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ModelMuse Version 4: A graphical user interface for MODFLOW 6

ModelMuse, a graphical user interface for groundwater-modeling software, was modified to support MODFLOW 6. ModelMuse works with two types of spatial discretization in MODFLOW 6: structured grids (DIS) and discretization by vertices (DISV). Quadtree refinement is used to generate a DISV model from a structured-grid model. The locations and weights for ghost nodes used to improve DISV model accuracy are computed automatically by ModelMuse using a new algorithm. ModelMuse does not support other types of DISV grids and unstructured grids. ModelMuse supports options in MODFLOW 6 that designate individual cells as confined or convertible and remove inactive cells associated with discontinuous layers, thereby reducing the computational burden. ModelMuse can specify fully three-dimensional (3D), spatially variable anisotropy in hydraulic conductivity. Although MODFLOW 6 does not support the parameters supported by MODFLOW–2005, ModelMuse provides backward compatibility by allowing ModelMuse parameters to specify scale-factor variables in MODFLOW 6 time-series files within packages that support time-series files. ModelMuse can automatically convert the data for many of the packages from other MODFLOW models to the new data for these packages in MODFLOW 6. Some packages, such as the Streamflow-Routing (SFR) package, changed significantly enough that only a partial conversion is possible. Head and flow observations in older models are also converted to observation locations in the MODFLOW 6 Observation utility. ModelMuse accommodates the ability of MODFLOW 6 to store specific discharge components by allowing the user to visualize the components of a specific discharge on the model grid. ModelMuse supports the versions of MODPATH and ZONEBUDGET compatible with MODFLOW 6.

Scientific Investigations Report↗

Hydrogeology and model-simulated groundwater availability in the Salt Fork Red River aquifer, southwestern Oklahoma, 1980–2015

The 1973 Oklahoma Water Law (82 OK Stat § 82-1020.5) requires that the Oklahoma Water Resources Board (OWRB) conduct hydrologic investigations of the State’s groundwater basins to support a determination of the maximum annual yield for each groundwater basin (hereinafter referred to as an “aquifer”). The maximum annual yield allocated per acre of land is known as the equal-proportionate-share (EPS) pumping rate. At present (2021), the OWRB has not yet established a maximum annual yield and EPS pumping rate for the Salt Fork Red River aquifer. To provide updated information to the OWRB that could support evaluation and determination of an appropriate maximum annual yield, the U.S. Geological Survey (USGS), in cooperation with the OWRB, conducted a hydrologic investigation and evaluated the effects of potential groundwater withdrawals on groundwater availability in the Salt Fork Red River aquifer. The Salt Fork Red River aquifer in Greer, Harmon, and Jackson Counties of southwestern Oklahoma is composed of about 274.5 square miles of alluvium and terrace deposits associated with the Salt Fork Red River. The mean annual recharge rate to the Salt Fork Red River aquifer for the period 1980–2015 was estimated to be about 2.94 inches per year, or 10.0 percent of the mean annual precipitation for the same period (29.4 inches per year). This 1980–2015 mean annual recharge rate is equivalent to a mean annual recharge rate of about 38,000 acre-feet per year (acre-ft/yr) for the Salt Fork Red River aquifer excluding about 19,764 acres comprising the Mulberry Creek and Horse Creek terraces. The mean annual recharge rates upgradient and downgradient from USGS streamgage 07300500 Salt Fork Red River at Mangum, Okla. (hereinafter referred to as the “Mangum gage”), apportioned by aquifer area (41.5 and 58.5 percent, respectively), were about 16,000 and 22,000 acre-ft/yr, respectively. Mean annual groundwater use for the study period (1980–2015) was 3,532.7 acre-ft/yr; about 77 percent of that groundwater use was for irrigation, and about 23 percent was for public supply. Most groundwater use for irrigation was associated with wells in the Martha terrace. A hydrogeologic framework was developed for the Salt Fork Red River aquifer and included a definition of the aquifer extent and potentiometric surface, as well as a description of the textural and hydraulic properties of aquifer materials. The hydrogeologic framework was used in the construction of the numerical groundwater-flow model of the Salt Fork Red River aquifer described in this report. A conceptual model for the Salt Fork Red River aquifer that reasonably represents the groundwater-flow system was developed to constrain the construction and calibration of the numerical model. The conceptual-model water budget estimated mean annual inflows to, and outflows from, the Salt Fork Red River aquifer for the period 1980–2015 and included a subaccounting of mean annual inflows and outflows for the portions of the aquifer that were upgradient and downgradient from the Mangum gage. The numerical groundwater-flow model of the Salt Fork Red River aquifer was constructed by using MODFLOW-2005 with the Newton formulation solver. The model of the Salt Fork Red River aquifer was spatially discretized into 1,050 rows, 1,125 columns, about 170,000 active cells measuring 200 by 200 feet (ft), and a single convertible layer. The model was temporally discretized into 432 monthly transient stress periods (each with two time steps to improve model stability). An initial steady-state stress period represented mean annual inflows to, and outflows from, the aquifer and produced a solution that was used as the initial condition for subsequent transient stress periods as well as some groundwater-availability scenarios. The model was calibrated to water-table-altitude observations at selected wells and base-flow observations at selected streamgages. The simulated saturated thickness of the Salt Fork Red River aquifer was determined by subtracting the altitude of the aquifer base from the simulated water-table altitude at the end of the numerical-model period (2015). The simulated saturated thickness was more than 75 ft in a paleochannel in the Dodson terrace near the Texas border. The mean aquifer thickness (sum of saturated and unsaturated) was 49.62 ft, and the mean saturated thickness was 28.55 ft. A simulated mean transmissivity of 1,024 feet squared per day was computed from the calibrated hydraulic conductivity and saturated thickness of each cell. The simulated available water in storage at the end of the numerical-model period (2015) was 526,117 acre-feet (acre-ft); about 42 percent of that total was available upgradient from the Mangum gage, and about 58 percent of that total was available downgradient from the Mangum gage (including the Mangum terrace). Three types of groundwater-availability scenarios were run using the calibrated numerical model. These scenarios were used to (1) estimate the EPS pumping rate that ensures a minimum 20-, 40-, and 50-year life of the aquifer, (2) quantify the potential effects of projected well withdrawals on groundwater storage over a 50-year period, and (3) simulate the potential effects of a hypothetical 10-year drought on base flow and groundwater storage. The 20-, 40-, and 50-year EPS pumping rates under normal recharge conditions were about 0.51, 0.48, and 0.48 acre-foot per acre per year, respectively. Given the 155,929-acre modeled aquifer area, these rates correspond to annual yields of about 78,800, 74,900, and 74,700 acre-ft/yr, respectively. For the 20-year EPS scenario, decreasing and increasing recharge by 10 percent resulted in a 6-percent change in the EPS pumping rate in both cases; for the 40- and 50-year EPS scenarios, decreasing and increasing recharge by 10 percent resulted in a 7-percent change in the EPS pumping rate in both cases. Projected 50-year pumping scenarios were used to simulate the effects of selected well withdrawal rates on groundwater storage of the Salt Fork Red River aquifer and base flows in the Salt Fork Red River. The effects of well withdrawals were evaluated by quantifying differences in groundwater storage and base flow in four 50-year scenarios, which applied (1) no groundwater pumping, (2) mean pumping rates for the study period (1980–2015), (3) 2015 pumping rates, and (4) increasing demand pumping rates at simulated wells. The increasing demand pumping rates assumed a cumulative 20.4-percent increase in pumping over 50 years based on 2010–60 demand projections for southwestern Oklahoma. Groundwater storage after 50 years with no pumping was 535,000 acre-ft, or 8,900 acre-ft (1.7 percent) greater than the initial groundwater storage; this groundwater storage increase is equivalent to a mean water-table-altitude increase of 0.48 ft. Groundwater storage after 50 years of pumping at the mean rate for the study period (1980–2015) was 519,900 acre-ft, or 6,200 acre-ft (1.2 percent) less than the initial groundwater storage; this groundwater storage decrease is equivalent to a mean water-table-altitude decline of 0.34 ft. Groundwater storage at the end of the 50-year period with 2015 pumping rates was 513,100 acre-ft, or 13,000 acre-ft (2.5 percent) less than the initial storage; this groundwater storage decrease is equivalent to a mean water-table-altitude decline of 0.71 ft. Groundwater storage at the end of the 50-year period with increasing demand pumping rates was 509,700 acre-ft, or 16,500 acre-ft (3.1 percent) less than the initial storage; this groundwater storage decrease is equivalent to a mean water-table-altitude decline of 0.89 ft. A hypothetical 10-year drought scenario was used to simulate the effects of a prolonged period of reduced recharge on groundwater storage. The period January 1983–December 1992 was chosen as the simulated drought period. Drought effects were quantified by comparing the results of the drought scenario to those of the calibrated numerical model (no drought) at the end of the simulated drought period (1992). To simulate the hypothetical drought, recharge in the calibrated numerical model was reduced by 50 percent during the simulated drought period (1983–92). Upstream inflows from the Salt Fork Red River, Turkey Creek, and Bitter Creek were reduced by 75 percent. Groundwater storage at the end of the drought period (1992) was 479,200 acre-ft, or 53,200 acre-ft (10.0 percent) less than the groundwater storage of the calibrated numerical model at the end of the drought period. This decrease in groundwater storage is equivalent to a mean water-table-altitude decline of 2.9 ft. At the end of the 10-year hypothetical drought period, simulated base flows at the Mangum gage and USGS streamgage 07301110 Salt Fork Red River near Elmer, Okla., had decreased by about 80 and 70 percent, respectively.

