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iMOD is an easy to use Graphical User Interface + an accelerated Deltares-version of MODFLOW
with fast, flexible and consistent sub-domain modeling techniques. iMOD facilitates very large, high resolution MODFLOW groundwater modeling and also geo-editing of the subsurface.

Disclaimer/warning:
This is a html-version of the iMOD User Manual; we do not guarantee that its content is exactly the same as the official distributed pdf-version of the iMOD User Manual which is available for downloading on http://oss.deltares.nl/web/imod/user-manual. Also, this online version is not being updated every night (as opposed to the automated daily update of the draft-version of the pdf of the manual). Users are encouraged to report any error or inconsistency between the pdf- and html-version of the manual by sending an email to imod.support@deltares.nl.

iMOD User Manual version 5.0 (html)

(for the pdf of the iMOD User Manual, see https://oss.deltares.nl/web/imod/user-manual)

P.T.M. Vermeulen, F.J. Roelofsen, B. Minnema, L.M.T. Burgering, J. Verkaik, A.D. Rakotonirina and G.M.C.M. Janssen. Deltares, Delft, The Netherlands.
December 24, 2019
iMOD User Manual version 5.0 (html) — Introduction

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iMOD User Manual version 5.0 (html)


1Introduction

Welcome to iMOD. This chapter gives a brief introduction to:

iMOD User Manual version 5.0 (html) — Motivation

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iMOD User Manual version 5.0 (html)


1.1Motivation

Stakeholders (e.g. water companies, water boards, industrial users) and decision makers (e.g. municipalities, provincial governments) are increasingly participating in jointly developing numerical groundwater flow models that cover land areas of common interest. The reason for this is twofold:

In an effort to facilitate this the concepts of MODFLOW were used by Deltares to develop iMOD (interactive MODeling) to:

A major difference, compared to other conventional modeling packages, is the generic geo-referenced data structure that for spatial data may contain files with unequal resolutions and can be used to generate sub-models at different scales and resolutions applying up- and down-scaling concepts. This is done internally without creating sub-sets of the original model data. For modelers and stakeholders, this offers high performance, flexibility and transparency.

iMOD User Manual version 5.0 (html) — The iMOD approach

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iMOD User Manual version 5.0 (html)


1.2The iMOD approach

High resolution groundwater flow modeling, necessary to evaluate effects on a local scale, has traditionally been restricted to small regions given the computational limitations of the CPU memory to handle large numerical MODFLOW-grids. Although CPU-memory size doubles every two years (‘Moore’s law’) the restriction still holds from a hardware point of view. This restriction has traditionally forced a model builder to always choose between (1) building a model for a large area with a coarse grid resolution or (2) building a model for a small area with a fine grid resolution. For some time it appeared that finite element models could fill the gap by refining the grid only where hydrological gradients were anticipated. However, unanticipated stress may also occur in parts of the model area where the grid is not yet refined resulting in a possible undesired underestimation of these effects. Theoretically the modeler could choose to design a finite element network with a high resolution everywhere, but then it becomes more economic to use finite differences. This is why Deltares has based its innovative modeling techniques on MODFLOW considering it is largely seen world-wide as the standard finite difference source code. Still, modelers ideally need an approach that allows: (1) flexibility to generate high resolution model grids everywhere when needed, (2) flexibility to use or start with a coarser model grid, (3) reasonable runtimes / high performance computing and (4) conceptual consistency over time for any part of the area within their administrative boundary. Deltares has invested in understanding all of these requirements and has developed the iMOD software package to advance the methods and approach used by modelers and regulators.

The development of the iMOD approach took off in The Netherlands in 2005 when Deltares and a group of 17 stakeholders decided to jointly build a numerical groundwater model for their common area of interest [Vermeulen(2006), Berendrecht and others(2007), Minnema(2013)]. The groundwater model encompasses the entire north of the Netherlands at a resolution of 25 x 25 m\({}^{2 }\)and was constructed together via an internet accessible user-interface. This makes it possible for the modelers to easily access the model data, intermediate results and participate in the model construction. The iMOD approach allows gathering the available input data to be stored at its finest available resolution; these data don’t have to be clipped to any pre-defined area of interest or pre-processed to any model grid resolution.

