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iMOD User Manual version 5.2 (html)


5.5iMOD Project Manager

The files needed in a model simulation are defined in the iMOD Project Manager. On the menubar click View and then choose the option iMOD Project Manager to open the corresponding window.

The iMOD Project Manager window shows a list of all possible model input topics. iMOD saves the characteristics in a project file, a so called *.PRJ file. From a project file different model simulations can be run e.g. standard MF2005, MODFLOW6, SEAWAT etc. Before that it is possible to change e.g. the number of model layers and the configuration of packages, the time and space characteristics of the simulation and the output settings (see section 5.5.5). Moreover, an existing runfile can be read and used to write a *.PRJ file.


5.5.1TreeView - list of Topics

Example of the iMOD Project Manager window: TreeView All tab

Initially:                 After reading a project (*.PRJ) file:

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Note: The Project Manager does not yet support the PKS package or the variant PKST and PKSF for iMOD-WQ.


TreeView
All

All acronyms bracketed are described in more detail in chapter 10. Once a project file *.PRJ (or a runfile *.RUN) has been read, the topics that contain model information (recognized by the small “plus” signs) can be expanded to access the underlying files/information.
"All" means that All available topic are listed. On the tab Configuration it is possible to select a sub-set of the topics based on the desired model simulation type.


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Refresh
Click this button to refresh the Project Definition table. All definitions will be removed.


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Delete
Click this button to delete the selected entry. If the main category is selected, the entire category will be deleted. If a single entry is selected, the corresponding package entry will be deleted.

Question to confirm the desired removal of a category.

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Question to confirm the desired removal of a single entry.

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Question to confirm the desired removal of all entries for a selected date.

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Open Project file (*.prj)
Click this button to select a project file (*.PRJ). iMOD will read the project file and fills the treeview in the Project Definition table.


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Save Project file (*.prj)
Click this button to save the project file (*.PRJ) on disk.


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Open Runfile (*.run)
Click this button to select a runfile (*.RUN). iMOD will read the entire runfile and fills the treeview accordingly in the Project Definition table.


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Start the Simulation Manager
Click this button to open the window to configure and start the model simulation for one of the supported simulators MODFLOW2005, MODFLOW6, SEAWAT etc. It starts the Simulation Manager window, see section 5.5.5.


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Draw
Click this button to port the files within the selected topic to the iMOD Manager and to display the files. The action of the Draw button depends on the selection in the tree view. It will port all files underneath the selected branch. Whenever a branch is expanded individual files can be selected that need to be ported to the iMOD Manager.

Draw all files in the expanded branch:     Draw the selected file only:

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Packages that are defined by constant values instead of spatial datasets, such as IDF, IPF, ISG and/or GEN-files (e.g. lay=3;fct=1.0;imp=0.0;constant=15.0) will not be ported to the iMOD Manager.


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Special Open:

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In this case, the files that are assigned to the \(3\) layers will be opened in the order top elevation, transmissivity and bottom elevation for each model layer, up to the \(3^{\rm rd}\) model layer. More options are:

  • • TOP1 - BOT1 - TOP2 - ...
    Ports the IDF files for the top and bottom elevations to the iMOD Manager;

  • • TOP1 - KDW1 - BOT1 - TOP2 - KDW2 - BOT2 ...
    Ports the IDF files for the top, transmissivity and bottom elevations to the iMOD Manager;

  • • TOP1 - KDW1 - BOT1 - VCW1 - TOP2 - BOT2 - VCW2 - TOP3 ...
    Ports the IDF files for the top, transmissivity, bottom elevations and vertical resistance to the iMOD Manager;

  • • TOP1 - BOT1 - VCW1 - TOP2 - BOT2 - VCW2 - TOP3 ...
    Ports the IDF files for the top, bottom elevation and vertical resistance to the iMOD Manager;

  • • TOP1 - SHD1 - BOT1 - TOP2 - SHD2 - BOT2 ...
    Ports the IDF files for the top, starting head and bottom elevations to the iMOD Manager;

  • • TOP1 - KHV1 - BOT1 - TOP2 - KHV2 - BOT2 ...
    Ports the IDF files for the top, horizontal permeability and bottom elevations to the iMOD Manager;

  • • TOP1 - BOT1 - KVV1 - TOP2 - BOT2 - KVV2 - TOP3 ...
    Ports the IDF files for the top, bottom elevations and vertical permeability of the interbed to the iMOD Manager;


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Define Characteristics:
Click this button to open the Define Characteristics window, see section 5.5.2.


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Define Characteristics Automatically:
Click this button to open the Define Characteristics Automatically window, see section 5.5.4.2.


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Calculator
Click this button to start the Predefined Calculations window in which it is possible to complete standard calculations on model parameters, such as computed vertical resistances between model layers based upon permeability values and top- and bottom of model interfaces.

Predefined Calculations:

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The following predefined calculations are implemented:

  • Transmissivities
    Based upon the horizontal permeability (m/d) values per modellayer and the top- and bottom of model layers, the transmissivity (m\(^2\)/d) is computed;

  • Vertical Resistances Aquitards
    Based upon the vertical permeability (m/d) in between model layers, the vertical resistance (d) of the intermediate model layer (aquitard) is computed;

  • Total Vertical Resistances
    Based upon the horizontal permeability (m/d), the top- and bottom, the vertical anisotropy (-) per model layer and the vertical permeability (m/d) in between model layers, the total vertical resistance (d) between model layers is computed.

The computation can be carried out for the total modeling domain or for the current zoom window of the graphical canvas. Also, it can be done for a selected (sub)set of model layers.

Help ...

