IHMS—Integrated Hydrological Modelling System. Part 1. Hydrological processes and general structure

A newly Integrated Hydrological Modelling System (IHMS) has been developed to study the impact of changes in climate, land use and water management on groundwater and seawater intrusion (SWI) into coastal areas. The system represents the combination of three models, which can, if required, be run separately. It has been designed to assess the combined impact of climate, land use and groundwater abstraction changes on river, drainage and groundwater flows, groundwater levels and, where appropriate, SWI. The approach is interdisciplinary and reflects an integrated water management approach. The system comprises three packages: the Distributed Catchment Scale Model (DiCaSM), MODFLOW (96 and 2000) and SWI models. In addition to estimating all water balance components, DiCaSM, produces the recharge data that are used as input to the groundwater flow model of the US Geological Survey, MODFLOW. The latter subsequently generates the head distribution and groundwater flows that are used as input to the SWI model, SWI. Thus, any changes in land use, rainfall, water management, abstraction, etc. at the surface are first handled by DiCaSM, then by MODFLOW and finally by the SWI. The three models operate at different spatial and temporal scales and a facility (interface utilities between models) to aggregate/disaggregate input/output data to meet a desired spatial and temporal scale was developed allowing smooth and easy communication between the three models. As MODFLOW and SWI are published and in the public domain, this article focuses on DiCaSM, the newly developed unsaturated zone DiCaSM and equally important the interfacing utilities between the three models. DiCaSM simulates a number of hydrological processes: rainfall interception, evapotranspiration, surface runoff, infiltration, soil water movement in the root zone, plant water uptake, crop growth, stream flow and groundwater recharge. Input requirements include distributed data sets of rainfall, land use, soil types and digital terrain; climate data input can be either distributed or non‐distributed. The model produces distributed and time series output of all water balance components including potential evapotranspiration, actual evapotranspiration, rainfall interception, infiltration, plant water uptake, transpiration, soil water content, soil moisture (SM) deficit, groundwater recharge rate, stream flow and surface runoff. This article focuses on details of the hydrological processes and the various equations used in DiCaSM, as well as the nature of the interface to the MODFLOW and SWI models. Furthermore, the results of preliminary tests of DiCaSM are reported; these include tests related to the ability of the model to predict the SM content of surface and subsurface soil layers, as well as groundwater levels. The latter demonstrates how the groundwater recharge calculated from DiCaSM can be used as input into the groundwater model MODFLOW using aggregation and disaggregation algorithms (built into the interface utility). SWI has also been run successfully with hypothetical examples and was able to reproduce the results of some of the original examples of Bakker and Schaars ( 2005 ). In the subsequent articles, the results of applications to different catchments will be reported. Copyright © 2010 John Wiley & Sons, Ltd.     

ListingAnalyst: A Program for Analyzing the Main Output File from MODFLOW

ListingAnalyst is a Windows® program for viewing the main output file from MODFLOW‐2005, MODFLOW‐NWT, or MODFLOW‐LGR. It organizes and displays large files quickly without using excessive memory. The sections and subsections of the file are displayed in a tree‐view control, which allows the user to navigate quickly to desired locations in the files. ListingAnalyst gathers error and warning messages scattered throughout the main output file and displays them all together in an error and a warning tab. A grid view displays tables in a readable format and allows the user to copy the table into a spreadsheet. The user can also search the file for terms of interest.     

MODFLOW/MT3DMS-based simulation of variable-density ground water flow and transport

This paper presents an approach for coupling MODFLOW and MT3DMS for the simulation of variable-density ground water flow. MODFLOW routines were modified to solve a variable-density form of the ground water flow equation in which the density terms are calculated using an equation of state and the simulated MT3DMS solute concentrations. Changes to the MODFLOW and MT3DMS input files were kept to a minimum, and thus existing data files and data files created with most pre- and postprocessors can be used directly with the SEAWAT code. The approach was tested by simulating the Henry problem and two of the saltpool laboratory experiments (low- and high-density cases). For the Henry problem, the simulated results compared well with the steady-state semianalytic solution and also the transient isochlor movement as simulated by a finite-element model. For the saltpool problem, the simulated breakthrough curves compared better with the laboratory measurements for the low-density case than for the high-density case but showed good agreement with the measured salinity isosurfaces for both cases. Results from the test cases presented here indicate that the MODFLOW/MT3DMS approach provides accurate solutions for problems involving variable-density ground water flow and solute transport.     