The iMOD approach: one input data set:

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Resolutions of parameters can differ and the distribution of the resolution of one parameter can also be heterogeneous. In addition, the spatial extents of the input parameters don’t have to be the same. iMOD will perform up- and down scaling [Vermeulen(2006)] whenever the resolution of the simulation is lower or higher than that of the available data. This approach allows the modeler to interactively generate models of any sub-domain within the area covered by the data set. When priorities change in time (e.g. due to changing political agenda’s) the modeler can simply move to that new area of interest and apply any desired grid resolution. In addition the modeler can edit the existing data set and / or add new data types to the data set. Utilizing the internal up- and down-scaling techniques ensures that sub-domain models remain consistent with the bigger regional model or that the regional model can locally be updated with the details added in the sub-domain model.

Suppose the modeler needs to simulate groundwater flow for the total area covered by the data set, but the theoretical size of the model is far too big to fit in any CPU-memory. iMOD facilitates generating sub models for parts of the whole area of interest with a user-defined resolution depending on how large the available CPU-memory is and how long the modeler permits her/himself to wait for the model calculations to last. To generate a high resolution result for the whole model domain a number of partly overlapping but adjacent sub models are invoked and the result of the non-overlapping parts of the models are assembled to generate the whole picture. The modeler should of course be cautious that the overlap is large enough to avoid edge effects, but this overlap is easily adjustable in iMOD. A big advantage of this approach is that running a number of small models instead of running one large model (if it would fit in memory, which it often will not) takes much less computation time; computation time (T) depends on the number of model cells (n) exponentially: T = f(n\({}^{1,5-2,0}\)). The approach also allows the utilization of parallel computing, but this is not obligatory. Using this approach means that the modeling workflow is very flexible and not limited anymore by hardware when utilizing iMOD.

iMOD User Manual version 5.0 (html) — Main functionalities

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iMOD User Manual version 5.0 (html)


1.3Main functionalities

The capability of iMOD to rapidly view and edit model inputs is essential to build effective models in reasonable timeframes. The rapid and integrated views of the geologic / hydrostratigraphic models as well as dynamic model output is critical for the public, stakeholders and regulators to understand and trust the model as a valid decision support tool. iMOD is fast even when working from very large data files because it uses a random accessible data format for 2D grids which facilitates instant visualization or editing subsets of such a large grid file. Also iMOD contains very economic zoom-extent-dependent visualization techniques that allow subsets of grids being visualized instantaneously both in 2D and 3D. Another feature is that iMOD generates MODFLOW input direct in memory, skipping the time-consuming production of standard MODFLOW input files (generating standard MODFLOW input files in ASCII format for large transient models may take hours to a full working day); this efficiency is especially useful during the model building phase when checking newly processed or imported data.

iMOD includes the MetaSWAP-module developed by Wageningen Environmental Research (Alterra); for references to the separate MetaSWAP-documentation see section A.2.8.

iMOD includes the functionality to perform calculations for density-dependent flow and reactive transport. This functionality comes as a stand-alone feature. More specifically, density-dependent flow and reactive transport calculations are performed with a separate executable called iMOD-WQ (iMOD-WaterQuality). iMOD-WQ is a combination of three codes:

iMOD User Manual version 5.0 (html) — Minimal System Requirements

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iMOD User Manual version 5.0 (html)


1.4Minimal System Requirements

iMOD works on IBM-compatible personal computers equipped with at least:

Please note: it is permitted to install the Model System on a different Hardware Platform as long as it is a computer with similar minimum features as listed above. The transfer of the Model System to a dissimilar computer may endanger the working of the Model System and require adjustments in the Configuration.

iMOD can run on 64-bits systems, but iMOD itself is 32-bits. iMOD supports 32- and 64-bit machines working under the following platforms: Windows XP / Windows Server 2003 / Vista Business / Vista Ultimate / Windows Server 2008 / Windows 7 / Windows Server 2016 / Windows 10.

