FREE and Open Source Software Tools for

WATer Resource Management

FREEWAT User Manual - Volume 2

Heat and Solute Transport in Subsurface Water Flow

Version 0.5

July 27th, 2017

This version is confidential, only for FREEWAT Project Partners

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FREEWAT User Manual - Volume 2

Heat and Solute Transport in Subsurface Water Flow

Version 0.5

July 27th, 2017

By I. Borsi(1)

(1) TEA SISTEMI S.p.A., Pisa (IT)

This project has received funding from the European Union’s Horizon 2020 research

and innovation programme under grant agreement No 642224

This project document reflects only the authors' views and the European Union is not

liable for any use that may be made of the information contained therein.

FREEWAT Development has received funding from the following projects:

1. Hydrological part has been developed starting from a former project, named SID&GRID, funded by

Regione Toscana through EU POR-FSE 2007-2013 (sidgrid.isti.cnr.it)

2. Porting of SID&GRID under QGis has been performed through funds provided by Regione Toscana to

Scuola Superiore S.Anna - Project Evoluzione del sistema open source SID&GRID di elaborazione dei

dati geografici vettoriali e raster per il porting negli ambienti QGis e Spatialite in uso presso la Regione

Toscana (CIG: ZA50E4058A)

3. Saturated zone solute transport simulation capability has been developed within the EU FP7-ENV-

2013-WATER-INNO-DEMO MARSOL. MARSOL project receives funding from the European Union's

Seventh Framework Programme for Research, Technological Development and Demonstration under

grant agreement n. 619120 (www.marsol.eu)

4. Latest Version of FREEWAT is under development within EU H2020 project FREEWAT - Free and Open

Source Software Tools for Water Resource Management. FREEWAT project has received funding from

the European Union’s Horizon 2020 research and innovation programme under grant agreement n.

642224 (www.freewat.eu)

Suggested citation:

Borsi, I. FREEWAT User Manual, Volume 2 - Heat and Solute Transport in Subsurface Water Flow,

version 0.5, July 27, 2017.

License:

FREEWAT documentation is licensed as Creative Commons Attribution – Share Alike (CC BY-SA,

https://creativecommons.org/licenses/by-sa/3.0/).

FOREWORD

FREEWAT is a HORIZON 2020 project financed by the EU Commission under the call WATER

INNOVATION: BOOSTING ITS VALUE FOR EUROPE. FREEWAT main result is an open source and public

domain GIS-integrated modeling environment for the simulation of water quantity and quality in

surface water and groundwater with an integrated water management and planning module. Specific

objectives of the FREEWAT project are: to coordinate previous EU and national funded research to

integrate existing software modules for water management in a single environment into the GIS-based

FREEWAT platform and to support the FREEWAT application in an innovative participatory approach,

gathering technical staff and relevant stakeholders in designing scenarios for the proper application of

water policies.

The open source characteristics of the platform allow considering this an initiative "ad includendum",

as further research institutions, private developers etc. may contribute to the platform development.

FREEWAT is conceived as a composite plugin for the well-known GIS open source desktop software

QGIS (http://qgis.org). The selected reference version of QGIS is the latest LTR (Long Term Release),

namely QGIS 2.14: even if this release will be maintained as the reference one, it is worth mentioning

that any test performed so far with subsequent versions (e.g. 2.16 and 2.18) worked without

experiencing any problem.

As composite plugin, FREEWAT is designed as a modular ensemble of different tools: some of them can

be used independently, while some modules require the preliminary execution of other tools.

Capabilities integrated in FREEWAT are:

Simulation of models related to the hydrological cycle (Volume 1)

A module for simulating solute transport in the unsaturated/saturated zone, including density

and viscosity dependent flow (Volume 2)

A module for water resource management and optimization of conjunctive use, including issues

related to irrigation management in rural environment (Volume 3)

Tools for the analysis, interpretation and visualization of hydrogeological and hydrochemical

data and quality issues (Volume 4)

A module for time-series processing to support input data processing and advanced model

calibration (Volume 5)

A module for calibration, uncertainty and sensitivity analysis (Volume 6)

The following diagram shows how these different modules are interconnected, taking as reference a

standard modeling procedure.