Oklahoma↗

Simulation of groundwater budgets and travel times for watersheds on the north shore of Long Island Sound, with implications for nitrogen-transport studies

Aquatic systems in and around the Long Island Sound (LIS) provide a variety of ecological and economic benefits, but in some areas of the LIS, aquatic ecosystems have become degraded by excess nitrogen. A substantial fraction of the nitrogen inputs to the LIS are transported through the groundwater-flow system. Because groundwater travel times in surficial aquifers can exceed 100 years, multiyear lags are introduced between inputs at the water table in recharge areas and discharge to inland or coastal receiving waters. The U.S. Geological Survey, in cooperation with the Connecticut Department of Energy and Environmental Protection and the U.S. Environmental Protection Agency’s Long Island Sound Study, developed a steady-state groundwater model of the watersheds draining from the northern shore of the LIS for the purpose of calculating groundwater budgets and travel times to coastal waters. The model was developed by using the MODFLOW–NWT software and existing spatial data on aquifers, river networks, land-surface altitudes, land cover, groundwater recharge, and water use. Coastal waters were delineated on the basis of the National Wetland Inventory; all non-coastal waters were collectively termed “inland waters.” A coarse-resolution model was calibrated by using the PEST++ software, long-term records of water levels in 65 wells, stream altitudes from 477 streams, base-flow records for 14 streamgages that are relatively unaffected by withdrawals, and error metrics based on incorrectly simulated flooding and incorrectly simulated dry streams. The calibrated values were used in a fine-resolution model in which the mean absolute residuals were 4.5 meters for groundwater levels, 1.3 meters for stream altitudes, and 7,200 cubic meters per day (2.9 cubic feet per second) for base flow. About 89 percent of the terrestrial cells were correctly simulated with the water table below land surface, and nearly 90 percent of the cells representing streams were correctly simulated as having the water table above the stream bottom. Together, these metrics suggest that this model is robust for simulating regional-scale groundwater patterns. Simulated groundwater budgets were compiled for the entire study area, for each HUC12 (Hydrologic Unit Code no. 12) watershed and its adjacent coastal waters, if applicable, within the study area, and for 14 coastal-embayment watersheds. Most groundwater (90.6 percent of inflows) discharged to inland waters, with smaller fractions to coastal waters (7.0 percent) and well withdrawals (2.4 percent). When computed for HUC12 watersheds with coastal discharge, the portions of groundwater discharging to coastal waters ranged from 0.02 to 66 percent of groundwater outflows, with a median of 13 percent. Within priority-embayment watersheds, the portions of groundwater discharging to coastal waters ranged from 2 to 56 percent, with a median of 15 percent. Groundwater travel times also were simulated for the entire study area, for each HUC12 watershed and its adjacent coastal waters, if applicable, within the study area and for 14 priority coastal embayments. Within the entire study area, the median groundwater travel time was 1.9 years, with an interquartile range of 0.1 to 5.9 years. Sensitivity analysis of groundwater travel times within a subbasin in the study area indicates that the travel times are a function of the grid resolution, with coarser grids resulting in shorter median travel times. Travel times for groundwater discharging to coastal waters were similar to travel times for groundwater discharging to inland waters, with a median of 1.9 years. Median travel times for the HUC12 watersheds ranged from 0.9 to 53.5 years, with a median of 1.8 years. Among HUC12 watersheds that include coastal areas, travel times for groundwater discharging to coastal waters ranged from less than 1 to 61.6 years, with a median of 2.8 years. The HUC12 watersheds with the longest simulated travel times were in the urban area near New York City where the model performance is less accurate. Median travel times for groundwater discharging to coastal waters within the priority-embayment watersheds ranged from less than 1 to 18.6 years, with a median of 2.3 years. A more focused analysis was conducted for the Niantic River watershed to demonstrate the applicability of the regional model to local-scale nitrogen-transport analyses by using nitrogen-input and -attenuation rates from literature sources. Nitrogen inputs were estimated by using land-cover-based loading factors, and attenuation was estimated by using attenuation factors based on geologic zones and soil properties. Based on this analysis, groundwater transports an estimated 22,000 kilograms of nitrogen per year (2.9 kilograms of nitrogen per hectare per year) to streams, rivers, and coastal waters within the Niantic River watershed. Approximately 36 percent of discharging nitrogen is from atmospheric-deposition sources, 38 percent is from fertilizers, and 26 percent is from septic systems. Most of the groundwater-transported nitrogen (88 percent) discharges first to streams and rivers, with only 12 percent discharging directly to coastal waters. Travel times for groundwater-transported nitrogen ranged from less than 1 day to more than 100 years, with a median of 1.6 years.

