Technologies used in PHISHES

To learn more: MIKE ECO Lab | Ecological Modelling Software

MIKE ECO Lab is a versatile software tool that facilitates ecological modelling and environmental impact assessments across aquatic ecosystems. Tailored for simulating and analysing the intricate dynamics of marine, freshwater, and estuarine environments, it empowers users to model diverse ecological processes like nutrient cycling, primary production, and plankton dynamics. Leveraging advanced algorithms, MIKE ECO Lab accurately simulates the behaviour and distribution of organisms and chemical compounds in ecological systems and biogeochemical systems.

MIKE ECO Lab can be used for a wide range of applications including environmental impact assessments, ecosystem management, water quality modelling, and fisheries management. Its user-friendly interface and powerful modelling capabilities, enables scientists, environmental consultants, and decision-makers to assess the impact of human activities, climate change, and pollution on aquatic ecosystems, and to develop sustainable management strategies.

To learn more: AgroECO-HPM University of Copenhagen

GeoDaisy is part of the new high-performance data-driven agroecosystem modelling platform being created for Daisy. The aim of the infrastructure platform is to develop an advanced geo-referenced modelling platform (GeoDaisy) that integrates the acquisition and management of multivariate, spatio-temporal datasets, advanced data science methods, and mechanistic model simulations of water, carbon, and nutrient pools and fluxes. This includes crop production, carbon sequestration, nitrogen leaching, gaseous losses (CO₂, N2/ N₂O), and all field-relevant solutes such as pesticides and plant toxins. With automated data flows and integration with High-Performance Computing (HPC), GeoDaisy will enable detailed simulations across time and space, down to subfield resolution. 

GeoDaisy will foster cooperation across scientific fields and scales, accelerate research projects, and provide novel evaluations of the environmental impact of agricultural practices and land-use changes in Denmark and across Europe.

To learn more: PC-PROGRESS – HYDRUS 

The Hydrus software suite has become standard tools for addressing many soil, agricultural, environmental, and hydrological problems requiring the evaluation of various subsurface physical, chemical, and biological processes. Hydrus is a standalone software designed for simulating water, heat, and solute movement in 1D, 2D, or 3D variably saturated porous media. An advanced formalism of the Richards equation dealing with (constant or time-varying) boundary conditions and non-uniformity of the simulated domain is solved. conditions. These conditions can be prescribed as either pressure head or flux boundaries, as well as boundaries controlled by atmospheric conditions. During the simulation, soil surface boundary conditions may shift from prescribed flux to prescribed head-type conditions (and vice versa), accounting for infiltration, ponding, surface runoff or actual soil evaporation processes. Moreover, a special boundary condition simulating plant water uptake as a sink term with an explicit distribution of the root zone along the soil profile can be applied to the water flow equation. Hydrus software also incorporates hysteresis, assuming that scanning curves are scaled from the main drying curve and wetting curves from the main wetting curve. The code further implements a scaling procedure to approximate variability in the hydraulic properties along a soil profile using a set of linear scaling transformations. To simulate fate and transport of contaminant as well as several soil functions related to carbon and nutrient cycles or organic matter dynamics, a specific add-on of the Hydrus software suite can be used, called HPx, coupling Hydrus with PHREEQC geochemical code. Due to the flexibility of the PHREEQC code, a broad range of low-temperature (bio)-geochemical reactions can be simulated. HPx has been used to simulate the fate and transport of a broad range of contaminant in soils, including nitrogen, phosphorus, pesticides, metals and metalloids as well as emerging contaminants. A recent development of Hydrus has been also conducted for modifying Richards and advection-dispersion-reaction equations to simulate PFAS mobility in soils.