RIPGIS-NET: a GIS tool for riparian groundwater evapotranspiration in MODFLOW

RIPGIS-NET, an Environmental System Research Institute (ESRI's) ArcGIS 9.2/9.3 custom application, was developed to derive parameters and visualize results of spatially explicit riparian groundwater evapotranspiration (ETg), evapotranspiration from saturated zone, in groundwater flow models for ecohydrology, riparian ecosystem management, and stream restoration. Specifically RIPGIS-NET works with riparian evapotranspiration (RIP-ET), a modeling package that works with the MODFLOW groundwater flow model. RIP-ET improves ETg simulations by using a set of eco-physiologically based ETg curves for plant functional subgroups (PFSGs), and separates ground evaporation and plant transpiration processes from the water table. The RIPGIS-NET program was developed in Visual Basic 2005, .NET framework 2.0, and runs in ArcMap 9.2 and 9.3 applications. RIPGIS-NET, a pre- and post-processor for RIP-ET, incorporates spatial variability of riparian vegetation and land surface elevation into ETg estimation in MODFLOW groundwater models. RIPGIS-NET derives RIP-ET input parameters including PFSG evapotranspiration curve parameters, fractional coverage areas of each PFSG in a MODFLOW cell, and average surface elevation per riparian vegetation polygon using a digital elevation model. RIPGIS-NET also provides visualization tools for modelers to create head maps, depth to water table (DTWT) maps, and plot DTWT for a PFSG in a polygon in the Geographic Information System based on MODFLOW simulation results.     

Improving Groundwater Model Calibration with Repeat Microgravity Measurements

Groundwater-flow models depend on hydraulic head and flux observations for evaluation and calibration. A different type of observation—change in storage measured using repeat microgravity—can also be used for parameter estimation by simulating the expected change in gravity from a groundwater model and including the observation misfit in the objective function. The method is demonstrated using new software linked to MODFLOW input and output files and field data from the vicinity of the All American Canal in southeast California, USA. Over a 10-year period following lining of the previously highly permeable canal with concrete, gravity decreased by over 100 μGal (equivalent to about 2.5 m of free-standing water) at some locations as seepage decreased and the remnant groundwater mound dissipated into the aquifer or was removed by groundwater pumping. Simulated gravity from a MODFLOW model closely matched observations, and repeat microgravity data proved useful for constraining both hydraulic conductivity and specific yield estimates. Specific yield estimated using the infinite-horizontal slab approximation agreed well with model-derived values, and the departure from the linear, flat-water-table approximation was small, less than 2%, despite relatively large and dynamic water-table slope. First-order second-moment parameter uncertainty analysis shows reduction in uncertainty for all hydraulic conductivity and specific yield parameter estimates with the addition of repeat microgravity data, as compared to drawdown data alone.     

SFRmaker and Linesink-Maker: Rapid Construction of Streamflow Routing Networks from Hydrography Data

Groundwater models have evolved to encompass more aspects of the water cycle, but the incorporation of realistic boundary conditions representing surface water remains time-consuming and error-prone. We present two Python packages that robustly automate this process using readily available hydrography data as the primary input. SFRmaker creates input for the MODFLOW SFR package, while Linesink-maker creates linesink string input for the GFLOW analytic element program. These programs can reduce weeks or even months of manual effort to a few minutes of execution time, and carry the added advantages of reduced potential for error, improved reproducibility and facilitation of step-wise modeling through reduced dependency on a particular conceptual model or discretization. Two real-world examples at the county to multi-state scales are presented.     

Spatial Periodic Boundary Condition for MODFLOW

Small‐scale hyporheic zone (HZ) models often use a spatial periodic boundary (SPB) pair to simulate an infinite repetition of bedforms. SPB's are common features of commercially available multiphysics modeling packages. MODFLOW's lack of this boundary type has precluded it from being effectively utilized in this area of HZ research. We present a method to implement the SPB in MODFLOW by development of the appropriate block‐centered finite‐difference expressions. The implementation is analogous to MODFLOW's general head boundary package. The difference is that the terms on the right hand side of the solution equations must be updated with each iteration. Consequently, models that implement the SPB converge best with solvers that perform both inner and outer iterations. The correct functioning of the SPB condition in MODFLOW is verified by two examples. This boundary condition allows users to build HZ‐bedform models in MODFLOW, facilitating further research using related codes such as MT3DMS and PHT3D.     

