Release notes - iMod

Release notes

The release notes of iMOD 3.0, 3.1, 3.2 and 3.4 can be found as the last 2 chapters in the iMOD User Manual.

• Technical release notes iMOD-GUI, releases 3.0 - 3.4
   
• Technical release notes iMODFLOW, releases 3.0 - 3.4

For iMOD 3.4 both technical release notes (see above) and a descriptive summary of all new, changed, extended and fixes functionalities (see below) is available.

• Release notes iMOD 3.4:
  • Summary of new and improved features and bug fixes
  • Current developments for upcoming releases
  • Other ongoing developments

Starting from iMOD 3.6 we provide a descriptive summary of the release notes only, see below.

• Release notes iMOD 3.6:
  • Summary of new and improved features and bug fixes
  • Current developments for upcoming releases
  • Other ongoing developments

• Release notes iMOD 4.0:
  • Summary of new and improved features and bug fixes
  • Current developments for upcoming releases
  • Other ongoing developments

• Release notes iMOD 4.0.1:
  • Summary of bug fix

• Release notes iMOD 4.1:
  • Summary of new and improved features and bug fixes
  • Current developments for upcoming releases
  • Other ongoing developments

• Release notes iMOD 4.1.1:
  • Summary of new and improved features and bug fixes
• Release notes iMOD 4.2:
  • Summary of new and improved features and bug fixes
  • Current developments for upcoming releases
  • Other ongoing developments
• Release notes iMOD 4.2.1:
  • Summary of bug fix

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The main reason of this release is the new GeoConnect Tool functionality. iMOD 3.4 also contains improved features and bugfixes.

Below please find:

1. A summary of new and improved features, and a summary of most important bugfixes.
2. A summary of current developments.

Ad 1) Summary of new and improved features and bugfixes in iMOD 3.4.

In the Graphical User Interface of iMOD (iMOD-GUI):

• The new GeoConnect Tool:
  • In many cases groundwater model layer parameters are based on assembled (e.g. summed) detailed geological aquifer- and aquitard-properties (elevation, thickness, geometry (extent), hydraulic conductivity, etc.). 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. For more info, see section 7.8 of the iMOD User Manual.
• Redesign of the 3D Tool:
  • The 3D Tool window and the 3D-Tool menu-options have been merged to one window that optionally synchronizes with the zooming in the 2D-window.
• Output of Pathline calculations:
  • The number of the deepest model layer the pathline passes through is now recorded (as in the past).
• Contouring and legends:
  • Improved contour algorithm for delineation of flat areas.
  • A legend-label now uses a proper number of decimals.
  • Legends can now be generated using a user-specified interval.
• Solid Tool:
  • During interpolation, separate IPF-files can now be included, with associated txt-files that specify the elevation of each interface.
• IMF-files:
  • In IMF-files, relative directory names can now be used.
• Thanks to the iMOD-forum discussions, several bugfixes were identified and solved:
  • Assignment of the appropriate output filename when starting iMODPATH.
  • PST-module now mentioned correctly in the runfile.
  • The Water Balance Tool now recognizes filenames containing *sys*.

In iMODFLOW:

• As was the case in iMOD 3.3, iMOD 3.4 includes MetaSWAP SVN-version 1047. Compared with the previous version of MetaSWAP only some in- and output statements for post-processing purposes have been improved.
• Automatic assignment to layers of faults in HFB (Horizontal Flow Barrier) package:
  • When using GEN-files as a representation of the location of faults, it was already possible to have horizontal flow barriers assigned automatically to the nearest cell faces resulting in interconnected series of HFB-cell faces. We have extended this functionality with automatic assignment to layers; it requires a GEN-file including elevation data (a so-called 3D-GEN-file) and TOP and BOT elevations of the model layers. For input instructions, see section 10.14 "Data Set 11: Input ?le assignment" ; for theory and examples see section 12.15 in the iMOD User Manual.
• New value for HNOFLOW cells:
  • To avoid possible confusion when modelling deep systems the HNOFLOW value is now set to 1.43E+37 (the old value was -999).
• On-the-fly correction of input data:
  • Starting from iMOD 3.0 the iMODFLOW computational core is based on MODFLOW2005. Although we prefer to keep the pre-processing and processing separate, and thus not deviate from the standard MODFLOW2005-code, we have implemented 2 on-the-fly corrections on input data:
    1. If the elevation of the riverbed is higher than the waterlevel, the riverbed elevation is set to the river waterlevel. We intend to migrate this on-the-fly correction to a to be developed iMOD batch function that allows for the mentioned correction and similar checks on input data as an optional pre-processing step.
    2. MODFLOW2005 cannot handle active cells with zero thickness. In iMODFLOW these cells can optionally be assigned a minimum transmissivity value; for input instructions see section 10.6 "Data Set 4: Simulation mode".
• Saving OLF output separately:
  • OverLand Flow is now saved in separate budget files. For more info, see section 7.15 "Compute Waterbalance" in the iMOD User Manual.
• Bug fix in waterbalance post-processing regarding diagonal ANI-fluxes
  • Diagonal fluxes between 'ANI-cells' and 'diagonal-adjacent' fixed head cells are now computed correctly and processed in the (cumulative) water balance.
• Bug fix in ANI, incorrect nodata values:
  • When the ANI package was activated, this could cause errors near closed model boundaries (IBOUND=0) for anisotropy factors < 1. The reason for this is that for stability reasons small minimal horizontal conductivities (1E-07) were initially imposed by this package for all MODFLOW cells, causing a) arti?cial diagonal ?uxes being computed near closed boundaries from the small horizontal conductivities and large default HNOFLO (1.43E+37), and b) incorrect coef?cient matrix cleaning in the PCG solver due to a bug in this package (see below).
• Bug fix in PCG, cleaning matrix coef?cients:
  • The cleaning of the matrix coef?cients was corrected. The cleaning routine of CC/CR/CV was a sequence-dependent method for closed model boundaries
    (IBOUND=0). Also cleaning was done in the same loop as the initialization of the coef?cients matrix. In case of closed East and South boundaries, a certain initial residual was included in the calculation. The issue only occurred with models that included the ANI package, because with this package it is possible to initialize CC and CR with very small values.
• Bug fix regarding inactive package handling:
  • In the runfile it is possible to temporarily inactive packages. Sometimes this option was erroneously interpreted as "re-use"; this is now corrected.
• Bug fix in SFT/ISG:
  • When utilizing the StreamFlow Thickness package a correction regarding the calculated total length of the river reaches in a cell is implemented.

