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inst/doc/AquaEnv.R
In AquaEnv: Integrated Development Toolbox for Aquatic Chemical Model Generation
### R code from vignette source 'AquaEnv.rnw'
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### code chunk number 1: Preliminaries
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library("AquaEnv")
library("deSolve")
options(width=80)
Plotit <- AquaEnv:::plot.aquaenv
plot.aquaenv <- function(...) {
if ("newdevice" %in% list(...))
Plotit(...)
else
Plotit(newdevice = FALSE, ...) # else Sweave does not work...
}
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### code chunk number 2: AquaenvElements
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test <- aquaenv(S = 35, t = 10)
test$t
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### code chunk number 3: CallingKFuncsDirectly
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K_CO2(S = 15, t = 30)
K0_CO2(S = 15, t = 30)
Ksp_calcite(S = 15, t = 30, p = 100)
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### code chunk number 4: Avector
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K_CO2(S = 10:15, t = 30)
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### code chunk number 5: MinimalAquaenv
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ae <- aquaenv(S = 30, t = 15)
ae$K_CO2
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### code chunk number 6: AquaenvWithDepth
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ae <- aquaenv(S = 30, t = 15, p = 10)
names(ae)
ae$Ksp_calcite
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### code chunk number 7: AquaenvPressures
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ae <- aquaenv(S = 30, t = 15, p = 10)
ae[c("p", "P")]
ae <- aquaenv(S = 30, t = 15, P = 10)
unlist(ae[c("p", "P")])
ae <- aquaenv(S = 30, t = 15, P = 10, Pa = 0.5)
unlist(ae[c("p", "P")])
ae <- aquaenv(S = 30, t = 15, d = 100)
unlist(ae[c("p", "P")])
ae <- aquaenv(S = 30, t = 15, d = 100, lat = 51)
unlist(ae[c("p", "P")])
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### code chunk number 8: SkeletonAquaenv
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ae <- aquaenv(S = 30, t = 15, p = 10, skeleton = TRUE)
names(ae)
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### code chunk number 9: CompleteAquaenvSystem
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S <- 30
t <- 15
p <- 10
SumCO2 <- 0.0020
pH <- 8
TA <- 0.002142233
fCO2 <- 0.0005272996
CO2 <- 2.031241e-05
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH)
ae$TA
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, TA = TA)
ae$pH
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, CO2 = CO2)
ae$pH
names(ae)
###################################################
### code chunk number 10: SpeciationSkeletonAquaenv
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ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH, speciation = FALSE)
names(ae)
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH, speciation = FALSE,
skeleton = TRUE)
names(ae)
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### code chunk number 11: DSAAquaenv
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ae <- aquaenv(S, t, p, SumCO2 = SumCO2, fCO2 = fCO2, dsa = TRUE)
ae$dTAdH
ae$revelle
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### code chunk number 12: ErrorMessagesAquaenv
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ae <- aquaenv(S, t, p, SumCO2 = SumCO2, CO2 = CO2, fCO2 = fCO2)
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH, TA = TA)
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH, CO2 = CO2)
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH, fCO2 = fCO2)
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, TA = TA, CO2 = CO2)
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, TA = TA, fCO2 = fCO2)
###################################################
### code chunk number 13: SumCO2Calculating
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fCO2 <- 0.0006943363
CO2 <- 2.674693e-05
pH <- 7.884892
TA <- 0.0021
S <- 30
t <- 15
p <- 10
ae <- aquaenv(S, t, p, SumCO2 = NULL, pH = pH, CO2 = CO2)
ae$SumCO2
ae <- aquaenv(S, t, p, SumCO2 = NULL, pH = pH, fCO2 = fCO2)
ae$SumCO2
ae <- aquaenv(S, t, p, SumCO2 = NULL, pH = pH, TA = TA)
ae$SumCO2
ae <- aquaenv(S, t, p, SumCO2 = NULL, TA = TA, CO2 = CO2)
ae$SumCO2
ae <- aquaenv(S, t, p, SumCO2 = NULL, TA = TA, fCO2 = fCO2)
ae$SumCO2
###################################################
### code chunk number 14: CloningAquaenv
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S <- 30
t <- 15
SumCO2 <- 0.0020
TA <- 0.00214
ae <- aquaenv(S, t, SumCO2 = SumCO2, TA = TA)
ae$pH
ae1 <- aquaenv(ae = ae) # this is the same
ae1$pH
ae2 <- aquaenv(ae = ae, pH = 9)
c(ae$TA, ae2$TA)
ae3 <- aquaenv(ae = ae, TA = 0.002)
c(ae$pH, ae3$pH)
K_CO2 <- 1e-6
ae4 <- aquaenv(ae = ae, k_co2 = 1e-6)
c(ae$TA, ae4$TA)
###################################################
### code chunk number 15: PreparingInput
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S <- 10
t <- 15
pH_NBS <- 8.142777
SumCO2molar <- 0.002016803
(pH_free <- convert(pH_NBS, "pHscale", "nbs2free", S = S, t = t))
(SumCO2molin <- convert(SumCO2molar, "conc", "molar2molin", S = S, t = t))
ae <- aquaenv(S, t, SumCO2 = SumCO2molin, pH = pH_free)
ae$pH
ae$SumCO2
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### code chunk number 16: InputVectors
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SumCO2 <- 0.0020
pH <- 8
S <- 30
t <- 1:5
p <- 10
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH)
rbind(t = ae$t, TA = ae$TA)
###################################################
### code chunk number 17: Selectplot
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plot(ae, xval = t, xlab = "t/(deg C)",
what = c("pH", "CO2", "HCO3", "CO3"),
mfrow = c(1, 4))
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### code chunk number 18: MoreInputVectors1 (eval = FALSE)
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## ae <- aquaenv(S=20:24, t=15, p=10, SumCO2 = SumCO2, pH = pH, dsa = TRUE)
## rbind(ae$S, ae$TA)
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### code chunk number 19: MoreInputVectors6
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ae <- aquaenv(20, 10, SumCO2=seq(0.001, 0.002, 0.00025), TA = 0.002)
rbind(ae$SumCO2, ae$pH, ae$HCO3)
###################################################
### code chunk number 20: SumCO2CalcInputVecs1
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ae <- aquaenv(S = 30, t = 11:15, SumCO2 = NULL, pH = pH, CO2 = CO2,
dsa = TRUE)
ae$SumCO2
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### code chunk number 21: Dataframe
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ae <- aquaenv(S = 30, t = 11:15, SumCO2 = NULL, pH = 8, CO2 = 2e-5)
aedataframe <- as.data.frame(ae)
dim(aedataframe)
aedataframe[, 1:3]
aetest <- aquaenv(ae = aedataframe, from.data.frame = TRUE)
###################################################
### code chunk number 22: Elementconversion
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ae <- aquaenv(S = 30, t = 10)
ae$SumBOH3
ae <- convert(ae, "mol/kg-soln", "umol/kg-H2O", 1e6/ae$molal2molin, "unit")
ae$SumBOH3
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### code chunk number 23: DSAQuantities1
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ae <- aquaenv(S = 30, t = 15, d = 10, SumCO2 = 0.002, pH = 8, dsa = TRUE)
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### code chunk number 24: DSAQuantities2
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ae$dTAdH
ae$dTAdSumCO2
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### code chunk number 25: DSAQuantities3
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ae$dTAdKdKdS
ae$dTAdKdKdSumH2SO4
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### code chunk number 26: DSAQuantities4
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ae$c1
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### code chunk number 27: BufferFactors1
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BF <- BufferFactors()
names(BF)
BF$dtotX.dpH
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### code chunk number 28: BufferFactors2
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ae <- aquaenv(S = 30, t = 15, d = 10, SumCO2 = 0.002, pH = 8.1,
skeleton = TRUE)
BF <- BufferFactors(ae = ae)
BF$RF
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### code chunk number 29: BufferFactors3
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ae <- aquaenv(S = 30, t = 15, d = 10, SumCO2 = 0.002, pH = 8.1, dsa = TRUE)
BF <- BufferFactors(ae = ae)
cbind(ae$dTAdH,BF$beta.H)
###################################################
### code chunk number 30: BufferFactors4
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parameters <- c(DIC = 0.002, Alk = 0.0022)
BF <- BufferFactors(parameters = parameters)
BF$RF
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### code chunk number 31: BufferFactors5
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ae <- aquaenv(S = 30, t = 15, d = 10, SumCO2 = 0.002, pH = 8.1,
skeleton = TRUE)
BF <- BufferFactors(ae = ae)
BF$RF
parameters <- c(Alk = 0.0022)
BF_2 <- BufferFactors(ae = ae, parameters = parameters)
BF_2$RF
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### code chunk number 32: BufferFactors6
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BF <- BufferFactors(species = c("CO2", "HCO3", "CO3", "SumNH4"))
BF$dtotX.dX
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### code chunk number 33: BufferFactors7
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ae <- aquaenv(S = 30, t = 15, d = 10, SumCO2 = 0.002, pH = 8.1,
skeleton = TRUE)