Connecticut, New York, Rhode Island↗

Groundwater model of the Harney Basin, southeastern Oregon

Groundwater development, mainly for large-scale irrigation, has increased substantially in the Harney Basin of southeastern Oregon since 2010. Concurrently, some areas of the basin experienced groundwater-level declines of more than 100 feet, and some shallow wells have gone dry. The Oregon Water Resources Department has limited new groundwater development in the basin until an improved understanding of the groundwater-flow system is available. The groundwater resources report by Gingerich and others (2022, U.S. Geological Survey Scientific Investigations Report 2021–5103, https://doi.org/10.3133/sir20215103 ) provides that understanding. This report describes the development of a numerical groundwater-flow model that can be used as a tool to help improve that understanding. The Harney Basin Groundwater Model was developed using the finite-difference groundwater-modeling software U.S. Geological Survey modular finite-difference groundwater-flow model (MODFLOW 6) and associated Python pre- and post-processing routines. The groundwater model encompasses the entire 5,240-square-mile Harney Basin and adjacent areas and is calibrated to the hydrologic conditions from 1930 to 2018. The model has a uniform grid consisting of 78,064 nearly square cells, each covering 2,005 by 2,007 feet (about 92 acres) and has 10 layers (780,640 total cells) representing the vertical distribution of hydrogeologic units. The results from the calibrated model simulations indicate that groundwater pumpage exceeded recharge since about the mid-1980s, resulting in an estimated net cumulative depletion of groundwater storage (discharge minus recharge) of about 840,000 acre-feet and also indicated declines in groundwater evapotranspiration and spring and stream discharge. Model simulations show as much as 100 feet of groundwater-level decline in some areas and more than 40 feet of decline in widespread areas in recent decades. Model simulations are consistent with field observations of groundwater levels through time.

Oregon↗

Numerical model of the groundwater-flow system near the southeastern part of Puget Sound, Washington

Groundwater flow in the active model area (AMA) was simulated using a groundwater-flow model. A steady-state model version of the model simulates equilibrium conditions, and a transient model version simulates monthly variability. The model corresponds to the physical and temporal dimensions of the conceptual model and groundwater budget. The steady-state model version represents average conditions for an 11-year period (January 1, 2005–December 31, 2015), and the transient model represents monthly hydrologic variability within that period. The 13-layer model was constructed using MODFLOW-NWT with a uniformly spaced grid consisting of 416 rows, 433 columns, and cells with a horizontal dimension of 500 feet (ft) on a side. The model was calibrated to measured values of water levels in wells and lakes and estimated base flow for selected streamflow measurement stations, commonly referred to as streamgages. Model calibration was accomplished using a combination of manual and automatic methods, including the Model-Independent Parameter Estimation (PEST) program that adjusted model input parameters with the aim of minimizing the difference between estimated and model-simulated values of hydraulic head and base flow. Model boundary conditions consist of all simulated groundwater inflow to and outflow from the AMA. For example, a stream reach that simulates a gain from or loss to groundwater is a boundary condition that allows water to exit or enter, respectively, the groundwater system. Other boundary conditions include springs, seeps, precipitation recharge, groundwater exchange with lakes and Puget Sound, and groundwater pumping. A comparison of the estimated groundwater budget to that simulated by the steady-state model version indicates that the relative percentages of total inflow or total outflow for six major categories of boundary conditions are similar for the two budgets. The model was used to simulate three suites of scenarios of potential drought and water-use changes. Scenario 1 suite consisted of the steady-state model version that was run with 0, 15, 20, and 25 percent reduction of precipitation recharge to assess the corresponding reductions in base flow with decreasing recharge. The last simulation for the scenario 1 suite consisted of the transient model version simulating 3 years of consecutive seasonal drought, defined by the months of May through September, to assess the corresponding base-flow reductions. Scenario 2 suite consisted of the steady-state model version with all simulated groundwater use removed, compared with a simulation that includes current groundwater use to evaluate changes to potentiometric surfaces and base flows. Scenario 3 suite consisted of a transient model version of the model that simulated pumping increases for four different categories of water-supply wells (compared to no pumping increases) to evaluate resulting reductions in base flow. Although, these scenarios provide examples of model applications and useful insights, many other scenarios could be simulated. A description of how to download the model is described in the body of this report. Uncertainty is associated with most model inputs. Groundwater levels, lake levels, and land-surface altitudes are relatively certain; other model inputs are far less certain, including precipitation recharge, base flow, hydraulic properties, water use, and the three-dimensional structure of subsurface hydrogeologic units. Models are useful not because of high levels of accuracy of all model inputs, but because they combine the best information and estimates available, thereby providing the best predictions available related to physical processes. The model described in this report simulates groundwater flow on a regional scale, which has inherent limitations for simulating hydrologic scenarios at local scales. Model structures and inputs were generalized to be consistent with this regional scale. For example, the actual groundwater system has much greater heterogeneity of hydraulic conductivity than is possible within the model’s degrees of freedom. Variations in hydraulic gradients over distances less than 500 ft cannot be simulated. The distances between model features, such as a pumping well and a stream, must be placed at 500-ft intervals and are co-located if both features are within the same model cell.