To learn more: MODFLOW 6 – USGS Modular Hydrological Models

For nearly four decades, MODFLOW has been a trusted tool among academics, private consultants, and government scientists for its accuracy, reliability, and efficiency in simulating groundwater flow. MODFLOW 6 is an object-oriented program and framework designed to support multiple models and model types within a single simulation. The “6” represents the sixth major version of MODFLOW released by the USGS, following previous versions from 1984, 1988, 1996, 2000, and 2005. MODFLOW 6 enables the inclusion of multiple models in a simulation, which can operate independently, exchange information, or be tightly coupled at the matrix level through a shared numerical solution. Information transfer between models is managed through exchange objects, enabling independent model development and use. This flexible framework supports diverse modeling approaches, such as coupling a regional-scale groundwater model with multiple local-scale models or integrating a surface-water flow model with multiple groundwater flow models.  

In the PHISHES project, conceptual models of current and future pathways involving surface water, groundwater, and the unsaturated zone in the soil will be analyzed using numerical models.  Since MODFLOW 6 has already been used for the saturated zone in the case study of Rotterdam, solute transport in this zone will be applied. However, particular attention is needed for the interaction between storage in the infiltration facility and the unsaturated zone.

Link to “learn more” : MIKE SHE | Integrated Hydrological Modelling Software

MIKE SHE is integrated catchment hydrological modelling software designed to simulate surface water and groundwater interactions in complex systems.

Developed by leading experts in the field, MIKE SHE is widely used by hydrologists, engineers, and researchers to evaluate water resources, predict flooding events, and optimise water management strategies.

It incorporates advanced algorithms to simulate rainfall-runoff processes, groundwater flow, soil moisture dynamics, and surface water routing.

By integrating these components, MIKE SHE enables users to assess the impact of various factors like land use changes, climate variability, and water management interventions on water resources and ecosystems.

Link to “learn more”: MIKE ECO Lab | Ecological Modelling Software

MIKE ECO Lab is a versatile software tool that facilitates ecological modelling and environmental impact assessments across aquatic ecosystems. Tailored for simulating and analysing the intricate dynamics of marine, freshwater, and estuarine environments, it empowers users to model diverse ecological processes like nutrient cycling, primary production, and plankton dynamics. Leveraging advanced algorithms, MIKE ECO Lab accurately simulates the behavior and distribution of organisms and chemical compounds in ecological systems and biogeochemical systems.

MIKE ECO Lab can be used for a wide range of applications including environmental impact assessments, ecosystem management, water quality modeling, and fisheries management. Its user-friendly interface and powerful modelling capabilities, enables scientists, environmental consultants, and decision-makers to assess the impact of human activities, climate change, and pollution on aquatic ecosystems, and to develop sustainable management strategies.

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The Hydrus software suite has become standard tools for addressing many soil, agricultural, environmental, and hydrological problems requiring the evaluation of various subsurface physical, chemical, and biological processes. The HYDRUS software package standalone software for simulating water, heat, and solute movement in 1D, 2D, or 3D variably saturated porous media. The program was additionally extended with many special (old and new) standard add-on modules.

The HYDRUS program numerically solves the Richards equation used to simulate variably saturated water flow in porous medium. The software can model 1D, 2D, 3D flows in complex layered systems. The program can handle flow regions delineated by irregular boundaries. The flow region, furthermore, may be composed of non-uniform layers with an arbitrary degree of local anisotropy. An advanced formalism of the Richards equation dealing with (constant or time-varying) boundary conditions is solved. The boundary conditions are prescribed either as pressure head or flux boundaries, as well as boundaries controlled by atmospheric conditions. Soil surface boundary conditions may change during the simulation from prescribed flux to prescribed head-type conditions (and vice versa), accounting for infiltration, ponding, surface runoff or actual soil evaporation processes.

The code can also handle a seepage face boundary, through which water leaves the saturated part of the flow domain, and free drainage boundary conditions. In addition, a special boundary condition simulating plant water uptake as a sink term with an explicit distribution of the root zone along the soil profile can be applied to the water flow equation. The Richards equation is highly nonlinear, soil hydraulic functions have to be used to close the equation. Several analytical functions are available (Brooks and Corey, Durner, Van Genutchen or Kosugi as well as modified Van Genutchen-type analytical that improve description of the hydraulic properties near saturation). Hydrus software also incorporates hysteresis, assuming that during scanning curves are scaled form the main drying curve and wetting curves from the main wetting curve.