BF <- BufferFactors(ae = ae, species = c("SumCO2", "SumNH4"))
BF$dtotX.dX
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### code chunk number 34: BufferFactors7
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BF <- BufferFactors(k1k2 = "roy")
BF$RF
BF <- BufferFactors(k_co2 = 1e-6)
BF$RF
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### code chunk number 35: Plot1
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ae <- aquaenv(20:30, 10)
plot(ae, xval = 20:30, xlab = "S", what = c("K_CO2", "K_HCO3", "K_BOH3"),
size = c(10, 2), mfrow = c(1,3))
###################################################
### code chunk number 36: OrdDynModParamList (eval = FALSE)
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## parameters <- list(
## S = 25 , # psu
## t_min = 5 , # degrees C
## t_max = 25 , # degrees C
##
## k = 0.4 , # 1/d proportionality factor for air-water exchange
## rOx = 0.0000003 , # mol-N/(kg*d) maximal rate of oxic mineralisation
## rNitri = 0.0000002 , # mol-N/(kg*d) maximal rate of nitrification
## rPP = 0.000006 , # mol-N/(kg*d) maximal rate of primary production
##
## ksDINPP = 0.000001 , # mol-N/kg
## ksNH4PP = 0.000001 , # mol-N/kg
##
## D = 0.1 , # 1/d (dispersive) transport coefficient
##
## O2_io = 0.000296 , # mol/kg-soln
## NO3_io = 0.000035 , # mol/kg-soln
## SumNH4_io = 0.000008 , # mol/kg-soln
## SumCO2_io = 0.002320 , # mol/kg-soln
## TA_io = 0.002435 , # mol/kg-soln
##
## C_Nratio = 8 , # mol C/mol N C:N ratio of organic matter
##
## a = 30 , # time at which PP begins
## b = 50 , # time at which PP stops again
##
## modeltime = 100 # duration of the model
## )
###################################################
### code chunk number 37: OrdDynModFunction (eval = FALSE)
###################################################
##
## temperature <- with (parameters,
## approxfun(x = 0:101,
## y = c(seq(t_min, t_max, (t_max-t_min)/50),
## seq(t_max, t_min, -(t_max-t_min)/50)))
## )
##
## boxmodel <- function(time, state, parameters) {
## with (
## as.list(c(state, parameters)), {
## t <- temperature(time)
## ae <- aquaenv(S = S, t = t, SumCO2 = SumCO2,
## SumNH4 = SumNH4, TA = TA)
##
## ECO2 <- k * (ae$CO2_sat - ae$CO2)
## EO2 <- k * (ae$O2_sat - O2)
##
## # dilution
## TO2 <- D*(O2_io - O2)
## TNO3 <- D*(NO3_io - NO3)
## TSumNH4 <- D*(SumNH4_io - SumNH4)
## TTA <- D*(TA_io - TA)
## TSumCO2 <- D*(SumCO2_io - SumCO2)
##
## RNit <- rNitri * SumNH4/(SumNH4+1e-8)
##
## ROx <- rOx
## ROxCarbon <- ROx * C_Nratio
##
## pNH4PP <- 0
## RPP <- 0
##
## if ((time > a) && (time < b)) {
## RPP <- rPP * ((SumNH4+NO3)/(ksDINPP + (SumNH4+NO3)))
## pNH4PP <- SumNH4/(SumNH4+NO3)
## }
##
## RPPCarbon <- RPP * C_Nratio
##
## dO2 <- TO2 + EO2 - ROxCarbon - 2*RNit + (2-2*pNH4PP)*RPP + RPPCarbon
## dNO3 <- TNO3 + RNit -(1-pNH4PP)*RPP
##
## dSumCO2 <- TSumCO2 + ECO2 + ROxCarbon - RPPCarbon
## dSumNH4 <- TSumNH4 + ROx - RNit - pNH4PP*RPP
##
## dTA <- TTA + ROx - 2*RNit -(2*pNH4PP-1)*RPP
##
## ratesofchanges <- c(dO2, dNO3, dSumNH4, dSumCO2, dTA)
##
## return(list(ratesofchanges, ae[c("t", "NH4", "NH3", "pH")]))
## } )
## }
###################################################
### code chunk number 38: OrdDynModSolution (eval = FALSE)
###################################################
## initialstate <- with (parameters,
## c(O2=O2_io, NO3=NO3_io, SumNH4=SumNH4_io, SumCO2=SumCO2_io, TA=TA_io))
##
## times <- 1:100
## output <- vode(initialstate,times,boxmodel,parameters, hmax = 1)
###################################################
### code chunk number 39: OrdDynModePlotting (eval = FALSE)
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## plot(output)
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### code chunk number 40: SinglePHModParams
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parameters <- list(
S = 25 , # psu
t = 15 , # degrees C
k = 0.4 , # 1/d proportionality factor for air-water exchange
rOx = 0.0000003 , # mol-N/(kg*d) maximal rate of oxic mineralisation
rNitri = 0.0000002 , # mol-N/(kg*d) maximal rate of nitrification
rPP = 0.0000006 , # mol-N/(kg*d) maximal rate of primary production
ksSumNH4 = 0.000001 , # mol-N/kg
D = 0.1 , # 1/d (dispersive) transport coefficient
SumNH4_io = 0.000008 , # mol/kg-soln
SumCO2_io = 0.002320 , # mol/kg-soln
TA_io = 0.002435 , # mol/kg-soln
C_Nratio = 8 , # mol C/mol N C:N ratio of organic matter
a = 5 , # time from which PP begins
b = 20 , # time where PP shuts off again
modeltime = 30 # duration of the model
)
###################################################
### code chunk number 41: SinglePHModFunction
###################################################
boxmodel <- function(timestep, currentstate, parameters)
{
with (
as.list(c(currentstate,parameters)),
{
# the "classical" implicit pH calculation method is applied in aquaenv
ae <- aquaenv(S=S, t=t, SumCO2=sumCO2,
SumNH4=sumNH4, TA=alkalinity, dsa=TRUE)
ECO2 <- k * (ae$CO2_sat - ae$CO2)
RNit <- rNitri
ROx <- rOx
if ((timestep > a) && (timestep < b))
RPP <- rPP * (sumNH4/(ksSumNH4 + sumNH4))
else
RPP <- 0
dsumCO2 <- ECO2 + C_Nratio*ROx - C_Nratio*RPP
dsumNH4 <- ROx - RNit - RPP
dalkalinity <- ROx - 2*RNit - RPP
# The DSA pH
dH <- (dalkalinity - (dsumCO2*ae$dTAdSumCO2 + dsumNH4*ae$dTAdSumNH4))/ae$dTAdH
DSApH <- -log10(H)
# The DSA pH using pH dependent fractional stoichiometry (= using partitioning coefficients)
rhoHECO2 <- ae$c2 + 2*ae$c3
rhoHRNit <- 1 + ae$n1
rhoHROx <- C_Nratio * (ae$c2 + 2*ae$c3) - ae$n1
rhoHRPP <- -(C_Nratio * (ae$c2 + 2*ae$c3)) + ae$n1
dH_ECO2 <- rhoHECO2*ECO2/(-ae$dTAdH)
dH_RNit <- rhoHRNit*RNit/(-ae$dTAdH)
dH_ROx <- rhoHROx*ROx /(-ae$dTAdH)
dH_RPP <- rhoHRPP*RPP /(-ae$dTAdH)
dH_stoich <- dH_ECO2 + dH_RNit + dH_ROx + dH_RPP
DSAstoichpH <- -log10(H_stoich)
ratesofchanges <- c(dsumNH4, dsumCO2, dalkalinity, dH, dH_stoich)
processrates <- c(ECO2=ECO2, RNit=RNit, ROx=ROx, RPP=RPP)
DSA <- c(DSApH=DSApH, rhoHECO2=rhoHECO2, rhoHRNit=rhoHRNit, rhoHROx=rhoHROx,
rhoHRPP=rhoHRPP, dH_ECO2=dH_ECO2, dH_RNit=dH_RNit, dH_ROx=dH_ROx,
dH_RPP=dH_RPP, DSAstoichpH=DSAstoichpH)
return(list(ratesofchanges, processrates, DSA, ae))
}
)
}
###################################################
### code chunk number 42: SinglPHModSolution
###################################################
with (as.list(parameters),
{
H_init <<- 10^(-(aquaenv(S=S, t=t, SumCO2=SumCO2_io, SumNH4=SumNH4_io, TA=TA_io,
speciation=FALSE)$pH))
initialstate <<- c(sumNH4=SumNH4_io, sumCO2=SumCO2_io, alkalinity =TA_io, H=H_init,
H_stoich=H_init)
times <<- c(0:modeltime)
})
output <- vode(initialstate, times, boxmodel, parameters, hmax=1)
###################################################
### code chunk number 43: SinglePHModePlotting1
###################################################
select <- c("sumCO2", "alkalinity", "sumNH4", "RPP", "dTAdH", "dTAdSumCO2",
"dTAdSumNH4","rhoHECO2", "rhoHRNit", "rhoHROx","dH_ECO2","dH_RNit",
"dH_RPP","pH", "DSApH", "DSAstoichpH")
plot(output, which = select, xlab="time/d", mfrow=c(4,4))
###################################################
### code chunk number 44: SinglepHModPlotting2
###################################################
what <- c("dH_ECO2", "dH_RNit", "dH_ROx", "dH_RPP")
plot(aquaenv(ae=as.data.frame(output), from.data.frame=TRUE),
xval = times, what = what, xlab = "time/d", size = c(7,5),
ylab = "mol-H/(kg-soln*d)", legendposition = "bottomright", cumulative = TRUE)
###################################################
### code chunk number 45: SinplePHModConsistencyCheck
###################################################
matplot(output[, "time"],
output[, c("pH", "DSApH", "DSAstoichpH")], type = "l", lty = 1, lwd = 2)
###################################################
### code chunk number 46: ImplicitPHModParams (eval = FALSE)
###################################################
## parameters <- list(
## t = 15 , # degrees C
## S = 35 , # psu
##
## SumCO2_t0 = 0.002 , # mol/kg-soln (comparable to Wang2005)
## TA_t0 = 0.0022 , # mol/kg-soln (comparable to Millero1998)
##
## kc = 0.5 , # 1/d proportionality factor for air-water exchange
## kp = 0.000001 , # mol/(kg-soln*d) max rate of calcium carbonate precipitation
## n = 2.0 , # - exponent for kinetic rate law of precipitation
##
## modeltime = 20 , # d duration of the model
## outputsteps = 100 # number of outputsteps
## )
###################################################
### code chunk number 47: ImplicitPHModFunction (eval = FALSE)
###################################################
## boxmodel <- function(timestep, currentstate, parameters)
## {
## with (
## as.list(c(currentstate,parameters)),
## {
## ae <- aquaenv(S=S, t=t, SumCO2=SumCO2, TA=TA, SumSiOH4=0,
## SumBOH3=0, SumH2SO4=0, SumHF=0)
##
## Rc <- kc * ((ae$CO2_sat) - (ae$CO2))
## Rp <- kp * (1-ae$omega_calcite)^n
##
## dSumCO2 <- Rc - Rp
## dTA <- -2*Rp
##
## ratesofchanges <- c(dSumCO2, dTA)
##
## processrates <- c(Rc=Rc, Rp=Rp)
##
## return(list(ratesofchanges, list(processrates, ae)))
## }
## )
## }
###################################################
### code chunk number 48: ImplicitPHModSolution (eval = FALSE)
###################################################
## with (as.list(parameters),
## {
## initialstate <<- c(SumCO2=SumCO2_t0, TA=TA_t0)
## times <<- seq(0,modeltime,(modeltime/outputsteps))
## })
## output <<- vode(initialstate,times,boxmodel,parameters, hmax=1)
###################################################
### code chunk number 49: ExplicitPHModParams (eval = FALSE)
###################################################