Click this button to start the iMOD Help Functionality.

Close

Click this button to close the iMOD Project Manager.

Example of the iMOD Project Manager window: Configuration tab

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Configuration

Tab with the option to select a subset of the complete list of all topics available in iMOD. This will reduce the listed topics on the TreeView ALL tab for a better overview and fast navigation.

Model Configuration

Menu to select a specific subset of topics for one of the specific Model Configurations e.g. MODFLOW2005, MODFLOW6, SEAWAT and MT3D.

Topic

The list of all topics, both obligatory and optional, for the selected Model Configuration.


Visible

Checkbox to reduce or enlarge the topics to be displayed on the TreeView ALL tab. Initially, when no topic is filled yet, all available topics are listed automatically. In case an existing *.PRJ file is loaded, only the topics read from that file are checked.

The selection on this tab only influences the TreeView and not which (optional) topic is included in the actual modelrun. The (de)selection of topics in a modelrun is facilitated on the Simulation Manager window (see section 5.5.5.1).


5.5.2Define Characteristics layer based

The Define Characteristics pictures/h1-h3/image192.png ) option of the iMOD Project Manager window opens a window which enables to define the characteristics of the model input topics as described below.

Define Characteristics window:

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Package is ACTIVE for coming simulations, deselect to Deactivate Parameter

Check this option to exclude, in case it is ACTIVE, or include, in case it is DEACTIVE (red bar), this model topic when saving a runfile (*.RUN).

Steady-state

Check this button to define a steady state model input for the selected topic.


Transient, start from

Check this button to define input for use in a transient model. Enter the start date for the input in the input fields to the right. Besides defining the date there is also the option of defining the time [hh]:[mm]:[ss]. E.g. entering \(10^{\rm th}\) of June 2014 08 00 00 means that the input files as specified under Parameter Assignment: are starting at the \(10^{\rm th}\) of June 2014 at 08:00:00 am forward. The packages end, whenever another input is defined ahead of time.


Transient period:

Select a predefined period to indicate the start period for the current topic. This period will be endless in time, unless another input is defined ahead in time.

Define Periods...

Click this button to open the window in which it is possible to add and/or alter period definitions, see section 5.5.2.2.

Define Species...

Click this button to open the window in which it is possible to add of remove species for use in SEAWAT/MT3D (see section 5.5.2.1).


Parameter:

Choose the parameter for which the Parameter Assignment will be defined. Depending on the model input topic the number of parameters is 1 (e.g. for WEL), 2 (e.g. for ANI), 3 (e.g. for EVT) or 4 (e.g. for RIV). See chapter 10 for detailed information about these different input per topic.


Assign parameter to
model layer …

Enter the model layer number to which the input is assigned in the model. Three options are possible:

  • • Layer = 0 (for time variant input)
    A zero-value will assign the characteristics automatically to the model layers intersected by the depth of the model topic (e.g. the depth of the screen for wells or the depth of stage to bottom level for rivers);

  • • Layer < 0 (for time variant input)
    A negative value will assign the characteristics to the upper most active model layer as defined in the Boundary Condition. Whenever the RCH and/or EVT packages are selected, the appropriate flags in the corresponding MF2005 packages will be set to 3 to indicate this automatic layer assignment;

  • • Layer > 0
    A positive value will assign the characteristics to the corresponding model layer.


Extra files:

Click this option to add extra files to the topic. This option is only available whenever the MSW (Unsaturated Zone) package is selected.

Extra Files:

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In this case, the files are listed to be copied in a simulation with MetaSWAP.

Inherent from previous definition:

Select this option to inherent the input for the selected topic from the previous (in time) definition for this topic.

Assign Parameter
Multiplication Factor:

Change the multiplication factor from the default value 1.0 in case the model input needs to be multiplied. Multiplication goes before the additional value.

Assign Parameter
Addition Value:

Change the addition factor from the default value 0.0 in case the model input needs to be increased (added) with a constant value. Multiplication goes before the additional value.

Add constant value

Check this button and enter a constant value for the parameter for the whole model area.

Add file:

Check this option and enter a file name to be used for the parameter. It depends on the package whether an IDF, IPF, ISG or GEN file need to be entered.


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Open File
Click this button to open the a Windows Explorer to locate the file name for the parameter, this can be an IDF, IPF, ISG or GEN file that depends on the topic considered.


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Open
Click this button to select a folder, remember to add a wild-card to the folder name in order to select appropriate file names by iMOD.

Help ...

Click this button to start the iMOD Help Functionality.


Add System
Adjust System

Check this button to save the entered input for the selected topic and return to the Project Manager window. This can mean that the parameter for an existing topic are adjusted, or a new system is added to a topic. The tree-view in this window will collapse all topics and expand the selected and modified topic. For large project configurations with many time-definitions it can take several minutes to (re)fill in the tree-view field.

Note: For transient (time variant) topics, individual stressperiods (specific dates and/or periods) can be assigned to packages as a whole. They become accessible in the iMOD Project Manager. Those (and time invariant topics) may contain more than one levels (subtopics) of necessary input, such as topic ANISOTROPY that consists of FACTORS and ANGLES and topic DRAINAGE that consists of CONDUCTANCE and DRAINAGELEVEL. Use the Define Characteristics Automatically button (  pictures/h1-h3/properties_auto.png ) option to efficiently configure the time variant model input and/or multi-layered input (see also section 5.5.4.2).

Anisotropy with more subtopics:     Drainage/Constant Head with time variant information:

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5.5.2.1Define Species

The definition of Species is obligatory for model simulations SEAWAT or MT3D.
This options to add or remove species is available on each Define Characteristics window that is layer based. Once a species is defined for one topic it becomes available for each topic that has an input related to species e.g. SCO (starting concentration) or FSC (first sorption constant).

