1 MULTISCALE ADAPTIVE GROUNDWATER NETWORK (MAGNET) MAGNET VERSION 3.0_ Hydrosimulatics, / Michigan State University Copyright © 2018 by Hydrosimulatics / Michigan State University. All rights reserved. MSU/Hydrosimulatics makes no warranties either expressed or implied regarding the program MAGNET and its fitness for any particular purpose, or for the validity of the information contained in this document. User’s Manual for MAGNET 3.0 prepared by Hydrosimulatics Authors / Editors: Zachary Curtis Dr. Hua-Sheng Liao Dr. Shuguang Li LAST REVISED: January 28, 2019 www.magnet4water.com 2 TABLE OF CONTENTS TABLE OF CONTENTS ..................................................................................................................................... 2 TABLE OF FIGURES .................................................................................................................................. 4 Chapter 1 INTRODUCTION & ACCESS ................................................................................................ 7 1.1 Overview of MAGNET ................................................................................................................ 7 1.2 Datasets ......................................................................................................................................... 8 1.3 User Accounts ............................................................................................................................... 8 1.4 MAGNET Premium .................................................................................................................... 13 Chapter 2 MAGNET MODELING ENVIRONMENT ........................................................................... 15 2.1 Maps Display and Working Area ................................................................................................ 16 2.2 Status Bar .................................................................................................................................... 17 2.3 Map Display Tools ...................................................................................................................... 17 2.4 Simulation Tools ......................................................................................................................... 18 2.5 Model Creation and Visualization Tools .................................................................................... 18 2.6 Conceptual Features Tools .......................................................................................................... 19 2.7 Utilities and Analysis Tools ........................................................................................................ 19 Chapter 3 MODEL CREATION AND PARAMETER OPTIONS ......................................................... 21 3.1 Delineating the Model Domain .................................................................................................. 21 3.2 Model Grid and Solver Settings ................................................................................................. 23 3.3 Aquifer Elevations ..................................................................................................................... 24 3.4 Hydraulic Conductivity .............................................................................................................. 27 3.5 Recharge and Surface Seepage .................................................................................................. 28 3.6 Boundary Conditions & Hierarchical Modeling ........................................................................ 29 3.7 Transient Model Settings & Initial Conditions .......................................................................... 30 Chapter 4 CONCEPTUAL FEATURES: LINES, ZONES & WELLS .................................................. 32 4.1 Line Features & Attributes ......................................................................................................... 32 4.2 Zone Features & Attributes ........................................................................................................ 39 4.3 Well Features & Attributes ......................................................................................................... 52 Chapter 5 SIMULATION AND VISUALIZATION .............................................................................. 59 5.1 Submitting a Model for Simulation ........................................................................................... 59 5.2 Display Options .......................................................................................................................... 62 5.3 Model Values at a Node .............................................................................................................. 67 5.4 Cross-sections ............................................................................................................................. 68 5.5 3D Visualizations ........................................................................................................................ 71 5.6 Particle Tracking ......................................................................................................................... 73 3 Chapter 6 ANALYSIS & MODEL PERFORMANCE ........................................................................... 77 6.1 Monitoring Well Time-Series and Breakthrough Curves ........................................................... 77 6.2 Water Balance Analyses ............................................................................................................ 78 6.3 Model Results vs. Observations (Manual Calibration) .............................................................. 82 Chapter 7 UTILITIES & FILE FUNCTIONS ......................................................................................... 91 7.1 Saving and Loading Models ....................................................................................................... 91 7.2 Publishing & Editing MAGNET Network Models ..................................................................... 92 7.3 Background Images .................................................................................................................... 98 7.4 Geometry Lock/Unlock............................................................................................................... 99 4 TABLE OF FIGURES Figure 1-1: Account login/sign-up interface. ................................................................................................ 9 Figure 1-2: Hydrosimulatics Sign Up Form. .............................................................................................. 10 Figure 1-3: Options for describing user job title/type and affiliation. ........................................................ 