## parameters <- list(
## S = 35 , # psu
## t = 15 , # degrees C
##
## SumCO2_t0 = 0.002 , # mol/kg-soln (comparable to Wang2005)
## TA_t0 = 0.0022 , # mol/kg-soln (comparable to Millero1998)
##
## kc = 0.5 , # 1/d proportionality factor for air-water exchange
## kp = 0.000001 , # mol/(kg-soln*d) max rate of calcium carbonate precipitation
## n = 2.0 , # - exponent for kinetic rate law of precipitation
##
## modeltime = 20 , # d duration of the model
## outputsteps = 100 # number of outputsteps
## )
###################################################
### code chunk number 50: ExplicitPHModFunction (eval = FALSE)
###################################################
## boxmodel <- function(timestep, currentstate, parameters)
## {
## with (
## as.list(c(currentstate,parameters)),
## {
## ae <- aquaenv(S=S, t=t, SumCO2=SumCO2, pH=-log10(H), SumSiOH4=0,
## SumBOH3=0, SumH2SO4=0, SumHF=0, dsa=TRUE)
##
## Rc <- kc * ((ae$CO2_sat) - (ae$CO2))
## Rp <- kp * (1-ae$omega_calcite)^n
##
## dSumCO2 <- Rc - Rp
##
## dHRc <- ( -(ae$dTAdSumCO2*Rc ))/ae$dTAdH
## dHRp <- (-2*Rp -(ae$dTAdSumCO2*(-Rp)))/ae$dTAdH
## dH <- dHRc + dHRp
##
## ratesofchanges <- c(dSumCO2, dH)
##
## processrates <- c(Rc=Rc, Rp=Rp)
## outputvars <- c(dHRc=dHRc, dHRp=dHRp)
##
## return(list(ratesofchanges, list(processrates, outputvars, ae)))
## }
## )
## }
###################################################
### code chunk number 51: ExplicitPHModSolution (eval = FALSE)
###################################################
## with (as.list(parameters),
## {
## aetmp <- aquaenv(S=S, t=t, SumCO2=SumCO2_t0, TA=TA_t0, SumSiOH4=0, SumBOH3=0, SumH2SO4=0, SumHF=0)
## H_t0 <- 10^(-aetmp$pH)
##
## initialstate <<- c(SumCO2=SumCO2_t0, H=H_t0)
## times <<- seq(0,modeltime,(modeltime/outputsteps))
## })
## output <- vode(initialstate,times,boxmodel,parameters, hmax=1)
###################################################
### code chunk number 52: FracStoichModParams (eval = FALSE)
###################################################
## parameters <- list(
## S = 35 , # psu
## t = 15 , # degrees C
##
## SumCO2_t0 = 0.002 , # mol/kg-soln (comparable to Wang2005)
## TA_t0 = 0.0022 , # mol/kg-soln (comparable to Millero1998)
##
## kc = 0.5 , # 1/d proportionality factor for air-water exchange
## kp = 0.000001 , # mol/(kg-soln*d) max rate of calcium carbonate precipitation
## n = 2.0 , # - exponent for kinetic rate law of precipitation
##
## modeltime = 20 , # d duration of the model
## outputsteps = 100 # number of outputsteps
## )
###################################################
### code chunk number 53: FracStoichModFunction (eval = FALSE)
###################################################
## boxmodel <- function(timestep, currentstate, parameters)
## {
## with (
## as.list(c(currentstate,parameters)),
## {
## ae <- aquaenv(S=S, t=t, SumCO2=SumCO2, pH=-log10(H), SumSiOH4=0,
## SumBOH3=0, SumH2SO4=0, SumHF=0, dsa=TRUE)
##
## Rc <- kc * ((ae$CO2_sat) - (ae$CO2))
## Rp <- kp * (1-ae$omega_calcite)^n
##
## dSumCO2 <- Rc - Rp
##
## rhoc <- ae$c2 + 2*ae$c3
## rhop <- 2*ae$c1 + ae$c2
##
## dHRc <- rhoc*Rc/(-ae$dTAdH)
## dHRp <- rhop*Rp/(-ae$dTAdH)
## dH <- dHRc + dHRp
##
## ratesofchanges <- c(dSumCO2, dH)
##
## processrates <- c(Rc=Rc, Rp=Rp)
## outputvars <- c(dHRc=dHRc, dHRp=dHRp, rhoc=rhoc, rhop=rhop)
##
## return(list(ratesofchanges, list(processrates, outputvars, ae)))
## }
## )
## }
###################################################
### code chunk number 54: FracStoichModSolution (eval = FALSE)
###################################################
## with (as.list(parameters),
## {
## aetmp <- aquaenv(S=S, t=t, SumCO2=SumCO2_t0, TA=TA_t0, SumSiOH4=0,
## SumBOH3=0, SumH2SO4=0, SumHF=0)
## H_t0 <- 10^(-aetmp$pH)
##
## initialstate <<- c(SumCO2=SumCO2_t0, H=H_t0)
## times <<- seq(0,modeltime,(modeltime/outputsteps))
## output <<- as.data.frame(vode(initialstate,times,boxmodel,parameters, hmax=1))
## })
###################################################
### code chunk number 55: HClTit1
###################################################
ae_init <- aquaenv(S = 35, t = 15, SumCO2 = 0.0035, SumNH4 = 0.00002, pH = 11.3)
###################################################
### code chunk number 56: HClTit2
###################################################
ae <- titration(ae_init, mass_sample = 0.01, mass_titrant = 0.02,
conc_titrant = 0.01, S_titrant = 0.5, steps = 100)
###################################################
### code chunk number 57: HClTit3
###################################################
what <- c("TA", "pH", "CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
"NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "fCO2")
plot(ae, xval = ae$delta_mass_titrant, xlab = "HCl solution added [kg]",
what = what, size = c(12,8), mfrow = c(4,4))
###################################################
### code chunk number 58: HClTit4 (eval = FALSE)
###################################################
## plot(ae, xval = ae$delta_conc_titrant, what = what,
## xlab = "[HCl] offset added [mol/kg-soln]",
## size = c(14,10), mfrow = c(4,4))
## plot(ae, xval=ae$delta_moles_titrant, xlab = "HCl added [mol]",
## what = what, size = c(14,10), mfrow = c(4,4))
###################################################
### code chunk number 59: HClTit5
###################################################
plot(ae, xval = ae$pH, xlab = "free scale pH", what = what,
size = c(12,8), mfrow = c(4,4))
###################################################
### code chunk number 60: HClTit6
###################################################
plot(ae, bjerrum = TRUE)
###################################################
### code chunk number 61: HClTit7
###################################################
what <- c("CO2", "HCO3", "CO3")
plot(ae, what = what, bjerrum = TRUE, lwd = 4,
palette = c("cyan", "magenta", "yellow"),
bg = "gray", legendinset = 0.1, legendposition = "topleft")
###################################################
### code chunk number 62: HClTit9
###################################################
what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
"NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F")
plot(ae, what = what, bjerrum = TRUE, log = TRUE)
###################################################
### code chunk number 63: HClTit10
###################################################
plot(ae, what = what, bjerrum = TRUE, log = TRUE, ylim = c(-6,-1),
legendinset = 0, lwd = 3,
palette = c(1, 3, 4, 5, 6, colors()[seq(100,250,6)]))
###################################################
### code chunk number 64: NaOHTit1 (eval = FALSE)
###################################################
## ae <- titration(aquaenv(S = 35, t = 15, SumCO2 = 0.0035, SumNH4 = 0.00002, pH = 2),
## mass_sample = 0.01, mass_titrant = 0.02, conc_titrant = 0.01,
## S_titrant = 0.5, steps = 50, type = "NaOH")
###################################################
### code chunk number 65: NaOHTit2 (eval = FALSE)
###################################################
## plot(ae, xval = ae$delta_mass_titrant, xlab = "NaOH solution added [kg]",
## mfrow = c(10,10))
###################################################
### code chunk number 66: NaOHTit3 (eval = FALSE)
###################################################
## what <- c("TA", "pH", "CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
## "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "fCO2")
## plot(ae, xval = ae$delta_mass_titrant, xlab = "NaOH solution added [kg]",
## what = what, size = c(12,8), mfrow = c(4,4))
## plot(ae, xval = ae$pH, xlab = "free scale pH", what = what,
## size = c(12,8), mfrow = c(4,4))
###################################################
### code chunk number 67: NaOHTit4 (eval = FALSE)
###################################################
## what <- c("CO2", "HCO3", "CO3")
## plot(ae, what=what, bjerrum=TRUE)
###################################################
### code chunk number 68: NaOHTit5 (eval = FALSE)
###################################################
## what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
## "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F")
## plot(ae, what = what, bjerrum = TRUE, log = TRUE, ylim = c(-6,-1),
## legendinset = 0, lwd = 3, palette = c(1,3,4,5,6,colors()[seq(100,250,6)]))
###################################################
### code chunk number 69: TextbookTit1
###################################################
ae <- titration(aquaenv(S = 35, t = 15, SumCO2 = 0.0035, SumNH4 = 0.00002, pH = 11.3),
mass_sample = 100, mass_titrant = 0.5, conc_titrant = 3,
S_titrant = 0.5, steps = 100)
###################################################
### code chunk number 70: TextbookTit2 (eval = FALSE)
###################################################
## plot(ae, xval = ae$delta_mass_titrant,
## xlab = "HCl solution added [kg]", mfrow = c(10, 10))
###################################################
### code chunk number 71: TextbookTit3 (eval = FALSE)
###################################################
## what <- c("TA", "pH", "CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
## "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "fCO2")
## plot(ae, xval = ae$delta_mass_titrant, xlab = "HCl solution added [kg]",
## what = what, size = c(12, 8), mfrow = c(4,4))
## plot(ae, xval = ae$pH, xlab = "free scale pH", what = what,
## size = c(12,8), mfrow = c(4,4))
## plot(ae, xval = ae$delta_conc_titrant, xlab = "[HCl] offset added [mol/kg-soln]",
## what = what, size = c(12,8), mfrow = c(4,4))
## plot(ae, xval = ae$delta_moles_titrant, xlab = "HCl added [mol]",
## what = what, size = c(12,8), mfrow = c(4,4))
###################################################
### code chunk number 72: TextbookTit4 (eval = FALSE)
###################################################
