HydroBioGeoChem123D Input Guide, release 1.1

About HydroBioGeoChem123D (HBGC123D)

HBGC123D is a computer code for the simulation of coupled non-isothermal hydrologic transport and biogeochemical kinetic and/or equilibrium reactions in variably saturated media. HBGC123D iteratively solves the 1-, 2-, or 3-dimensional heat transfer equations, transport equations, and the ordinary differential and algebraic equations of mixed biogeochemical reactions. The transport equations are solved for all aqueous chemical components and kinetically controlled species. A Lagrangian-Eulerian finite element method is used to solve the heat transfer and transport equations. The computer code accommodates hexahedral (6 faces), pentahedral (5 faces), and tetrahedral (4 faces) elements in three-dimensional domains, quadrilateral (4 sides) and triangular (3 sides) elements in two-dimensional domains, and line elements in one-dimensional domains. The Newton-Raphson method is used to solve the biogeochemical system of equations.

HBGC123D is designed for generic applications to reactive transport problems in subsurface media that are affected by microbiological and geochemical reactions. Input to the program includes the geometry of the media, the spatial distribution of finite elements and nodes, the properties of the media, the possible chemical and microbial reactions, and the initial and boundary conditions. The output includes the spatial distribution of chemical and microbial concentrations as a function of time and space, and the chemical speciation at user-specified nodes.

HBGC123D is also a high-performance computer code that utilizes the multiprocessor power of today's parallel computers. In the early design phase, we realized that there are needs to increase the speed of a multiprocessor code such as HBGC123D. HBGC123D 1.1 has been rigorously tested on SGI shared-memory multiprocessor workstations, PC's running Linux, other UNIX workstations, and Windows 95/NT PC's. Work is currently under way to include distributed-memory platforms such as the IBM SP and workstation clusters. These improvements will be available in subsequent releases.

HydroBioGeoChem(postscript||pdf), a two-dimensional code and the predecessor of HBGC123D, was developed by Dr. Karen Salvage, Dr. George Yeh, and their co-workers at the Pennsylvania State University. HBGC123D is the multidimensional and enhanced release of HydroBioGeoChem by the Oak Ridge National Laboratory (ORNL). The development of HBGC123D is one of the tasks supporting the DOE Environmental Technology Partnership Initiative project Influence of Coupled Processes on the Fate and Transport of Industrial Mixed Waste Plumes in Structured Media. In conjunction with field scale multitracer injection, a three-dimensional computer model of the field site at Waste Area Grouping 5, ORNL is being developed. HBGC123D is being used to study the coupled, multiscale (laboratory undisturbed soil columns to the field site) processes of microbiology and subsurface multicomponent reactive transport.

Acknowledgement

This work is funded by the Environmental Technology Partnership program of the US Department of Energy (DOE). The development team is especially grateful to the guidance of Dr. Paul Bayer in the Office of Biological and Environmental Research of the US DOE Office of Science. This work is also partially supported by the ORNL Partnership in Computational Sciences (PICS) program, supported by the Department of Energy's Mathematical, Information, and Computational Sciences (MICS) Division of the Office of Computational and Technology Research. Implementation of the microbial kinetics and geochemical kinetics into HydroBioGeoChem (two-dimensional) code was supported by The Department of Energy, Battelle Pacific Northwest Laboratory. This implementation is under the guidance of Dr. Frank Wobber, also at the US DOE Office of Biological and Environmental Research. The present version of HydroBioGeoChem123D reflects the many contributions made by an army of colleagues from the Civil and Environmental Engineering Department at the Pennsylvania State University, the Oak Ridge Institute for Science and Education, and the Computer Science and Mathematics Division, the Computer Science and Mathematics Division, and the Environmental Sciences Division of Oak Ridge National Laboratory.

Release Notes

• Density effects on heat transfer and transport caused by biogeochemical speciation and species concentration variations are not accounted for in this release.
• For the Microsoft Windows 95/98/NT precompiled executable, hbgc123d.exe, a Pentium PC or above with at least 32 MB of memory is recommended. For other memory constraints due to hardware configuration and problem size, it is advisable that the source be downloaded and recompiled.
• For efficient computer memory use, the user is recommended to adjust the total number of array elements allocated to dmem(dmemdim) and imem(imemdim) in the header file memcom.h. The number of elements in these two arrays that are used for the current problem is always reported on the screen and near the top of the ASCII output file.
• Version 1.1 allows the user to input a time series profile for velocities and water contents, e.g. when flow interrupts were performed during a laboratory column experiment.
• The distribution of Version 1.1 includes the non-graphical postprocessor PostHBGC to prepare the output data of HBGC123D for visualization software like Excel, Gnuplot, Surfer, and GMS.

The Consultant

Gour-Tsyh Yeh, Pennsylvania State University.

The ORNL Development Team

J. P. (Jack) Gwo, Department of Civil and Environmental Engineering, University of Maryland, Baltimore County.
Hartmut Frenzel, Oak Ridge Institute for Science and Education.
Ed D'Azevedo, Computer Science and Mathematics Division.
Forrest M. Hoffman, Environmental Sciences Division.

v1.1 - 6/29/1999

Jin-Ping Gwo, email: jgwo@umbc.edu