Define Species window:

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Number of Species

Select the number of Species to be included in the modelling. A maximum of 10 species can be defined.

Adjust

After increasing or decreasing the number of species click this button to update the table below. By default new species are named SPECIES (Number).

Number

Automatic numbering of defined species (fixed).

Species

Species name. User can modify this name.

Mobile

Select the species property Mobile or Immobile (Mobile by default).

Apply

Click this button to close this window and update the project manager with the given changes. All topics with a species entree are changed.

Help ...

Click this button to start the iMOD Help Functionality.

Apply

Click this button to close this window, any modification to a period definition will be stored.

Note: Be careful: once a species is removed it is removed for all topics. Previously added topic specific parameters (values or IDF’s) for this species will be removed.


5.5.2.2Define Periods

A period is defined by a starting date and time for which a package, assigned to that period, will be repeatedly included in the runfile. A period start at a particular moment in time, but it will never end repeating itself. The only way of ending a package defined by a period, is by defining another package after or equal to the starting date of the period.

Define Periods window:

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New
Click this button to define a new period. In the following window it is possible to enter a name for the period.

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Use the OK button to agree with the entered period name, click the Cancel button to cancel the creation of a new period. Click Help to open the iMOD help functionality.


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Rename
Click this button to rename an existing period name. Usage of the window as described by New will be used.


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Delete
Click this button to delete the selected period. Whenever the last period is delete, iMOD will ask to enter a period name as described by New and if this cancelled, the Define Period window will be closed.

Summer

Select one of the predefined period from the dropdown list. If none available, create one first by means of the New button.

From

Modify the starting date and time for the selected predefined period. In this example the period Summer is a period starting from 1990 and thereafter each year at the \(1^{\rm st}\) of April at 08:00:00 am. Any modification will effect any systems for topics that are assigned to that period definition.

Help ...

Click this button to start the iMOD Help Functionality.

Apply

Click this button to close this window, any modification to a period definition will be stored.


5.5.2.3Multi Periods Handling

Packages are assigned to a particular date and time at which they start. They will never end, but can be overruled by another packages that is defined ahead of them. In the following figure it is explained what this means whenever more packages become available and interact whenever periods are defined.

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In the figure shown above, a) describes the situation in which only a single package T\(_1\) is defined half-way a simulation between Start and End. In b), another package T\(_2\) is defined and overrules T\(_1\) at the start of T\(_2\). In c), a third package T\(_3\) is defined before T\(_1\) and even before the start of the simulation. Consequently, the package T\(_3\) becomes active, directly at the start of the simulation. In d), a period P\(_1\) and P\(_2\) are defined at a certain moment within a single year, they will be repeated for each year, automatically. Finally, in e) a package T\(_4\) is defined besides the period definitions P\(_1\) and P\(_2\). As a consequence, the package T\(_4\) will split period P\(_1\) halfway, up to the moment period P\(_2\) is defined again.


5.5.3Define Characteristics topic specific


5.5.3.1PCG: Preconditioned Conjugate-Gradient

Within the PCG Settings window it is possible to configure the settings for the PCG solver. Several options are available.

PCG Settings window:

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Number of outer iterations
(MXITER)

Is the maximum number of outer iterations (calls to the solution routine). For a linear problem MXITER should be 1, unless more than 50 inner iterations are required, when MXITER could be as large as 10. A larger number (generally less than 100) is required for a nonlinear problem. If the Lake package is used, more iterations may be required.

Number of inner iterations
(ITER1)

Is the number of inner iterations. For nonlinear problems, ITER1 usually ranges from 10 to 30; a value of 30 will be sufficient for most linear problems.

Head closure criterion
(HCLOSE)

Is the head change criterion for convergence, in units of length. When the maximum absolute value of head change from all nodes during an iteration is less than or equal to HCLOSE, and the criterion for RCLOSE is also satisfied (see below), iteration stops.

Budget closure criterion
(RCLOSE)

Is the residual criterion for convergence, in units of cubic length per time. When the maximum absolute value of the residual at all nodes during an iteration is less than or equal to RCLOSE, and the criterion for HCLOSE is also satisfied (see above), iteration stops. For nonlinear problems, convergence is achieved when the convergence criteria are satisfied for the first inner iteration.

Relaxation parameter
(RELAX)

Is the relaxation parameter used with NPCOND = 1. Usually, RELAX = 1.0, but for some problems a value of 0.99, 0.98, or 0.97 will reduce the number of iterations required for convergence. RELAX is not used unless NPCOND is 1.

Preconditioning
(NPCOND

Is the flag used to select the matrix conditioning method. The first choice (Modified Incomplete Cholesky) is almost always chosen. Second is the Polynomial matrix conditioning method.

Printout Interval
(IPRPCG)

Is the printout interval for PCG. If IPRPCG is equal to zero, it is changed to 999. The maximum head change (positive or negative) and residual change are printed for each iteration of a time step whenever the time step is an even multiple of IPRPCG. This printout also occurs at the end of each stress period regardless of the value of IPRPCG.

Printing of Convergence Information
(MUTPCG)

Is a flag that controls printing of convergence information from the solver with 4 options.

Damping Factor Steady-State
(DAMPPCG)

Is the damping factor for steady state stress periods. It is typically set equal to one, which indicates no damping. A value less than 1 and greater than 0 causes damping. DAMPPCG does not affect inner iterations; instead, it affects outer iterations.