• Additional runfile-options:
  • We are implementing a number of additional runfile-options; for a specification of these runfile-options scheduled for a next iMOD-release, please have a look in chapter 10 of the iMOD User Manual.
• Implementation of the SFR2- and LAK-packages:
  • SFR2- and LAK-package are being implemented in iMOD as part of ongoing projects and will become available in one of the upcoming iMOD-releases. 
• A new Parallel Krylov Solver package (PKS):
  • We are currently developing a new parallel solver package for MODFLOW called PKS (Parallel Krylov Solver). It is based on overlapping domain decomposition combining both the techniques of MPI and OpenMP. This development is done together with the USGS and Wageningen Environmental Research (Alterra) in cooperation with Utrecht University and Delft University of Technology. This year we are piloting this new PKS package in iMOD to test running large iMOD models on powerful multi-core computers allowing a drastic reduction in runtimes. We hope we will be able to make this new solver available in one of the upcoming iMOD-releases.

Other ongoing developments (status on the release date of iMOD 3.4):

• A new SUB-CR package (including 'creep'):
  • The existing SUBsidence-package has been extended with 'creep' for clay and peat; the implemented concept is consistent with D-Settlement (geotechnical software). We hope we will be able to include this extension in an upcoming iMOD-release.
• Coupling of iMOD and DgFlow:
  • Proof of Concept: iMODFLOW has been off-line coupled to DgFlow, a finite-element code developed by Deltares for simulating the consolidation process of dikes/embankments. An explicit head-flux boundary coupling has been realised, demonstrating the added value of incorporating regional, transient, groundwater flow boundary conditions for dike stability analysis. For more info, please contact Deltares.
• We also plan to make iMOD-MT3DMS/SEAWAT open source and include it in the iMOD-framework. This modified version of MT3DMS/SEAWAT uses an easy-to-use runfile for specifying model data for many layers and supports the common iMOD file-formats. We hope to finalize this open source process at the end of 2017, depending on the availability of resources.
• We are working on extending the list of iMOD-supported MODFLOW2005-packages, among others the MNW2-, UZF- and SWR1-packages; a fixed schedule of implementation/prioritization is not available yet.

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This release contains the iMOD-implementation of five existing USGS MODFLOW-packages: the SFR-package (Surface Flow Routing), the LAK-package (Lake), the UZF-package (Unsaturated Zone Flow), the FHB-package (Flow and Head Boundary) and the MNW-package (Multi Node Well). Implementation of these packages was realized within the framework of foreign projects.

This iMOD 3.6 release also contains a new version of MetaSWAP which facilitates the use of an extensive database containing 370 soil profiles; the new version of MetaSWAP was made possible by the The Netherlands Hydrological Instrument - project. 

iMOD 3.6 also contains some significant improvements of existing functionalities.

Below please find:

1. A summary of new and improved features, and a summary of most important bug fixes.
2. A summary of current developments.

• SFR-package:
  The existing Surface Flow Routing package of MODFLOW2005 has been implemented in iMOD. With this package it is possible to route surface water through a network of segments. These segments are stored in an additional type of ISG file that contains more records than the conventional ISG. These additional records are specific for the SFR package and describe the relationship between individual segments and how the water depth in the segments needs to be computed. The water depth is a function of the computed hydraulic head, the SFR is therefore a significant improvement in the interaction between surface- and groundwater.
• LAK-package:
  The existing Lake package of MODFLOW2005 has been implemented in iMOD. With this package it is possible to compute lake stages in relation to the groundwater head. Given a bathymetry of the lake, iMOD will assign the lake to the appropriate model layers and assign the correct conductances to the lake. The SFR can be connected to locations where a lake is defined to route water in- and from a lake.
• UZF-package:
  The existing Unsaturated Zone Flow package of MODFLOW2005 has been implemented in iMOD. Percolation of precipitation through unsaturated zones is important for recharge of ground water. Rain and snow melt at land surface are partitioned into different pathways including runoff, infiltration, evapotranspiration, unsaturated-zone storage, and recharge. The package was developed to simulate water flow and storage in the unsaturated zone and to partition flow into evapotranspiration and recharge. The package also accounts for land surface runoff to streams and lakes. A kinematic wave approximation to Richards' equation is solved by the method of characteristics to simulate vertical unsaturated flow. The approach assumes that unsaturated flow occurs in response to gravity potential gradients only and ignores negative potential gradients (upward capillary flow); the approach further assumes uniform hydraulic properties in the unsaturated zone for each vertical column of model cells.
• FHB-package:
  The existing Flow and Head Boundary package of MODFLOW2005 was implemented in iMOD. With this package it is possible to combine constant head- and constant flux boundaries for all model layers independently. For each model cell it is possible to define whether it becomes a constant head or constant flux boundary condition.
• MNW-package:
  The existing Multi Node Well package of MODFLOW2005 was implemented in iMOD, among others to be able to couple with RIBASIM (Deltares-software for planning and analysis of water resources). The Multi-Node Well package is used to simulate "long" wells that are connected to more than one model layer; the abstraction rate is vertically distributed  proportional to the transmissivity adjacent to the well screen; e.g. when a hydraulic head gradually drops below the top of a well screen the yield of this shallow part of the well will also gradually drop. This package also connects to overlying aquifers via the well screen; an example of this behaviour is given in the new MNW-tutorial in the iMOD User Manual.
• In the iMOD-GUI:
  • Configuration of the SFR-, LAK-, MNW- and UZF-packages has been implemented in the iMOD Project Manager. These packages are not used through by the so-called 'runfile' (*.RUN) but by an iMOD-project file (*.PRJ) only. Based on the iMOD-project file-definitions iMOD generates/exports the input files for iMODFLOW.
  • An iMODBatch function had been added that allows converting the model output to ISG-format thus facilitating visualizing results vector-wise.
  • We now also facilitate the use of unconfined layers.
• In iMODFLOW:
  • An option to sum flux-output of sub-systems (e.g. summing bdgisg_sys1_*.idf + bdgisg_sys2_*.idf to bdgisg_sys_*.idf) has been added for RIV, DRN and ISG.
  • The volumetric water balance term 'DXC FLUXES' (summed data exchange fluxes for coupled non-USGS-packages) can now be stored as separate idf-output (e.g. MetaSWAP-fluxes).
  • The debug option IDEBUG has been reactivated.
• In MetaSWAP:
  The MetaSWAP update is compatible with the new distributed format of the unsaturated zone database. The distributed format has a separate database for each of the soil types. This format has the advantage that new soil types can more easily be added, and the files are kept a manageable size.  Extracting the zip archive does yield a large number of files in a directory tree; these files form part of the documentation of how the database was generated. In the para_sim.inp file the path  to the root of the tree should be specified.
  Compatibility with the old database format has technically been maintained. But one should be aware of the fact that exhaustive testing of all combinations with all old databases is not feasible. In the case of problems we will first advise to update to the latest database. Apart from containing the latest available soil information the database also generates storage coefficients that are not smaller than 0.01, which speeds up the running of the model.
  The MetaSWAP code has been made more robust for situations with extremely sensitive relationships in the MODFLOW model. Since the model no longer crashes in such a situation, this makes it easier to diagnose where the sensitivity is located and thus address the issue.
  The most recent database with 72 soil types can be downloaded here: ftp://ftp.wur.nl/simgro/tests/PreMetaSWAP_V7_3_13_BOFEK2012_Fits2_a/out/LHM2016_v01.zip, info on the database with 370 soil type can be found in the MetaSWAP-release notes.

