Reactive Chemical Transport under Multiphase System

Open Access
Fang, Yilin
Graduate Program:
Civil Engineering
Doctor of Philosophy
Document Type:
Date of Defense:
March 31, 2003
Committee Members:
  • Dr Gour Tsyh Yeh, Committee Chair
  • William D Burgos, Committee Chair
  • Christopher J Duffy, Committee Member
  • Derek Elsworth, Committee Member
  • Andrew Scanlon, Committee Member
  • Conservative Form
  • Multiphase System
  • Reactive Chemical Transport
  • Matrix Decomposition
  • Reaction Network
  • Biogeochemical Modeling
  • Advective Form
This thesis presents the development of BIOGEOCHEM, a numerical model to simulate biochemical and geochemical reactions in a batch system and HYDROBIOGEOCHEM, a numerical model to simulate HYDROlogic transport and BIOchemical and GEOCHEMical reactions under nonisothermal multiphase systems in 2-dimensions and 3-dimensions. HYDROBIOGEOCHEM is a coupled hydrologic transport and biogeochemical reaction code, reaction module of which is BIOGEOCHEM, to predict the spatio-temporal distributions of all the important chemical species. The formulation of BIOGEOCHEM and HYDROBIOGEOCHM is new in that it is based on a general paradigm which uses the well accepted diagonalizetion-decomposition procedure. The unique features of the general paradigm are that it can simultaneously (1) facilitate the segregation (isolation) of linearly independent kinetic reactions and, thus, enable the formulation and parameterization of individual rates one reaction by one reaction when linearly dependent kinetic reactions are absent; (2) enable the inclusion of virtually any type of equilibrium expressions and kinetic rates users want to specify; (3) reduce problem stiffness by eliminating all fast reactions from the set of ordinary differential equations governing the evolution of kinetic variables; (4) perform systematic operations to remove redundant fast reactions and irrelevant kinetic reactions; (5) systematically define chemical components and explicitly enforce mass conservation; (6) accomplish automation in decoupling fast reactions from slow reactions; and (7) increase the robustness of numerical integration of the governing equations with species switching schemes. The new formulation in HYDROBIOGEOCHEM uses Gauss-Jordan decomposition to diagonalize the governing matrix equations for hydrologic transport to reduce primary dependent variables (PDVs), resulting in mobile components and mobile kinetic variables as PDVs. Methods for coupling biogeochemical reaction and hydrologic transport, such as the sequential iteration approach (SIA) and predictor corrector approach are incorporated into the code to make the model versatile. The governing transport equation can be written in conservative form and nonconservative form. Five different numerical schemes based on the two forms of equations are incorporated in HYDROBIOGEOCHEM to better understand different physical processes. They are (1) FEM on advective form of equation, (2) FEM on conservative form of equation, (3) Hybrid Lagrangian-Eulerian FEM for interior elements + FEM on advective form of equation for boundary elements , (4) hybrid Lagrangian-Eulerian FEM, and (5) Hybrid Lagrangian-Eulerian FEM for interior elements + FEM on conservative form of equation for boundary elements. Heat transfer is considered in HYDROBIOGEOCHEM to account for the temperature variations that may impact hydrologic transport by affecting the hydrologic and chemical conditions in the subsurface system. Weak coupling will be applied to solve a system of chemical transport and heat transfer to save computing resources. HYDROBIOGEOCHEM is designed to assess migration of subsurface contamination and help design remediation technologies. The prospective field application of the model is demonstrated by examples.