Damping Factor Transient
(DAMPPCGT)

Is the damping factor for transient stress periods. In other respects it is like DAMPPCG.

Help ...

Click this button to start the iMOD Help Functionality.

Apply

Click this button to close this window, any modification to a period definition will be stored.

Cancel

Click this button to cancel the creationg of this topic.


5.5.3.2PEST: Parameter Estimation

Within the PEST Settings window it is possible to configure the settings for a parameter estimation. Several options are available, such as defining the main settings, the number and characteristics of parameters, the zones and measurements, see section 12.33 for more detailed information on parameter estimation. Most of the parameters are described in more detail in section 10.15 as well.

PEST Settings window:

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Apply Parrallel iPEST

Select this option to use parrallel iPEST. In this case iMOD will steer the optimization and start all simulations that are needed for the sensitivity computations. Whenever this option is unchecked, iMODFLOW is steering the optimization.

Hide Command Windows
Select this option to hide the command-windows in which the individual model run. This is strongly recommended as (re)starting of all individual models disturb usage of the computer for other activities. Uncheck this option in the case individual sub models won’t run and it is needed to inspect any errors.

Number of Processors:
Enter the number of processors that is available at the current computer. The entered number determines the number of individual models that start in parallel.

Number of Line Searches:
Enter the number of Line Searches

Maximum Number of Sequences

Enter the number of sequences (iteration) of the parameter estimation routine. Enter a zero will start a sensitivity analysis only.

Stop Criterion Reduction of Objective Function

Enter a percentage for which the objective function needs to be reduced between adjacent iteration in order to terminate the parameter estimation process. The percentage is computed as the ratio between the previous and current objective function value.

Stop Criterion Parameter Adjustment

Enter a value for this stop criterion between 0.0 and 1.0 to terminate the parameter estimation whenever it becomes less than the specified value. The stop criterion is computed as

Ignore parameter with maximal Sensitivity

Enter a percentage of the sensitivity of a parameter which will be excluded from the current parameter estimation cycle, whenever its sensitivity is less than the specified value.

Minimal Acceptable Residual

Enter a value to skip measurements in the formulation of the objectie function whenever the absolute residual is less than the specified value.

Enter a fraction for each Target

Enter a weight value for two targets of the objective function; the first target is the sum of the square root residuals, the second the sum of the square root residual of the dynamic in a measurement (see section 12.33.1). Its is not necessary to scale them to a sum of 1.0, internally the entered fraction will be scaled to a total sum of 1.0, this includes any Batchfiles included (see NUmber of Batchfiles further below).

Specify Scaling / SVD

Scaling can be used whenever parameters yield significant different sensitivities; SVD (Eigenvalue Decomposition) is a process in which parameters can be grouped mathematically of excluded/ignored in the parameter optimization. This can be done manually (using the parameter sensitivity) or automatically by means of some mathematically expressions. It is encouraged to apply SVD at all times. Select of the following options:

  • No Scaling / SVD
    No use of scaling and/or SVD;

  • Scaling
    Use Scaling, use this option whenever the amplitude of different residuals differ significantly, such as measurements of groundwater level and discharge;

  • Scaling and SVD
    Use Scaling and Eigenvalue Decomposition whenever it is very difficult to exclude parameters on their sensitivity or relevant contribution to the reduction of the objective function;

  • Eigenvalues
    Use Eigenvalue Decomposition whenever the parameter sensitivity alone, is not enough the estimate the relevance of a parameter to the parameter optimization.

Tikhonov Regulariation

This type of regularisation allows to include the modification of parameters in the penalty function (objective function). Large modifications are punished more than less modifications. It is advised to include this type of regularisation as it avoid parameters to differ too much from their posterior estimate.

Variable Weighting
As the misfit between measurements and computed heads can be weighted, so is the difference between the posterior estimate and the estimated values. The values of 1.0 indicates that a change in variables is penalised similar as a misfit between the measurements. If many measurements are included, the penalty of the estimated values need to be in magnitude with the reduction of the objective function. In the end the objective function value with and without the Tiknonov Regularation is printed in the log files, based on this, the size of the Variable Weighting can be estimated more realistically.

Kriging Type

Specify the type of Kriging (section 12.33.5.1) whenever the Pilot Point concept is used (section 12.33.5). Whether Pilot Points are used is steered by the fact that an IPF file will be entered by the zones (see Number of Zones) instead of IDF files. The following options are available:

  • Simple Kriging (section 12.33.5.1)
    Simple Kriging assumes stationarity of the mean, all variables have the same mean over the entire domain;

  • Ordinary Kriging (section 12.33.5.1)
    In Ordinary Kriging a unknown mean is assumed only over the search neighborhood, so the mean is recomputed for the values in the search neighborhood.

Define Periods ...

Click this button to define periods (see section 10.16) for which measurement need to be included in the computation of the objective function, e.g. \(1^{\rm st}\) of January 2010 to the \(31^{\rm st}\) of December 2010 and the \(1^{\rm st}\) of January 2012 to the \(31^{\rm st}\) of December 2012.

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Click the Define Periods to increase or decrease the number of available rows (entry fields) in the table, e.g. \(2\). There is a maximum of \(10\) rows. Click the Apply button to accept your entry, click the Cancel to ignore any changes, click the Help button to start the Help-functionality.

Define Batchfiles ...

Click this button to define batchfiles (see section 10.17) for which extra or additional measurement need to be included in the computation of the objective function.

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Click the Define Batchfiles to increase or decrease the number of available rows (entry fields) in the table, e.g. \(1\). There is a maximum of \(10\) rows. Click the Apply button to accept your entry, click the Cancel to ignore any changes, click the Help button to start the Help-functionality.