Washington↗

Phytoplankton responses to experimental nitrogen and phosphorus loading in the eutrophic and colored Caloosahatchee River, Florida

The Caloosahatchee River, located in southwest Florida, is a eutrophic and colored river that flows from Lake Okeechobee westward into its estuary and the Gulf of America. Cyanobacterial harmful algal blooms (HABs) are a documented problem along this freshwater-to-marine waterway where nutrient enrichment has been identified as a key factor in bloom occurrence but has not been experimentally tested in the river. This study is the first to test the effects of inorganic nutrient loading on phytoplankton assemblages in the Caloosahatchee River and the effects of different nutrient sources on phytoplankton dynamics at different times of the year. Three independent, in situ experiments were conducted to test the effects of daily, incrementally increased ammonium, nitrate, and phosphate loading on phytoplankton at different times of the year (summer, fall, winter). Over the 72-hour enclosure period, phytoplankton abundance metrics (cell concentration, chlorophyll- a , and phycocyanin), dissolved oxygen, and pH increased, and fluorescent dissolved organic matter and turbidity decreased in all treatments and controls. Increased phytoplankton abundance metrics relative to controls were observed after 72 hours of exposure to elevated ammonium and nitrate in summer and only ammonium in winter, suggesting periodic nitrogen limitation; however, no treatment effects on phytoplankton assemblage structure in terms of resemblance and diversity metrics were found. Increases in total cell concentrations were driven by elevated growth rates of already dominant taxa but not sufficiently to form a visible bloom. Cyanobacteria consistently dominated the phytoplankton, particularly Aphanocapsa and Merismopedia , whereas the common HAB-forming Microcystis maintained consistently low abundance. This study provides new information on the ecology of phytoplankton assemblages in the Caloosahatchee River and could be used by water resources managers to evaluate strategies for controlling cyanobacterial HABs in the river.

Florida↗

Duttonite, a new quadrivalent vanadium oxide from the Peanut mine, Montrose County, Colorado

Duttonite, a new quadrivalent vanadium oxide from the Peanut mine, Montrose County, Colo., has the formula VO(OH) 2 . The mineral occurs as crusts and coatings of pale-brown transparent platy crystals, as one of the first oxidation products of montroseite ore. It is associated with melanovanadite and abundant crystals of hexagonal native selenium. Duttonite is biaxial positive, 2V is about 60°, dispersion is r < v , moderate; X = a , pale pinkish brown; Y = c , pale yellow-brown; Z = b , pale brown; α = 1.810 ± 0.003, β = 1.900 ± 0.003, γ > 2.01. The hardness is about 2.5; the calculated specific gravity is 3.24. The chemical analysis shows, in percent: V 2 o 3 2.6, V 2 O 4 75.3, FeO 0.4, H 2 O 18.1, insoluble 4.2, total 100.6. Duttonite is monoclinic, a o = 8.80 ± 0.02A, b o - 3.95 ± 0.01A, c o - 5.96 ± 0.02A, β = 90°40 1 ± 5 1 . The space group is I 2/ c , ( C 6 2 h ); the cell contents are 4[VO(OH) 2 ]. The crystals are strongly pseudo-orthorhombic, and the structure departs only slightly from the space group Imcm . Duttonite is named for Captain Clarence Edward Dutton (1841-1912). A detailed study of the geology, geochemistry, and mineralogy of the vanadium-uranium ore at the Peanut mine, Montrose County, Colo., was begun early in 1954 by Carl H. Roach of the U. S. Geological Survey. A number of rare and new minerals were found in the ore and the study of these samples was undertaken by Mary E. Thompson. Duttonite is the first new vanadium mineral to be described from the Peanut mine. It is named for Captain Clarence Edward Dutton (1841-1912), who was one of the first geologists to work in the Colorado Plateau region and who was a member of the U. s. Geological Survey from 1879-91. We are indebted to the following members of the Geological Surbey: K. E. Valentine for spectrographic analyses of duttonite, and M. E. Mrose and H. T. Evans, Jr., for measurement of the unit cell constants. This work is part of a program being conducted by the U. S. Geological Survey on behalf of the Division of Raw Materials of the U. S. Atomic Energy Commission.

Colorado↗

User guide for the farm process (FMP1) for the U.S. Geological Survey's modular three-dimensional finite-difference ground-water flow model, MODFLOW-2000

There is a need to estimate dynamically integrated supply-and-demand components of irrigated agriculture as part of the simulation of surface-water and ground-water flow. To meet this need, a computer program called the Farm Process (FMP1) was developed for the U.S. Geological Survey three-dimensional finite-difference modular ground-water flow model, MODFLOW- 2000 (MF2K). The FMP1 allows MF2K users to simulate conjunctive use of surface- and ground water for irrigated agriculture for historical and future simulations, water-rights issues and operational decisions, nondrought and drought scenarios. By dynamically integrating farm delivery requirement, surface- and ground-water delivery, as well as irrigation-return flow, the FMP1 allows for the estimation of supplemental well pumpage. While farm delivery requirement and irrigation return flow are simulated by the FMP1, the surface-water delivery to the farm can be simulated optionally by coupling the FMP1 with the Streamflow Routing Package (SFR1) and the farm well pumping can be simulated optionally by coupling the FMP1 to the Multi-Node Well (MNW) Package. In addition, semi-routed deliveries can be specified that are associated with points of diversion in the SFR1 stream network. Nonrouted surface-water deliveries can be specified independently of any stream network. The FMP1 maintains a dual mass balance of a farm budget and as part of the ground-water budget. Irrigation demand, supply, and return flow are in part subject to head-dependent sources and sinks such as evapotranspiration from ground water and leakage between the conveyance system and the aquifer. Farm well discharge and farm net recharge are source/sink terms in the FMP1, which depend on transpiration uptake from ground water and other head dependent consumptive use components. For heads rising above the bottom of the root zone, the actual transpiration is taken to vary proportionally with the depth of the active root zone, which can be restricted by anoxia or wilting. Depths corresponding to anoxia- or wilting-related pressure heads within the root zone are found using analytical solutions of a vertical pseudo steady-state pressure- head distribution over the depth of the total root zone (Consumptive Use Concept 1). Alternatively, a simpler, conceptual model is available, which defines how consumptive use (CU) components vary with changing head (CU Concept 2). Subtracting the ground water and precipitation transpiration components from the total transpiration yields a transpiratory irrigation requirement for each cell. The total farm delivery requirement (TFDR) then is determined as cumulative transpiratory and evaporative irrigation requirements of all farm cells and increased sufficiently to compensate for inefficient use from irrigation with respect to plant consumption. The TFDR subsequently is satisfied with surface- and ground-water delivery, respectively constrained by allotments, water rights, or maximum capacities. Five economic and noneconomic drought response policies can be applied optionally, if the potential supply of surface water and ground water is insufficient to meet the crop demand: acreage-optimization with or without a water conservation pool, deficit irrigation with or without water-stacking, and zero policy.

