In this paper we describe the OpenGeoSys (OGS) project, which is a scientific open-source initiative for numerical simulation of thermo-hydro-mechanical-chemical processes in porous media. The basic ...concept is to provide a flexible numerical framework (using primarily the Finite Element Method (FEM)) for solving multifield problems in porous and fractured media for applications in geoscience and hydrology. To this purpose OGS is based on an object-oriented FEM concept including a broad spectrum of interfaces for pre- and postprocessing. The OGS idea has been in development since the mid-eighties. We provide a short historical note about the continuous process of concept and software development having evolved through Fortran, C, and C++ implementations. The idea behind OGS is to provide an open platform to the community, outfitted with professional software-engineering tools such as platform-independent compiling and automated benchmarking. A comprehensive benchmarking book has been prepared for publication. Benchmarking has been proven to be a valuable tool for cooperation between different developer teams, for example, for code comparison and validation purposes (DEVOVALEX and CO
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BENCH projects). On one hand, object-orientation (OO) provides a suitable framework for distributed code development; however, the parallelization of OO codes still lacks efficiency. High-performance-computing efficiency of OO codes is subject to future research.
We present a sensitivity analysis for infiltration excess (Hortonian) overland flow based on a classic laboratory experiment by Smith and Woolhiser Smith RE, Woolhiser DA. Overland flow on an ...infiltrating surface. Water Resour Res 1971;7(4):899–913. The model components of the compartment approach are comprised of a diffusive wave approximation to the Saint–Venant equations for overland flow, a Richards model for flow in the variably saturated zone, and an interface coupling concept that combines the two components. In the coupling scheme a hydraulic interface is introduced to allow the definition of an exchange flux between the surface and the unsaturated zone. The effects of friction processes, soil capillarity, hydraulic interface, and vertical soil discretization on both infiltration and runoff prediction are investigated in detail. The corresponding sensitivity analysis is conducted using a small-perturbation method. As a result the importance of the hydraulic processes and related parameters are evaluated for the coupled hydrosystem.
In this paper, we present a stand alone root water uptake model called aRoot, which calculates the sink term for any bulk soil water flow model taking into account water flow within and around a root ...network. The boundary conditions for the model are the atmospheric water demand and the bulk soil water content. The variable determining the plant regulation for water uptake is the soil water potential at the soil-root interface. In the current version, we present an implementation of aRoot coupled to a 3-D Richards model. The coupled model is applied to investigate the role of root architecture on the spatial distribution of root water uptake. For this, we modeled root water uptake for an ensemble (50 realizations) of root systems generated for the same species (one month old Sorghum). The investigation was divided into two Scenarios for aRoot, one with comparatively high (A) and one with low (B) root radial resistance. We compared the results of both aRoot Scenarios with root water uptake calculated using the traditional Feddes model. The vertical rooting density profiles of the generated root systems were similar. In contrast the vertical water uptake profiles differed considerably between individuals, and more so for Scenario B than A. Also, limitation of water uptake occurred at different bulk soil moisture for different modeled individuals, in particular for Scenario A. Moreover, the aRoot model simulations show a redistribution of water uptake from more densely to less densely rooted layers with time. This behavior is in agreement with observation, but was not reproduced by the Feddes model.
This paper deals with numerical modeling of density-dependent flow of saltwater intrusion in coastal groundwater systems. We present the implementation of an approach to solve a moving boundary ...problem for a dynamic water table within an invariant finite element mesh. The model is successfully validated against laboratory experiment data for an unconfined, density-dependent benchmark. The validated software is applied to a regional-scale study area and sufficiently calibrated for a steady state of pre-development conditions. Transient mass transport scenario simulations show good concordance with salinity measurements satisfyingly supporting the model setup.
CO2 capture and storage technology is often hampered by CO2 leakage through natural occurring fractures in the overlying caprock. This work suggests a two-dimensional test case of typical CO2 ...injection with possible leakage into freshwater resource. By using this test case in combination with a 1D verification example, the effects of sorption and decay processes are evaluated. Leakage value and buoyancy number reveal that buoyancy is the main mechanism for leakage, and the sorption process delays the arrival of CO2 at the fracture. The volume translated Peng-Robinson (VTPR) equation of state (EoS) has been modified for accurate material properties of CO2 and water in a multi-componential flow model.