Define Parameters ...

Click this button to define parameter to be optimized.

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Click the Define Parameters to increase or decrease the number of available rows (entry fields) in the table, e.g. \(2\). There is a maximum of \(1000\) parameters, see section 10.19 for the explanation of the variables. Click the Apply button to accept your entry, click the Cancel to ignore any changes, click the Help button to start the Help-functionality.

Define Zones ...

Click this button to define zones (see section 10.21) for which parameters need to be adjusted.

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Click the Define Zones to increase or decrease the number of available rows (entry fields) in the table, e.g. \(5\). There is a maximum of \(1000\) zones, constant values can be entered to denote a zone fore the entire model area, multiply zones can be combined in a single IDF file and/or IPF files can be entered for usage of Pilot Points (section 12.33.5). Click the Apply button to accept your entry, click the Cancel to ignore any changes, click the Help button to start the Help-functionality.

Define Measurements ...

Click this button to define measurements (see section 10.4) which are needed to compute the objective function. It is also possible to exclusively use Batchfiles instead.

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Click the Define Measurements to increase or decrease the number of available rows (entry fields) in the table, e.g. \(2\). There is a maximum of \(50\) zones, constant values can be entered to denote a zone fore the entire model area, multiply zones can be combined in a single IDF file and/or IPF files can be entered for usage of Pilot Points (section 12.33.5). Click the Apply button to accept your entry, click the Cancel to ignore any changes, click the Help button to start the Help-functionality.

Apply System Settings

Click this button to leave the Parameter Estimation Settings window and store the adjustments.

Cancel

Click this button to close the Parameter Estimation Settings window

Help ...

Click this button to start the Help-functionality


5.5.3.3GCG: Generalized Conjugate Gradient Solver

Within the GCG Settings window it is possible to configure the settings for the GCG solver.

GCG Settings window:

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Maximum number of outer iterations
(MAXITER)

The maximum number of outer iterations; it should be set to an integer greater than one only when a nonlinear sorption isotherm is included in simulation.

Maximum number of inner iterations (ITER1)

The maximum number of inner iterations; a value of 30-50 should be adequate for most problems.

Convergence criterion
(CCLOSE)

The convergence criterion in terms of relative concentration; a real value between 10\({}^{-4}\) and 10\({}^{-6}\) is generally adequate.

Preconditioning
(ISOLVE)

The type of preconditioners to be used with the Lanczos/ORTHOMIN acceleration scheme 1) Jacobi 2) SSOR or 3) Modified Incomplete Cholesky (MIC). MIC usually converges faster, but it needs significantly more memory.

Treatment of disp. cross terms
(NCRS)

An integer flag for treatment of dispersion tensor cross terms. Lumped to the right-hand-side or include full dispersion

Relaxation factor - for SSOR preconditioner
(ACCL)

The relaxation factor for the SSOR option; a value of 1.0 is generally adequate.

Interval for printing max. conc. changes
(IPRGCG)

The interval for printing the maximum concentration changes of each iteration. Set IPRGCG to zero as default for printing at the end of each stress period.

Apply

Click this button to leave the GCG settings window and store the adjustments.

Cancel

Click this button to close the GCG settings window

Help ...

Click this button to start the Help-functionality


5.5.3.4RCT: Chemical Reaction

Within the RCT Settings window it is possible to configure the settings for the RCT package for SEAWAT and MT3D.

RCT Settings window:

pictures/Ch-view-menu-options/PM-RCT_01.png

Type of sorption
(ISOTHM)

Indicates which type of sorption (or dual-domain mass transfer) is simulated:

  • • no sorption is simulated;

  • • Linear isotherm (equilibrium-controlled);

  • • Freundlich isotherm (equilibrium-controlled);

  • • Langmuir isotherm (equilibrium-controlled);

  • • First-order kinetic sorption (nonequilibrium);

  • • Dual-domain mass transfer (without sorption);

  • • Dual-domain mass transfer (with sorption).

Kinetic Rate Reaction
(IREACT)

Indicates which type of kinetic rate reaction is simulated:

  • • no kinetic rate reaction is simulated;

  • • first-order irreversible reaction. Note that this reaction package is not intended for modeling chemical reactions between species. An add-on reaction package developed specifically for that purpose may be used.

  • • zeroth-order reaction (decay or production).

Input option
(IGETSC)

Indicates whether the initial concentration for the nonequilibrium sorbed or immobile phase of all species should be read when nonequilibrium sorption (ISOTHM = 4) or dual-domain mass transfer (ISOTHM = 5 or 6) is simulated:

  • • 0: the initial concentration for the sorbed or immobile phase is not read. By default, the sorbed phase is assumed to be in equilibrium with the dissolved phase (ISOTHM = 4), and the immobile domain is assumed to have zero concentration (ISOTHM = 5 or 6).

  • • 1: the initial concentration for the sorbed phase or immobile liquid phase of all species will be read.

Apply

Click this button to leave the RCT settings window and store the adjustments.

Cancel

Click this button to close the RCT settings window

Help ...

Click this button to start the Help-functionality


5.5.3.5VDF: Variable Density Flow

Within the VDF Settings window it is possible to configure the settings for the VDF package for SEAWAT and MT3D.

VDF Settings window:

pictures/Ch-view-menu-options/PM-VDF_01.png

Minimum fluid density
(DENSEMIN)

If the resulting density value calculated with the equation of state is less than this value, the density value is set to the entered value.

Maximum fluid density
(DENSEMAX)

If the resulting density value calculated with the equation of state is greater than this value, the density value is set to the entered value.