Techniques and Methods↗

MODFLOW-NWT, a Newton formulation for MODFLOW-2005

This report documents a Newton formulation of MODFLOW-2005, called MODFLOW-NWT. MODFLOW-NWT is a standalone program that is intended for solving problems involving drying and rewetting nonlinearities of the unconfined groundwater-flow equation. MODFLOW-NWT must be used with the Upstream-Weighting (UPW) Package for calculating intercell conductances in a different manner than is done in the Block-Centered Flow (BCF), Layer Property Flow (LPF), or Hydrogeologic-Unit Flow (HUF; Anderman and Hill, 2000) Packages. The UPW Package treats nonlinearities of cell drying and rewetting by use of a continuous function of groundwater head, rather than the discrete approach of drying and rewetting that is used by the BCF, LPF, and HUF Packages. This further enables application of the Newton formulation for unconfined groundwater-flow problems because conductance derivatives required by the Newton method are smooth over the full range of head for a model cell. The NWT linearization approach generates an asymmetric matrix, which is different from the standard MODFLOW formulation that generates a symmetric matrix. Because all linear solvers presently available for use with MODFLOW-2005 solve only symmetric matrices, MODFLOW-NWT includes two previously developed asymmetric matrix-solver options. The matrix-solver options include a generalized-minimum-residual (GMRES) Solver and an Orthomin / stabilized conjugate-gradient (CGSTAB) Solver. The GMRES Solver is documented in a previously published report, such that only a brief description and input instructions are provided in this report. However, the CGSTAB Solver (called X MD) is documented in this report. Flow-property input for the UPW Package is designed based on the LPF Package and material-property input is identical to that for the LPF Package except that the rewetting and vertical-conductance correction options of the LPF Package are not available with the UPW Package. Input files constructed for the LPF Package can be used with slight modification as input for the UPW Package. This report presents the theory and methods used by MODFLOW-NWT, including the UPW Package. Additionally, this report provides comparisons of the new methodology to analytical solutions of groundwater flow and to standard MODFLOW-2005 results by use of an unconfined aquifer MODFLOW example problem. The standard MODFLOW-2005 simulation uses the LPF Package with the wet/dry option active. A new example problem also is presented to demonstrate MODFLOW-NWT's ability to provide a solution for a difficult unconfined groundwater-flow problem.

Techniques and Methods↗

Documentation of the Surface-Water Routing (SWR1) Process for modeling surface-water flow with the U.S. Geological Survey Modular Ground-Water Model (MODFLOW-2005)

A flexible Surface-Water Routing (SWR1) Process that solves the continuity equation for one-dimensional and two-dimensional surface-water flow routing has been developed for the U.S. Geological Survey three-dimensional groundwater model, MODFLOW-2005. Simple level- and tilted-pool reservoir routing and a diffusive-wave approximation of the Saint-Venant equations have been implemented. Both methods can be implemented in the same model and the solution method can be simplified to represent constant-stage elements that are functionally equivalent to the standard MODFLOW River or Drain Package boundary conditions. A generic approach has been used to represent surface-water features (reaches) and allows implementation of a variety of geometric forms. One-dimensional geometric forms include rectangular, trapezoidal, and irregular cross section reaches to simulate one-dimensional surface-water features, such as canals and streams. Two-dimensional geometric forms include reaches defined using specified stage-volume-area-perimeter (SVAP) tables and reaches covering entire finite-difference grid cells to simulate two-dimensional surface-water features, such as wetlands and lakes. Specified SVAP tables can be used to represent reaches that are smaller than the finite-difference grid cell (for example, isolated lakes), or reaches that cannot be represented accurately using the defined top of the model. Specified lateral flows (which can represent point and distributed flows) and stage-dependent rainfall and evaporation can be applied to each reach. The SWR1 Process can be used with the MODFLOW Unsaturated Zone Flow (UZF1) Package to permit dynamic simulation of runoff from the land surface to specified reaches. Surface-water/groundwater interactions in the SWR1 Process are mathematically defined to be a function of the difference between simulated stages and groundwater levels, and the specific form of the reach conductance equation used in each reach. Conductance can be specified directly or calculated as a function of the simulated wetted perimeter and defined reach bed hydraulic properties, or as a weighted combination of both reach bed hydraulic properties and horizontal hydraulic conductivity. Each reach can be explicitly coupled to a single specific groundwater-model layer or coupled to multiple groundwater-model layers based on the reach geometry and groundwater-model layer elevations in the row and column containing the reach. Surface-water flow between reservoirs is simulated using control structures. Surface-water flow between reaches, simulated by the diffusive-wave approximation, can also be simulated using control structures. A variety of control structures have been included in the SWR1 Process and include (1) excess-volume structures, (2) uncontrolled-discharge structures, (3) pumps, (4) defined stage-discharge relations, (5) culverts, (6) fixed- or movable-crest weirs, and (7) fixed or operable gated spillways. Multiple control structures can be implemented in individual reaches and are treated as composite flow structures. Solution of the continuity equation at the reach-group scale (a single reach or a user-defined collection of individual reaches) is achieved using exact Newton methods with direct solution methods or exact and inexact Newton methods with Krylov sub-space methods. Newton methods have been used in the SWR1 Process because of their ability to solve nonlinear problems. Multiple SWR1 time steps can be simulated for each MODFLOW time step, and a simple adaptive time-step algorithm, based on user-specified rainfall, stage, flow, or convergence constraints, has been implemented to better resolve surface-water response. A simple linear- or sigmoid-depth scaling approach also has been implemented to account for increased bed roughness at small surface-water depths and to increase numerical stability. A line-search algorithm also has been included to improve the quality of the Newton-step upgrade vector, if possible. The SWR1 Process has been benchmarked against one- and two-dimensional numerical solutions from existing one- and two-dimensional numerical codes that solve the dynamic-wave approximation of the Saint-Venant equations. Two-dimensional solutions test the ability of the SWR1 Process to simulate the response of a surface-water system to (1) steady flow conditions for an inclined surface (solution of Manning's equation), and (2) transient inflow and rainfall for an inclined surface. The one-dimensional solution tests the ability of the SWR1 Process to simulate a looped network with multiple upstream inflows and several control structures. The SWR1 Process also has been compared to a level-pool reservoir solution. A synthetic test problem was developed to evaluate a number of different SWR1 solution options and simulate surface-water/groundwater interaction. The solution approach used in the SWR1 Process may not be applicable for all surface-water/groundwater problems. The SWR1 Process is best suited for modeling long-term changes (days to years) in surface-water and groundwater flow. Use of the SWR1 Process is not recommended for modeling the transient exchange of water between streams and aquifers when local and convective acceleration and other secondary effects (for example, wind and Coriolis forces) are substantial. Dam break evaluations and two-dimensional evaluations of spatially extensive domains are examples where acceleration terms and secondary effects would be significant, respectively.