iMOD User Manual version 5.0 (html) — Getting Help

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iMOD User Manual version 5.0 (html)


1.5Getting Help

There are 2 types of support available:

Any questions? Contact the help-desk imod.support@deltares.nl.

iMOD User Manual version 5.0 (html) — Deltares

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iMOD User Manual version 5.0 (html)


1.6Deltares

Since January 1\(^{st}\) 2008, GeoDelft together with parts of Rijkswaterstaat-DWW, -RIKZ and -RIZA, WL | Delft Hydraulics and a part of TNO Built Environment and Geosciences are forming the Deltares Institute, a new and independent institute for applied research and specialist advice. For more information on Deltares, visit the Deltares website: www.deltares.nl.

iMOD User Manual version 5.0 (html) — Release Notes

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iMOD User Manual version 5.0 (html)


1.7Release Notes

Starting from iMOD 3.6 we summarize all new, changed, extended and fixed functionalities on the iMOD-website: http://oss.deltares.nl/web/imod/release-notes. Per release these release notes are also distributed per email to all iMOD-community members.

iMOD User Manual version 5.0 (html) — Acknowledgements

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iMOD User Manual version 5.0 (html)


1.8Acknowledgements

The development and enhancement of iMOD functionality is project-based. This section lists these project-based developments and specifies its funding and organisations Deltares has collaborated with during the implementation.

Functionality

Funding

Implementation

iMOD Maintenance & Support & iMOD-Helpdesk
In 2013 a group of five iMOD-consortia started the project "iMOD Beheer en Onderhoud, Helpdesk en Website" initiating and (co-)financing a coordinated further development of iMOD and enhanced maintenance and support. The current iMOD-consortia are AMIGO, AZURE, IBRAHYM, MIPWA and MORIA; info on the members of each iMOD-consortium can be found here.


iMOD-CGO
consortia


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MetaSWAP
iMOD includes the unsaturated zone MetaSWAP-module which covers the plant-atmosphere interactions and soil water. MetaSWAP is based on a quasi steady-state solution of the Richards equation. MetaSWAP is developed by Wageningen Environmental Research (Alterra) and was (among others) financed by The Netherlands Hydrological Instrument. For references to the MetaSWAP-documentation see section A.2.8.


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MODFLOW-MetaSWAP coupling
The coupling of MODFLOW and MetaSWAP was created in a collaboration between Deltares and Wageningen Environmental Research (Alterra) and was (among others) financed by The Netherlands Hydrological Instrument.


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Quick Scan Tool
The MIPWA consortium initiated and funded the QuickScan Tool which is an instrument to efficiently compute effects on groundwater levels and seepage fluxes to- and from drainage systems using a so-called Impulse-Response Database. This database stores pre-computed effects of several measures which can be combined in the QuickScan Tool using the principles of superposition.


MIPWA
consortium


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Perched Water Table package
The MIPWA consortium initiated and funded the development of the Purged Water Table (PWT) Package. With this package purged water table conditions can be simulated occurring on shallow (clayey) aquitards with a significant vertical resistance. The initial concept was developed in collaboration with Wageningen Environmental Research (Alterra).


MIPWA
consortium


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3D Tool
Waternet funded the development of the first version of the 3D Tool allowing an interactive 3D visualization of the subsurface in combination with the (litho-stratigraphy) of boreholes.



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Functionality

Funding

Implementation

Pumping Tool
Hoogheemraadschap De Stichtse Rijnlanden funded an initial version of the Pumping Tool developed specifically to simulate the effect of pumping. In addition to the Scenario Tool the Pumping Tool can be applied to configure new elements in an existing model configuration (runfile) and simulate and analyse the results easily.



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GeoConnect Tool
The GeoConnect Tool allows the modeller to define and utilize permanent links between 1) the (unassembled) geologic layers (incl. its properties) and 2) the aggregated model layers. With the GeoConnect Tool you can re-calculate the hydraulic conductivities of a model layer after adapting the individual weights of each contributing geological layer. The development of was funded by the IBRAHYM concortium (Waterschap Limburg, Provincie Limburg, Waterleiding Maatschappij Limburg).