Reference fluid density
(DENSEREF)

The fluid density at the reference concentration, temperature, and pressure.

The slope d(rho)/d(C)
(DRHODC/DENSESLP )

The slope of the linear equation of state that relates fluid density to solute concentration.

Apply

Click this button to leave the VDF settings window and store the adjustments.

Cancel

Click this button to close the VDF settings window

Help ...

Click this button to start the Help-functionality


5.5.4Define Characteristics automatically

The Define Characteristics Automatically pictures/h1-h3/properties_auto.png ) option on the iMOD Project Manager window opens a window which enables to define the characteristics of the model input topics in a more advanced way than the default Define Characteristics window (see section 5.5.2). The process consists out of two steps. In the first step you define the characteristic of the source for each topic, in the second step iMOD will list the found sources and it is possible to modify this list manually before adding them to the Project Manager window.


5.5.4.1Define Source for Topics

The first step is to define the type of sources for each topic.

Define Characteristics for: window

pictures/h72-end/pmanager_dc_auto.png

Define Package

This table show how each of the topics for the package (here the topics CON, RST, RBT and RIF for the RIV package) need to be specified. Three options are available

  • • Constant Value
    Specify a constant value for the topic to be used for all stress-periods or model layers, e.g. a value of 90.0 means that this topics is 90.0 for all stress-periods or model layers;

  • • File Name
    Specify a file name for the topic to be used for all stress-periods or model layers, e.g. a file name as D:\MODEL\DBASE\BOTTOM.IDF applies that this file is used for all stress-periods or model layers;

  • • Wild card
    Specify a file name with a wild card ( * ) to specify that all files that are part of this will be added. It depends whether a module or package is associated, for modules layers can be added this way, for packages multiple stress periods, e.g. D:\MODEL\DBASE\STAGE_*_.IDF will add all files that belong to this group.

iMOD will look for unique TIMESTEPS

Select this option to select unique timesteps and add the related files to your project.

iMOD will look for unique LAYERS

Select this option to only select unique layers and add the related files to your project.

Select files within given layer range

Select this option to be able to only select the files of the given layer range of your project.

Select files within given time frame only

Select this option to define the start- and end date for the input. Besides defining the date there is also the option of defining the time [hh]:[mm]:[ss]. E.g. entering \(10^{\rm th}\) of June 2014 08 00 00 means that the input files as selected at the \(10^{\rm th}\) of June 2014 at 08:00:00 am up to the specified end date.

Allocate Files ...

Click this button to apply the given sources for topics and pop-up a list of constant values and/or file namer per model layer or stress period.

Help ...

Click this button to start the iMOD Help Functionality.

Cancel ...

Click this button to close the Define Characteristics Automatically window and return to the Project Manager window.


5.5.4.2Modify List of Topics

The second step is to inspect the list of found files based on the given sources for each topic.

Define Characteristics for window:

pictures/h72-end/pmanager_dc_listfiles.png


5.5.5Simulation Manager

Within the Simulation Manager window it is possible to configure runs of all supported simulators. Several options are available, such as defining the location and size of clip models, time-discretisations, activate packages, select output etc.

Simulation Manager window, Main tab:

pictures/Ch-view-menu-options/Simulation-Manager-main-01.png

Available INI files

Open an existing INI file to automatically load a complete configuration of a previous run model in stead of the default options. This includes all options on the available tabs e.g. stress periods (instead of Steady State by default) and model window (instead of ’extend of 1st mentioned IDF’ by default).


Model Type

Check which model simulator to use. This influences specific simulator options on this or other tabs, see for instance the ’Output Folder’ section on the Main tab.

Create input files only

Check this box and iMOD only creates the result folder with a copy of the executable, the run file and a batch file to start the model manually.

Simulate on Foreground

Check this box and iMOD starts the model run in a new DOS window. On the background also a copy of the executable is placed in the result folder as well as the run file and a batch file to rerun the model manually.

Select Existing iMOD Results

In case MT3D is selected, also select an existing model result folder with a calculated flow field (BDGF*F files).

Enter or Select
Ouput / MT3D folder

Enter the name of a new output folder or select an existing folder. The content of an existing folder will be overwritten. The folders in the drop down menu are found in installfolder \USER \MODEL \.

Start...

Start the model run. iMOD uses the Executable as mentioned in the PRF file).


5.5.5.1Select Layers and Packages

Layers / Packages tab:

pictures/Ch-view-menu-options/Simulation-Manager-tab2-01.png

Act.

Actual. By default all topics are selected to be included in the model run. Click the check box to select and deselect topics. It is not recommended to deselect topics that are essential for a correct simulation of the model, such as the topic BND and GCG.

Topic

Only those topics from the Project Manager that contain data.

Int.

Interpolation. When selected, the grid values will be interpolated in case of a downscaling. When switched of iMOD uses the block value of the grid. By default grid values will be interpolated.

Model layers

Enter a number of modellayers for which the model configuration need to be built and click on the button Adjust. By default the maximum number of layers is given, based on the available layer data for one of the topics in the Project Manager.

Layer

Layer number (fixed).

Type

Select one of the 4 available layer types: Confined (TOP-BOT), Convertible (HNEW-BOT), Convertible (SHD-BOT) or Constant Head.

Adjust all

Click this button to apply the selected layer type from the in the dropdown menu to all modellayers in one action.


5.5.5.2Define Space dimensions

Space dimension tab:

pictures/Ch-view-menu-options/Simulation-Manager-tab3-01.png

Full Extent

Model window equals the extent of first mentioned IDF file in the PRJ file; boundary conditions.