Improvements, bug fixes and extension of existing functionalities in iMOD 3.6:

• In the iMOD-GUI:
  • Mainly improvement of legend-features, e.g. to use legends for multiple maps simultaneously more easily.
  • ISG Edit has been extended significantly. For figures containing water levels and cross-sections now axes have been added. For use in the SFR-context (SFR uses the extended ISG-file type) the set of SFR-definitions has been extended, e.g. interactively or automatically generating the definition of the connection of segments in a downstream direction. 
• In iMODFLOW:
  • The accuracy of the gridding of GEN-files for the definition of Horizontal Flow Barriers has been improved and is now similar to common GIS-gridding methods. Applying this improved gridding can cause significant differences in calculated heads in the vicinity of the Horizontal Flow Boundary.
  • The ISG-gridding has been made more robust, avoiding a divide-by-zero in rare cases where the water level coincides with a buckling point elevation of a specified cross-section.
  • A number of bugs in iPEST have been fixed, e.g. during conductance optimization of rivers and drains water levels were optimized instead, this is fixed now. Also the statistical information on the optimized parameter has been extended.
  • Names of output files can now also include the starting date of a time step as opposed to the end date of a time step; in a PRJ-file this is now default, the RUN-file still used the 'old' method.
• In the MODFLOW-MetaSWAP-coupling:
  • In the N:1 coupling of iMODFLOW and MetaSWAP the second MetaSWAP-column coupled to a MODFLOW-cell was not included correctly. These second MetaSWAP-column usually represents the paved/urban fraction of a cell area which results in a relatively small share of the water balance. This is corrected in the current version.
  • The standard parameterization for urban fraction of a cell has been made more realistic including a surface elevation comparable with the rest of the cell and including a small threshold (2 mm) to allow runoff calculated by MetaSWAP. Deltares and Wageningen Environmental Research (Alterra) will communicate more recommendations regarding runoff- and evaporation parameter values for urban areas in the near future.
• In MetaSWAP:
  • A 'MSWP-error: update rootzone - floating invalid'-issue seems to be fixed, by doing some dynamic array allocations more strictly than required by the Intel compiler.
  • Known issues: sprinkling using groundwater from multiple model layers of the same cell simultaneously does not work properly. Also a water balance problem may occur when using groundwater for sprinkling purposes from a different location than where it is sprinkled. In case you encounter the latter situation, a temporary workaround is available via the iMOD help desk. For both issues we are working on a solution to be made available in a next release.
  • For a the full list of release notes, please have a look at the MetaSWAP-release notes.

Ad 2) Developments (status on the release date of iMOD 3.6):
Current developments for upcoming releases:

• A new Parallel Krylov Solver package (PKS):
  • We are currently developing a new parallel solver package for MODFLOW called PKS (Parallel Krylov Solver). It is based on overlapping domain decomposition combining both the techniques of MPI and OpenMP. This development is done together with the USGS and Wageningen Environmental Research (Alterra) in cooperation with Utrecht University and Delft University of Technology. This year we are piloting this new PKS package in iMOD to test running large iMOD models on powerful multi-core computers allowing a drastic reduction in runtimes. 
  • We made considerable progress; preliminary results have been presented during the 2016 AGU Fall Meeting (San Francisco, USA) and the MODFLOW and more 2017 conference (Golden, USA). See also Deltares R&D Highlights 2016, page 64. During the Dutch Deltares Software Dagen we organize a beta-workshop 'iMOD Workshop Parallel Krylov Solver package' (in Dutch); participants can experiment with a beta-version of the PKS-package on their own laptop. The use of PKS-package will most likely also be programmed during the iMOD International User Day (to be scheduled in the last week of October / first week of November 2017).
  • We hope to make the PKS-package available in a next iMOD-release.
• Extension of the Waterbalance Tool:
  • The current water balance tool is extended significantly to allow constructing water balances for sub-regions, and selecting / de-selecting MODFLOW- and MetaSWAP-water balance components interactively. The new water balance tool also allows specifying only a subset of the output time-series and contains several time-related aggregation possibilities (e.g. averages per year, month, season).  Visualization includes interactive stack-bars time-series plots and schematic vertical cross-sectional overviews. This development is done together with Tauw and financed by the Dutch iMOD-CGO group.
• Movie tool:
  • Also part of the above mentioned 'Water balance Tool extension'-project a movie tool is developed. It facilitates visualizing a time-series of maps (e.g. calculated groundwater levels) and record it as a playable file.
• 3D fault assignment tool:
  • As part of a consortium-project led by the Province of Limburg, the automated 3D-assignment of fault-lines to the appropriate model layers is being improved. We are currently looking for opportunities to make releasing this beta-functionality possible.
• Fence-diagrams
  • The current 3D Tool is extended with an option to interactively create so-called fence-diagrams by using clipping planes along the major eucledian axes. This development is funded by the Alberta Geological Survey.
• Deviated wells:
  • The current 3D Tool is extended with the option to visualize deviated wells. This development is funded by the Alberta Geological Survey.
• Additional runfile-options:
  • We are implementing a number of additional runfile-options; for a specification of these runfile-options scheduled for a next iMOD-release, please have a look in chapter 10 of the iMOD User Manual.
• iMODBatch:
  • Further improvement of the iMODBatch function XYZTOIDF including the computation of voxel models from bore hole data.