Effect of elevation resolution on evapotranspiration simulations using MODFLOW

Surface elevations represented in MODFLOW head-dependent packages are usually derived from digital elevation models (DEMs) that are available at much high resolution. Conventional grid refinement techniques to simulate the model at DEM resolution increases computational time, input file size, and in many cases are not feasible for regional applications. This research aims at utilizing the increasingly available high resolution DEMs for effective simulation of evapotranspiration (ET) in MODFLOW as an alternative to grid refinement techniques. The source code of the evapotranspiration package is modified by considering for a fixed MODFLOW grid resolution and for different DEM resolutions, the effect of variability in elevation data on ET estimates. Piezometric head at each DEM cell location is corrected by considering the gradient along row and column directions. Applicability of the research is tested for the lower Rio Grande (LRG) Basin in southern New Mexico. The DEM at 10 m resolution is aggregated to resampled DEM grid resolutions which are integer multiples of MODFLOW grid resolution. Cumulative outflows and ET rates are compared at different coarse resolution grids. Results of the analysis conclude that variability in depth-to-groundwater within the MODFLOW cell is a major contributing parameter to ET outflows in shallow groundwater regions. DEM aggregation methods for the LRG Basin have resulted in decreased volumetric outflow due to the formation of a smoothing error, which lowered the position of water table to a level below the extinction depth.     

Generating MODFLOW grids from boundary representation solid models

Complex stratigraphy can be difficult to simulate in MODFLOW models. MODFLOW uses a structured grid that requires that each grid layer be continuous throughout the model domain. This makes it difficult to explicitly represent common features such as pinchouts and embedded seams in a MODFLOW model. In this paper, we describe a method for automatically generating MODFLOW-compatible grids from boundary-representation solid models. Solid models are data structures developed originally for computer-aided design applications that define the geometry of three-dimensional objects. Solid models can be used to represent arbitrarily complex stratigraphy. The elevations defined by the solids are then extracted from the solids in a manner that preserves the continuous-layer requirement imposed by MODFLOW. Two basic approaches are described: The first method adjusts the MODFLOW grid dimensions (layer elevations) to fit the solid model boundaries, and the second method creates a regular MODFLOW grid and adjusts the material properties to match the changes in stratigraphy. One of the main benefits of using solid models to define stratigraphy for MODFLOW models is that it provides a grid-independent definition of the layer elevations that can be used to immediately re-create the MODFLOW grid geometry after any change to the grid resolution.     

MODFLOW 2000 head uncertainty,a first-order second moment method

A computationally efficient method to estimate the variance and covariance in piezometric head results computed through MODFLOW 2000 using a first-order second moment (FOSM) approach is presented. This methodology employs a first-order Taylor series expansion to combine model sensitivity with uncertainty in geologic data. MODFLOW 2000 is used to calculate both the ground water head and the sensitivity of head to changes in input data. From a limited number of samples, geologic data are extrapolated and their associated uncertainties are computed through a conditional probability calculation. Combining the spatially related sensitivity and input uncertainty produces the variance-covariance matrix, the diagonal of which is used to yield the standard deviation in MODFLOW 2000 head. The variance in piezometric head can be used for calibrating the model, estimating confidence intervals, directing exploration, and evaluating the reliability of a design. A case study illustrates the approach, where aquifer transmissivity is the spatially related uncertain geologic input data. The FOSM methodology is shown to be applicable for calculating output uncertainty for (1) spatially related input and output data, and (2) multiple input parameters (transmissivity and recharge).     

Field Test of a Hybrid Finite‐Difference and Analytic Element Regional Model

Regional finite‐difference models often have cell sizes that are too large to sufficiently model well‐stream interactions. Here, a steady‐state hybrid model is applied whereby the upper layer or layers of a coarse MODFLOW model are replaced by the analytic element model GFLOW, which represents surface waters and wells as line and point sinks. The two models are coupled by transferring cell‐by‐cell leakage obtained from the original MODFLOW model to the bottom of the GFLOW model. A real‐world test of the hybrid model approach is applied on a subdomain of an existing model of the Lake Michigan Basin. The original (coarse) MODFLOW model consists of six layers, the top four of which are aggregated into GFLOW as a single layer, while the bottom two layers remain part of MODFLOW in the hybrid model. The hybrid model and a refined “benchmark” MODFLOW model simulate similar baseflows. The hybrid and benchmark models also simulate similar baseflow reductions due to nearby pumping when the well is located within the layers represented by GFLOW. However, the benchmark model requires refinement of the model grid in the local area of interest, while the hybrid approach uses a gridless top layer and is thus unaffected by grid discretization errors. The hybrid approach is well suited to facilitate cost‐effective retrofitting of existing coarse grid MODFLOW models commonly used for regional studies because it leverages the strengths of both finite‐difference and analytic element methods for predictions in mildly heterogeneous systems that can be simulated with steady‐state conditions.     

