This paper presents a generic biogeochemical simulator, BIOGEOCHEM. The simulator can read a thermodynamic database based on the EQ3/EQ6 database. It can also read user-specified equilibrium and kinetic reactions (reactions not defined in the format of that in EQ3/EQ6 database) symbolically. BIOGEOCHEM is developed with a general paradigm. It overcomes the requirement in most available reaction-based models that reactions and rate laws be specified in a limited number of canonical forms. The simulator interprets the reactions, and rate laws of virtually any type for input to the MAPLE symbolic mathematical software package. MAPLE then generates Fortran code for the analytical Jacobian matrix used in the Newton-Raphson technique, which are compiled and linked into the BIOGEOCHEM executable. With this feature, the users are exempted from recoding the simulator to accept new equilibrium expressions or kinetic rate laws. Two examples are used to demonstrate the new features of the simulator.
Revised: June 7, 2005 |
Published: June 17, 2004
Citation
Fang Y., S.B. Yabusaki, and G.T. Yeh. 2004.A generic reaction-based biogeochemical simulator. In Proceedings of the 15th International Conference on Computational Methods in Water Resources (CMWR XV), June 13-17, 2004 Chapel Hill, NC, USA. Computational Methods in Water Resources, edited by C.T. Miller, M.W. Farthing, W.G. Gray, and G.F. Pinder, 1, 869-878. Amsterdam:Elsevier.PNNL-SA-40458.