ L
3. ORGN mg/ L
4. ORGP mg/ L
5. NO3 mg/ L
6. NH3 mg/ L
7. NO2 mg/ L
8. MI NP mg/ L
9. CBOD mg/ L
10. DI SOX mg/ L
11. CHLA ug/ L
12. SOLPST mg/ L
13. SORPST mg/ L
14. BACTP ct / L
15. BACTLP ct / L
16. CMETAL1 mg/ LC
17. METAL2 mg/ LC
32
18. METAL3 mg/ L
19. TEMP deg C
20. Kj el dahl N mg/ L
21. Tot al N mg/ L
22. Tot al P mg/ L

Montly observations
year (1X5i) month (3x2i), 3x, measured values (1X11F.3)

1. FLOWm^3 / s
2. SED met r i c t ons / day
3. ORGN kg N / day
4. ORGP kg P day
5. NO3 kg N / day
6. NH3 kg N / day
7. NO2 kg N / day
8. MI NP kg P / day
9. CBOD kg / day
10. DI SOX kg / day
11. CHLA kg / day
12. SOLPST mg pest i ci de / day
13. SORPST mg pest i ci de / day
14. Kj el dahl kg N / day
15. Tot al kg N / day
16. Tot al kg N / day

All missing data should have a negative value (Figure 22). These will then be skipped by the calculation of
the objective function.

Figure 22: observation file
changepar

The changepar file (Figure 23) lists the parameters to be changed. These can be GENERAL parameters (1
parameter representing the entire basin, such as parameters listed in basins.bsn file) or HRU-parameters
(listed in the *.hru file) or subbasin parameters (listed in the *.rte file). The formats are different. General
33
parameters have 1 line each, HRU/subbasin parameters have one (when they are changed in a LUMPED
way all distributed parameters get the same change) or have 2 lines when they are changed in a
DISTRIBUTED way. In this case, a second line lists the HRU/subbasin numbers to be changed. There are
also a few routing parameters. Here, the number of each reach is listed.

General

Inputs for the changepar file are listed in Table 8.

Table 8: Inputs for the changepar file
Name line format space
lower border 1 xxxx.xxxxx 1-10
up border 1 xxxx.xxxxx 11-20
parameter code (see table) 1 xxxxx 21-25
method code (see table) 1 xxxxx 26-30
Number of HRU numbers listed
below (=0)
1 0 31-35

HRU/subbasin parameters

Formats for the changepar file and options for imet are listed in Tables 9 and 10, respectively.

Table 9: Formats for the changepar file
Name line format space
lower border 1 xxxx.xxxxx 1-10
up border 1 xxxx.xxxxx 11-20
parameter code (see table) 1 xxxxx 21-25
method code (see table) 1 xxxxx 26-30
Number of HRU/subbasins
numbers listed below
1 xxxxx 31-35
If nHRU/subbasins <=2000
HRU numbers or crop number
for changes in the crop.dat file
lines of 50 values 50 times(xxxxx)
If nHRU/subbasins >2000, all
HRUs of the model are
modified and no list of HRUs
should be given



Table 10: Options for imet
1 Replacement of parameter by value
2 Adding value to initial parameter
3 Multiplying initial parameter by value

The options for the parameters are listed in Table 1
34

Figure 23: Changepar.dat.
objmet.dat

This file (Figure 24) defines the variables and methods that will be used for the optimization. Each line
stands for a OF with a maximum of 20 OF. The OF is described by 3 control parameters:

OFMET1 determines which output variable will be used for the OF, OFMET2 determines which method
will be used and OFMET3 indicates if loads should be used in stead of concentrations, OFMET4 the number
of file (site locations). Inputs are outlined in Table 11.



Parameter bounds
Parameter code and name
Parmeter change method:
1: replace by value
2: addition of value
3: multiplication of value
35
Table 11: Inputs for objmet.dat.
OFMET1 i4 The code number of the variable to be saved for calibration:
1: water (m/s)
2: sediment
etc. (like watout)
+
20: Kjeldahl nitrogen
21: total nitrogen
22: total phosphorus
OFMET2 i4 chose 1 or 5 according to previous described methods for the calculation of the OF
(1=SSQ and 5=SSQR)
OFMET3 i4 This option can only be used for the pollutants (for daily or hourly). 0 indicates that the
concentrations are calibrated, 1 the loads. Monthly is always based on the loads.
OFMET4 I4 Code number for the autocalfile in *.fig (1 for autocal1.out, etc)
CALW F8.3 Given weight for objective function



































Figure 24: Objmet.dat.