Simulating ground water-lake interactions: approaches and insights

Approaches for modeling lake-ground water interactions have evolved significantly from early simulations that used fixed lake stages specified as constant head to sophisticated LAK packages for MODFLOW. Although model input can be complex, the LAK package capabilities and output are superior to methods that rely on a fixed lake stage and compare well to other simple methods where lake stage can be calculated. Regardless of the approach, guidelines presented here for model grid size, location of three-dimensional flow, and extent of vertical capture can facilitate the construction of appropriately detailed models that simulate important lake-ground water interactions without adding unnecessary complexity. In addition to MODFLOW approaches, lake simulation has been formulated in terms of analytic elements. The analytic element lake package had acceptable agreement with a published LAKI problem, even though there were differences in the total lake conductance and number of layers used in the two models. The grid size used in the original LAKI problem, however, violated a grid size guideline presented in this paper. Grid sensitivity analyses demonstrated that an appreciable discrepancy in the distribution of stream and lake flux was related to the large grid size used in the original LAKI problem. This artifact is expected regardless of MODFLOW LAK package used. When the grid size was reduced, a finite-difference formulation approached the analytic element results. These insights and guidelines can help ensure that the proper lake simulation tool is being selected and applied.     

Contamination Assessment and Site-Management Tool (CAST): A Browser-Based Tool for Site Assessment

Groundwater dependency is increasing globally, while millions of potentially contaminated sites are yet to be characterized for contamination levels. In particular, groundwater contamination due to light nonaqueous phase liquids (LNAPLs) continues to be a global challenge. Mathematical approaches (i.e., analytical, semi-analytical, empirical, numerical) are preferred for an initial site assessment to circumvent the high characterization costs and limited site data availability. However, the site-specific nature of contamination restricts the generalization of any single approach. Hence, the requirement is for an easy-to-use computing interface that provides site-specific data management, the selection and use of multiple-model interfaces for computing, and site characterization, with extension for the latest models as they become available. This work provides one such interface called CAST or Contamination Assessment and Site-management Tool. CAST is an open-source browser-based (online/offline) tool that provides an interface for six different analytical models (e.g., BIOSCREEN-AT), a MODFLOW based numerical model, and two empirical models (including a hybrid numerical-analytical model). Additionally, CAST includes interfaces for site data management, their evaluation, and scenario-based modeling. CAST's development is in a modular format, which simplifies the addition of new computing or data interfaces. Furthermore, the entire code-base of CAST is based on open-source (dominantly Python programming) libraries and standards. This further simplifies the modification or extension of this tool. This paper introduces CAST, its different computing, and data management interfaces and provides examples of the tool's functionality primarily for the initial evaluation of contaminated sites.     

MODFLOW as a Configurable Multi-Model Hydrologic Simulator

MODFLOW 6 is the latest in a line of six “core” versions of MODFLOW released by the U.S. Geological Survey. The MODFLOW 6 architecture supports incorporation of additional hydrologic processes, in addition to groundwater flow, and allows interaction between processes. The architecture supports multiple model instances and multiple types of models within a single simulation, a flexible approach to formulating and solving the equations that represent hydrologic processes, and recent advances in interoperability, which allow MODFLOW to be accessed and controlled by external programs. The present version of MODFLOW 6 consolidates popular capabilities available in MODFLOW variants, such as the unstructured grid support in MODFLOW-USG, the Newton-Raphson formulation in MODFLOW-NWT, and the support for partitioned stress boundaries in MODFLOW-CDSS. The flexible multi-model capability allows users to configure MODFLOW 6 simulations to represent the local-grid refinement (LGR) capabilities available in MODFLOW-LGR, the multi-species transport capabilities in MT3DMS, and the coupled variable-density capabilities available in SEAWAT. This paper provides a new, holistic and integrated overview of simulation capabilities made possible by the MODFLOW 6 architecture, and describes how ongoing and future development can take advantage of the program architecture to integrate new capabilities in a way that is minimally invasive and automatically compatible with the existing MODFLOW 6 code.     