Other ongoing developments (status on the release date of iMOD 3.6):

• A new SUB-CR package (including 'creep'):
  • The existing SUBsidence-package has been extended with 'creep' for clay and peat; the implemented concept is consistent with D-Settlement (geotechnical software). We hope we will be able to include this extension in an upcoming iMOD-release.
• Coupling of iMOD and DgFlow:
  • Proof of Concept: iMODFLOW has been off-line coupled to DgFlow, a finite-element code developed by Deltares for simulating the consolidation process of dikes/embankments. An explicit head-flux boundary coupling has been realized, demonstrating the added value of incorporating regional, transient, groundwater flow boundary conditions for dike stability analysis. For more info, please contact Deltares.
• We also plan to make iMOD-MT3DMS/SEAWAT open source and include it in the iMOD-framework. This modified version of MT3DMS/SEAWAT uses an easy-to-use runfile for specifying model data for many layers and supports the common iMOD file-formats. We are making progress but slower than we hoped for; we will update you on the progress later.

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Release notes iMOD 4.0, July 14^th 2017:

1. Install free 'third party' MPI-software MPICH.
2. Specify the PKS-solver settings.
3. Start your parallel run, either from within the iMOD-GUI or from the command prompt.

• The partitioning process of your model domain into subdomains is fully automated; it results in a number of subdomains equal to the assigned number of CPU's (or threads).
• Your model input does not need any restructuring (thanks to iMOD's subdomain modelling techniques).
• The PKS solver settings can be specified in the iMOD-GUI interactively (step 2).
• Existing iMOD-runfiles can be fully reused, only the solver settings need a few small modifications. Solver settings can simply be edited manually too, for an example see the Runfile-section 10.20.2 'Updating from iMOD 3.6 to iMOD 4.0' of the iMOD User Manual. 
• Tutorial 6, 'Model Simulation' now contains an exercise on how to approach load balancing your model on a multi-core machine.
• We have included a test program in the iMOD 4.0 allowing you to check your MPI-installation prior to using the PKS-package.

1. A summary of new and improved features.
2. A summary of current developments.

Ad 1) Summary of new and improved features and bug fixes.

New features:

• A new Parallel Krylov Solver package (PKS):
  Deltares, USGS and WEnR (Alterra) together with Utrecht University and Technical University Delft have developed the new parallel solver package for MODFLOW called PKS (Parallel Krylov Solver). It is based on overlapping domain decomposition combining both the techniques of MPI and OpenMP.  Preliminary results were presented during the 2016 AGU Fall Meeting (San Francisco, USA) and the MODFLOW and More 2017 conference (Golden, USA). Deltares R&D Highlights 2016 (page 64) summarizes first results for the Dutch National Hydrological Instrument and the global groundwater model PCR-GLOBWB. During the annual Dutch Deltares Software Days we organized a beta-release workshop 'iMOD Workshop Parallel Krylov Solver package' (June 14th, 2017, in Dutch); feedback from participants experimenting with a beta-version of the PKS-package on their own laptop was integrated in the current release.
  
  Scope, limitations and expectations:
  • The PKS package was implemented for the 64-bit version of iMODFLOW only. So the PKS package can be used on Windows-based multi-core 64-bit computer systems, starting for example from Windows-based laptops and desktops (containing e.g. Intel Core i5 or i7 processors) to dedicated Windows-based multi-core 64-bit supercomputers.
  • The PKS package uses MPI-techniques, therefore prior to using the PKS package so-called 'third party' MPI software (available free of charge) should be installed, see iMOD 4.0 installation instructions for details. We have included a test program in the iMOD 4.0 distribution allowing you to check your MPI-installation.
  • The expected overall speedup strongly depends on the available hardware, load balancing of the partitions and the data input/output intensity:
    • On a typical home computer / laptop with an Intel Core i5 processor inside (maximum 4 threads) the speedup will usually be limited. When assigning 3 (or 4) threads one may expect an acceleration factor of around 1.5 to 2; since MPI creates extra overhead communicating between the subdomains typically large and computational intensive models will potentially benefit from a parallel approach; also limiting the model output (frequency) contributes to the potential speedup. Relatively small models most likely will not benefit from a parallel approach due to the necessary extra communication between the subdomains.
    • Test runs for the Dutch National Hydrological Model were carried out on a Windows server consisting of 2 Haswell 16-core CPUs with 128GB RAM resulting in a speedup of approximately a factor 5; in this case overall speedup is limited because only the MODFLOW-MetaSWAP part could be run in parallel mode; the coupled surface water (MOZART/DM) effectively still runs in serial mode (see Deltares R&D Highlights 2016, page 64).
    • A test run for an artificial groundwater model covering the area of California (23897 column, 27974 rows, 335 million active cells, cell size 50 meters) using 128 cores on the SURFsara Cartesius Dutch supercomputer showed a reduction of an estimated single core runtime of 12 hours to approximately 17 minutes (a speedup factor of around 42) prior to load balancing efforts. 
    • Another test on the Cartesius supercomputer for the global PCR-GLOBWB model showed speedup factors ranging from ~17 to ~45 using 48 cores, depending on the partioning method (see Deltares R&D Highlights 2016, page 64).
    • To play it safe, for large models, expect speedup factors starting from 1/3 of the number of the assigned number of cores. To get maximum speedup for large high resolution models, tuning is necessary; for more practical considerations, see section 12.32.3 of the iMOD User Manual. 
  • The PKS package can be used in combination with most iMOD-packages except the LAK-, MNW-, PST-, SFR- and UZF-packages; when an iMOD-model contains one or more of these latter package the single-core PCG-solver has to be used. The PKS package has been implemented for models including the MetaSWAP concept. 
  • The iMOD-GUI (i.e. the 'Model Simulation' window) has been extended for the use of the PKS package. In addition, a parallel run can also be started from the command prompt. 
  • The PKS package is not yet supported in the Project Manager.
  • Tutorial 6, 'Model Simulation' of the iMOD User Manual has been extended with an exercise on:
    • how to configure the PKS package.
    • how to switch between the PCG- and PKS-solver.
    • how to approach load balancing your model on a multi-core machine.