10 Figure 1-4: Hydrosimulatics Account Edit Form........................................................................................ 12 Figure 1-5: View Message Box .................................................................................................................. 12 Figure 1-6: Activity Report interface. ......................................................................................................... 13 Figure 1-7: MAGNET User Available Download List. .............................................................................. 13 Figure 2-1: MAGNET Modeling Environment upon login. ....................................................................... 16 Figure 2-2: Using the Map Display Tools to customize the display. .......................................................... 18 Figure 2-3: Default Parameters and Options menu. .................................................................................... 20 Figure 3-1: Creating and adjusting the model domain using the ‘DomainRect’ and ‘DomainZone’ button. The blue in-set map highlights the ‘un-do’ button available after altering any node position. ................... 22 Figure 3-2: The Model Grid and Solver settings available in the Default Parameters and Options menu. Default values/settings are shown. .............................................................................................................. 23 Figure 3-3: Options and parameters for assigning aquifer elevations in MAGNET. Default values/settings are shown. ................................................................................................................................................... 25 Figure 3-4: Different possible settings for the aquifer bottom elevations. .................................................. 26 Figure 3-5: Options and settings for parametrizing the hydraulic conductivity of the aquifer. Default values/setting are shown. ............................................................................................................................ 27 Figure 3-6: Options for applying recharge along the top of the model boundary. Default values/settings are shown. ................................................................................................................................................... 28 Figure 3-7: Surface leakance parameter text box. ....................................................................................... 29 Figure 3-8: Options for applying boundary conditions for flow and/or solute transport modeling. ........... 29 Figure 3-9: Example of the hierarchical modeling approach for developing appropriate boundary conditions in the study area. ........................................................................................................................ 30 Figure 3-10: Options for unsteady (transient) modeling in MAGNET. Default values/parameters are shown. ......................................................................................................................................................... 31 Figure 3-11: Options for assigning an initial head distribution across the model domain. Default value/parameters are shown. ....................................................................................................................... 31 Figure 4-1: Polyline feature added to the model domain and the Polyline Attributes menu. ..................... 33 Figure 4-2: Sub-menu for editing Transient prescribed head data. ............................................................. 34 Figure 4-3: Edit Polyline Attributes sub-menu for assigning unique head values at different vertex locations. Default values/options are shown. .............................................................................................. 35 Figure 4-4: Edit Polyline Attributes sub-menu for assigning polyline attributes needed for computing two-way head dependent flux. Default values/options are shown. .................................................................... 36 Figure 4-5: Edit Polyline Attributes sub-menu for assigning polyline attributes needed for computing one-way head dependent flux. Default values/options are shown. .................................................................... 37 Figure 4-6: Sub-menu for editing Transient prescribed head data. ............................................................. 38 Figure 4-7: Editing attributes of a pre-existing polyline feature. ................................................................ 39 Figure 4-8: Zone feature added to the model domain and the Zone Attributes menu. ............................... 40 Figure 4-9: Elevation sub-menu (for Zone conceptual features). ............................................................... 42 Figure 4-10: Example Cross-section results (see Section 5.4) of using and not using Partial Penetration for a zone feature in MAGNET. When partial penetration is not used, the solute source is distributed 5 throughout the aquifer system (i.e., across all computational layers. When it is used, the solute source is restricted to the topmost computational layer. ............................................................................................ 42 Figure 4-11: Transport Property sub-menu (for Zone conceptual features). .............................................. 43 Figure 4-12: Biochemical sub-menu (for Zone conceptual features). ........................................................ 44 Figure 4-13: Sources and Sinks (Head Dependent) sub-menu (for Zone conceptual features). ................. 45 Figure 4-14: Sub-menu for editing transient lake (or other source/sink) stage data. .................................. 45 Figure 4-15: Sub-menu for editing transient lake concentration data. ........................................................ 46 Figure 4-16: Sources and Sinks (Prescribed) sub-menu (for Zone conceptual features). ........................... 47 Figure 4-17: Sub-menu for editing transient recharge data. ....................................................................... 48 Figure 4-18: Sub-menu for editing transient recharge concentration data. ................................................. 49 Figure 4-19: Sub-menu for editing transient prescribed head data. ............................................................ 50 Figure 4-20: Sub-menu for editing transient source concentration data. .................................................... 51 Figure 4-21: attributes of pre-existing zone features. ................................................................................. 52 Figure 4-22: Well Input Options menu. ...................................................................................................... 