Fast transport simulation with an adaptive grid refinement

One of the main difficulties in transport modeling and calibration is the extraordinarily long computing times necessary for simulation runs. Improved execution time is a prerequisite for calibration in transport modeling. In this paper we investigate the problem of code acceleration using an adaptive grid refinement, neglecting subdomains, and devising a method by which the Courant condition can be ignored while maintaining accurate solutions. Grid refinement is based on dividing selected cells into regular subcells and including the balance equations of subcells in the equation system. The connection of coarse and refined cells satisfies the mass balance with an interpolation scheme that is implicitly included in the equation system. The refined subdomain can move with the average transport velocity of the subdomain. Very small time steps are required on a fine or a refined grid, because of the combined effect of the Courant and Peclet conditions. Therefore, we have developed a special upwind technique in small grid cells with high velocities (velocity suppression). We have neglected grid subdomains with very small concentration gradients (zero suppression). The resulting software, MODCALIF, is a three-dimensional, modularly constructed FORTRAN code. For convenience, the package names used by the well-known MODFLOW and MT3D computer programs are adopted, and the same input file structure and format is used, but the program presented here is separate and independent. Also, MODCALIF includes algorithms for variable density modeling and model calibration. The method is tested by comparison with an analytical solution, and illustrated by means of a two-dimensional theoretical example and three-dimensional simulations of the variable-density Cape Cod and SALTPOOL experiments. Crossing from fine to coarse grid produces numerical dispersion when the whole subdomain of interest is refined; however, we show that accurate solutions can be obtained using a fraction of the execution time required by uniformly fine-grid solutions.     

A Hybrid Finite-Difference and Analytic Element Groundwater Model

Regional finite-difference models tend to have large cell sizes, often on the order of 1–2 km on a side. Although the regional flow patterns in deeper formations may be adequately represented by such a model, the intricate surface water and groundwater interactions in the shallower layers are not. Several stream reaches and nearby wells may occur in a single cell, precluding any meaningful modeling of the surface water and groundwater interactions between the individual features. We propose to replace the upper MODFLOW layer or layers, in which the surface water and groundwater interactions occur, by an analytic element model (GFLOW) that does not employ a model grid; instead, it represents wells and surface waters directly by the use of point-sinks and line-sinks. For many practical cases it suffices to provide GFLOW with the vertical leakage rates calculated in the original coarse MODFLOW model in order to obtain a good representation of surface water and groundwater interactions. However, when the combined transmissivities in the deeper (MODFLOW) layers dominate, the accuracy of the GFLOW solution diminishes. For those cases, an iterative coupling procedure, whereby the leakages between the GFLOW and MODFLOW model are updated, appreciably improves the overall solution, albeit at considerable computational cost. The coupled GFLOW–MODFLOW model is applicable to relatively large areas, in many cases to the entire model domain, thus forming an attractive alternative to local grid refinement or inset models.     

A New Package in MODFLOW to Simulate Unconfined Groundwater Flow in Sloping Aquifers

The nonhorizontal‐model‐layer (NHML) grid system is more accurate than the horizontal‐model‐layer grid system to describe groundwater flow in an unconfined sloping aquifer on the basis of MODFLOW‐2000. However, the finite‐difference scheme of NHML was based on the Dupuit‐Forchheimer assumption that the streamlines were horizontal, which was acceptable for slope less than 0.10. In this study, we presented a new finite‐difference scheme of NHML based on the Boussinesq assumption and developed a new package SLOPE which was incorporated into MODFLOW‐2000 to become the MODFLOW‐SP model. The accuracy of MODFLOW‐SP was tested against solution of Mac Cormack (1969). The differences between the solutions of MODFLOW‐2000 and MODFLOW‐SP were nearly negligible when the slope was less than 0.27, and they were noticeable during the transient flow stage and vanished in steady state when the slope increased above 0.27. We established a model considering the vertical flow using COMSOL Multiphysics to test the robustness of constrains used in MODFLOW‐SP. The results showed that streamlines quickly became parallel with the aquifer base except in the narrow regions near the boundaries when the initial flow was not parallel to the aquifer base. MODFLOW‐SP can be used to predict the hydraulic head of an unconfined aquifer along the profile perpendicular to the aquifer base when the slope was smaller than 0.50. The errors associated with constrains used in MODFLOW‐SP were small but noticeable when the slope increased to 0.75, and became significant for the slope of 1.0.