Improvements, bug fixes and extension of existing functionalities:

• In the iMOD-GUI:
  • The 'Solver Settings' tab of the 'Model Simulation' window has been extended for the PKS-package. Here you can specify in how many subdomains your model domain should be partitioned by specifying how many CPU's should be used. It is recommended not to assign all available cores since your computer should be left some computational power for overall operating purposes.
  • In the cross-section tool (ideal to compare single core and subdomain model results) the synchronization of overlying idf's has been tuned. 
• In iMODFLOW:
  • At downscaling:
    • Sometimes for interpolation there was a wrong supporting point for the edge of a subdomain, this has been fixed.
    • Sometimes cells with nodata-values were ignored and interpolated with surrounding data values, this has been fixed.
    • Sometimes values of the first column were wrongly copied to the last column if the window of the fine grid not exactly coincided with the grid-lines of the coarser grid, this has been fixed.
    • Sometimes for cells without precipitation an interpolation with surrounding cells values was performed resulting in precipitation awarded to cells originally having no precipitation, this has been fixed.
  • At upscaling: KHV en KVV were upscaled arithmetically instead of geometrically, this has been fixed.

Ad 2) Developments (status on the release date of iMOD 4.0):

Current developments for upcoming releases:

• Extension of the Waterbalance Tool:
  • The current water balance tool is extended significantly to allow constructing water balances for sub-regions, and selecting / deselecting MODFLOW- and MetaSWAP-water balance components interactively. The new water balance tool also allows specifying only a subset of the output time series and contains several time-related aggregation possibilities (e.g. averages per year, month and season). Visualization includes interactive stack-bars time series plots and schematic vertical cross-sectional overviews. This development is done together with Tauw and financed by the Dutch iMOD-CGO group.
• Movie tool:
  • Also part of the above mentioned 'Water balance Tool extension'-project a movie tool is developed. It facilitates visualizing a time series of maps (e.g. calculated groundwater levels) and records it as a playable file.
• 3D fault assignment tool:
  • As part of a consortium-project led by the Province of Limburg, the automated 3D-assignment of fault-lines to the appropriate model layers is being improved. We are currently looking for opportunities to make releasing this beta-functionality possible.
• Fence diagrams
  • The current 3D Tool is extended with an option to interactively create so-called fence-diagrams by using clipping planes along the major Euclidian axes. This development is funded by the Alberta Geological Survey.
• Deviated wells:
  • The current 3D Tool is extended with the option to visualize deviated wells. This development is funded by the Alberta Geological Survey.
• Additional runfile-options:
  • We are implementing a number of additional runfile-options; for a specification of these runfile-options scheduled for a next iMOD-release, please have a look in chapter 10 of the iMOD User Manual.
• iMODBatch:
  • Further improvement of the iMODBatch-function XYZTOIDF including the computation of voxel models from bore hole data.

Other ongoing developments (status on the release date of iMOD 4.0):

• A new SUB-CR package (including 'creep'):
  • The existing SUBsidence-package has been extended with 'creep' for clay and peat; the implemented concept is consistent with D-Settlement (geotechnical software). We hope we will be able to include this extension in an upcoming iMOD-release.
• Coupling of iMOD and DgFlow:
  • Proof of Concept: iMODFLOW has been offline coupled to DgFlow, a finite-element code developed by Deltares for simulating the consolidation process of dikes/embankments. An explicit head-flux boundary coupling has been realized, demonstrating the added value of incorporating regional, transient, groundwater flow boundary conditions for dike stability analysis. For more information, please contact Deltares.
• We also plan to make iMOD-MT3DMS/SEAWAT open source and include it in the iMOD-framework. This modified version of MT3DMS/SEAWAT uses an easy-to-use runfile for specifying model data for many layers and supports the common iMOD file-formats. We are making progress but slower than we hoped for; we will update you on the progress later.

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Release notes iMOD 4.0.1, September 8^th 2017:

iMOD 4.0.1 is a bugfix-release: in iMOD 4.0 output from MetaSWAP to idf-files was accidentally blocked, this has been repaired in this release.

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Release notes iMOD 4.1, October 27^th 2017:

iMOD 4.1 was released because the automated 3D-assignment of fault-lines to the appropriate model layers in the Horizontal Flow Barrier package has been improved. This release was financed by the Dutch IBRAHYM-consortium through a consortium-project led by the Province of Limburg. iMOD 4.1 also faciltates the use of non-uniform grids (not in combination with the PKS-package and in combination with ISG containing cross sections wider than the cell size).

Please find below: 

1. A summary of new and improved features.
2. A summary of current developments.
3. Other ongoing developments.

Ad 1) Summary of new and improved features and bug fixes.