FREEWAT architecture is based on the integration of different software tools (the so called FREEWAT

pillars): SQLITE relational database manager, external (free and open source) codes like MODFLOW and

MODFLOW-related programs as well as codes specifically developed for the FREEWAT. The way of

interconnecting such tools is done via Python programming language, with extensive use of the Python

library FloPy. A schematic representation of FREEWAT pillars and their interconnection is showed in the

following figure.

Contents

Abstract ii

1 Introduction 11.1 Simulated processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21.2 Limitations (related to the FREEWAT Version v.0.4 - March 2017) . . . . . . . . . . . . . . . . . . . 2

2 Building the transport model 32.1 Creating a new transport model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42.2 Basic properties of the transport model (ADV and DSP package) . . . . . . . . . . . . . . . . . . . . 52.3 Sink and Source Mixing Package - SSM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72.4 Reaction Package - RCT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82.5 Solving transport problem in unsaturated zone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

2.5.1 Unsaturated Solute Balance - USB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92.5.2 Unsaturated Zone Transport - UZT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

2.6 Density and Viscosity dependence (VDF and VSC) . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

3 Run the transport model 13

References 15

Release history 16

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Abstract

In FREEWAT the hydrological model can be coupled with a solute transport model, to simulate multispecies advectiveand dispersive transport, both in unsaturated and saturated zone. The possibility to simulate viscosity- and density-dependent flows is present as well. Such capabilities are particularly relevant to approach studies on seawater intrusionprocesses (where density variations of water due to salinity effect are crucial), or for assessing geothermal plants at lowand medium enthalpy.

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CHAPTER 1

Introduction

In FREEWAT (Free and Open Source Software Tools for Water Resource Management) the hydrological model can becoupled to a solute transport model, to simulate advective and dispersive transport of several species, both in unsaturatedand saturated zone. The possibility to simulate viscosity and density dependent flow is present as well. Such capabilitiesare particularly relevant to approach studies on seawater intrusion processes (where density variations of water dueto salinity effect are crucial), or for assessing geothermal plants at low- and medium-entalpy. Simulation of heattransport (also coupled with additional chemical species) is possible just treating heat as a species and defining diffusivecoefficient and other parameters in a coherent way.

Solute transport is solved in FREEWAT by applying the well-known MT3DMS code (A Modular Three-DimensionalMulti-species Transport Model for Simulation of Advection, Dispersion, and Chemical Reactions of Contam-inants in Groundwater Systems). The User can find details on the code and documentation material at:http://hydro.geo.ua.edu/mt3d

Furthermore, viscosity- and density-dependendent flows are solved by applying SEAWAT (Simulation of Three-Dimensional Variable-Density Ground-Water Flow and Transport), http://water.usgs.gov/ogw/seawat, which is a revisedversion of coupling MODFLOW with MT3DMS, taking into account variations in density and viscosity during thenumerical resolution of the groundwater flow equation (Langevin et al., 2007).

Finally, problems involving solute transport through vadoze zone are addressable in two ways:

• A simplified approach, computing an estimate of the pollutant leaching from the ground surface up to the watertable: here the amount of effective concentration is then used as boundary condition for the MT3DMS code inthe saturated zone.

• Activating in the transport model the package UZT (Unsaturated Zone Transport), included in the code MT3D-USGS (<https://water.usgs.gov/ogw/mt3d-usgs>), a USGS updated release of the groundwater solute transportcode MT3DMS.

Note: To support Unsaturated Zone Transport capabilities by the application of MT3D-USGS code, it requiresto solve the flow model by MODFLOW-NWT (https://water.usgs.gov/ogw/modflow-nwt), instead of the standardMODFLOW-2005. Therefore, the User is required to download this code and to input the path of its executable filewithin Program Locations table.

This manual is organized as follows. In Section Simulated processes, details on FREEWAT capabilities are presented,focusing on transport processes, while limitations and default settings are reported in Section Limitations. Descriptionof the simulation procedure is given in Chapter Building the transport model.

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1.1 Simulated processes

The following processes (each one corresponding to a specific package of MT3DMS or SEAWAT code) are implementedin FREEWAT.

• ADV (Advection package).