Techniques and Methods↗

User guide for MODPATH version 6—A particle-tracking model for MODFLOW

MODPATH is a particle-tracking post-processing model that computes three-dimensional flow paths using output from groundwater flow simulations based on MODFLOW, the U.S. Geological Survey (USGS) finite-difference groundwater flow model. This report documents MODPATH version 6. Previous versions were documented in USGS Open-File Reports 89-381 and 94-464. The program uses a semianalytical particle-tracking scheme that allows an analytical expression of a particle's flow path to be obtained within each finite-difference grid cell. A particle's path is computed by tracking the particle from one cell to the next until it reaches a boundary, an internal sink/source, or satisfies another termination criterion. Data input to MODPATH consists of a combination of MODFLOW input data files, MODFLOW head and flow output files, and other input files specific to MODPATH. Output from MODPATH consists of several output files, including a number of particle coordinate output files intended to serve as input data for other programs that process, analyze, and display the results in various ways. MODPATH is written in FORTRAN and can be compiled by any FORTRAN compiler that fully supports FORTRAN-2003 or by most commercially available FORTRAN-95 compilers that support the major FORTRAN-2003 language extensions.

Techniques and Methods↗

Two graphical user interfaces for managing and analyzing MODFLOW groundwater-model scenarios

Scenario Manager and Scenario Analyzer are graphical user interfaces that facilitate the use of calibrated, MODFLOW-based groundwater models for investigating possible responses to proposed stresses on a groundwater system. Scenario Manager allows a user, starting with a calibrated model, to design and run model scenarios by adding or modifying stresses simulated by the model. Scenario Analyzer facilitates the process of extracting data from model output and preparing such display elements as maps, charts, and tables. Both programs are designed for users who are familiar with the science on which groundwater modeling is based but who may not have a groundwater modeler’s expertise in building and calibrating a groundwater model from start to finish. With Scenario Manager, the user can manipulate model input to simulate withdrawal or injection wells, time-variant specified hydraulic heads, recharge, and such surface-water features as rivers and canals. Input for stresses to be simulated comes from user-provided geographic information system files and time-series data files. A Scenario Manager project can contain multiple scenarios and is self-documenting. Scenario Analyzer can be used to analyze output from any MODFLOW-based model; it is not limited to use with scenarios generated by Scenario Manager. Model-simulated values of hydraulic head, drawdown, solute concentration, and cell-by-cell flow rates can be presented in display elements. Map data can be represented as lines of equal value (contours) or as a gradated color fill. Charts and tables display time-series data obtained from output generated by a transient-state model run or from user-provided text files of time-series data. A display element can be based entirely on output of a single model run, or, to facilitate comparison of results of multiple scenarios, an element can be based on output from multiple model runs. Scenario Analyzer can export display elements and supporting metadata as a Portable Document Format file.

Techniques and Methods↗

MT3D-USGS version 1: A U.S. Geological Survey release of MT3DMS updated with new and expanded transport capabilities for use with MODFLOW

MT3D-USGS, a U.S. Geological Survey updated release of the groundwater solute transport code MT3DMS, includes new transport modeling capabilities to accommodate flow terms calculated by MODFLOW packages that were previously unsupported by MT3DMS and to provide greater flexibility in the simulation of solute transport and reactive solute transport. Unsaturated-zone transport and transport within streams and lakes, including solute exchange with connected groundwater, are among the new capabilities included in the MT3D-USGS code. MT3D-USGS also includes the capability to route a solute through dry cells that may occur in the Newton-Raphson formulation of MODFLOW (that is, MODFLOW-NWT). New chemical reaction Package options include the ability to simulate inter-species reactions and parent-daughter chain reactions. A new pump-and-treat recirculation package enables the simulation of dynamic recirculation with or without treatment for combinations of wells that are represented in the flow model, mimicking the above-ground treatment of extracted water. A reformulation of the treatment of transient mass storage improves conservation of mass and yields solutions for better agreement with analytical benchmarks. Several additional features of MT3D-USGS are (1) the separate specification of the partitioning coefficient ( K d ) within mobile and immobile domains; (2) the capability to assign prescribed concentrations to the top-most active layer; (3) the change in mass storage owing to the change in water volume now appears as its own budget item in the global mass balance summary; (4) the ability to ignore cross-dispersion terms; (5) the definition of Hydrocarbon Spill-Source Package (HSS) mass loading zones using regular and irregular polygons, in addition to the currently supported circular zones; and (6) the ability to specify an absolute minimum thickness rather than the default percent minimum thickness in dry-cell circumstances. Benchmark problems that implement the new features and packages test the accuracy of new code through comparison to analytical benchmarks, as well as to solutions from other published codes. The input file structure for MT3D-USGS adheres to MT3DMS conventions for backward compatibility: the new capabilities and packages described herein are readily invoked by adding three-letter package name acronyms to the name file or by setting input flags as needed. Memory is managed in MT3D-USGS using FORTRAN modules in order to simplify code development and expansion.