Cellsize

Option to (re)define the cell size for the model run. By default the cellsize of the IDF is displayed.

Snap Coordinates to Cellsize

Select this option to snap the coordinates of the model domain to the entered cellsizes. In this manner, the coordinates of the model will have ”nice-andround” coordinates.

Define Spatial Dimension Interactively

Select this option to determine the dimension and size of the rastercells (computational nodes) interactively.

Draw Simulation Area ...

Click this button to start drawing a rectangle on the graphical display to indicate the location of the simulation area (hatched area). Use your left-mouse button to position the first points of the rectangle, use the left/right-mouse button to identify the opposite border. Whenever you move the mouse cursor inside the hatched area, a cross-arrow appears indicating that the entire hatched area can be moved while clicking the left-mouse button. Similar the borders can be moved whenever the horizontal/vertical arrows appear.

Cellsize

Option to (re)define the cell size for the model run. By default the cellsize of the IDF is displayed.

Snap Coordinates to Cellsize

Select this option to snap the coordinates of the model domain to the entered cellsizes. In this manner, the coordinates of the model will have ”nice-andround” coordinates.

Include a Buffer-zone

Select one of the buffersizes from the dropdown menu or enter a value in the input field next to it. The Buffer-zone is an extra “ring” of modelcells around the chosen simulation area and indicated by a green rectangle.

Max Cellsizes in Buffer

Select this option to increase the cellsizes in the Buffer-zone upto a cellsize that can be selected from the dropdown menu or entered in the input field next to it.

Use Spatial Dimension Defined by

Select this option to determine the dimension and size of the rastercells (computational nodes) interactively.

GEN file
(only for Modflow 6)

A GEN file describing the polygons of the sub models. The 1\({}^{st}\) column is the ID of the sub model polygons. The 2\({}^{nd}\) column must contain the cellsize of the sub model.
Important:
It is recommended to make each cellsize a multiplication of the cellsize of the finest model. If this requirement is not met, iMOD will give a warning in a pop-up window and than continues.
The GEN file must have the binary format (see section 9.11.2).

Current Model Dimensions

These fields are automatically filled as a result of the options selected above.

X coordinate

MINimum X coordinate, MAXimum X coordinate, Delta X, number of columns.

Y coordinate

MINimum Y coordinate, MAXimum Y coordinate, Delta Y, number of rows.


5.5.5.3Define Time dimensions

Time dimension tab:

pictures/Ch-view-menu-options/Simulation-Manager-tab4-01.png

Temporal Configuration

Steady-State

Check this option to generate a run for a steady-simulation, the option becomes available only whenever at least one package is defined for a steady-state period. iMOD will collect all topics that are connected to a steady-state definition as specified in the Define Characteristics window.

Transient

Check this option to generate a transient run. iMOD will collect all topics that are within the specified Start Date and End Date. Besides defining the date there is also the option of defining the time [hh]:[mm]:[ss]. On default the start- and end time is set to 00:00:00

Include
Steady State
period

Select this option to include an initial steady-state period, prior to the start of the transient simulation. This option becomes available whenever at least one package is defined for a steady-state period, see section 5.5.2.

Start Date

Enter a start date and time for the transient simulation, this date will be start of the first stress-period. iMOD will fill in this Start Date initially with the earliest defined date in the packages. Whenever the Start Date is decreased, before the initial value, the model will include packages that remain inactive until the first dat at which they are defined.

End Date

Enter an end date and time for the transient simulation, this date will be the end of last stress-period. iMOD will fill in this End Date initially with the latest defined date in the packages. The End Date is the date at which the simulate will terminate, so it is the end of the last stress period. It is allowed to increase the End Date beyond the initial value to enforce the latest stress period to be include in the model.

TimeSteps

Select one of the option from the drop down menu:

  • Minutes
    Select this option to generate minute stress-periods;

  • Hourly
    Select this option to generate hourly stress-periods;

  • Daily
    Select this option to generate daily stress-periods;

  • Weekly
    Select this option to generate weekly stress-periods;

  • 14/28
    Select this option to generate stress-periods on the 14th and 28th day of each month;

  • Monthly
    Select this option to generate monthly stress-periods;

  • Yearly
    Select this option to generate yearly stress-periods;

  • Decade
    Select this option to generate stress-periods per decade;

  • Packages
    Select this option to generate stress-periods that are determined by the input data as specified by the available packages in the Define Characteristics window. It can yield a non-constant time sequence for stress periods, but will be most optimally to the amount of stress-periods;

  • Custom
    Select this option to refine or inspect time configuration priorly defined. This option is selected automatically after the first time the option Customize is selected.

Fill In Actual Stress Periods

Click this button and iMOD will process the choices in the section Temporal Configuration into a resulting list of stress periods that is displayed in the table below.

Actual Stress Period Configuration
Column names

  • • Column 1: Number of the stress period.

  • • Date: Start Date of the stress period with format YYYY-MM-DD hh:mm:ss.

  • • Length: Length of the stress period in days.

  • • Save: Indicator that defines whether output (as defined by tab Output) is generated for the current stress period.

  • • Steps: Number of transport time steps for this stress period (keyword iMOD-WQ: NSTP).

  • • Factor: Time step multiplier (keyword iMOD-WQ: TSMULT).

  • • TFactor: Transport time step multiplier (keyword iMOD-WQ: TTSMULT).

  • • Max.Step: Maximum transport steps allowed in one flow time-step (keyword iMOD-WQ: MXSTRN).

  • • T.Size: Transport time (keyword iMOD-WQ: DT0).

  • • Max.Steps: Maximum transport step size (keyword iMOD-WQ: TTSMAX).