53 Figure 4-23: Sub-menu for editing transient pumping/injection rate data. ................................................. 54 Figure 4-24: Sub-menu for editing transient injection source concentration data. ..................................... 55 Figure 4-25: Particle tracking options available in the Default Parameters and Options menu. Default values/settings are shown. ........................................................................................................................... 55 Figure 4-26: Sub-menu for editing transient head observations. ................................................................ 57 Figure 4-27: Sub-menu for editing transient concentration observations. .................................................. 57 Figure 4-28: Example of a well feature placed in a model. ........................................................................ 58 Figure 5-1: Projection option box in the Default Parameters and Options menu. ...................................... 60 Figure 5-2: Example of simulation results (head and concentration). Note that the solute concentration is indicated with the color overlay (red = high concentration; blue = low concentration). ............................ 61 Figure 5-4: Display options available in MAGNET. .................................................................................. 62 Figure 5-5: Different ways to display the groundwater flow results (head distribution and seepage velocities). ................................................................................................................................................... 63 Figure 5-6: Drop-down menu used to select an model input for display. ................................................... 64 Figure 5-7: Examples of displaying model inputs in the MDWA. ............................................................. 64 Figure 5-8: Example of using the ‘Seepage Area’ option from the ‘Display Input’ drop-down menu to indicate areas where groundwater is discharging at the land surface. ........................................................ 65 Figure 5-9: Example of displaying flow model results in Google Earth. ................................................... 66 Figure 5-10: Example of using the 'HideOverlay' button to temporarily remove the simulation results from the MDWA.................................................................................................................................................. 67 Figure 5-11: Example of placing nodal value flags in the model domain, with a sample variable table shown for the flag in the upper right of the model domain. ........................................................................ 68 Figure 5-12: Example charts generated when using the ‘Display Charts’. An example Cross-section plot is shown in the top-right, and an example Cross-section diagram (Full cross-section) is shown in the bottom-right. ............................................................................................................................................... 69 Figure 5-13: Different configurations of the Cross-section plot for the Cross-section shown in Figure 5-11. ............................................................................................................................................................ 70 Figure 5-14: Example Cross-section Diagram. Default options/settings are shown. ................................ 71 Figure 5-15: Customized Cross-section Diagram. The hydraulic conductivity (K) field is shown, with red colors indicating high K and bluer colors indicating low K. ...................................................................... 71 Figure 5-16: Example 3D visualization of a model in MAGNET. ............................................................. 72 Figure 5-17: Model variables available for display in the 3D Surface Plot. ............................................... 73 Figure 5-18: Particle Pop-up menu. ............................................................................................................ 74 Figure 5-19: Example of placing particles along a polyline and performing forward particle tracking. .... 75 6 Figure 5-20: Example of placing particles in a zone and performing reverse/backward particle tracking. 76 Figure 6-1: Example of using a monitoring well to generate a concentration breakthrough curve. ........... 78 Figure 6-2: Example of using a monitoring well to visualize time-series simulated head data. ................. 78 Figure 6-3: Example Zone (water) Balance charts. Top-right:: zone budget for entire domain polygon; bottom-left: zone budget for a zone added to the model domain; bottom-right: zone budget for a single model cell. ................................................................................................................................................... 81 Figure 6-4: The 45 Degree Line Based Calibration Chart used for “manual calibration” (comparing current model outputs with observations). .................................................................................................. 83 Figure 6-5: Calibration Data window, ready for direct input of observational data. .................................. 84 Figure 6-6: Example header line and line of observation inputs. ............................................................... 84 Figure 6-7: Calibration Data window after importing observation data from a file. .................................. 84 Figure 6-8: Filter for Well Data window for importing data from the IGW server ..................................... 85 Figure 6-9: Modeling Samples vs. Calibration plot, extracted model values and residuals (relative to the observations), and chart options.................................................................................................................. 86 Figure 6-10: Scheme used for 3D Weighted interpolation of simulated head for comparison with observations. ............................................................................................................................................... 87 Figure 6-11: Example Calibration plot with Confidence intervals (red dotted line) of one standard deviation and Band-mean indicators (yellow triangles). ............................................................................. 89 Figure 6-12: Examples of residual mapping display options. ..................................................................... 90 Figure 7-1: Utilities sub-menu. ................................................................................................................... 91 Figure 7-2: Example MAGNET model file. ............................................................................................... 