Kurzfassung
Hydrosysteme sind komplexe Systeme, in denen eine Vielzahl von Prozessen gleichzeitig auf unterschiedlichen Raum- und Zeitskalen ablaufen. In diesem Artikel stellen wir ein ...Kompartimentkonzept zur Simulation von Stoff- und Wärmetransportprozessen in gekoppelten Hydrosystemen vor. Das Konzept beinhaltet die Kopplung von Strömungs- und Transportprozessen über die Grenzflächen der Kompartimente (oder der Prozessdomäne) unter Beibehaltung der rechentechnischen Anforderungen und Optimierungen für die numerische Lösung jedes einzelnen Prozesses. Neu ist auch die Verwendung stochastischer Partikelmethoden (random walk particle tracking – RWPT) zur Analyse von Stofftransport in gekoppelten Hydrosystemen. Wir stellen zunächst kurz die verwendete RWPT-Methode und die maßgeblichen Gleichungen für Strömung, Wärme- und Stofftransport in der gesättigten und der ungesättigten Zone sowie auf der Landoberfläche vor. Fließvorgänge werden durch (z. T. nichtlineare) Diffusionsgleichungen beschrieben (Darcy-Gleichung für Grundwasserströmung, Richards-Gleichung für Strömung in der ungesättigten Zone und diffusive Wellengleichung für Oberflächenabfluss) und über Austauschterme (Flüsse) gekoppelt. Transportprozesse werden durch Advektions-Diffusionsgleichungen beschrieben und advektiv gekoppelt. Wir stellen drei Anwendungsbeispiele für Strömungs-, Stoff- und Wärmetransportvorgänge in gekoppelten Hydrosystemen vor basierend auf Hortonschen und Dunneschen Oberflächenabflüssen sowie hyporheischen Fließvorgängen.
Omnivorous animals, including mice and humans, tend to prefer energy-dense nutrients rich in fat over plant-based diets, especially for short periods of time, but the health consequences of this ...short-term consumption of energy-dense nutrients are unclear. Here, we show that short-term reiterative switching to 'feast diets', mimicking our social eating behavior, breaches the potential buffering effect of the intestinal microbiota and reorganizes the immunological architecture of mucosa-associated lymphoid tissues. The first dietary switch was sufficient to induce transient mucosal immune depression and suppress systemic immunity, leading to higher susceptibility to Salmonella enterica serovar Typhimurium and Listeria monocytogenes infections. The ability to respond to antigenic challenges with a model antigen was also impaired. These observations could be explained by a reduction of CD4
T cell metabolic fitness and cytokine production due to impaired mTOR activity in response to reduced microbial provision of fiber metabolites. Reintroducing dietary fiber rewired T cell metabolism and restored mucosal and systemic CD4
T cell functions and immunity. Finally, dietary intervention with human volunteers confirmed the effect of short-term dietary switches on human CD4
T cell functionality. Therefore, short-term nutritional changes cause a transient depression of mucosal and systemic immunity, creating a window of opportunity for pathogenic infection.
Extreme-ultraviolet to x-ray free-electron lasers (FELs) in operation for scientific applications are up to now single-user facilities. While most FELs generate around 100 photon pulses per second, ...FLASH at DESY can deliver almost two orders of magnitude more pulses in this time span due to its superconducting accelerator technology. This makes the facility a prime candidate to realize the next step in FELs-dividing the electron pulse trains into several FEL lines and delivering photon pulses to several users at the same time. Hence, FLASH has been extended with a second undulator line and self-amplified spontaneous emission (SASE) is demonstrated in both FELs simultaneously. FLASH can now deliver MHz pulse trains to two user experiments in parallel with individually selected photon beam characteristics. First results of the capabilities of this extension are shown with emphasis on independent variation of wavelength, repetition rate, and photon pulse length.
In this paper we present an object-oriented concept for numerical simulation of multi-field problems for coupled hydrosystem analysis. Individual (flow) processes modelled by a particular partial ...differential equation, i.e. overland flow by the shallow water equation, variably saturated flow by the Richards equation and saturated flow by the groundwater flow equation, are identified with their corresponding hydrologic compartments such as land surface, vadose zone and aquifers, respectively. The object-oriented framework of the compartment approach allows an uncomplicated coupling of these existing flow models. After a brief outline of the underlying mathematical models we focus on the numerical modelling and coupling of overland flow, variably saturated and groundwater flows via exchange flux terms. As each process object is associated with its own spatial discretisation mesh, temporal time-stepping scheme and appropriate numerical solution procedure. Flow processes in hydrosystems are coupled via their compartment (or process domain) boundaries without giving up the computational necessities and optimisations for the numerical solution of each individual process. However, the coupling requires a bridging of different temporal and spatial scales, which is solved here by the integration of fluxes (spatially and temporally). In closing we present three application examples: a benchmark test for overland flow on an infiltrating surface and two case studies - at the Borden site in Canada and the Beerze-Reusel drainage basin in the Netherlands.
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