• DSP (Hydrodynamic Dispersion), taking into account mechanical dispersion and molecular diffusion phenomena.

• SSM (Sinks and Sources Terms), simulating solute mass entering the model domain through sources or leavingthe model domain through sinks.

• RCT (Chemical Reactions), simulating equilibrium-controlled linear or nonlinear sorption, nonequilibrium(rate-limited) sorption, and first-order reaction that can represent radioactive decay or provide an approximaterepresentation of biodegradation. The general formulation sorption can also be used to model kinetic masstransfer between the mobile and immobile domains in a dual-domain advection-diffusion model. No reactionamong different species can be considered (namely no geochemical reaction).

• VDF (Variable Density Flow)

• VCS (Viscosity-depedent Flow)

• UZT (Unsaturated Zone Transport), which implies the application of the code MT3D-USG. As alternative toUZT, the leaching of contaminant through the vadoze zone may be solved also by the module USB (UnsaturatedSolute Balance), developed as original internal module of FREEWAT. Both (UZT and USB) require to apply theUZF (Unsaturated Zone Flow) package in the MODFLOW model.

1.2 Limitations (related to the FREEWAT Version v.0.4 - March 2017)

The following packages/options can not be activated directly from FREEWAT platform (to activate them, the Userneeds to write or modify input files generated by FREEWAT).

• RCT (Chemical Reactions) package can be activated only in case of single species simulations (this is a temporarlylimitation that will be solved in short time)

• HSS (Hydrocarbon Spill Source) package, to provide a seamless linkage to the MT3DMS transport simulator forthe Hydrocarbon Spill Screening Model (HSSM) http://www.epa.gov/water-research/hydrocarbon-spill-screening-model-hssm-windows-version, is not implemented in FREEWAT.

• Application of SEAWAT (density- and viscosity-dependent flow) is possible only in the saturated zone.

• Some User experienced problems in rendering raster output files correctly, when using the Multi-stress periodoption in FREEWAT>Post-processing>View Model Output. Just in case, please contact the FREEWAT DevelopersTeam to report potential bugs.

• UZT (Unsaturated Zone Transport) can be applied also to multi-species problem, but a deep testing of thisapplicability has not been carried out so far. Therefore, Users might experience some drawbacks on multi-speciesproblem with UZT active: in such cases, Users are kindly requested to feedback sthese problems to FREEWATDevelopers.

• The new code MT3D-USGS can be applied only to address unsaturated zone transport (UZT). Other specificpackages included in MT3D-USGS are not supported so far.

• Some testing models revealed problems in running MT3D-USGS when a significant amount of surface leakage isgenerated by UZF package. FREEWAT Developers are in contact with MT3D-USGS developers, who announceda new version cooming soon, in which such potential problems will be solved completely. FREEWAT Usersshould stay tuned at https://water.usgs.gov/ogw/mt3d-usgs to follow code updates.

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CHAPTER 2

Building the transport model

Through this chapter we assume that the User has already built and run a MODFLOW model (namely the groundwaterflow equation has been already solved) using FREEWAT utilities and tools described in Volume I of this manual.Concerning the code implementation, the User should be aware that the MODFLOW/MT3DMS strategy to link flowmodel and transport model is a binary file generated by MODFLOW (FTL file) where water flux (for each cell, and foreach time step in each stress period) is saved. Then, MT3DMS will use this file as input to pass the flow regime to thetransport equation solver (Zheng and Wang, 1999).

Therefore, it is assumed that the User has already created a Model (and related SpatiaLite DB), loaded in its properQGIS project.

Furthermore, it is also assumed that the flow model was run activating the LMT Package. If not, the User has to repeatthis step. In particular, go to FREEWAT -> Run Model, input all the boundary consitions and options desired for yourmodel, and be sure that the box Activate Link with MT3DMS (LMT) Package is checked. In particular:

• default sub-option Transport through Usaturated zone is not simulated is usually checked: this is the defaultoption, unless you want to activate the Unsaturated Zone Transport simulation. Pay attention that the latter refersto the UZT package only, and not to the USB one.