## plot(ae, bjerrum=TRUE)
## what <- c("CO2", "HCO3", "CO3")
## plot(ae, what = what, bjerrum = TRUE)
## plot(ae, what = what, bjerrum = TRUE, lwd = 4,
## palette=c("cyan", "magenta", "yellow"), bg = "gray",
## legendinset = 0.1, legendposition = "topleft")
## what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
## "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F")
## plot(ae, what = what, bjerrum = TRUE, log = TRUE)
###################################################
### code chunk number 73: TextbookTit5
###################################################
what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
"NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F")
plot(ae, what = what, bjerrum = TRUE, log = TRUE, ylim = c(-6,-1),
legendinset = 0, lwd = 3, palette = c(1,3,4,5,6,colors()[seq(100,250,6)]))
###################################################
### code chunk number 74: TAfit1
###################################################
ae_init <- aquaenv(S = 35, t = 15, SumCO2 = 0.0035, SumNH4 = 0.00002, pH = 11.3)
ae <- titration(ae_init, mass_sample = 0.01, mass_titrant = 0.02,
conc_titrant = 0.01, S_titrant = 0.5, steps = 100)
plot(ae, xval = ae$delta_mass_titrant, xlab = "HCl solution added [kg]",
what = "pH", xlim = c(0,0.015))
par(new = TRUE)
plot(ae$delta_mass_titrant[1:100], diff(ae$pH), type = "l",
col = "red", xlim = c(0,0.015), ylab = "", xlab = "", yaxt = "n")
par(new = TRUE)
plot(ae$delta_mass_titrant[2:100], diff(diff(ae$pH)), type = "l",
col = "blue", xlim = c(0,0.015), ylab = "", xlab = "", yaxt = "n")
abline(h =0, col = "blue")
abline(v = ae$TA[[1]])
abline(v = ae$TA[[1]] - ae$SumCO2[[1]])
###################################################
### code chunk number 75: TAfit2
###################################################
plot(ae, xval = ae$delta_mass_titrant, xlab = "HCl solution added [kg]",
what = "pH", xlim = c(0,0.015))
prot1 <- c()
for (i in 1:length(ae$pH))
prot1 <- c(prot1, (10^-(ae$pH[[i]])+ae$HSO4[[i]]+ae$HF[[i]]+
ae$CO2[[i]]-ae$CO3[[i]]-ae$BOH4[[i]]-ae$OH[[i]]))
par(new = TRUE)
plot(ae$delta_mass_titrant, prot1, type = "l", col = "blue", xlim = c(0,0.015),
ylab = "", xlab = "", yaxt = "n", ylim = c(-0.015,0.015))
prot2 <- c()
for (i in 1:length(ae$pH))
prot2 <- c(prot2, (10^-(ae$pH[[i]])+ae$HSO4[[i]]+ae$HF[[i]]-
ae$HCO3[[i]]-2*ae$CO3[[i]]-ae$BOH4[[i]]-ae$OH[[i]]))
par(new = TRUE)
plot(ae$delta_mass_titrant, prot2, type = "l", col = "green", xlim = c(0,0.015),
ylab = "", xlab = "", yaxt = "n", ylim = c(-0.015,0.015))
abline(v = ae$TA[[1]])
abline(v = ae$TA[[1]] - ae$SumCO2[[1]])
abline(h = 0)
###################################################
### code chunk number 76: TAfit3
###################################################
ae <- titration(aquaenv(S = 35, t = 15, SumCO2 = 0.0035, SumNH4 = 0.00002,
pH = 11.3),
mass_sample = 100, mass_titrant = 0.5, conc_titrant = 3,
S_titrant = 0.5, steps = 100)
plot(ae, xval = ae$delta_mass_titrant, xlab = "HCl solution added [kg]",
what = "pH", xlim = c(0, 0.5))
prot1 <- c()
for (i in 1:length(ae$pH))
prot1 <- c(prot1, (10^-(ae$pH[[i]])+ae$HSO4[[i]]+ae$HF[[i]]+
ae$CO2[[i]]-ae$CO3[[i]]-ae$BOH4[[i]]-ae$OH[[i]]))
par(new = TRUE)
plot(ae$delta_mass_titrant, prot1, type = "l", col = "blue",
xlim = c(0,0.5), ylab = "", xlab = "", yaxt = "n",
ylim = c(-0.015, 0.015))
prot2 <- c()
for (i in 1:length(ae$pH))
prot2 <- c(prot2, (10^-(ae$pH[[i]])+ae$HSO4[[i]]+ae$HF[[i]]-
ae$HCO3[[i]]-2*ae$CO3[[i]]-ae$BOH4[[i]]-ae$OH[[i]]))
par(new = TRUE)
plot(ae$delta_mass_titrant, prot2, type = "l", col = "green",
xlim = c(0,0.5), ylab = "", xlab = "", yaxt = "n",
ylim = c(-0.015,0.015))
abline(v = (ae$TA[[1]]*100/3))
abline(v = ((ae$TA[[1]] - ae$SumCO2[[1]])*100/3))
abline(h = 0)
###################################################
### code chunk number 77: TAfit4
###################################################
initial_ae <- aquaenv(S = 35, t = 15, SumCO2 = 0.002, TA = 0.0022)
ae <- titration(initial_ae, mass_sample = 0.01, mass_titrant = 0.003,
conc_titrant = 0.01, S_titrant = 0.5, steps = 20)
###################################################
### code chunk number 78: TAfit5
###################################################
titcurve <- cbind(ae$delta_mass_titrant, ae$pH)
###################################################
### code chunk number 79: TAfit6
###################################################
fit1 <- TAfit(initial_ae, titcurve, conc_titrant = 0.01,
mass_sample = 0.01, S_titrant = 0.5)
fit1
###################################################
### code chunk number 80: TAfit6a (eval = FALSE)
###################################################
## initial_ae_ <- aquaenv(S = 35, t = 15, SumCO2 = 0.002, TA = 0.0022,
## k1k2 = "lueker", khf = "perez")
## ae_ <- titration(initial_ae_, mass_sample = 0.01, mass_titrant = 0.003,
## conc_titrant = 0.01,
## S_titrant = 0.5, steps = 20, k1k2 = "roy",
## khf = "perez")
## titcurve_ <- cbind(ae_$delta_mass_titrant, ae_$pH)
## fit1_ <- TAfit(initial_ae_, titcurve_, conc_titrant = 0.01,
## mass_sample = 0.01, S_titrant = 0.5, k1k2 = "roy",
## khf = "perez", verbose = TRUE)
## fit1_
###################################################
### code chunk number 81: TAfit7 (eval = FALSE)
###################################################
## ae <- titration(initial_ae, mass_sample = 0.01, mass_titrant = 0.003,
## conc_titrant = 0.01, steps = 20, seawater_titrant = TRUE)
## titcurve <- cbind(ae$delta_mass_titrant, ae$pH)
## tottitcurve <- cbind(ae$pH, convert(ae$pH, "pHscale", "free2tot", S = 35, t = 15))
## Etitcurve <- cbind(ae$delta_mass_titrant,
## (0.4 - ((PhysChemConst$R/10)*initial_ae$T/PhysChemConst$F)*
## log(10^-tottitcurve[,2])))
###################################################
### code chunk number 82: TAfit8 (eval = FALSE)
###################################################
## fit2 <- TAfit(initial_ae, Etitcurve, conc_titrant = 0.01, mass_sample = 0.01,
## Evals = TRUE, verbose = TRUE, seawater_titrant = TRUE)
## fit2
###################################################
### code chunk number 83: TAfit9
###################################################
fit3 <- TAfit(initial_ae, titcurve, conc_titrant = 0.01, mass_sample = 0.01,
S_titrant = 0.5, K_CO2fit = TRUE)
fit3
initial_ae$K_CO2
###################################################
### code chunk number 84: TAfit10
###################################################
ae <- titration(initial_ae, mass_sample = 0.01, mass_titrant = 0.003,
conc_titrant = 0.01, steps = 20, seawater_titrant = TRUE)
titcurve <- cbind(ae$delta_mass_titrant, ae$pH)
fit4 <- TAfit(initial_ae, titcurve, conc_titrant = 0.01, mass_sample = 0.01,
K_CO2fit = TRUE, seawater_titrant = TRUE)
fit4
###################################################
### code chunk number 85: TAfit11 (eval = FALSE)
###################################################
## Etitcurve <- cbind(titcurve[,1], (0.4 - ((PhysChemConst$R/10)*initial_ae$T/
## PhysChemConst$F)*log(10^-titcurve[,2])))
## fit5 <- TAfit(initial_ae, Etitcurve, conc_titrant = 0.01, mass_sample = 0.01,
## K_CO2fit = TRUE, seawater_titrant = TRUE, Evals = TRUE)
## fit5
###################################################
### code chunk number 86: TAfit12 (eval = FALSE)
###################################################
## neqsptitcurve <- rbind(titcurve[1:9,], titcurve[11:20,])
## fit6 <- TAfit(initial_ae, neqsptitcurve, conc_titrant = 0.01,
## mass_sample = 0.01, seawater_titrant = TRUE, equalspaced = FALSE,
## verbose = TRUE, debug = TRUE)
## fit6
###################################################
### code chunk number 87: TAfit13
###################################################
noisetitcurve <- titcurve * rnorm(length(titcurve), mean = 1, sd = 0.01) #one percent error possible
fit7 <- TAfit(initial_ae, noisetitcurve, conc_titrant = 0.01, mass_sample = 0.01,
seawater_titrant = TRUE, verbose = FALSE, debug = TRUE)
fit7
###################################################
### code chunk number 88: TAfit14
###################################################
ylim <- range(noisetitcurve[,2], calc)
xlim <- range(tit$delta_mass_titrant, noisetitcurve[,1])
plot(noisetitcurve[,1], noisetitcurve[,2], xlim = xlim, ylim = ylim,
type = "l", xlab = "delta mass titrant", ylab = "pH (free scale)")
par(new = TRUE)
plot(tit$delta_mass_titrant, calc, xlim = xlim, ylim = ylim, type = "l",
col = "red", xlab = "", ylab = "")
###################################################
### code chunk number 89: TAfit15
###################################################
conc_titrant <- 0.3 # mol/kg-soln
mass_sample <- 0.2 # kg
S_titrant <- 14.835 # is aequivalent to the ionic strength of 0.3 mol/kg-soln
SumBOH3 <- 0.00042 # mol/kg-soln
SumH2SO4 <- 0.02824 # mol/kg-soln
SumHF <- 0.00007 # mol/kg-soln
###################################################
### code chunk number 90: TAfit16
###################################################
sam <- cbind(sample_dickson1981[,1]/1000, sample_dickson1981[,2]) # convert mass of titrant from g to kg
###################################################
### code chunk number 91: TAfit17
###################################################
dicksonfit <- TAfit(aquaenv(S = 35, t = 25, SumBOH3 = SumBOH3,
SumH2SO4 = SumH2SO4, SumHF=SumHF), sam, conc_titrant,
mass_sample, S_titrant = S_titrant, debug = TRUE)
dicksonfit
###################################################
### code chunk number 92: TAfit18
###################################################
dicksontitration1 <- titration(aquaenv(S = 35, t = 25, SumCO2 = 0.00220,
SumBOH3 = SumBOH3, SumH2SO4 = SumH2SO4, SumHF = SumHF, TA = 0.00245),
mass_sample = mass_sample, mass_titrant = 0.0025,
conc_titrant = conc_titrant, steps = 50, type = "HCl")
###################################################
### code chunk number 93: TAfit19
###################################################
dicksontitration2 <- titration(aquaenv(S = 35, t = 25, SumCO2 = 0.00220,