Techniques and Methods↗

T-COMP — A suite of programs for extracting transmissivity from MODFLOW models

Simulated transmissivities are constrained poorly by assigning permissible ranges of hydraulic conductivities from aquifer-test results to hydrogeologic units in groundwater-flow models. These wide ranges are derived from interpretations of many aquifer tests that are categorized by hydrogeologic unit. Uncertainty is added where contributing thicknesses differ between field estimates and numerical models. Wide ranges of hydraulic conductivities and discordant thicknesses result in simulated transmissivities that frequently are much greater than aquifer-test results. Multiple orders of magnitude differences frequently occur between simulated and observed transmissivities where observed transmissivities are less than 1,000 feet squared per day. Transmissivity observations from individual aquifer tests can constrain model calibration as head and flow observations do. This approach is superior to diluting aquifer-test results into generalized ranges of hydraulic conductivities. Observed and simulated transmissivities can be compared directly with T-COMP, a suite of three FORTRAN programs. Transmissivity observations require that simulated hydraulic conductivities and thicknesses in the volume investigated by an aquifer test be extracted and integrated into a simulated transmissivity. Transmissivities of MODFLOW model cells are sampled within the volume affected by an aquifer test as defined by a well-specific, radial-flow model of each aquifer test. Sampled transmissivities of model cells are averaged within a layer and summed across layers. Accuracy of the approach was tested with hypothetical, multiple-aquifer models where specified transmissivities ranged between 250 and 20,000 feet squared per day. More than 90 percent of simulated transmissivities were within a factor of 2 of specified transmissivities.

Nevada↗

Probabilistic methodology for the assessment of original and recoverable coal resources, illustrated with an application to a coal bed in the Fort Union Formation, Wyoming

Executive Summary The U.S. Geological Survey (USGS) has been using its Circular 891 for evaluating uncertainty in coal resource assessments for more than 35 years. Calculated cell tonnages are assigned to four qualitative reliability classes depending exclusively on distance to the nearest drill hole. The main appeal of this methodology, simplicity, is also its main drawback. Reliability may depend so marginally on distance to the nearest drill hole that, over time, it has become evident that Circular 891 is inadequate for modeling reliability and is limited by other shortcomings. The present publication describes the use of geostatistics as an approach allowing a more satisfactory performance than that which is achieved following Circular 891. Geostatistics takes advantage of partly random and partly organized fluctuations in attributes such as coal thickness, coal density, and elevation of the top of a coal bed, borrowing concepts and tools that have been standard features in statistics and risk analysis for decades. Considering that readers interested in this study may not have the background to go directly into the details of the methodology, we start by explaining geostatistical concepts and modeling techniques. The remainder of the publication is devoted to formulating the assessment methodology, applying it to data from the Fillmore Ranch coal bed in the Fort Union Formation in Wyoming, and explaining the computer software applied for performing calculations and displays. The assessment methodology has been designed to report three different forms of resources: coal in place, coal mineable by surface mining methods, and coal mineable by underground mining methods. These three types of resources are reported graphically by displaying both the magnitude and the reliability of total coal resources and resources at the cell scale. In the case of the Fillmore Ranch coal bed example, there is a 90-percent probability that the resources in place are 9.687 ± 0.383 billion short tons (bst), while the coal available for underground mining is 2.279 ± 0.160 bst, and that available for surface mining is only 0.240 ± 0.025 bst because of the steep dip to the west away from the outcrop. These magnitudes are derived from numerical probability distributions not following any specific form.

Wyoming↗

Assessment of freshwater mussels in the Allegheny River at Foxburg, Pennsylvania, 1998

The upper reaches of the Allegheny River are a high-quality resource that supports populations of a number of endangered species. Two endangered species of freshwater mussel, the northern riffleshell, Epioblasma torulosa rangiana , and clubshell, Pleurobema clava , are present in this river reach. Prior to a bridge-replacement project at the Allegheny River at Foxburg, Pa. (river mile 86.2), a mussel survey was conducted to determine if either of the protected endangered species are present and to assess the quality of the mussel bed at this site. Shore and near-shore searches followed by SCUBA diving transects determined that a mussel bed is present at this location. The freshwater-mussel community consists of at least 14 species and includes both endangered species. Substrate type, stream velocity, and channel morphology combined with results from the transect searches documented that the mussel bed is largely limited to the east side of the river. A two-stage sampling design was employed to estimate the overall mussel abundance within the bed. Twelve 4-m 2 (square meter) cells were sampled with four 0.25-m 2 quadrants per cell. The mean population density within the mussel bed is 8.4 mussel per square meter. The overall mussel population in the survey area is 225,567 individuals (95-percent confidence interval, 135,973 to 374,195). River-bed scour and acid mine drainage appear to limit mussel distribution in the center and left section of the channel. Overall, a healthy and diverse mussel bed exists at this site.

Water-Resources Investigations Report↗

Characterization and simulation of ground-water flow in the Kansas River Valley at Fort Riley, Kansas, 1990-98