• the other sub-option Transport through Unsaturated zone is simulated must be checked if you want to activateUZT package using the MT3D-USGS code

Note: The particular case of the second sub-option (namely Transport through Unsaturated zone is simulated) impliesthe following:

• The flow model is solved using MODFLOW-NWT instead of MODFLOW-2005. Therefore, in this case the Userhas to download the executable of MODFLOW-NWT (https://water.usgs.gov/ogw/modflow-nwt) and enter theright path in Program Locations table, FREEWAT -> Program Locations. If this step has not been concluded, awarning window pops up, informing the User about this error.

• Activation of UZT package is possible by solving the transport problem by MT3D-USGS code (Bedekaret al., 2016). Therefore, before to go ahead, the User has to download the executable of MT3D-USGS(https://water.usgs.gov/ogw/mt3d-usgs) and enter the right path in Program Locations table, FREEWAT ->Program Locations. If this step has not been done, a warning window pops up, informing the User about thiserror.

The reason of this combination is that MT3DMS-USGS can read only flux terms file (FTL) generated by MODFLOW-NWT, in which the possibility to save (also) flux terms related to the unstaurated zone have been included. This wasone of the new capability of packgage LMT8, developed within MODFLOW-NWT (Noswonger et al., 2011), startingfrom version 1.1.0.

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2.1 Creating a new transport model

The first step is the creation of a new transport model, selecting FREEWAT -> Solute Transport Process -> CreateTransport Model menu:

The Create Transport Model GUI opens,

requesting the following information:

• Selection of the groundwater flow model (MODFLOW model) the User wants to couple with the transportprocess.

• Inserting a name for the new transport model.

• Selecting the units of measure for mass (Kg or Lb)

• Setting the species_name (name of the species the User wants to simulate), also specifying if it is a mobile orimmobile species (setting yes or no, respectively, in the mobile field).

If the User has more than 5 species to be inserted, there is the possibility to upload a CSV file, having exactly the samestructure as the table here presented: in particular, the three fields in firs row have to be declared with same name as in

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the GUI.

After running this tool, two new tables are created in the model DB:

1. The transport_modelname table (where modelname is the name of the groundwater flow model). In this tablethe list of transport models linked to the groundwater flow model modelname are listed. Therefore, if the Userdecides to create another one (or more than one) transport models, this table will be updated, and having as manyrecords as the number of transport model associated to the selected groundwater flow model.

2. The species_transportname table (where transportname is the name of the transport model set before, mymodel+in the example). This table reports the species selected for the model: their name and the property mobile *yes or not.The User can modify this table (add or remove or modify) by setting the layer in editing mode and then saving thechanges before closing the editing session.

Next step is to assign basic properties to the model.

2.2 Basic properties of the transport model (ADV and DSP package)

Once the model is defined, the User has to set the basic properties, such as initial condition, active/non-active cells,effective porosity. Such pieces of information are passed to the model by defining new Model Data Objects (MDOs),the transport layer(s): they are a replication of the model layer(s) defined for the corresponding groundwater flowmodel, and they are used to set basic properties (for each hydrological layer presents in the model), as described below.

From the main menu, FREEWAT -> Solute Transport Process -> Create Transport Layer(s)

The following GUI appears

where the name for both groundwater and transport model are requested, along with the reference grid layer. Once thebottom Run has been pushed, the algorithm creates as many MDOs as the number of model layers of the flow model,assigning the standard name transportname_lay_1, transportname_lay_2, ..., transportname_lay_N according to

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the number (N) of model layers defined. Each transport layer reports (for each cell of the model grid), the followingfields (see also the screen shot below, as example):

• ACTIVE: set -1, 0 or 1, to set the cell as constant-concentration cell, inactive, or active, respectively (as for themodel layer)

• LONG_D: value of longitudinal dispersivity (a L ).

• TRPT: ratio of the horizontal transverse dispersivity, a TH , to the longitudinal dispersivity.

• TRPV: ratio of the vertical transverse dispersivity, a TV , to the longitudinal dispersivity.

• For each species:

1. SCONC: initial concentration.

2. DMCOEFF: coefficient of molecular diffusion.

Note: the other crucial parameter to solve the transport equation is the effective porosity. Such a value, to be setfor each layer, is defined in the flow model layer, and identified as NE. Therefore, once the above properties for eachtransport layer have been set, the User has to go to the flow model layers and set the NE value there.