SumBOH3 = SumBOH3, SumH2SO4 = SumH2SO4, SumHF = SumHF, TA = 0.00245),
mass_sample = mass_sample, mass_titrant = 0.0025,
conc_titrant = conc_titrant, S_titrant = S_titrant, steps = 50, type = "HCl")
###################################################
### code chunk number 94: TAfit20
###################################################
plot(dicksontitration1, xval = dicksontitration1$delta_mass_titrant,
what = "pH", xlim = c(0,0.0025), ylim = c(3,8.2), col = "red",
xlab = "delta mass titrant")
par(new = TRUE)
plot(dicksontitration2, xval = dicksontitration2$delta_mass_titrant,
what = "pH", xlim = c(0,0.0025), ylim = c(3,8.2), col = "blue", xlab = "")
par(new = TRUE)
plot(sam[,1], sam[,2], type = "l", xlim = c(0,0.0025),
ylim = c(3,8.2), xlab = "", ylab = "")
###################################################
### code chunk number 95: TAfit21
###################################################
plot(dicksontitration2$pH - sam[,2])
###################################################
### code chunk number 96: TAfit22
###################################################
dicksonfit2 <- TAfit(aquaenv(S = 35, t = 25, SumBOH3 = SumBOH3,
SumH2SO4 = SumH2SO4, SumHF = SumHF), sam, conc_titrant,
mass_sample, S_titrant = S_titrant, debug = TRUE, K_CO2fit = TRUE)
dicksonfit2
###################################################
### code chunk number 97: AquaEnv.rnw:1763-1764
###################################################
###################################################
### code chunk number 98: TAfit23
###################################################
dicksontitration3 <- titration(aquaenv(S = 35, t = 25, SumCO2 = 0.00220,
SumBOH3 = SumBOH3, SumH2SO4 = SumH2SO4, SumHF = SumHF, TA = 0.00245,
k_w = 4.32e-14, k_co2 = 1e-6, k_hco3 = 8.20e-10, k_boh3 = 1.78e-9,
k_hso4 = (1/1.23e1), k_hf = (1/4.08e2)),
mass_sample = mass_sample, mass_titrant = 0.0025, conc_titrant = conc_titrant,
steps = 50, type = "HCl", S_titrant = S_titrant,
k_w = 4.32e-14, k_co2 = 1e-6, k_hco3 = 8.20e-10, k_boh3 = 1.78e-9,
k_hso4 = (1/1.23e1), k_hf = (1/4.08e2))
plot(dicksontitration3, xval = dicksontitration3$delta_mass_titrant,
what = "pH", xlim = c(0,0.0025), ylim = c(3,8.2), col = "blue",
xlab = "delta mass titrant")
par(new = TRUE)
plot(sam[,1], sam[,2], type = "l", xlim = c(0,0.0025), ylim = c(3,8.2),
xlab = "", ylab = "")
###################################################
### code chunk number 99: TAfit24
###################################################
plot(dicksontitration3$pH - sam[,2])
###################################################
### code chunk number 100: TAfit25
###################################################
dicksonfit3 <- TAfit(aquaenv(S = 35, t = 25, SumBOH3 = SumBOH3, SumH2SO4 = SumH2SO4,
SumHF = SumHF, k_w = 4.32e-14, k_co2 = 1e-6, k_hco3 = 8.20e-10,
k_boh3 = 1.78e-9, k_hso4 = (1/1.23e1), k_hf = (1/4.08e2)),
sam, conc_titrant, mass_sample, S_titrant = S_titrant, debug = TRUE,
k_w = 4.32e-14, k_co2 = 1e-6, k_hco3 = 8.20e-10, k_boh3 = 1.78e-9,
k_hso4 = (1/1.23e1), k_hf = (1/4.08e2))
dicksonfit3
###################################################
### code chunk number 101: extend1
###################################################
simpletitration <- function(aquaenv, # an object of class aquaenv: minimal definition,
# contains all information about the system:
# T, S, d, total concentrations of nutrients etc
volume, # the volume of the (theoretical) titration vessel in l
amount, # the amount of titrant added in mol
steps, # the amount of steps the amount of titrant is added in
type) # the type of titrant: either "HCl" or "NaOH"
{
directionTAchange <- switch(type, HCl = -1, NaOH = +1)
TAconcchangeperstep <- convert(((amount/steps)/volume), "conc", "molar2molin", aquaenv$t, aquaenv$S)
aquaenvtemp <- aquaenv
for (i in 1:steps)
{
TA <- aquaenvtemp$TA + (directionTAchange * TAconcchangeperstep)
aquaenvtemp <- aquaenv(ae=aquaenvtemp, TA=TA)
aquaenv <- merge(aquaenv, aquaenvtemp)
}
aquaenv[["DeltaCTitrant"]] <- convert((amount/volume)/steps*(1:(steps+1)),
"conc", "molar2molin", aquaenv$t, aquaenv$S)
return(aquaenv) # object of class aquaenv which contains a titration simulation
}
###################################################
### code chunk number 102: extend2
###################################################
ae <- simpletitration(aquaenv(S = 35, t = 15, SumCO2 = 0.003500,
SumNH4 = 0.000020, pH = 11.3),
volume =100, amount = 1.5, steps = 100, type = "HCl")
what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "NH4", "NH3",
"H2SO4", "HSO4", "SO4", "HF", "F")
plot(ae, what = what, bjerrum = TRUE, log = TRUE, ylim = c(-6,-1),
legendinset = 0, lwd = 3, palette = c(1,3,4,5,6,colors()[seq(100,250,6)]))
###################################################
### code chunk number 103: extend3
###################################################
simpleTAfit <- function(ae, # an object of class aquaenv: minimal definition,
# contains all information about the system:
# T, S, d, total concentrations of nutrients etc
pHmeasurements, # a table containing the titration curve:
# basically a series of pH values (pH on free proton scale)
volume, # the volume of the titration vessel
amount, # the total amount of the titrant added
TAguess=0.0025, # a first guess for [TA] and [SumCO2] to be used as
# initial values for the optimization procedure
type="HCl") # the type of titrant: either "HCl" or "NaOH"
{
ae$Na <- NULL # make sure ae gets cloned as "skeleton": cloneaquaenv determines "skeleton"
# TRUE or FALSE from the presence of a value for Na
residuals <- function(state)
{
ae$SumCO2 <- state[[1]]
pHcalc <- simpletitration(aquaenv(ae=ae, TA=state[[2]]), volume=volume,
amount=amount, steps=(length(pHmeasurements)-1), type=type)$pH
residuals <- pHmeasurements-pHcalc
return(residuals)
}
require(minpack.lm)
out <- nls.lm(fn=residuals, par=c(TAguess, TAguess)) #guess for TA is also used as guess for SumCO2
result <- list(out$par[[2]], out$par[[1]], out$deviance)
attr(result[[1]], "unit") <- "mol/kg-soln"
attr(result[[2]], "unit") <- "mol/kg-soln"
names(result) <- c("TA", "SumCO2", "sumofsquares")
return(result) # a list of three values
# ([TA] in mol/kg-solution, [SumCO2] in mol/kg-solution, sum of the squared residuals)
}
###################################################
### code chunk number 104: extend4
###################################################
pHmeasurements <- ae$pH
fit <- simpleTAfit(aquaenv(S = 35, t = 15, SumNH4 = 0.00002),
pHmeasurements, volume = 100, amount = 1.5)
fit
###################################################
### code chunk number 105: CleaningUp
###################################################
graphics.off()
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### R code from vignette source 'AquaEnv.rnw'
###################################################
### code chunk number 1: Preliminaries
###################################################
library("AquaEnv")
library("deSolve")
options(width=80)
Plotit <- AquaEnv:::plot.aquaenv
plot.aquaenv <- function(...) {
if ("newdevice" %in% list(...))
Plotit(...)
else
Plotit(newdevice = FALSE, ...) # else Sweave does not work...
}
###################################################
### code chunk number 2: AquaenvElements
###################################################
test <- aquaenv(S = 35, t = 10)
test$t
###################################################
### code chunk number 3: CallingKFuncsDirectly
###################################################
K_CO2(S = 15, t = 30)
K0_CO2(S = 15, t = 30)
Ksp_calcite(S = 15, t = 30, p = 100)
###################################################
### code chunk number 4: Avector
###################################################
K_CO2(S = 10:15, t = 30)
###################################################
### code chunk number 5: MinimalAquaenv
###################################################
ae <- aquaenv(S = 30, t = 15)
ae$K_CO2
###################################################
### code chunk number 6: AquaenvWithDepth
###################################################
ae <- aquaenv(S = 30, t = 15, p = 10)
names(ae)
ae$Ksp_calcite
###################################################
### code chunk number 7: AquaenvPressures
###################################################
ae <- aquaenv(S = 30, t = 15, p = 10)
ae[c("p", "P")]
ae <- aquaenv(S = 30, t = 15, P = 10)
unlist(ae[c("p", "P")])
ae <- aquaenv(S = 30, t = 15, P = 10, Pa = 0.5)
unlist(ae[c("p", "P")])
ae <- aquaenv(S = 30, t = 15, d = 100)
unlist(ae[c("p", "P")])
ae <- aquaenv(S = 30, t = 15, d = 100, lat = 51)
unlist(ae[c("p", "P")])
###################################################
### code chunk number 8: SkeletonAquaenv
###################################################
ae <- aquaenv(S = 30, t = 15, p = 10, skeleton = TRUE)
names(ae)
###################################################
### code chunk number 9: CompleteAquaenvSystem
###################################################
S <- 30
t <- 15
p <- 10
SumCO2 <- 0.0020
pH <- 8
TA <- 0.002142233
fCO2 <- 0.0005272996
CO2 <- 2.031241e-05
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH)
ae$TA
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, TA = TA)
ae$pH
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, CO2 = CO2)
ae$pH
names(ae)
###################################################
### code chunk number 10: SpeciationSkeletonAquaenv
###################################################
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH, speciation = FALSE)
names(ae)
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH, speciation = FALSE,
skeleton = TRUE)
names(ae)
###################################################
### code chunk number 11: DSAAquaenv
###################################################