• Extension and improvement of the 3D-parameterization of faults in the Horizontal Flow Barrier package:
  • The automatic 3D-fault-parameterization has been extended: it is now possible to use 3D GEN-files to assign fault to the appropriate model layers. Also the concept of how to calculate the fault resistances has been refined (see section 12.15 in the iMOD User Manual).
  • When using 3D GEN-files each intersection of a cell face will result in additional resistance harmonically. When all 3D line segments have been processed the resistance is corrected for situations the fault is partly unconfined; a default resistance value equal to 1 is assigned to that unconfined part of the fault and included in the harmonic calculation of the overall fault resistance.
  • Contrary to using 3D GEN-files: when using 2D GEN-files the resistance is now solely determined by the first line segment intersecting the cell face. In the earlier release resistance was added when the GEN-file contained an additional line segment intersecting the same cell face, this is not the case anymore; as a result final resistances may be significant lower.
  • To allow inspection the resulting parameterization is exported in GEN- and DAT-files.
• Non-uniform grids
  • Earlier 2.x versions of iMOD featured the use of non-uniform grids. During the transition to open source in 2013 this feature was not included. In iMOD 4.1 this functionality has been revived. Around the area of interest a buffer can be defined where cell sizes gradually increase in the direction of the outer boundary of the model area. This is also facilitated in the iMOD-GUI. Optionally pre-defined irregular finite difference grids can be used. Limitation: non-uniform grids cannot be combined with 1) the PKS-package and 2) the ISG-package containing 1D- or 2D-cross sections wider than the cell sizes.

• Refinement of automated layer-assignments:
  • In earlier versions a minimum of 5% of the total penetration depth of a river reach or well screen was used to assign a river reach or well to a particular model layer. In iMOD 4.1 this minimum criterion is not used anymore because it results in more realistic schematizations when rivers or wells penetrate very thin layers.
  • For areas containing many thin shallow lying aquifers containing clayey sediments this may result in significant different river results. For wells this effect will be smaller because the vertical discharge distribution was and still is proportional to the penetrated thickness times the conductivity. The conductivities values are now based on the user input transmissivities, not on the average of the CC- and CR-terms anymore; this may cause a vertical redistribution of the assigned well rates.
• Correction of the ‘brush'-option of the ISG-gridding:
  • The ‘brush'-option of the ISG-gridding has been corrected for cases 1D cross-sections are wider than a model cell by maximizing the conductance according to the cell width. This may result in lower overall conductances causing less interaction between ground- and surface water.
  • When using the ‘brush'-option now only cells covered with a minimum fraction of 50% will be assigned a river reach.

• iPEST:
  •  iPEST output parameters are now generated with additional significant digits.
  • The contents of the logfile have been extended.
  • Before iPEST stopped as soon the steepest gradient and the gauss-newton direction conflicted, now iPEST continues ignoring the generated parameter values of that cyclus.
  • KHV, KVV en KVA are exported for re-use purposes.
  • iPEST can now be invoked through the additional argument ‘–ipest *.pst‘
  • Now the Brook-Coley parameter of the UZF-package can be included in iPEST.
• SFT-package:
  • Constant input values are now processed correctly.
  • The SFT-package can now be ignored when IFVDL is active; in that case river conductances are calculated using the ‘De Lange formula' using thicknesses and transmissivities of model layer 1 instead of the CC- and CR-terms.
• Starting conditions:
  • Now a non-steady state run can start with one steady-state ‘stress period'; This is particularly useful if you want to start a non-steady state simulation where the groundwater system is in full equilibrium with its initial boundary conditions.
  • A run is set as transient based on the definition of the stress periods in the DIS-file (SS or TR), not on the length of the first stress period anymore.
• Generation of NAM-files:
  • The value of MAXWBALERROR is equal to 0 by default. If a value > 0 is specified this value is also copied to the STOPERROR keyword in the BAS-file.
  • The OCD-file now contains correct output layer numbers.
• Extension of output filenames:
  • The keyword 'ISAVEEND' has been added to the MODFLOW MET file. This facilitates the option to use the end time of a time step in the output filenames.
• Improvement of the optional drain level correction:
  • Via the ICONCHK keyword DRN-levels can be corrected each time new DRN-input is  being read. However, this correction was not performed if only new RIV- or ISG-input was processed (in case no new DRN-input was read for that particular time step); this has been corrected.
  • If ICONCHK is active this is logged in the LST output file.
  • ICONCHK has been reprogrammed for memory efficiency.
• Well data:
  • Associated TXT files containing well data now optionally can contain additional 2 columns without causing iMOD to generate an error. iMOD continues using the first 2 column only.
• Time discretisation:
  • The iMOD-Batch function RUNFILE now supports ‘hours', ‘minutes' and ‘seconds'.
  • The Time Series Tool in the iMOD-GUI has been extended to support processing folders containing filenames with and without ‘hours', ‘minutes' and ‘seconds'.
• Downscaling (going from coarse data to a finer model network) of conductances contained an error, this has been corrected.

• The combination of a constant + factor + a to be added impuls was processed correctly only when an IDF file was used; this has been corrected.

• Water balance terms of inactive cells are now assigned the HNOFLO-value (‘huge number').

• The maximum value of a resistance has now been increased form 1.0E6 to 1.0E8 days.

• A constant head cell becomes an inactive cell if fully surrounded by inactive cells or constant head cells.

• The iMOD Manager has been extended with the option to (de-)select files using wildcards.

Ad 2) Developments (status on the release date of iMOD 4.1):

Current developments for upcoming releases:

• Extension of the Waterbalance Tool:
  • The water balance tool is extended significantly to allow constructing water balances for sub-regions, and selecting / deselecting MODFLOW- and MetaSWAP-water balance components interactively. The new water balance tool also allows specifying only a subset of the output time series and contains several time-related aggregation possibilities (e.g. averages per year, month and season). Visualization includes interactive stack-bars time series plots and schematic vertical cross-sectional overviews. This development is done together with Tauw and financed by the Dutch iMOD-CGO group.
• Movie tool:
  • Also part of the above mentioned 'Water balance Tool extension'-project a movie tool is developed. It facilitates visualizing a time series of maps (e.g. calculated groundwater levels) and records it as a playable file.