Hydrologic data and a ground-water flow model were used to characterize ground-water flow in the Kansas River alluvial aquifer at Fort Riley in northeast Kansas. The ground-water flow model was developed as a tool to project ground-water flow and potential contaminant-transport paths in the alluvial aquifer on the basis of past hydrologic conditions. The model also was used to estimate historical and hypothetical ground-water flow paths with respect to a private- and several public-supply wells. The ground-water flow model area extends from the Smoky Hill and Republican Rivers downstream to about 2.5 miles downstream from the city of Ogden. The Kansas River Valley has low relief and, except for the area within the Fort Riley Military Reservation, is used primarily for crop production. Sedimentary deposits in the Kansas River Valley, formed after the ancestral Kansas River eroded into bedrock, primarily are alluvial sediment deposited by the river during Quaternary time. The alluvial sediment consists of as much as about 75 feet of poorly sorted, coarse-to-fine sand, silt, and clay, 55 feet of which can be saturated with ground water. The alluvial aquifer is unconfined and is bounded on the sides and bottom by Permian-age shale and limestone bedrock. Hydrologic data indicate that ground water in the Kansas River Valley generally flows in a downstream direction, but flow direction can be quite variable near the Kansas River due to changes in river stage. Ground-water-level changes caused by infiltration of precipitation are difficult to detect because they are masked by larger changes caused by fluctuation in Kansas River stage. Ratios of strontium isotopes Sr87 and Sr86 in water collected from wells in the Camp Funston Area indicate that the ground water along the northern valley wall originates, in part, from upland areas north of the river valley. Water from Threemile Creek, which flows out of the uplands north of the river valley, had Sr87:Sr86 ratios similar to those in ground water from wells in the northern Camp Funston Area. In addition, comparison of observed water levels from wells CF90-06, CF97-101, and CF97-401 in the Camp Funston Area and ground-water levels simulated for these wells using floodwave-response analysis indicates that ground-water inflow from bedrock is a hydraulic stress that, in addition to the changing stage in the Kansas River, acts on the aquifer. This hydraulic stress seems to be located near the northern valley wall because the effect of this stress is greater for well CF97-101, which is the well closest to the valley wall. Ground-water flow was simulated using a modular, three-dimensional, finite-difference ground-water flow model (MODFLOW). Particle tracking, used to visualize ground-water flow paths in the alluvial aquifer, was accomplished using MODPATH. Forward-in-time particle tracking indicated that, in general, particles released near the Kansas River followed much more variable paths than particles released near the valley wall. Although particle tracking does not simulate solute transport, this increased path variability indicates that, near the river, ground-water contaminants could follow many possible paths towards the river, whereas more distant from the river, ground-water contaminants likely would follow a narrower corridor. Particle tracks in the Camp Funston Area indicate that, for the 1990-98 simulation period, contaminants from the ground-water study sites in the Camp Funston Area would be unlikely to move into the vicinity of Ogden's supply wells. Backward-in-time particle tracking indicated that the flow-path and recharge areas for model cells corresponding to Ogden's supply wells lie near the northern valley wall and extend into the northern Camp Funston Area. The flow-path and recharge areas for model cells corresponding to Morris County Rural Water District wells lie within Clarks Creek Valley and probably extend outside the model area. Three hypothetical simulations, i

Water-Resources Investigations Report↗

Quality-assurance design applied to an assessment of agricultural pesticides in ground water from carbonate bedrock aquifers in the Great Valley of eastern Pennsylvania

Assessments to determine whether agricultural pesticides are present in ground water are performed by the Commonwealth of Pennsylvania under the aquifer monitoring provisions of the State Pesticides and Ground Water Strategy. Pennsylvania's Department of Agriculture conducts the monitoring and collects samples; the Department of Environmental Protection (PaDEP) Laboratory analyzes the samples to measure pesticide concentration. To evaluate the quality of the measurements of pesticide concentration for a groundwater assessment, a quality-assurance design was developed and applied to a selected assessment area in Pennsylvania. This report describes the quality-assurance design, describes how and where the design was applied, describes procedures used to collect and analyze samples and to evaluate the results, and summarizes the quality assurance results along with the assessment results. The design was applied in an agricultural area of the Delaware River Basin in Berks, Lebanon, Lehigh, and Northampton Counties to evaluate the bias and variability in laboratory results for pesticides. The design—with random spatial and temporal components—included four data-quality objectives for bias and variability. The spatial design was primary and represented an area comprising 30 sampling cells. A quality-assurance sampling frequency of 20 percent of cells was selected to ensure a sample number of five or more for analysis. Quality-control samples included blanks, spikes, and replicates of laboratory water and spikes, replicates, and 2-lab splits of groundwater. Two analytical laboratories, the PaDEP Laboratory and a U.S. Geological Survey Laboratory, were part of the design. Bias and variability were evaluated by use of data collected from October 1997 through January 1998 for alachlor, atrazine, cyanazine, metolachlor, simazine, pendimethalin, metribuzin, and chlorpyrifos. Results of analyses of field blanks indicate that collection, processing, transport, and laboratory analysis procedures did not contaminate the samples; there were no false-positive results. Pesticides were detected in water when pesticides were spiked into (added to) samples. There were no false negatives for the eight pesticides in all spiked samples. Negative bias was characteristic of analytical results for the eight pesticides, and bias was generally in excess of 10 percent from the ‘true’ or expected concentration (34 of 39 analyses, or 87 percent of the ground-water results) for pesticide concentrations ranging from 0.31 to 0.51 mg/L (micrograms per liter). The magnitude of the negative bias for the eight pesticides, with the exception of cyanazine, would result in reported concentrations commonly 75-80 percent of the expected concentration in the water sample. The bias for cyanazine was negative and within 10 percent of the expected concentration. A comparison of spiked pesticide-concentration recoveries in laboratory water and ground water indicated no effect of the ground-water matrix, and matrix interference was not a source of the negative bias. Results for the laboratory-water spikes submitted in triplicate showed large variability for recoveries of atrazine, cyanazine, and pendimethalin. The relative standard deviation (RSD) was used as a measure of method variability over the course of the study for laboratory waters at a concentration of 0.4 mg/L. An RSD of about 11 percent (or about ?0.05 mg/L)characterizes the method results for alachlor, chlorpyrifos, metolachlor, metribuzin, and simazine. Atrazine and pendimethalin have RSD values of about 17 and 23 percent, respectively. Cyanazine showed the largest RSD at nearly 51 percent. The pesticides with low variability in laboratory-water spikes also had low variability in ground water. The assessment results showed that atrazinewas the most commonly detected pesticide in ground water in the assessment area. Atrazine was detected in water from 22 of the 28 wells sampled, and recovery results for atrazine were some of the worst (largest negative bias). Concentrations of the eight pesticides in ground water from wells were generally less than 0.3 µg/L. Only six individual measurements of the concentrations in water from six of the wells were at or above 0.3 µg/L, five for atrazine and one for metolachlor. There were eight additional detections of metolachlor and simazine at concentrations less than 0.1 µg/L. No well water contained more than one pesticide at concentra-tions at or above 0.3 µg/L. Evidence exists, how-ever, for a pattern of co-occurrence of metolachlor and simazine at low concentrations with higher concentrations of atrazine. Large variability in replicate samples and negative bias for pesticide recovery from spiked samples indicate the need to use data for pesticide recovery in the interpretation of measured pesti-cide concentrations in ground water. Data from samples spiked with known amounts of pesticides were a critical component of a quality-assurance design for the monitoring component of the Pesti-cides and Ground Water Strategy. Trigger concentrations, the concentrations that require action under the Pesticides and Ground Water Strategy, should be considered maximums for action. This consideration is needed because of the magnitude of negative bias.

Water-Resources Investigations Report↗