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, fCO2 = fCO2, dsa = TRUE)
ae$dTAdH
ae$revelle
###################################################
### code chunk number 12: ErrorMessagesAquaenv
###################################################
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, CO2 = CO2, fCO2 = fCO2)
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH, TA = TA)
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH, CO2 = CO2)
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH, fCO2 = fCO2)
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, TA = TA, CO2 = CO2)
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, TA = TA, fCO2 = fCO2)
###################################################
### code chunk number 13: SumCO2Calculating
###################################################
fCO2 <- 0.0006943363
CO2 <- 2.674693e-05
pH <- 7.884892
TA <- 0.0021
S <- 30
t <- 15
p <- 10
ae <- aquaenv(S, t, p, SumCO2 = NULL, pH = pH, CO2 = CO2)
ae$SumCO2
ae <- aquaenv(S, t, p, SumCO2 = NULL, pH = pH, fCO2 = fCO2)
ae$SumCO2
ae <- aquaenv(S, t, p, SumCO2 = NULL, pH = pH, TA = TA)
ae$SumCO2
ae <- aquaenv(S, t, p, SumCO2 = NULL, TA = TA, CO2 = CO2)
ae$SumCO2
ae <- aquaenv(S, t, p, SumCO2 = NULL, TA = TA, fCO2 = fCO2)
ae$SumCO2
###################################################
### code chunk number 14: CloningAquaenv
###################################################
S <- 30
t <- 15
SumCO2 <- 0.0020
TA <- 0.00214
ae <- aquaenv(S, t, SumCO2 = SumCO2, TA = TA)
ae$pH
ae1 <- aquaenv(ae = ae) # this is the same
ae1$pH
ae2 <- aquaenv(ae = ae, pH = 9)
c(ae$TA, ae2$TA)
ae3 <- aquaenv(ae = ae, TA = 0.002)
c(ae$pH, ae3$pH)
K_CO2 <- 1e-6
ae4 <- aquaenv(ae = ae, k_co2 = 1e-6)
c(ae$TA, ae4$TA)
###################################################
### code chunk number 15: PreparingInput
###################################################
S <- 10
t <- 15
pH_NBS <- 8.142777
SumCO2molar <- 0.002016803
(pH_free <- convert(pH_NBS, "pHscale", "nbs2free", S = S, t = t))
(SumCO2molin <- convert(SumCO2molar, "conc", "molar2molin", S = S, t = t))
ae <- aquaenv(S, t, SumCO2 = SumCO2molin, pH = pH_free)
ae$pH
ae$SumCO2
###################################################
### code chunk number 16: InputVectors
###################################################
SumCO2 <- 0.0020
pH <- 8
S <- 30
t <- 1:5
p <- 10
ae <- aquaenv(S, t, p, SumCO2 = SumCO2, pH = pH)
rbind(t = ae$t, TA = ae$TA)
###################################################
### code chunk number 17: Selectplot
###################################################
plot(ae, xval = t, xlab = "t/(deg C)",
what = c("pH", "CO2", "HCO3", "CO3"),
mfrow = c(1, 4))
###################################################
### code chunk number 18: MoreInputVectors1 (eval = FALSE)
###################################################
## ae <- aquaenv(S=20:24, t=15, p=10, SumCO2 = SumCO2, pH = pH, dsa = TRUE)
## rbind(ae$S, ae$TA)
###################################################
### code chunk number 19: MoreInputVectors6
###################################################
ae <- aquaenv(20, 10, SumCO2=seq(0.001, 0.002, 0.00025), TA = 0.002)
rbind(ae$SumCO2, ae$pH, ae$HCO3)
###################################################
### code chunk number 20: SumCO2CalcInputVecs1
###################################################
ae <- aquaenv(S = 30, t = 11:15, SumCO2 = NULL, pH = pH, CO2 = CO2,
dsa = TRUE)
ae$SumCO2
###################################################
### code chunk number 21: Dataframe
###################################################
ae <- aquaenv(S = 30, t = 11:15, SumCO2 = NULL, pH = 8, CO2 = 2e-5)
aedataframe <- as.data.frame(ae)
dim(aedataframe)
aedataframe[, 1:3]
aetest <- aquaenv(ae = aedataframe, from.data.frame = TRUE)
###################################################
### code chunk number 22: Elementconversion
###################################################
ae <- aquaenv(S = 30, t = 10)
ae$SumBOH3
ae <- convert(ae, "mol/kg-soln", "umol/kg-H2O", 1e6/ae$molal2molin, "unit")
ae$SumBOH3
###################################################
### code chunk number 23: DSAQuantities1
###################################################
ae <- aquaenv(S = 30, t = 15, d = 10, SumCO2 = 0.002, pH = 8, dsa = TRUE)
###################################################
### code chunk number 24: DSAQuantities2
###################################################
ae$dTAdH
ae$dTAdSumCO2
###################################################
### code chunk number 25: DSAQuantities3
###################################################
ae$dTAdKdKdS
ae$dTAdKdKdSumH2SO4
###################################################
### code chunk number 26: DSAQuantities4
###################################################
ae$c1
###################################################
### code chunk number 27: BufferFactors1
###################################################
BF <- BufferFactors()
names(BF)
BF$dtotX.dpH
###################################################
### code chunk number 28: BufferFactors2
###################################################
ae <- aquaenv(S = 30, t = 15, d = 10, SumCO2 = 0.002, pH = 8.1,
skeleton = TRUE)
BF <- BufferFactors(ae = ae)
BF$RF
###################################################
### code chunk number 29: BufferFactors3
###################################################
ae <- aquaenv(S = 30, t = 15, d = 10, SumCO2 = 0.002, pH = 8.1, dsa = TRUE)
BF <- BufferFactors(ae = ae)
cbind(ae$dTAdH,BF$beta.H)
###################################################
### code chunk number 30: BufferFactors4
###################################################
parameters <- c(DIC = 0.002, Alk = 0.0022)
BF <- BufferFactors(parameters = parameters)
BF$RF
###################################################
### code chunk number 31: BufferFactors5
###################################################
ae <- aquaenv(S = 30, t = 15, d = 10, SumCO2 = 0.002, pH = 8.1,
skeleton = TRUE)
BF <- BufferFactors(ae = ae)
BF$RF
parameters <- c(Alk = 0.0022)
BF_2 <- BufferFactors(ae = ae, parameters = parameters)
BF_2$RF
###################################################
### code chunk number 32: BufferFactors6
###################################################
BF <- BufferFactors(species = c("CO2", "HCO3", "CO3", "SumNH4"))
BF$dtotX.dX
###################################################
### code chunk number 33: BufferFactors7
###################################################
ae <- aquaenv(S = 30, t = 15, d = 10, SumCO2 = 0.002, pH = 8.1,
skeleton = TRUE)
BF <- BufferFactors(ae = ae, species = c("SumCO2", "SumNH4"))
BF$dtotX.dX
###################################################
### code chunk number 34: BufferFactors7
###################################################
BF <- BufferFactors(k1k2 = "roy")
BF$RF
BF <- BufferFactors(k_co2 = 1e-6)
BF$RF
###################################################
### code chunk number 35: Plot1
###################################################
ae <- aquaenv(20:30, 10)
plot(ae, xval = 20:30, xlab = "S", what = c("K_CO2", "K_HCO3", "K_BOH3"),
size = c(10, 2), mfrow = c(1,3))
###################################################
### code chunk number 36: OrdDynModParamList (eval = FALSE)
###################################################
## parameters <- list(
## S = 25 , # psu
## t_min = 5 , # degrees C
## t_max = 25 , # degrees C
##
## k = 0.4 , # 1/d proportionality factor for air-water exchange
## rOx = 0.0000003 , # mol-N/(kg*d) maximal rate of oxic mineralisation
## rNitri = 0.0000002 , # mol-N/(kg*d) maximal rate of nitrification
## rPP = 0.000006 , # mol-N/(kg*d) maximal rate of primary production
##
## ksDINPP = 0.000001 , # mol-N/kg
## ksNH4PP = 0.000001 , # mol-N/kg
##
## D = 0.1 , # 1/d (dispersive) transport coefficient
##
## O2_io = 0.000296 , # mol/kg-soln
## NO3_io = 0.000035 , # mol/kg-soln
## SumNH4_io = 0.000008 , # mol/kg-soln
## SumCO2_io = 0.002320 , # mol/kg-soln
## TA_io = 0.002435 , # mol/kg-soln
##
## C_Nratio = 8 , # mol C/mol N C:N ratio of organic matter
##
## a = 30 , # time at which PP begins
## b = 50 , # time at which PP stops again
##
## modeltime = 100 # duration of the model
## )
###################################################
### code chunk number 37: OrdDynModFunction (eval = FALSE)
###################################################
##
## temperature <- with (parameters,
## approxfun(x = 0:101,
## y = c(seq(t_min, t_max, (t_max-t_min)/50),
## seq(t_max, t_min, -(t_max-t_min)/50)))
## )
##
## boxmodel <- function(time, state, parameters) {
## with (
## as.list(c(state, parameters)), {
## t <- temperature(time)
## ae <- aquaenv(S = S, t = t, SumCO2 = SumCO2,
## SumNH4 = SumNH4, TA = TA)
##
## ECO2 <- k * (ae$CO2_sat - ae$CO2)
## EO2 <- k * (ae$O2_sat - O2)
##
## # dilution
## TO2 <- D*(O2_io - O2)
## TNO3 <- D*(NO3_io - NO3)
## TSumNH4 <- D*(SumNH4_io - SumNH4)
## TTA <- D*(TA_io - TA)
## TSumCO2 <- D*(SumCO2_io - SumCO2)
##
## RNit <- rNitri * SumNH4/(SumNH4+1e-8)
##
## ROx <- rOx
## ROxCarbon <- ROx * C_Nratio
##
## pNH4PP <- 0
## RPP <- 0
##
## if ((time > a) && (time < b)) {
## RPP <- rPP * ((SumNH4+NO3)/(ksDINPP + (SumNH4+NO3)))
## pNH4PP <- SumNH4/(SumNH4+NO3)
## }
##
## RPPCarbon <- RPP * C_Nratio
##
## dO2 <- TO2 + EO2 - ROxCarbon - 2*RNit + (2-2*pNH4PP)*RPP + RPPCarbon
## dNO3 <- TNO3 + RNit -(1-pNH4PP)*RPP
##
## dSumCO2 <- TSumCO2 + ECO2 + ROxCarbon - RPPCarbon
## dSumNH4 <- TSumNH4 + ROx - RNit - pNH4PP*RPP
##
## dTA <- TTA + ROx - 2*RNit -(2*pNH4PP-1)*RPP
##
## ratesofchanges <- c(dO2, dNO3, dSumNH4, dSumCO2, dTA)
##
## return(list(ratesofchanges, ae[c("t", "NH4", "NH3", "pH")]))
## } )
## }
###################################################
### code chunk number 38: OrdDynModSolution (eval = FALSE)
###################################################