The code further implements a scaling procedure to approximate variability in the hydraulic properties along a soil profile using a set of linear scaling transformations. The scaling factors can be either normally or log-normally distributed. The governing equation are solved numerically by discretizing the continuous simulated domain in several blocks (called cells). Galerkin-type linear finite element method was used to mesh the simulated domain. Integration in time is achieved using an implicit finite difference scheme. The equations are solved by linearization and subsequent Gaussian elimination for banded matrices, a conjugate gradient method for symmetric matrices or the ORTHOMIN method for asymmetric matrices. To speed up resolution time, automatic time step adjustment and conservation of the Courant and Peclet numbers within preset levels are used.

Hydrus computational modules are coupled to the PHREEQC-3 geochemical code, namely HPx. HPx is a comprehensive simulation module that can be used to simulate (1) transient water flow, (2) the transport of multiple components, including diffusion in the gas phase and exchange with the atmosphere, (3) mixed equilibrium/kinetic biogeochemical reactions, and (4) heat transport in 1D or 2D variably saturated porous media. The HPx modules can simulate a broad range of low-temperature biogeochemical reactions in water, the vadose zone, and/or groundwater systems, including interactions with minerals, gases, exchangers, and sorption surfaces based on thermodynamic equilibrium, kinetic, or mixed equilibrium/kinetic reactions. Additionally, the framework allows the use of flow and transport parameters based on the geochemical state at a given time and location in the domain.

The GIS modelling tools developed by BRGM are devoted to estimate soil contamination in urban context, notably urban soil geochemical background. These tools are needed to estimate spatial distribution of soil contamination in urban context.

These tools are devoted to a robust assessment of soil contamination in an urban context and included in a framework combining two steps. First, a preprocessing step focus on collecting and conducting a ‘data fusion’ procedure to accommodate several sources of environmental data, the propagation of QA/QC uncertainty in the estimation, taking into account the influence of scales of proxy maps (covariates, geophysical-geochemical coupling, historical databases), the development of improved algorithmics for detecting anomalous values, censored data, clustered patches of data and optimal data transformation, and many other variables.

The second step mobilize a set of interpolation algorithms, including nearest neighbour method, inverse distance weighted method, quantile random forest method, inequality kriging, EPH experimental probabilistic hypersurface and Dampster-Shafer-Belief framework and ongoing interpolation algorithms based on currently new theories. These interpolation algorithms use several available information (covariates, scales), taking into account associated uncertainties. These sets of algorithms can be used in parallel to converge towards the most robust results, i.e. spatial distribution of soil quality, justified by available information.

Link to “learn more”: MODFLOW| Trusted tool

For nearly four decades, MODFLOW has been a trusted tool among academics, private consultants, and government scientists for accurately, reliably, and efficiently simulating of groundwater flow. MODFLOW 6 is an object-oriented program and framework designed to support multiple models and model types within a single simulation (Hughes et al., 2017; Langevin et al., 2024). It is named “6” as it represents the sixth core version of MODFLOW released by the USGS, following previous versions from 1984, 1988, 1996, 2000, and 2005. MODFLOW 6 allows for the inclusion of multiple models in a simulation, which can function independently, exchange information, or be tightly coupled at the matrix level through a shared numerical solution. Information transfer between models is managed through exchange objects, enabling independent model development and use. This flexible framework supports diverse modeling approaches, such as coupling a regional-scale groundwater model with multiple local-scale models or integrating a surface-water flow model with multiple groundwater flow models.

In PHISHES refined conceptual models of current and future pathways involving surface water, groundwater, and the unsaturated zone in the soil will be analyzed using numerical models.

Since MODFLOW 6 has already been used for the saturated zone in the testcase of Rotterdam, solute transport in this zone will be applied. However, particular attention is needed for the interaction between storage in the infiltration facility and the unsaturated zone.