Total number of stress periods

Maximum number of stress periods for the chosen configuration.


5.5.5.4Select Output options

Output tab:

pictures/Ch-view-menu-options/Simulation-Manager-tab5-01.png

Result Variable

This list will display the available output variables that are within the selected runfile from the Main Configuration tab. Select one of the following:

File (*.idf)

Variable

Description

SIMGRO

Flux in/out Simgro elements

BDGBND

BOUNDARY

Flux in/out constant head boundaries

HEAD

GROUNDWATERHEAD

Groundwater head

BDGFFF/
BDGFRF

FLUX FRONT/RIGHT FACE

Flux in/out front/right cell faces

BDGFLF

FLUX LOWER FACE

Flux in/out bottom cell face

BDGSTO

STORAGE

Flux in/out storage

PURGED WATER TABLE

Absent

ANISOTROPY

Absent

HORIZ.FLOW BARRIER

Absent

TOP

Absent

BOT

Absent

CONCENTRATION

Absent

HORIZ.K VALUE

Absent

VERT.K VALUE

Absent

BDGWEL

WELLS

Flux in/out well systems

BDGDRN

DRAINAGE

Flux out drainage systems

BDGRIV

RIVERS

Flux in/out river systems

BDGEVT

EVAPOTRANSPIRATION

Flux out evapotranspiration

BDGGHB

GENERAL HEAD BOUNDARY

Flux in/out general head boundaries

BDGRCH

RECHARGE

Flux in recharge

BDGOLF

OVERLAND FLOW

Flux out overland flow

BDGBND

CONSTANT HEAD

Flux in/out constant head boundaries (identical to BOUNDARY)

BDGISG

SEGMENT RIVERS

Flux in/out river systems

BDGIBS

INTERBED STORAGE

Flux in/out interbeds

Selected Layers

Select the modellayers for which the current selected variable need to be saved. The number of modellayers to choose from is determined by the Number of Modellayers selected in the Model Dimensions tab.

SaveBudget Terms for each Boundary System

Select this item to save budget terms for each of the defined sub-systems in the selected runfile. The order of subsystems is added to the filename, e.g. bdgriv_sys1_steady-state_l1.idf and bdgriv_sys2_steady-state_l1.idf. By default, the budgets of all defined RIV sub systems are summed.

Saved Result Variable inclusive the given Buffer Size

Select this item to save the results within the specified buffer size entered in the Include a Buffer-zone of field on the Model Dimensions tab.

Save Results in Double Precision

Select this option to save all results in double precision accuracy instead of single precision (which is the default). Bear in mind that all files will be doubled in size as well as the option for double precision is selected. Also, result files saved in double precision cannot be read in iMOD version older than v3.4.

Save Result with Timestamps of the End of the Stress Period

....

NOTE. In MODFLOW the output of fluxes between cells (front/right/bottom cell faces) is coupled together. Whenever one of the following Result Variables is chosen, all fluxes (BDGFRF, BDGFFF and BDGFLF) are saved:


5.5.5.5Define Simulator specific input

Misc tab: MODFLOW

pictures/Ch-view-menu-options/Simulation-Manager-tab61-01.png

BCF

Aquifer properties with the Block-Centered Flow package based on topics KDW and VCW.

LPF

Aquifer properties with the Layer-Property Flow package based on topics TOP, BOT, KHV, KVA and KVV.

ICHKCHD

modifying CHD for DRY cells (or thickness = 0.0)

ICONCHK

modifying DRN that are below RIV STAGES

IFWDL

Apply Conductance Correction

DWEL

Export WEL for each stress period

DISG

Export ISG for each stress period

DSFR

Export SFR for each stress period

Subsoil Consistency Checking

Options:

  • • 0 No Checking

  • • 1 Smiple Checking

  • • 2 Complex Modification

Apply Minimal
Transmissivity (MINKD)

To assign a minimal horizontal conductance KD (m\(^2\)/d) to maximize the computed conductances, internally, e.g. MINKD=0.01, by default MINKD=0.0.

Apply Minimal
Vertical Resistance (MINC)

To assign a minimal vertical resistance C (d) to maximize the computed vertical resistances, internally, e.g. MINC=1.0, by default MINC=0.0.

Misc tab: SEAWAT/MT3D

pictures/Ch-view-menu-options/Simulation-Manager-tab62-01.png

BCF

Aquifer properties with the Block-Centered Flow package based on topics KDW and VCW.

LPF

Aquifer properties with the Layer-Property Flow package based on topics TOP, BOT, KHV, KVA and KVV.

Observation point output frequency (NPROBS)

An integer indicating how frequently the concentration at the specified observation points should be saved in the observation file MT3Dnnn.OBS. Concentrations are saved every NPROBS step.

Output frequency
(NPRMAS)

An integer indicating how frequently the mass budget information should be saved in the mass balance summary file MT3Dnnn.MAS. Mass budget information is saved every NPRMAS step.

Advection solution option (MIXELM)

An integer flag for the advection solution option.
Options:

  • • TVD (Total-Variation-Diminishing)

  • • Finite-Difference

  • • MOC (Method of Characteristics) (not available)

  • • MMOC (Modified Method of Characteristics) (not available)

  • • HMOC (Hybrid Method of Characteristics) (not available)

Weighting scheme Finite-difference (NADVFD)

Weighting scheme for the Finite-difference method.
Options:

  • • upstream weighting (default);

  • • central-in-space weighting.

Courant number
(PERCEL)

Number of cells that advection is allowed to move in one transport step.

Max number point sinks/sources (MXSS)

Maximum number of all point sinks and sources included in the flow model.