## initialstate <- with (parameters,
## c(O2=O2_io, NO3=NO3_io, SumNH4=SumNH4_io, SumCO2=SumCO2_io, TA=TA_io))
##
## times <- 1:100
## output <- vode(initialstate,times,boxmodel,parameters, hmax = 1)
###################################################
### code chunk number 39: OrdDynModePlotting (eval = FALSE)
###################################################
## plot(output)
###################################################
### code chunk number 40: SinglePHModParams
###################################################
parameters <- list(
S = 25 , # psu
t = 15 , # degrees C
k = 0.4 , # 1/d proportionality factor for air-water exchange
rOx = 0.0000003 , # mol-N/(kg*d) maximal rate of oxic mineralisation
rNitri = 0.0000002 , # mol-N/(kg*d) maximal rate of nitrification
rPP = 0.0000006 , # mol-N/(kg*d) maximal rate of primary production
ksSumNH4 = 0.000001 , # mol-N/kg
D = 0.1 , # 1/d (dispersive) transport coefficient
SumNH4_io = 0.000008 , # mol/kg-soln
SumCO2_io = 0.002320 , # mol/kg-soln
TA_io = 0.002435 , # mol/kg-soln
C_Nratio = 8 , # mol C/mol N C:N ratio of organic matter
a = 5 , # time from which PP begins
b = 20 , # time where PP shuts off again
modeltime = 30 # duration of the model
)
###################################################
### code chunk number 41: SinglePHModFunction
###################################################
boxmodel <- function(timestep, currentstate, parameters)
{
with (
as.list(c(currentstate,parameters)),
{
# the "classical" implicit pH calculation method is applied in aquaenv
ae <- aquaenv(S=S, t=t, SumCO2=sumCO2,
SumNH4=sumNH4, TA=alkalinity, dsa=TRUE)
ECO2 <- k * (ae$CO2_sat - ae$CO2)
RNit <- rNitri
ROx <- rOx
if ((timestep > a) && (timestep < b))
RPP <- rPP * (sumNH4/(ksSumNH4 + sumNH4))
else
RPP <- 0
dsumCO2 <- ECO2 + C_Nratio*ROx - C_Nratio*RPP
dsumNH4 <- ROx - RNit - RPP
dalkalinity <- ROx - 2*RNit - RPP
# The DSA pH
dH <- (dalkalinity - (dsumCO2*ae$dTAdSumCO2 + dsumNH4*ae$dTAdSumNH4))/ae$dTAdH
DSApH <- -log10(H)
# The DSA pH using pH dependent fractional stoichiometry (= using partitioning coefficients)
rhoHECO2 <- ae$c2 + 2*ae$c3
rhoHRNit <- 1 + ae$n1
rhoHROx <- C_Nratio * (ae$c2 + 2*ae$c3) - ae$n1
rhoHRPP <- -(C_Nratio * (ae$c2 + 2*ae$c3)) + ae$n1
dH_ECO2 <- rhoHECO2*ECO2/(-ae$dTAdH)
dH_RNit <- rhoHRNit*RNit/(-ae$dTAdH)
dH_ROx <- rhoHROx*ROx /(-ae$dTAdH)
dH_RPP <- rhoHRPP*RPP /(-ae$dTAdH)
dH_stoich <- dH_ECO2 + dH_RNit + dH_ROx + dH_RPP
DSAstoichpH <- -log10(H_stoich)
ratesofchanges <- c(dsumNH4, dsumCO2, dalkalinity, dH, dH_stoich)
processrates <- c(ECO2=ECO2, RNit=RNit, ROx=ROx, RPP=RPP)
DSA <- c(DSApH=DSApH, rhoHECO2=rhoHECO2, rhoHRNit=rhoHRNit, rhoHROx=rhoHROx,
rhoHRPP=rhoHRPP, dH_ECO2=dH_ECO2, dH_RNit=dH_RNit, dH_ROx=dH_ROx,
dH_RPP=dH_RPP, DSAstoichpH=DSAstoichpH)
return(list(ratesofchanges, processrates, DSA, ae))
}
)
}
###################################################
### code chunk number 42: SinglPHModSolution
###################################################
with (as.list(parameters),
{
H_init <<- 10^(-(aquaenv(S=S, t=t, SumCO2=SumCO2_io, SumNH4=SumNH4_io, TA=TA_io,
speciation=FALSE)$pH))
initialstate <<- c(sumNH4=SumNH4_io, sumCO2=SumCO2_io, alkalinity =TA_io, H=H_init,
H_stoich=H_init)
times <<- c(0:modeltime)
})
output <- vode(initialstate, times, boxmodel, parameters, hmax=1)
###################################################
### code chunk number 43: SinglePHModePlotting1
###################################################
select <- c("sumCO2", "alkalinity", "sumNH4", "RPP", "dTAdH", "dTAdSumCO2",
"dTAdSumNH4","rhoHECO2", "rhoHRNit", "rhoHROx","dH_ECO2","dH_RNit",
"dH_RPP","pH", "DSApH", "DSAstoichpH")
plot(output, which = select, xlab="time/d", mfrow=c(4,4))
###################################################
### code chunk number 44: SinglepHModPlotting2
###################################################
what <- c("dH_ECO2", "dH_RNit", "dH_ROx", "dH_RPP")
plot(aquaenv(ae=as.data.frame(output), from.data.frame=TRUE),
xval = times, what = what, xlab = "time/d", size = c(7,5),
ylab = "mol-H/(kg-soln*d)", legendposition = "bottomright", cumulative = TRUE)
###################################################
### code chunk number 45: SinplePHModConsistencyCheck
###################################################
matplot(output[, "time"],
output[, c("pH", "DSApH", "DSAstoichpH")], type = "l", lty = 1, lwd = 2)
###################################################
### code chunk number 46: ImplicitPHModParams (eval = FALSE)
###################################################
## parameters <- list(
## t = 15 , # degrees C
## S = 35 , # psu
##
## SumCO2_t0 = 0.002 , # mol/kg-soln (comparable to Wang2005)
## TA_t0 = 0.0022 , # mol/kg-soln (comparable to Millero1998)
##
## kc = 0.5 , # 1/d proportionality factor for air-water exchange
## kp = 0.000001 , # mol/(kg-soln*d) max rate of calcium carbonate precipitation
## n = 2.0 , # - exponent for kinetic rate law of precipitation
##
## modeltime = 20 , # d duration of the model
## outputsteps = 100 # number of outputsteps
## )
###################################################
### code chunk number 47: ImplicitPHModFunction (eval = FALSE)
###################################################
## boxmodel <- function(timestep, currentstate, parameters)
## {
## with (
## as.list(c(currentstate,parameters)),
## {
## ae <- aquaenv(S=S, t=t, SumCO2=SumCO2, TA=TA, SumSiOH4=0,
## SumBOH3=0, SumH2SO4=0, SumHF=0)
##
## Rc <- kc * ((ae$CO2_sat) - (ae$CO2))
## Rp <- kp * (1-ae$omega_calcite)^n
##
## dSumCO2 <- Rc - Rp
## dTA <- -2*Rp
##
## ratesofchanges <- c(dSumCO2, dTA)
##
## processrates <- c(Rc=Rc, Rp=Rp)
##
## return(list(ratesofchanges, list(processrates, ae)))
## }
## )
## }
###################################################
### code chunk number 48: ImplicitPHModSolution (eval = FALSE)
###################################################
## with (as.list(parameters),
## {
## initialstate <<- c(SumCO2=SumCO2_t0, TA=TA_t0)
## times <<- seq(0,modeltime,(modeltime/outputsteps))
## })
## output <<- vode(initialstate,times,boxmodel,parameters, hmax=1)
###################################################
### code chunk number 49: ExplicitPHModParams (eval = FALSE)
###################################################
## parameters <- list(
## S = 35 , # psu
## t = 15 , # degrees C
##
## SumCO2_t0 = 0.002 , # mol/kg-soln (comparable to Wang2005)
## TA_t0 = 0.0022 , # mol/kg-soln (comparable to Millero1998)
##
## kc = 0.5 , # 1/d proportionality factor for air-water exchange
## kp = 0.000001 , # mol/(kg-soln*d) max rate of calcium carbonate precipitation
## n = 2.0 , # - exponent for kinetic rate law of precipitation
##
## modeltime = 20 , # d duration of the model
## outputsteps = 100 # number of outputsteps
## )
###################################################
### code chunk number 50: ExplicitPHModFunction (eval = FALSE)
###################################################
## boxmodel <- function(timestep, currentstate, parameters)
## {
## with (
## as.list(c(currentstate,parameters)),
## {
## ae <- aquaenv(S=S, t=t, SumCO2=SumCO2, pH=-log10(H), SumSiOH4=0,
## SumBOH3=0, SumH2SO4=0, SumHF=0, dsa=TRUE)
##
## Rc <- kc * ((ae$CO2_sat) - (ae$CO2))
## Rp <- kp * (1-ae$omega_calcite)^n
##
## dSumCO2 <- Rc - Rp
##
## dHRc <- ( -(ae$dTAdSumCO2*Rc ))/ae$dTAdH
## dHRp <- (-2*Rp -(ae$dTAdSumCO2*(-Rp)))/ae$dTAdH
## dH <- dHRc + dHRp
##
## ratesofchanges <- c(dSumCO2, dH)
##
## processrates <- c(Rc=Rc, Rp=Rp)
## outputvars <- c(dHRc=dHRc, dHRp=dHRp)
##
## return(list(ratesofchanges, list(processrates, outputvars, ae)))
## }
## )
## }
###################################################
### code chunk number 51: ExplicitPHModSolution (eval = FALSE)
###################################################
## with (as.list(parameters),
## {
## aetmp <- aquaenv(S=S, t=t, SumCO2=SumCO2_t0, TA=TA_t0, SumSiOH4=0, SumBOH3=0, SumH2SO4=0, SumHF=0)
## H_t0 <- 10^(-aetmp$pH)
##
## initialstate <<- c(SumCO2=SumCO2_t0, H=H_t0)
## times <<- seq(0,modeltime,(modeltime/outputsteps))
## })
## output <- vode(initialstate,times,boxmodel,parameters, hmax=1)
###################################################
### code chunk number 52: FracStoichModParams (eval = FALSE)
###################################################
## parameters <- list(
## S = 35 , # psu
## t = 15 , # degrees C
##
## SumCO2_t0 = 0.002 , # mol/kg-soln (comparable to Wang2005)
## TA_t0 = 0.0022 , # mol/kg-soln (comparable to Millero1998)
##
## kc = 0.5 , # 1/d proportionality factor for air-water exchange
## kp = 0.000001 , # mol/(kg-soln*d) max rate of calcium carbonate precipitation
## n = 2.0 , # - exponent for kinetic rate law of precipitation
##
## modeltime = 20 , # d duration of the model
## outputsteps = 100 # number of outputsteps
## )
###################################################
### code chunk number 53: FracStoichModFunction (eval = FALSE)
###################################################
## boxmodel <- function(timestep, currentstate, parameters)
## {
## with (
## as.list(c(currentstate,parameters)),
## {
## ae <- aquaenv(S=S, t=t, SumCO2=SumCO2, pH=-log10(H), SumSiOH4=0,
## SumBOH3=0, SumH2SO4=0, SumHF=0, dsa=TRUE)
##
## Rc <- kc * ((ae$CO2_sat) - (ae$CO2))
## Rp <- kp * (1-ae$omega_calcite)^n
##
## dSumCO2 <- Rc - Rp
##
## rhoc <- ae$c2 + 2*ae$c3
## rhop <- 2*ae$c1 + ae$c2
##
## dHRc <- rhoc*Rc/(-ae$dTAdH)
## dHRp <- rhop*Rp/(-ae$dTAdH)
## dH <- dHRc + dHRp
##
## ratesofchanges <- c(dSumCO2, dH)
##
## processrates <- c(Rc=Rc, Rp=Rp)
## outputvars <- c(dHRc=dHRc, dHRp=dHRp, rhoc=rhoc, rhop=rhop)
##
## return(list(ratesofchanges, list(processrates, outputvars, ae)))
## }
## )
## }
###################################################
### code chunk number 54: FracStoichModSolution (eval = FALSE)
###################################################