• Fence diagrams
  • The current 3D Tool is extended with an option to interactively create so-called fence-diagrams by using clipping planes along the major Euclidian axes. This development is funded by the Alberta Geological Survey.
• Deviated wells:
  • The current 3D Tool is extended with the option to visualize deviated wells. This development is funded by the Alberta Geological Survey.
• Additional runfile-options:
  • We are implementing a number of additional runfile-options; for a specification of these runfile-options scheduled for a next iMOD-release, please have a look in chapter 10 of the iMOD User Manual.
• iMODBatch:
  • Further improvement of the iMODBatch-function XYZTOIDF including the computation of voxel models from bore hole data.

Ad 3) Other ongoing developments (status on the release date of iMOD 4.1)::

• A new SUB-CR package (including 'creep'):
  • The existing SUBsidence-package has been extended with 'creep' for clay and peat; the implemented concept is consistent with D-Settlement (geotechnical software). We hope we will be able to include this extension in an upcoming iMOD-release.
• Coupling of iMOD and DgFlow:
  • Proof of Concept: iMODFLOW has been offline coupled to DgFlow, a finite-element code developed by Deltares for simulating the consolidation process of dikes/embankments. An explicit head-flux boundary coupling has been realized, demonstrating the added value of incorporating regional, transient, groundwater flow boundary conditions for dike stability analysis. For more information, please contact Deltares.
• We also plan to make iMOD-MT3DMS/SEAWAT open source and include it in the iMOD-framework. This modified version of MT3DMS/SEAWAT uses an easy-to-use runfile for specifying model data for many layers and supports the common iMOD file-formats. We are making progress but slower than we hoped for; we will update you on the progress later.

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Release notes iMOD 4.1.1, November 24^th 2017:

iMOD 4.1.1 is a bugfix-release: an error in the GENSNAPTOGRID-functionality of iMOD 4.1 used to parameterize the Horizontal Flow Barrier has been fixed. The iMOD 4.1 and iMOD 4.1.1 releases were financed by the Dutch IBRAHYM-consortium through a consortium-project led by the Province of Limburg. iMOD 4.1.1 also contains a number of other improved features and minor bugfixes.

Ad 1) Summary of new and improved features and bug fixes.

Improvements, bug fixes and extension of existing functionalities:

In iMOD-GUI:

• GENSNAPTOGRID triggered a crash when used without top/bot IDF files, this has been fixed.
• Visualizing length-profiles for ISG-files in combination with location of structures / cross-sections etc. reactivated sorting calculations points along a segment for correct visualisation on a profile, this has been fixed.
• Sometimes usage of NaN's inside an IDF file gave a crash; this has been resolved by skipping these values.
• The package definition of the project manager gave wrong results in case files were used with time information but needed to be treated as time contstant in the file selection procedure. Also there was a crash when no appropriate files were found and the user continued; this has been fixed.
• Invoking the iMODbatch PLOT function for only one IPF, GEN of IFF-file without specifying a window resulted in an improper plot, this has been corrected.
• iMOD crashed when trying to create a legend with a single class, this has been fixed.
• Displaying IPF-points with 7 significant numbers triggered an infinite loop when trying to generate a scale bar; this has been fixed.
• Plotting of IPF files went wrong in case the number of IPF files sequentially drawn was less and in a different order than of a previous plotting sequence, this has been fixed.
• In the ‘Start iMOD'-window the user can now sort the available IMF-files alphabetically, by size or by date. 
• The user cannot start iMOD accidentally anymore via the option ‘Open an existing iMOD project' without selecting an existing IMF-file.
• Plotting of time series:
  • In the status bar the space for displaying the mouse position coordinates has been increased;
  • two digits for displaying dates are added whenever the mouse is moved;
  • the to be plotted time series need to be sorted; iMOD stops plotting the remainder of the time series when encountering dates earlier than already plotted.
  • nodata lines in TXT files will be skipped.
• Whenever the Model Export Configuration is 'MODFLOW2005' (NAM file for simulation) and the simulation time extends the input of the txt files for wells, the well rate remains equal to the last entry.
• When plotting ISG profiles the plot-sequence has been revised: first the left parameter (a) is plotted followed by the right parameter (b). Also the assignment of the parameters colours has been corrected.
• The function to import CSV's in ISGEDIT with segment/calculation number has been extended to include remaining attributes. It allows to insert time series of data sequentially to different number of selected segments/calculation nodes. Futhermore ISGEDIT can now also export to CSV including these additional attributes. 
• Further improvement of the iMODBatch-function XYZTOIDF including the computation of voxel models from bore hole data.
• IPF Analyse now doesn't crash when the user visualizes an IPF accidentally containing associated TXT files definitions that do not exist.
• The Interactive Pathline Simulator (IPS) now allows the use of the $DBASE$ keyword in iMODPATH.RUN files.
• The PKS-settings in iMOD-GUI 4.1 were inconsistent, this has been fixed.
• Shapefiles containing POLYLINEZ shapes are now converted correctly.
• The 3D Tool has been extended with the optioin 'Deactivate Associated Files' to make visualizing IPF's containing secondary Z-coordinates in 3D possible.
• In the Project Manager in the 'Define Characteristics' window for the RCH and EVT packages the value 'Assign parameter to modellayer' = 0 (assign to modellayers automatically) is not allowed anymore.

In iMODFLOW:

• Whenever the simulation time extends the input of the txt files for wells, the well rate remains equal to the last entry.
• The use of NSCL=0 (network specified by an IDF file) generated an error, this has been fixed.
• When ISAVE_DATE = 1 (save results for enddate) and hours, minutes and seconds are not specified (zero's) the names of the IDF's will not contain zero's; the filenames will contain e.g. '20171117' instead of '21071117000000'.
• The multiplication of RCH in iPEST was also done in case the recharge was not reread from file, causing an erroneous repetition of multiplications, this has been fixed.
• Now by default the switch "simgro_opt = -1" is included in the MetaSWAP inputfile para_sim.inp; "simgro_opt= -1" is the switch to have MetaSWAP generate IDF-output.

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Release notes iMOD 4.2, December 21^st, 2017:

iMOD 4.2 contains the following new functionalities:

1. Extension of the water balance tool, funded by the Dutch iMOD-CGO group and implemented in collaboration with Tauw.
2. A new movie tool, also funded by the Dutch iMOD-CGO group.
3. Extension of the 3D Tool with Fence diagrams & deviated wells, funded by Alberta Energy Regulator | Alberta Geological Survey.