Variable code (1=flow
Objective
function
1: SSQ
5: ranked SSQ
File number (cfr.
fig.fig):
36
responsmet.dat

This file (Figure 25) defines the variables and methods that will be used for the sensitivity analysis. Each
line (Table 12) stands for an output value with a maximum of 100. The output value is described by the
control parameters:

RESPONSMET1 determines which output variable will be used, RESPONSMET2 what value has to be
calculated for the output variable (average concentration, total mass,).

Table 12: Inputs for Responsmet.dat
RESPONSMET1 i4 The code number of the variable of interest
1: water (m/s)
2: sediment (g/l)
etc. (like watout)
+
20: Kjeldahl nitrogen
21: total nitrogen
22: total phosphorus
RESPONSMET2 i4 chose 1-2 according interest
1: average
2: percent of time < then sensw threshold
RESPONSMET3 i4 This option can only be used for the pollutants. 0 indicates that the concentrations
are calibrated, 1 the loads
RESPONSMET4 I4 Code number for the autocalfile in basi.fig (1 for autocal1.out, etc)
responsw F8
.3
Threshold value for case responsmet2=2

37
Figure 25: Responsmet.dat.

Variable code (1=flow
Response function
1: mean value
2: percentage < threshold

File number (cfr. fig.fig).

Threshold value

38
Running the MC-OAT Sensitivity Analysis

Inputs

The sensitivity analysis needs input files listed in Table 13.

Table 13: Input files for MC-OAT sensitivity analysis.
File.cio Iclb=1 Adapt file (See above)
Basins.fig Indication of the location of the output
within the model structure
Adapt file (See above)
Objmet.dat Definition of error fuctions Create file (See above)
Responsmet.dat (optional) Definition of output criteria Create file (See above)
Sensin.dat Control parameters

Create file (See above)
Changepar.dat Indication of the parameters to be
changed


SENSIN.dat (INPUT)

Sensin.dat lists the control parameters.
Control parameters: Each control parameter uses one line with free format (Table 14).

Table 14: Inputs for sensin.dat
parameter descripion default
NINTVAL Number of intervals in the Latin
Hypercube
20
ISEED Random seed number 2003
OATVAR parameter change for OAT
(fraction)
0.05
Outputs

Table 15 lists the output files.

Table 15: Output files for LH-OAT.
File name Description
Sensobjf.out Objective functions values for each run
Sensrespons.out Model output values for each run
lathyppar.out Latin hypercube sampling points (normalized values)
OATpar.out OAT sampling points (normalized values)
Senspar.out Parameter values
sensout.out Detailed output with mean, variance and partial sensisitivities
for each latin hypercube cluster.

Sensresult.out

This file (Figure 26) list the parameter ranks.
39


Figure 26: Sensresult.out
40
Running PARASOL

Inputs

Parasol performs a combined optimisation and uncertainty analysis. It requires the input files that are listed
in Table 16.

Table 16: inputs needed for ParaSol.
File.cio iclb=2 Adapt file (See above)
Basins.fig Indication of the location of the output
within the model structure
Adapt file (See above)
Objmet.dat Definition of error fuctions Create file (See above)
Responsmet.dat (optional) Definition of output criteria Create file (See above)
parasolin.dat Control parameters +
Indication of the parameters to be
changed
Create file (See above)

PARASOLIN.dat (INPUT)

liss Parasolin.dat lists the control parameters. Each control parameter uses one line with free format (Table
17).

Table 17: Format for parasolin.dat
MAXN
20000 max no. of trials allowed before optimization is terminated
KSTOP
5 maximum number of shuffling loops in which the criterion value
PCENTO
0.01 percentage by which the criterion value must change...
NGS
10 number of complexes in the initial population
ISEED
1677 initial random seed
Empty line

Empty line

NSPL
5 number of evolution steps allowed for each complex before comp
ISTAT
1 Statistical method (1=Xi-squared; 2=Bayesian)
IPROB
3
iprob, when iprob=1 90% probability ; iprob=2 95% probability;
iprob=3 97.5% probability
IGOC 0
number of objective functions to be included in global optimization
(default=0 and means that all objective functions listed in objmet.dat)
NINTVAL 10 nintval in hypercube (for Bayesian method only)

Outputs

Table 18 lists the output files.

Table 18: Output files for ParaSol.
File name Description
Sceobjf.out Objective functions values for each optimization run
scerespons.out Model output values for all simulation runs
scepar.out Parameter values of all simulation runs
41
sceparobj.out Parameter values of all simulation runs and global optimization
criterion
Uncobjf.good Objective function values for the good parameter sets in
goodpar.out
Senspar.out Parameter values
parasolout.out Detailed output for each optimization loop and uncertainty
outputs
autocalxx.out this files lists the simulated values that will be used for the
calibration of point xx
Goodpar.out See below
Bestspar.out See below

ParaSolout.out

The main output file is ParaSolout.out (Figure 27). The first part consists of a report on the input files, the
second part reports for every loop of the SCE algorithm, and the third part reports the results of the
parameter uncertainty analysis.
bestpar.out

This file lists the best parameter values.
goodpar.out

This file lists the good parameter values.