Note: the coefficients above described (namley: LONG_D, TRPT, TRPV and DMCOEFF) must be specified onlyif the User wants to activate the dispersion package (DSP). Otherwise, the User can leace the default values, due to

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the fact that the code will not consider such values. The possibility to activate/inactivate DSP is given in the GUI RunModel (see below 3_runmodel).

2.3 Sink and Source Mixing Package - SSM

Whenever in the flow model is present (at least) a sink-source pacckage (like WEL, CHD, RIV, etc.), the User has tospecify the behaviour of the solutes with respect to these stresses, since they rapresent a potential sink/source term ofthe transport equation (Zeng and Wang, 1999). In this case, the User has to create an MDO for each point-wise or linearsource (like WEL, CHD or RIV, for instance) and for distributed sources (like RCH or EVT).

Note: The User is required to create a SSM term whenever one of the above packages is active, even if the transportmodel does not imply any type of source/sink (Zeng and Wang, 1999). In this case the User has to create (at least) afake MDO related to one of this package, by entering 0 as concentration flux. In this case, MT3D code creates the SSMpackage, but with no effect on the sinulation.

To input such an information, go to FREEWAT -> Solute Transport Process -> Create Sink and Source Layer

and the following GUI appears:

For any source/sink type (namely for each stress package of the flow model), the User has to select in the menus thecorresponding MDO created for the flow model. Furthermore, for each package the stress periods where this source/sinkis active has to be selected in the Select Stress Period(s) menu, checking the stress period(s) to be included.

The algorithm will produce a number of new MDOs as the number of packages selected. These MDOs will be used toinput data relative to the corresponding SSM stress.

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2.4 Reaction Package - RCT

The reaction package can be activated from FREEWAT -> Solute Transport Process -> Create Sink and Source Layer

The GUI to create this MDO requires as input the model name, the grid layer and the name the User wants to assign tothe new MDO.

In this MDOs the User has to set the parameters needed for the sorption and reaction terms, namely:

• RHOB: bulk density of the soil (for each layer)

• PRSITY2: porosity of the immobile domain (for each layer), i.e., the ratio of pore spaces filled with immobilefluids over the bulk volume of the aquifer medium, when the simulation is intended to represent a dual-domainsystem.

• Sorption and reaction parameters (for each layer and for each species ), according to the sorption and reactionmodels considered for the model [mt3dms]

2.5 Solving transport problem in unsaturated zone

As stated in Introduction, starting from version v.0.4, FREWAT’s User has two possibility for addressing solute transportthrough the vadoze zone:

• A simplified approach, computing an estimate of the pollutant leaching from the ground surface up to the watertable: here the amount of effective concentration is then used as boundary condition for the MT3DMS code inthe saturated zone. This is done by the USB (Unsaturated Solute Balance) module.

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• Activating in the transport model the package UZT (Unsaturated Zone Transport), included in MT3D-USGScode (https://water.usgs.gov/ogw/mt3d-usgs), a USGS updated release of the groundwater solute transport codeMT3DMS.

Both of them require that UZF (Unsaturated Zone Flow) package is active in the MODFLOW model. Conversely, themain difference is that USB uses, at each stress period, a formula to estimate the leaching of surface pollutant towardsthe water table; instead, UZT takes the saved UZF fluxes and infiltration front to solve the advection-diffusion equation(with variable saturation degree) within the vadose zone (Morway et al., 2013; Bedekar et al., 2016).

2.5.1 Unsaturated Solute Balance - USB

To take into account the leaching process of a contaminant present at the ground surface, the User can apply the USBmodule, which solves the following problem: if one (or more) area(s) on the ground surface are affected by the presenceof a pollutant species, it is necessary to estimate (for each stress period in the model) how much concentration of thispollutant reaches the water table, and eventually spread out following the ground water flow. USB will compute thisestimate.

Note: In case the simulation involves more than one component (contaminant), the following steps must be repeatedfor each component.

