Björn Zehner

OpenGeoSys: an open-source initiative for numerical simulation of thermo-hydro-mechanical/chemical (THM/C) processes in porous media

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 CO2 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.

Visualization of gridded scalar data with uncertainty in geosciences

Characterization of the earths subsurface involves the construction of 3D models from sparse data and so leads to simulation results that involve some degree of uncertainty. This uncertainty is often neglected in the subsequent visualization, due to the fact that no established methods or available software exist. We describe a visualization method to render scalar fields with a probability density function at each data point. We render these data as isosurfaces and make use of a colour scheme, which intuitively gives the viewer an idea of which parts of the surface are more reliable than others. We further show how to extract an envelope that indicates within which volume the isosurface will lie with a certain confidence, and augment the isosurfaces with additional geometry in order to show this information. The resulting visualization is easy and intuitive to understand and is suitable for rendering multiple distinguishable isosurfaces at a time. It can moreover be easily used together with other visualized objects, such as the geological context. Finally we show how we have integrated this into a visualization pipeline that is based on the Visualization Toolkit (VTK) and the open source scenegraph OpenSG, allowing us to render the results on a desktop and in different kinds of virtual environments.

TESSIN VISLab—laboratory for scientific visualization

Scientific visualization is an integral part of the modeling workflow, enabling researchers to understand complex or large data sets and simulation results. A high-resolution stereoscopic virtual reality (VR) environment further enhances the possibilities of visualization. Such an environment also allows collaboration in work groups including people of different backgrounds and to present results of research projects to stakeholders or the public. The requirements for the computing equipment driving the VR environment demand specialized software applications which can be run in a parallel fashion on a set of interconnected machines. Another challenge is to devise a useful data workflow from source data sets onto the display system. Therefore, we develop software applications like the OpenGeoSys Data Explorer, custom data conversion tools for established visualization packages such as ParaView and Visualization Toolkit as well as presentation and interaction techniques for 3D applications like Unity. We demonstrate our workflow by presenting visualization results for case studies from a broad range of applications. An outlook on how visualization techniques can be deeply integrated into the simulation process is given and future technical improvements such as a simplified hardware setup are outlined.

A parallel finite element method for two-phase flow processes in porous media: OpenGeoSys with PETSc

In past decades, high performance computing has became a valuable tool in many fields of environmental science and technology to utilize computational power for better characterization of the complexity of environmental systems as well as predicting their evolution in time. In this work, a parallel computing technique is presented for the numerical simulation of two-phase flow processes in porous media. The Galerkin finite element method (FEM) is used to solve the initial boundary value problem arising from the underlying mathematical model. The PETSc package is utilized for parallelization of the computational task in both the global assembly of the system of linear equations and the linear solver. In order to parallelize the global assembly of the linear equation system, the overlapping domain decomposition method is used. The preset parallel FEM approach is realized within the framework of OpenGeoSys, an open source C++ finite element code for numerical simulation of thermal, hydraulic, mechanical and chemical processes in fractured porous media. The computational efficiency of the approach has been tested with three examples of increasing complexity, the five spot benchmark, dense non-aquaeous phase liquid infiltration into a inhomogeneous porous medium and a real-world application to the

A Dynamic Flow Simulation Code Intercomparison based on the Revised Static Model of the Ketzin Pilot Site

\mathrm {CO}_2

MIXING VIRTUAL REALITY AND 2D VISUALIZATION - Using Virtual Environments as Visual 3D Information Systems for Discussion of Data from Geo- and Environmental Sciences

CO2 storage research site: Ketzin, in Germany.

Interactive exploration of tensor fields in geosciences using volume rendering

3D geological underground models are often presented by vector data, such as triangulated networks representing boundaries of geological bodies and geological structures. Since models are to be used for numerical simulations based on the finite difference method, they have to be converted into a representation discretizing the full volume of the model into hexahedral cells. Often the simulations require a high grid resolution and are done using parallel computing. The storage of such a high-resolution raster model would require a large amount of storage space and it is difficult to create such a model using the standard geomodelling packages. Since the raster representation is only required for the calculation, but not for the geometry description, we present an algorithm and concept for rasterizing geological models on the fly for the use in finite difference codes that are parallelized by domain decomposition. As a proof of concept we implemented a rasterizer library and integrated it into seismic simulation software that is run as parallel code on a UNIX cluster using the Message Passing Interface. We can thus run the simulation with realistic and complicated surface-based geological models that are created using 3D geomodelling software, instead of using a simplified representation of the geological subsurface using mathematical functions or geometric primitives. We tested this set-up using an example model that we provide along with the implemented library. Graphical abstractDisplay Omitted HighlightsConverting 3D surface based geological models into 3D structured grids for simulation.Suitable for complex structural situations with diapirs, faults and overturned folds.Parallel computation - conversion is done on the fly and no limitation on grid size.Integration of the library into parallel seismic simulation software as proof of concept.3D simulation of seismic wave propagation using a model of a salt diapir as input.