calc.stoich.basis | R Documentation |
Calculate the basis of the stoichiometry space that is compatible with mass balances of elementary constituents and additional constraints
calc.stoich.basis(alpha, subst = NA, constraints = list(), eps = 1e-5, verbose = TRUE)
alpha |
Substance composition matrix of all substances (labelled columns)
and mass fractions of elementary constituents (labelled rows).
Typically calculated by the function |
subst |
Character vector of names of substances to be used for analysis (this must be a subset of the column names of alpha). |
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. |
This function is primarily used in the function calc.stoich.coef
.
However, it can also be used to check the number of required stoichiometric
constraints in addition to mass conservation of elementary constituents
for a given process.
In this case the composition matrix should only contain the substances
relevant for this process.
The number of required constraints is then equal to the row dimension of the
output matrix minus 1.
Matrix of basis vectors (in rows) that span the compatible stoichiometric space.
Peter Reichert <peter.reichert@emeriti.eawag.ch>
Reichert, P. and Schuwirth, N., A generic framework for deriving process stoichiometry in environmental models, Environmental Modelling and Software 25, 1241-1251, 2010.
calc.comp.matrix
, calc.stoich.coef
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)
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))
basis.gro.ZOO <-
calc.stoich.basis(alpha,subst.gro.ZOO,const.gro.ZOO)
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