First, the User has to define the zone(s) on which the contaminant is present. To do that, go to the grid MDO and selectthe cells that form the zone(s) of interest. With this selection active, activate the USB source definition from FREEWAT-> Solute Transport Process -> Create Unsat Solute Balance Layer

The GUI to create this MDO requires as input the model name, the grid layer and the name the User wants to assign tothe new MDO.

In this MDO the User has to set the initial condition for each stress period, namely the value of solute concentration atthe ground surface, in terms of Mass per volume of water (e.g. 𝐾𝑔/𝑚3) , and the decay constant, i.e. :

• init_conc_1: solute concentration (for each stress period)

• decay_cnst: decay constant, as a rate term (𝑇−1).

Using such a datum, it is possible to estimate how much of this source (at the ground level) can reach the water table,and eventually acting as source for the saturated flow transport problem. This is done by the USB algorithm included inFREEWAT. To to do that, open FREEWAT -> Solute Transport Process -> Run Unsat Solute Balance Calculus

In this GUI the following info are needed:

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• Model name: the name of the flow model

• Grid: the name reference grid layer

• USB Layer: the MDO created before where initial concentration at the ground surface have been set

• Name of the new layer: the name to assign to the new MDO

Furthermore, through this GUI, the model including the UZF package must be run again, since the aim is to print outthe UZF budget for all the cells intersecting the source zone.

Therefore, after running again the model (this is done automatically by the code), USB algorithms ends with a creationof a new MDO, in which for each stress period the amount of concentration that reached the water table is reported, asunsat_conc_n field, where n is the n-th stress period.

Finally, to set this quantity as constant concentration at layer 1 of the model, as boundary condition for MT3DMSsimulation, the User performs the following steps:

1. Create a MDO for the SSM package, corresponding to Constant Concentration type (if not already defined), asdescribed in Sink and Source Mixing Package - SSM: this should be done only considering the cells correspondingto the source zone. To do that, the User can also use the USB source MDO, which reports only the grid cells ofthe source; alternatively, the User can use the reference grid layer, after selecting only those cells.

2. Use the tool FREEWAT -> Tools -> Copy from Vector Layer to copy the field unsat_conc_n to CSSMS_sp_n_m,where n is the n-th stress period and m is the m-th component.

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Remark 4: In case of a multi-component simulation, as stated in Remark 3, the User has to recall that a single MDOcontaining the USB output has to be created for each component. Therefore, step 2 above has to be repeated for eachcomponent, passing on a case-by-case basis only the concentrations relative to the component addressed.

Finally, the User can run the transport model using this SSM MDO, proceeding as described in Section 3.

2.5.2 Unsaturated Zone Transport - UZT

Note: To support Unsaturated Zone Transport capabilities by the application of MT3D-USGS code, it requiresto solve the flow model by MODFLOW-NWT (https://water.usgs.gov/ogw/modflow-nwt), instead of the standardMODFLOW-2005. Therefore, the User is required to download this code and to input the path of its executable filewithin Program Locations table.

An advanced way of accounting pollutant source occuring at the ground surface is the application of UZT package ofMT3D_USGS (Bedekar et al., 2016). This requires the creation of a specific MDO for UZT.

To perform this task, activate the UZT creation from FREEWAT -> Solute Transport Process -> Create UnsaturatedZone Transport Layer

The GUI to create this MDO requires as input the model name, the grid layer and the name the User wants to assign tothe new MDO.

In this MDO the User has to set the following values:

• IUZFBND: is a flag (integer) which is 1 for cells where UZT should be applied, 0 elsewhere.

• WC: is the starting water content (𝑇−1). For cells above the water table, this value can range between residualand saturated water contents. In cells below the water table, this value will be equal to saturated water content(i.e., effective porosity).

• CUZINF_sp_i_spec_j: is concentration of the infiltrating flux for species j, in stress period i, (𝑀/𝐿3), repeatedfor each species and for each stress period.

• CUZET_sp_i_spec_j: is concentration of ET fluxes originating from the unsaturated zone for species j, in stressperiod i, (𝑀/𝐿3), repeated for each species and for each stress period.

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In particular, variable IUZFBND has to be set as 1 only on cells where the sourface contaminant is present. To do that,since the default value for IUZFBND is 1, the User could go to the UZT MDO and select the cells that form the zone(s)of interest, do Invert Selection and set 0 on these cells.

