stoichcalc-package {stoichcalc}

R-Functions for Solving Stoichiometric Equations

Description

Given a list of substance compositions, a list of substances involved in a process, and a list of constraints in addition to mass conservation of elementary constituents, the package contains functions to build the substance composition matrix, to analyze the uniqueness of process stoichiometry, and to calculate stoichiometric coefficients if process stoichiometry is unique (see reference given below for more details).

Details

Package:	stoichcalc
Type:	Package
Version:	1.1-5
Date:	2023-08-28
License:	GPL >= 2
LazyLoad:	yes

The package contains the following three functions:
calc.comp.matrix constructs the substance composition matrix froma a list of substance composition vectors,
calc.stoich.basis calculates the basis of the stoichiometry space that is compatible with mass balances of elementary constituents and additional constraints, calc.stoich.coef calculates the stoichiometric coefficients of a process from involved substances, their composition and constraints.

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, calc.stoich.coef

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)