92 Figure 7-3: Example of publishing a model to the MAGNET network using the Model Publishing Options window. ....................................................................................................................................................... 93 Figure 7-4: MAGNET Model Network, available at www.magnet4water.com/modelnetwork/ . .............. 95 Figure 7-5: Selected model details in the MAGNET Model Network web interface. ................................ 96 Figure 7-6: Model Results and Comments page. ........................................................................................ 97 Figure 7-7: Window for editing user published models. ............................................................................. 98 Figure 7-8: 'Overlay an Image on Maps' menu. .......................................................................................... 99 7 Chapter 1 INTRODUCTION & ACCESS Understanding groundwater systems has traditionally been hampered by a lack of data - both for the analysis or characterization of the system and for conceptualizing, building, calibrating and validating numerical models. In recent times, though, the geospatial and digital revolutions have led to the availability of massive datasets such as high-resolution Digital Elevation Models (DEMs) or detailed climate information (precipitation, temperature). In spite of the availability of this “big data”, its size renders it immovable and hard to maneuver. As a result, the tools and techniques required to efficiently utilize this data have not kept pace with the rate of data “creation.” Moreover, the time required for processing the data makes it highly impractical to accomplish, especially considering that the same process must be repeated for every project. Obviously, this is an impractical way of efficiently using this data and needs improvement. 1.1 Overview of MAGNET MAGNET is a data-enabled modeling system built on pre-processed, fully-assembled framework data, i.e., data needed to conceptualize and characterize the system (e.g., DEM, recharge estimates, etc.) in a ready-to-use form at the “global scale”. Even though the data provided by the system may not completely satisfy the requirements of a particular study, it provides the vast majority of data needed to build a preliminary model. Thus, the modeler can use the “data-ready” system to refine or modify the preliminary model as desired by adding site-specific details, and also guide further data collection efforts. The system allows users not only to access and utilize pre-processed big datasets, but also to do so in real-time and interactively. Within the GIS-enabled modeling environment, users can zoom in anywhere to create a data-enabled model groundwater flow and contaminant transport, and immediately evaluate model performance using physical groundwater data available within the study area. All model inputs and representations (e.g. conceptual/structural, sources and sinks, number of layers, grid resolution, and display parameters) can be interactively modified and further customized based on study objectives and other available (local) data, as well as user experience and expertise. The users can: 1) change assumptions, conceptual framework, resolution, or representation, and immediately see the integrated effects, the ultimate implications, and the complex interrelationships presented intelligently in a meaningful context; 2) initiate or pause contaminant particle tracking or reactive plume modeling; and 3) perform well (head and concentration) monitoring and perform mass balance analyses. The MAGNET modeling environment is designed in such a way that modeler feels as though they are using a single model that provides multiple options. The process starts with a global Google Map that allows users to select an area of interest, after which a geo-referencing model is determined based on the area selected. A GIS-based interface is provided for the user to fine-tune the computational domain and to add additional data such as i) polyline or polygon data used to represent a stream/lake in the model, or ii) geo-referenced images used as a base-map for digitizing a geological formation. For example, a polyline layer could be either treated as a stream with attributes of stage, leakance and bed elevation or as an injection trench with a prescribed flux; and a polygon layer could be defined as a lake with attributes of lake level and leakance, or as a contaminant source. The remaining chapters of this User Manual explain the different functionalities of the MAGNET modeling platform. Chapter 2 overviews the MAGNET Modeling Environment and the assortment of modeling, visualization and analytical tools that are available. Chapters 3 through 6 guide users through the different 8 stages of model development and application – from model creation and parametrization, to adding conceptual features, running the simulation, and visualizing and analyzing the model results. Chapter 7 details the file function and model sharing utilities available in MAGNET. 1.2 Datasets Table 1 provides a list of datasets that are currently enabled on the modeling system. PARAMETER RESOLUTION/Data Points COVERAGE USAGE DEM 90 m Global Modeling 30 m USA 10 m USA 3 m USA* 1 m USA* Rock Top Elevation 500 m Michigan Modeling Surficial Aquifer Thickness -- Michigan, Global+ Modeling Conductivity 500 m Michigan, Global+ Modeling Recharge 1 mi Michigan Modeling/Calibration/Analysis Static Water Levels ~500 million Michigan Calibration/Analysis Soil Type 60 m USA Mapping Land Use/Land Cover 30 m USA Mapping 1.3 User Accounts All users of MAGNET must register an account, including a user name and user profile, at the Hydrosimulatics INC website: www.magnet4water.com/magnetV3.asp A palette of buttons is available along the left-side of the web interface (see Figure 2-1in next Chapter). Click the ‘Utilities’ button, then click ‘My Account’ in the submenu that appears. This launches the Account Login/Sign-up Interface (see Error! Reference source not found.). 9 Figure 1-1: Account login/sign-up interface. New users should click the green ‘Sign Up’ button to create a user name and profile with the Hydrosimulatics User Sign Up Form (see Error! Reference source not found.). Specify a username that will be provided when submitting a job to the MAGNET server (see Section 5.1) and a valid email account. Also specify a password that is needed when logging in with the provided username. Users need to provide a basic description of their job title/type and affiliation. This is done with the two drop-down menus in the User Sign Up Form. The list of different job types and different types of affiliations are shown in Figure 1-3. Next >