Finally, the User can run the transport model using this UZT MDO, proceeding as described in Section 3.

2.6 Density and Viscosity dependence (VDF and VSC)

For these packages no gridded or tabled data are needed, but only the specification of some coefficient and option isrequired.

Therefore, no MDO creation is required, and the User will set the desired option directly in the Run Model GUI (seeRun the transport model)

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CHAPTER 3

Run the transport model

Once tables and MDOs for the transport model have been created (see Building the transport model), the Run ModelGUI can be accessed, selecting the tag named Solute Transport

This GUI allows to input all the additional information needed to run a MT3DMS (or SEAWAT) simulation, namely:

• The name of flow model associated to the transport model.

• Options for the numerical solution of the advection term.

• Possibility to activate the dispersion term (by checking the flag Dispersion is Active)

• MDO and option for the reaction process

• MDOs for the Sink and Source Mixing package. The UZT MDO (if present) is included in this section, since itrepresents a particular case of source term.

• Possibility to activate the Density Dependent Flow (VDF), and corresponding options and parameters

• Possibility to activate the Viscosity Dependent Flow (VCS), and corresponding options and parameters

• Options and parameters for the numericla solver (GCG)

Note: If VDF and/or VCS are selected, before to click on Run button, the User has to include under Program Locationsthe executable of SEAWAT code.

Note: Activation of UZT package is possible by solving the flow model using MODFLOW-NWT (Niswongeret al., 2011) instead of MODFLOW-2005, and solving transport problem by MT3D-USGS code (Bedekar et

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al., 2016). Therefore, before to go ahead, the User has to download the executable of MODFLOW-NWT(https://water.usgs.gov/ogw/modflow-nwt) and MT3D-USGS (https://water.usgs.gov/ogw/mt3d-usgs) and enter theirpaths in Program Locations table, FREEWAT -> Program Locations. If these steps have not been done, warningwindows pop up, informing the User about this error.

From this step on, the User can follow the same instruction valid for the flow model (i.e. writing only input file, runningthe model, opening the text report).

Finally, simulation results can be converted in raster output using the view Model Output sub-menu, opening thePost-processing menu, and performing the same procedure followed for the flow model simulation.

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References

Bedekar V., Morway E.D., Langevin C.D., Tonkin M. (2016), MT3D-USGS version 1: A U.S. Geological Surveyrelease of MT3DMS updated with new and expanded transport capabilities for use with MODFLOW: U.S. GeologicalSurvey Techniques and Methods 6-A53, 69 p.

Langevin C.D., Thorne D.T. Jr., Dausman A.M., Sukop M.C. and Guo Weixing (2007). SEAWAT Version 4: AComputer Program for Simulation of Multi-Species Solute and Heat Transport: U.S. Geological Survey Techniques andMethods Book 6, Chapter A22, 39 p.

Morway Eric D., Niswonger Richard G., Langevin Christian D., Bailey Ryan T., Healy Richard W. (2013). ModelingVariably Saturated Subsurface Solute Transport with MODFLOW-UZF and MT3DMS, GROUNDWATER, Vol. 51, no.2.

Niswonger, R.G., Panday, Sorab, and Ibaraki, Motomu, 2011, MODFLOW-NWT, A Newton formulation forMODFLOW-2005: U.S. Geological Survey Techniques and Methods 6–A37, 44 p

Zheng Chunmiao, and P. Patrick Wang (1999). MT3DMS, A modular three-dimensional multi-species transport modelfor simulation of advection, dispersion and chemical reactions of contaminants in groundwater systems; documentationand user’s guide, U.S. Army Engineer Research and Development Center Contract Report SERDP-99-1, Vicksburg,MS, 202 p.

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Release history

31/07/2016 release of vesion 0.1

15/10/2016 release of version 0.2

(minor changes in the text)

5/12/2016 release of version 0.3

(minor changes in the text)

31/01/2017 release of version 0.3.1

(minor changes in the text)

31/03/2017 release of version 0.4

(inclusion of instructions to use the UZT package; minor changes in the text)

27/07/2017 release of version 0.5

(updating the cover)

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