process-class {ecosim}

Class "process"

Description

This class represents a transformation process of substances/organisms in the modelled system. Such a process is characterized by a transformation rate and a list of stoichiometric coefficients for the affected substances and organisms. It is recommended to calculate the stoichiometric coefficients with the function calc.stoich.coef of the package stoichcalc from substance and organism compositions. The output of this function can directly be used for the process definition.

Objects from the Class

Objects can be created by calls of the form new("process", ...).

Slots

name:

Character string specifying the name of the process.

rate:

Expression characterizing the dependence of the transformation rate on substance/organism concentrations and external influence factors

stoich:

List of expressions or numbers defining the stoichiometric coefficient of the substance/organism given by the label of the list component.

pervol:

Logical variable defining the process rate as per volume of the reactor (pervol=TRUE) or per surface area (pervol=FALSE).

Methods

calc.trans.rates

Calculates transformation rates; internal use only.

Author(s)

Peter Reichert <[e-mail]>

References

Omlin, M., Reichert, P. and Forster, R., Biogeochemical model of lake Zurich: Model equations and results, Ecological Modelling 141(1-3), 77-103, 2001.

Reichert, P., Borchardt, D., Henze, M., Rauch, W., Shanahan, P., Somlyody, L. and Vanrolleghem, P., River Water Quality Model no. 1 (RWQM1): II. Biochemical process equations, Water Sci. Tech. 43(5), 11-30, 2001.

Reichert, P. and Schuwirth, N., A generic framework for deriving process stoichiometry in environmental models, Environmental Modelling & Software, 25, 1241-1251, 2010.

See Also

reactor-class, link-class, system-class, calcres, plotres.

Examples

# Definition of parameters:
# =========================

param    <- list(k.gro.ALG   = 1,        # 1/d
                 k.gro.ZOO   = 0.8,      # m3/gDM/d
                 k.death.ALG = 0.4,      # 1/d
                 k.death.ZOO = 0.08,     # 1/d
                 K.HPO4      = 0.002,    # gP/m3
                 Y.ZOO       = 0.2,      # gDM/gDM
                 alpha.P.ALG = 0.002,    # gP/gDM
                 A           = 8.5e+006, # m2
                 h.epi       = 4,        # m
                 Q.in        = 4,        # m3/s
                 C.ALG.ini   = 0.05,     # gDM/m3
                 C.ZOO.ini   = 0.1,      # gDM/m3
                 C.HPO4.ini  = 0.02,     # gP/m3
                 C.HPO4.in   = 0.04)     # gP/m3             

# Definition of transformation processes:
# =======================================

# Growth of algae:
# ----------------

gro.ALG   <- new(Class  = "process",
                 name   = "Growth of algae",
                 rate   = expression(k.gro.ALG
                                     *C.HPO4/(K.HPO4+C.HPO4)
                                     *C.ALG),
                 stoich = list(C.ALG  = expression(1),              # gDM/gDM
                               C.HPO4 = expression(-alpha.P.ALG)))  # gP/gDM

# Death of algae:
# ---------------

death.ALG <- new(Class = "process",
                 name   = "Death of algae",
                 rate   = expression(k.death.ALG*C.ALG),
                 stoich = list(C.ALG  = expression(-1)))            # gDM/gDM

# Growth of zooplankton:
# ----------------------

gro.ZOO   <- new(Class  = "process",
                 name   = "Growth of zooplankton",
                 rate   = expression(k.gro.ZOO
                                     *C.ALG
                                     *C.ZOO),
                 stoich = list(C.ZOO  = expression(1),              # gDM/gDM
                               C.ALG  = expression(-1/Y.ZOO)))      # gP/gDM

# Death of zooplankton:
# ---------------------

death.ZOO <- new(Class  = "process",
                 name   = "Death of zooplankton",
                 rate   = expression(k.death.ZOO*C.ZOO),
                 stoich = list(C.ZOO  = expression(-1)))            # gDM/gDM