1. A summary of new and improved features.
2. A summary of current developments.
3. Other ongoing developments.

• Extension of the Waterbalance Tool
  The current water balance tool was extended significantly to allow constructing water balances for sub-regions, and selecting / deselecting MODFLOW- and MetaSWAP-water balance components interactively. The new water balance tool also allows specifying only a subset of the output time series and contains several time-related aggregation possibilities (e.g. averages per year, month and season). Visualization includes interactive stack-bars time series plots and schematic vertical cross-sectional overviews. This extension was implemented in collaboration with Tauw and financed by the Dutch iMOD-CGO group.
• A new movie tool
  Also part of the above mentioned 'Water balance Tool extension'-project a movie tool was developed. It facilitates visualizing a time series of maps (e.g. calculated groundwater levels) and records it as a playable file.
• Extension of the 3D Tool, funded by the Alberta Energy Regulator | Alberta Geological Survey:
  • Fence diagrams
    It is now possible to create 3D fence-diagrams. The fence-diagrams can both be defined interactively using clipping planes along the major Euclidian axes and can be generated automatically. Clipping can also be activated for IPF- and IFF data. Section 7.3 '3D Tool' of the iMOD User Manual has been upgraded accordingly.
  • Deviated wells
    The current 3D Tool was extended with the option to visualize deviated wells. An additional format in associated txt files was added to support the use of deviated wells; the values can vary in depth by x and y.
  • An 'Explode IDF'-option has been added. It allows to increase the vertical distance between selected IDF's in a 3D view interactively. For each individual IDF ?le this vertical distance can be specified by setting a slider interactively. See section 7.3.3 of the iMOD User Manual.
  • It is now possible to Import PETREL pillar-files and convert them to 3D-GEN files.
  • iMOD now displays boreholes in the 3D Tool in a fancy way by default when less than 1000 points are read, previously this was 500.
• The keyword IBLNTYPE was added to the IMODBATCH function XYZTOIDF to allow using BLNFILES not only as a fault but also as a polygon.
• When the ‘CheckRun' is performed in the ‘Start Model Simulation' window now also a result-message is written to the logfile when all files listed in the runfile exist (so not only when files do not exist).
• Now it is also possible to search for time dependent files without timesteps using wildcards; those files will be assigned a steady-state timestamp.

• Non-uniform grids can now be used with the ISG-package containing 1D- or 2D-cross sections wider than the cell sizes.
• Prior to closing the ISGEDIT window iMOD now askes whether to save changes.
• When exporting a model to a namfile, iMOD assigns a NODATA value to the VCW and KVV parameters in the LPF package in case the cell underneath is inactive.
• In SFR now a warning is given if the upstream bottom level is lower/equal to the downstream bottom level since this is not allowed by the SFR package.
• Now you cannot assign a layer number equal to 0 anymore in the RCH- and EVT-package since this is not a logical thing to do.
• The keyword IDATE in the PLOTRESIDUAL IMODBATCH function has been removed since a transient model yields an average not involving a particular date anymore.

• The waterbalance analyse tool crashed when the Modflow/Metaswap buttons were used and no files were available, this has been fixed.
• An error in 'search for segment number' in ISGEDIT was corrected.
• Reading an MDF file with non-existing IDF file(s) generated a crash in the profile-tool, this has been fixed.
• The IMODBATCH function IPFSPOTIFY generated results from non-initialised variables when a geological layer was not present in a model layer, this has been resolved by initialising those fractions as 0.0.
• Plotting of IUPSEG and IUDWN for SFR was mixed up, this has been fixed.
• Labels can be displayed in 3D again.

• An error in creating Metaswap input files for non-uniform grids (available since the iMOD 4.1 release) has been fixed.
• A more efficient allocation of zones to parameters has been implemented in iPEST.
• When using iPEST the RCH parameter was modified for each stress period regardless it was reread from disc, this has been fixed.

• Larger coordinates
  As a spin-off in a modelling project funded by Landesamt für Landwirtschaft, Umwelt und ländliche Räume, Geologischer Dienst Schleswig-Holstein, Germany, iMOD will be extended for the use of larger coordinates. This extension will become very handy with respect to the planned European transition to the ETRS89 coordinate system including an extra two-digit zonal prefix. The extension for larger coordinates will be part of a release scheduled for the spring of 2018.

• Additional runfile-options
  We are implementing a number of additional runfile-options; for a specification of these runfile-options scheduled for a next iMOD-release, please have a look in chapter 10 of the iMOD User Manual.
• A new SUB-CR package (including 'creep')
  The existing SUBsidence-package has been extended with 'creep' for clay and peat; the implemented concept is consistent with D-Settlement (geotechnical software). We hope we will be able to include this extension in an upcoming iMOD-release.
• Coupling of iMOD and DgFlow
  Proof of Concept: iMODFLOW has been offline coupled to DgFlow, a finite-element code developed by Deltares for simulating the consolidation process of dikes/embankments. An explicit head-flux boundary coupling has been realized, demonstrating the added value of incorporating regional, transient, groundwater flow boundary conditions for dike stability analysis. For more information, please contact Deltares.
• We also are working on making iMOD-MT3DMS/SEAWAT open source and include it in the iMOD-framework. This modified version of MT3DMS/SEAWAT uses an easy-to-use runfile for specifying model data for many layers and supports the common iMOD file-formats. We are making progress but slower than hoped for; we will update you on the progress later.

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Release notes iMOD 4.2.1, January 31^st, 2018:

iMOD 4.2.1 is a bugfix-release, it fixes a rare OpenGL-error present in the GUI of iMOD 4.2 only.

Current iMOD 4.2 users not experiencing OpenGL-errors don't have to upgrade to iMOD 4.2.1 because the source codes of iMOD 4.2.1 and iMOD 4.2 are exactly the same.

Compared to earlier releases the compiler-settings used for the GUI of iMOD 4.2 were a bit more strict. Recently in a couple of individual cases these stricter settings cause an OpenGL-error. For the iMOD 4.2.1-release the pre-iMOD 4.2-compiler settings have been used.