IBRAHYM
consortium


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ISG
The IBRAHYM consortium initiated the development of the concept of line elements (vector format) as a basis to discretize streams as an alternative for grid based parameterization. This yielded considerable data handling efficiency and much more flexibility when parameterization for different model grids sizes. It also facilitated more user-friendliness regarding inspecting and editing the stream data.


IBRAHYM
consortium


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Runfile Editor & Plug-In Tool
The project manager was extended to support editing of a runfile and project files. Also the iMOD-GUI was extended with Plug-In functionality allowing to invoke external programs in the iMOD-GUI using iMOD files. These functionalities were funded by the iMOD-CGO group.


iMOD-CGO
consortia


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Parallel Krylov Solver Package
Deltares, USGS and Wageningen Environmental Research (Alterra) together with Utrecht University and Technical University Delft have developed the new parallel solver package for iMOD called PKS (Parallel Krylov Solver). It is based on overlapping domain decomposition combining both the techniques of MPI and OpenMP.


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3D-assignment of fault-lines
Extension and improvement of the 3D-parameterization of faults in the Horizontal Flow Barrier package. This extension was funded by the IBRAHYM-consortium led by the Province of Limburg.


IBRAHYM
consortium


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Functionality

Funding

Implementation

Extension of the water balance tool
The extension of the water balance tool (released in iMOD 4.2) was created in a collaboration between Deltares and Tauw and financed by the Dutch iMOD-CGO group; it allows visualization (interactive stack-bars time series plots and schematic vertical cross-sectional overviews) of water balances for sub-regions and contains several time-aggregation possibilities (e.g. averages per year, month and season).


iMOD-CGO
consortia


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Fence diagrams & Deviated wells
The 3D Tool was extended with an option to interactively create so-called fence-diagrams by using clipping planes along the major Euclidian axes. The 3D Tool was also extended with the option to visualize deviated wells. These developments were funded by the Alberta Energy Regulator | Alberta Geological Survey and came available starting from the iMOD 4.2 release.


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Large coordinates
As a spin-off in a modelling project funded by Landesamt für Landwirtschaft, Umwelt und ländliche Räume, Geologischer Dienst Schleswig-Holstein, Germany, iMOD has been extended for the use of large coordinates. This extension is very handy with respect to the planned European transition to the ETRS89 coordinate system including an extra two-digit zonal prefix. iMOD now supports large coordinates with 12 significant numbers for displaying IDF, IPF, ISG and GEN files. Also IDF’s can be stored in a double precision format. Large coordinates came available starting from the iMOD 4.3 release.


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Extended queries and artificial boreholes in 3D tool
The 3D Tool was extended with the option to allow querying using specific items of boreholes to define a subset. It is now also possible to generate artificial boreholes from a 3D model of the subsurface by sampling the set of IDF’s at user-defined x-, y-locations. These developments were funded by the Alberta Energy Regulator | Alberta Geological Survey and came available starting from the iMOD 4.3 release.


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MetaSWAP Analyser tool
The new MetaSWAP Analyser tool (released in iMOD 4.4) was created by Deltares and financed by the Dutch iMOD-CGO group; it allows quick visualization (spatial and temporal) of all the input parameters for the MetaSWAP part of a groundwater model.


iMOD-CGO
consortia


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iMOD User Manual version 5.0 (html) — Getting Started

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iMOD User Manual version 5.0 (html)


2Getting Started

This chapter describes:

The other sections focus on how to operate iMOD and how new users can familiarize themselves with iMOD:

Additionally, the Tutorials in chapter 11 provide a selection of iMOD case studies to introduce the program’s functions. New iMOD users are advised to use the Tutorials to familiarize themselves with iMOD.

iMOD User Manual version 5.0 (html) — Get the Deltares-software executables of iMOD

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iMOD User Manual version 5.0 (html)