calc.stoich.coef {stoichcalc}

Calculate Stoichiometric Coefficients

Description

Calculate stoichiometric coefficients of a process from involved substances, their composition and constraints

Usage

calc.stoich.coef(alpha, name, subst, subst.norm, nu.norm = 1, constraints = list(), 
                 eps = 1e-5, verbose = TRUE)

Arguments

alpha

Substance composition matrix of all substances (labelled columns) and mass fractions of elementary constituents (labelled rows). Typically calculated by the function calc.comp.matrix.

name

Name of the process

subst

Character vector of names of substances affected by the process (this must be a subset of the column names of alpha)

subst.norm

Name of the substance that should have a normalized (given) stoichiometric coefficient

nu.norm

Stoichiometric coefficient of the substance the name of which is specified in the argument subst.norm

constraints

List of stoichiometric constraints in addition to mass conservation of elementary constituents. Each stoichiometric constraint must be stored as a vector containing the coefficients of the linear equation in elementary constituents that defines the constraint. The elements of this vector must be labelled by the names of the corresponding elementary constituents.

eps

relative tolerance for checking ratios of stoichiometric coefficients (only used for informing user about substance pairs with fixed stoichiometric ratio)

verbose

indicator for whether or not to write basic information to the console.

Details

This is the key function of the package for the calculation of stoichiometric coefficients of individual processes. The results for different processes can easily be bound to the comprehensive stoichiometric matrix of all processes by using rbind.

Value

Matrix consisting of one row of stoichiometric coefficients of the process or an error message if the process stoichiometry is not uniquely defined. The row name of the matrix is equal to the process name specified as an argument (to allow binding the stoichiometries of several processes to a comprehensive stoichiometric matrix), the column names are equal to the substance names provided by the substance composition matrix alpha.

Author(s)

Peter Reichert <[e-mail]>

References

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

See Also

calc.comp.matrix, calc.stoich.basis

Examples

subst.comp <- 
  list(NH4  = c(H      = 4*1/14,  # gH/gNH4-N
                N      = 1,       # gN/gNH4-N
                charge = 1/14),   # chu/gNH4-N
       NO3  = c(O      = 3*16/14, # gO/gNO3-N
                N      = 1,       # gN/gNO3-N
                charge = -1/14),  # chu/gNO3-N
       HPO4 = c(O      = 4*16/31, # gO/gHPO4-P
                H      = 1*1/31,  # gH/gHPO4-P
                P      = 1,       # gP/gHPO4-P
                charge = -2/31),  # chu/gHPO4-P
       HCO3 = c(C      = 1,       # gC/gHCO3-C
                O      = 3*16/12, # gO/gHCO3-C
                H      = 1*1/12,  # gH/gHCO3-C
                charge = -1/12),  # chu/gHCO3-C
       O2   = c(O      = 1),      # gO/gO2-O
       H    = c(H      = 1,       # gH/molH
                charge = 1),      # chu/molH
       H2O  = c(O      = 1*12,    # gO/molH2O
                H      = 2*1),    # gH/molH2O
       ALG  = c(N      = 0.06,    # gN/gALG
                P      = 0.005,   # gP/gALG
                O      = 0.50,    # gO/gALG
                H      = 0.07,    # gH/gALG
                C      = 0.365),  # gC/gALG
       ZOO  = c(N      = 0.06,    # gN/gZOO
                P      = 0.01,    # gP/gZOO
                O      = 0.50,    # gO/gZOO
                H      = 0.07,    # gH/gZOO
                C      = 0.36),   # gC/gZOO
       POM  = c(N      = 0.04,    # gN/gPOM
                P      = 0.007,   # gP/gPOM
                O      = 0.40,    # gO/gPOM
                H      = 0.07,    # gH/gPOM
                C      = 0.483),  # gC/gPOM
       DOM  = c(N      = 0.04,    # gN/gDOM
                P      = 0.007,   # gP/gDOM
                O      = 0.40,    # gO/gDOM
                H      = 0.07,    # gH/gDOM
                C      = 0.483))  # gC/gDOM
                
Y.ZOO <- 0.2; f.POM <- 0.2; f.DOM <- 0.1

alpha <- calc.comp.matrix(subst.comp)

subst.gro.ALG.NO3 <- c("NO3","HPO4","HCO3",
                       "O2","H","H2O","ALG")

basis.gro.ALG.NO3 <- 
  calc.stoich.basis(alpha,subst.gro.ALG.NO3)

nu.gro.ALG.NO3    <- 
  calc.stoich.coef(alpha       = alpha,
                   name        = "gro.ALG.NO3",
                   subst       = subst.gro.ALG.NO3,
                   subst.norm  = "ALG",
                   nu.norm     = 1)

subst.gro.ZOO <- c("NH4","HPO4","HCO3","O2","H",
                   "H2O","ALG","ZOO","POM","DOM")

basis.gro.ZOO <- 
  calc.stoich.basis(alpha,subst.gro.ZOO)

const.gro.ZOO <- list(c("ZOO" = 1,"ALG" = Y.ZOO),
                      c("POM" = 1,"ALG" = f.POM),
                      c("DOM" = 1,"ALG" = f.DOM)) 

nu.gro.ZOO    <- 
  calc.stoich.coef(alpha       = alpha,
                   name        = "gro.ZOO",
                   subst       = subst.gro.ZOO,
                   subst.norm  = "ZOO",
                   nu.norm     = 1,
                   constraints = const.gro.ZOO)

nu <- rbind(nu.gro.ALG.NO3,
            nu.gro.ZOO)

print(nu,digits=2)