42

Figure 27: ParaSolout.out.

















Minimum value of GOC as printed in the last column of file
Minimum and maximum for all
simulations done by SCE,
As printed in the files
sceobjf.out and scerespons.out
Threshold as in equation
Minimum and maximum of the
parameters in goodpar.out
43

Running in batch (Running the good parameter sets)

This option enables to run a bunch of parameter sets. It is especially useful to rerun goodpar.out for
another period, other scenarios or to analyse certain objective functions or model outputs. During the runs,
the minima and maxima of the indicated output variables are stored. These can then be used to plot
confidence intervals for these output variables.
Inputs

Table 19 lists the input files.

Table 19: Input files for running in batch.
File.cio Iclb=5 Adapt file (See above)
Basins.fig Indication of the location of the output
within the model structure
Adapt file (See above)
changepar.dat Indication of the parameters to be
changed
Create file (See above)
Objmet.dat Definition of the Objective Functions Create file (See above)
Responsmet.dat (optional) Definition of Response Functions Create file (See above)
batchin.dat Control parameters Create file (See above)
Goodpar.out File with parameter values. Create file (See above)

Objmet.dat or responsmet.dat could need to be adapted (as well as simulation period in File.cio).

Goodpar.out

This file is an output file of parasol, but it can also be made manually.

Format: 5blancs, (e12.5)*number of parameter
Output Files MINVAL.out and MAXVAL.out

These files list the minima and maxima of the output values, following the order as listed in objmet.dat.

44
Running SUNGLASSES

SUNGLASSES requires split observation files. This means that
1. Out of 1 observation file, 2 observation files have to be created
2. These observations files have to be indicated at the *.fig file
3. These objective functions need to be added to the Objmet.dat file
4. Indicate the IGOC in sunglasses.in. IGOC should be equal to the objective functions for the 1
st

period. In most cases, this will be equal to the number of objective functions indicated in objmet.dat,
divided by 2.
Inputs

Table 20 lists the SUNGLASSES inputs.

Table 20: Inputs for SUNGLASSES
File.cio iclb=8 Adapt file (See above)
*.fig Indication of the location of the output
within the model structure
Adapt file (See above)
changepar.dat Indication of the parameters to be
changed
Create file (See above)
Objmet.dat Definition of Objective Functions Create file (See above)
Responsmet.dat (option!) Definition of Response Functions Create file (See above)
sunglasses.in Control parameters Create file (See above)


























45
*.fig file

Figure 28 shows how the .fig file can be adapted for split observation files.


Figure 28: .fig file.

SUNGLASSES.in (INPUT)

The control parameters for sunglasses are equal to parasolin.dat and are listed in Table 21.

Table 21: Control parameters for sunglasses.
MAXN
20000 max no. of trials allowed before optimization is terminated
KSTOP
5 maximum number of shuffling loops in which the criterion value
PCENTO
0.01 percentage by which the criterion value must change...
NGS
10 number of complexes in the initial population
ISEED
1677 initial random seed
Empty line

Empty line

NSPL
5 number of evolution steps allowed for each complex before comp
ISTAT
1 Statistical method (1=Xi-squared; 2=Bayesian)
IPROB
3
iprob, when iprob=1 90% probability ; iprob=2 95% probability;
iprob=3 97.5% probability
IGOC 0
number of objective functions to be included in global optimization (default=0 and
means that all objective functions listed in objmet.dat)
NINTVAL 10 nintval in hypercube (for Bayesian method only)

46
Outputs
bestpar.out

This file lists the best parameter values.
goodpar.out

This file lists the good parameter values.
Other outputs

Some additional files are mainly printed for internal calculations but may be analysed in case of
problems/errors in the method (Table 22).

Table 22: List of additional output files.
File name Description
Sceobjf.out Objective functions values for each optimization run
scerespons.out Model output values for all simulation runs
scepar.out Parameter values of all simulation runs
sceparobj.out Parameter values of all simulation runs and global optimization
criterion
Uncobjf.good Objective function values for the good parameter sets in
goodpar.out
parasolout.out Detailed output for each optimization loop and uncertainty
outputs
autocalxx.out this files lists the simulated values that will be used for the
calibration of point xx

47
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