## with (as.list(parameters),
## {
## aetmp <- aquaenv(S=S, t=t, SumCO2=SumCO2_t0, TA=TA_t0, SumSiOH4=0,
## SumBOH3=0, SumH2SO4=0, SumHF=0)
## H_t0 <- 10^(-aetmp$pH)
##
## initialstate <<- c(SumCO2=SumCO2_t0, H=H_t0)
## times <<- seq(0,modeltime,(modeltime/outputsteps))
## output <<- as.data.frame(vode(initialstate,times,boxmodel,parameters, hmax=1))
## })
###################################################
### code chunk number 55: HClTit1
###################################################
ae_init <- aquaenv(S = 35, t = 15, SumCO2 = 0.0035, SumNH4 = 0.00002, pH = 11.3)
###################################################
### code chunk number 56: HClTit2
###################################################
ae <- titration(ae_init, mass_sample = 0.01, mass_titrant = 0.02,
conc_titrant = 0.01, S_titrant = 0.5, steps = 100)
###################################################
### code chunk number 57: HClTit3
###################################################
what <- c("TA", "pH", "CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
"NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "fCO2")
plot(ae, xval = ae$delta_mass_titrant, xlab = "HCl solution added [kg]",
what = what, size = c(12,8), mfrow = c(4,4))
###################################################
### code chunk number 58: HClTit4 (eval = FALSE)
###################################################
## plot(ae, xval = ae$delta_conc_titrant, what = what,
## xlab = "[HCl] offset added [mol/kg-soln]",
## size = c(14,10), mfrow = c(4,4))
## plot(ae, xval=ae$delta_moles_titrant, xlab = "HCl added [mol]",
## what = what, size = c(14,10), mfrow = c(4,4))
###################################################
### code chunk number 59: HClTit5
###################################################
plot(ae, xval = ae$pH, xlab = "free scale pH", what = what,
size = c(12,8), mfrow = c(4,4))
###################################################
### code chunk number 60: HClTit6
###################################################
plot(ae, bjerrum = TRUE)
###################################################
### code chunk number 61: HClTit7
###################################################
what <- c("CO2", "HCO3", "CO3")
plot(ae, what = what, bjerrum = TRUE, lwd = 4,
palette = c("cyan", "magenta", "yellow"),
bg = "gray", legendinset = 0.1, legendposition = "topleft")
###################################################
### code chunk number 62: HClTit9
###################################################
what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
"NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F")
plot(ae, what = what, bjerrum = TRUE, log = TRUE)
###################################################
### code chunk number 63: HClTit10
###################################################
plot(ae, what = what, bjerrum = TRUE, log = TRUE, ylim = c(-6,-1),
legendinset = 0, lwd = 3,
palette = c(1, 3, 4, 5, 6, colors()[seq(100,250,6)]))
###################################################
### code chunk number 64: NaOHTit1 (eval = FALSE)
###################################################
## ae <- titration(aquaenv(S = 35, t = 15, SumCO2 = 0.0035, SumNH4 = 0.00002, pH = 2),
## mass_sample = 0.01, mass_titrant = 0.02, conc_titrant = 0.01,
## S_titrant = 0.5, steps = 50, type = "NaOH")
###################################################
### code chunk number 65: NaOHTit2 (eval = FALSE)
###################################################
## plot(ae, xval = ae$delta_mass_titrant, xlab = "NaOH solution added [kg]",
## mfrow = c(10,10))
###################################################
### code chunk number 66: NaOHTit3 (eval = FALSE)
###################################################
## what <- c("TA", "pH", "CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
## "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "fCO2")
## plot(ae, xval = ae$delta_mass_titrant, xlab = "NaOH solution added [kg]",
## what = what, size = c(12,8), mfrow = c(4,4))
## plot(ae, xval = ae$pH, xlab = "free scale pH", what = what,
## size = c(12,8), mfrow = c(4,4))
###################################################
### code chunk number 67: NaOHTit4 (eval = FALSE)
###################################################
## what <- c("CO2", "HCO3", "CO3")
## plot(ae, what=what, bjerrum=TRUE)
###################################################
### code chunk number 68: NaOHTit5 (eval = FALSE)
###################################################
## what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
## "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F")
## plot(ae, what = what, bjerrum = TRUE, log = TRUE, ylim = c(-6,-1),
## legendinset = 0, lwd = 3, palette = c(1,3,4,5,6,colors()[seq(100,250,6)]))
###################################################
### code chunk number 69: TextbookTit1
###################################################
ae <- titration(aquaenv(S = 35, t = 15, SumCO2 = 0.0035, SumNH4 = 0.00002, pH = 11.3),
mass_sample = 100, mass_titrant = 0.5, conc_titrant = 3,
S_titrant = 0.5, steps = 100)
###################################################
### code chunk number 70: TextbookTit2 (eval = FALSE)
###################################################
## plot(ae, xval = ae$delta_mass_titrant,
## xlab = "HCl solution added [kg]", mfrow = c(10, 10))
###################################################
### code chunk number 71: TextbookTit3 (eval = FALSE)
###################################################
## what <- c("TA", "pH", "CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
## "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "fCO2")
## plot(ae, xval = ae$delta_mass_titrant, xlab = "HCl solution added [kg]",
## what = what, size = c(12, 8), mfrow = c(4,4))
## plot(ae, xval = ae$pH, xlab = "free scale pH", what = what,
## size = c(12,8), mfrow = c(4,4))
## plot(ae, xval = ae$delta_conc_titrant, xlab = "[HCl] offset added [mol/kg-soln]",
## what = what, size = c(12,8), mfrow = c(4,4))
## plot(ae, xval = ae$delta_moles_titrant, xlab = "HCl added [mol]",
## what = what, size = c(12,8), mfrow = c(4,4))
###################################################
### code chunk number 72: TextbookTit4 (eval = FALSE)
###################################################
## plot(ae, bjerrum=TRUE)
## what <- c("CO2", "HCO3", "CO3")
## plot(ae, what = what, bjerrum = TRUE)
## plot(ae, what = what, bjerrum = TRUE, lwd = 4,
## palette=c("cyan", "magenta", "yellow"), bg = "gray",
## legendinset = 0.1, legendposition = "topleft")
## what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
## "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F")
## plot(ae, what = what, bjerrum = TRUE, log = TRUE)
###################################################
### code chunk number 73: TextbookTit5
###################################################
what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
"NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F")
plot(ae, what = what, bjerrum = TRUE, log = TRUE, ylim = c(-6,-1),
legendinset = 0, lwd = 3, palette = c(1,3,4,5,6,colors()[seq(100,250,6)]))
###################################################
### code chunk number 74: TAfit1
###################################################
ae_init <- aquaenv(S = 35, t = 15, SumCO2 = 0.0035, SumNH4 = 0.00002, pH = 11.3)
ae <- titration(ae_init, mass_sample = 0.01, mass_titrant = 0.02,
conc_titrant = 0.01, S_titrant = 0.5, steps = 100)
plot(ae, xval = ae$delta_mass_titrant, xlab = "HCl solution added [kg]",
what = "pH", xlim = c(0,0.015))
par(new = TRUE)
plot(ae$delta_mass_titrant[1:100], diff(ae$pH), type = "l",
col = "red", xlim = c(0,0.015), ylab = "", xlab = "", yaxt = "n")
par(new = TRUE)
plot(ae$delta_mass_titrant[2:100], diff(diff(ae$pH)), type = "l",
col = "blue", xlim = c(0,0.015), ylab = "", xlab = "", yaxt = "n")
abline(h =0, col = "blue")
abline(v = ae$TA[[1]])
abline(v = ae$TA[[1]] - ae$SumCO2[[1]])
###################################################
### code chunk number 75: TAfit2
###################################################
plot(ae, xval = ae$delta_mass_titrant, xlab = "HCl solution added [kg]",
what = "pH", xlim = c(0,0.015))
prot1 <- c()
for (i in 1:length(ae$pH))
prot1 <- c(prot1, (10^-(ae$pH[[i]])+ae$HSO4[[i]]+ae$HF[[i]]+
ae$CO2[[i]]-ae$CO3[[i]]-ae$BOH4[[i]]-ae$OH[[i]]))
par(new = TRUE)
plot(ae$delta_mass_titrant, prot1, type = "l", col = "blue", xlim = c(0,0.015),
ylab = "", xlab = "", yaxt = "n", ylim = c(-0.015,0.015))
prot2 <- c()
for (i in 1:length(ae$pH))
prot2 <- c(prot2, (10^-(ae$pH[[i]])+ae$HSO4[[i]]+ae$HF[[i]]-
ae$HCO3[[i]]-2*ae$CO3[[i]]-ae$BOH4[[i]]-ae$OH[[i]]))
par(new = TRUE)
plot(ae$delta_mass_titrant, prot2, type = "l", col = "green", xlim = c(0,0.015),
ylab = "", xlab = "", yaxt = "n", ylim = c(-0.015,0.015))
abline(v = ae$TA[[1]])
abline(v = ae$TA[[1]] - ae$SumCO2[[1]])
abline(h = 0)
###################################################
### code chunk number 76: TAfit3
###################################################
ae <- titration(aquaenv(S = 35, t = 15, SumCO2 = 0.0035, SumNH4 = 0.00002,
pH = 11.3),
mass_sample = 100, mass_titrant = 0.5, conc_titrant = 3,
S_titrant = 0.5, steps = 100)
plot(ae, xval = ae$delta_mass_titrant, xlab = "HCl solution added [kg]",
what = "pH", xlim = c(0, 0.5))
prot1 <- c()
for (i in 1:length(ae$pH))
prot1 <- c(prot1, (10^-(ae$pH[[i]])+ae$HSO4[[i]]+ae$HF[[i]]+
ae$CO2[[i]]-ae$CO3[[i]]-ae$BOH4[[i]]-ae$OH[[i]]))
par(new = TRUE)
plot(ae$delta_mass_titrant, prot1, type = "l", col = "blue",
xlim = c(0,0.5), ylab = "", xlab = "", yaxt = "n",
ylim = c(-0.015, 0.015))
prot2 <- c()
for (i in 1:length(ae$pH))
prot2 <- c(prot2, (10^-(ae$pH[[i]])+ae$HSO4[[i]]+ae$HF[[i]]-
ae$HCO3[[i]]-2*ae$CO3[[i]]-ae$BOH4[[i]]-ae$OH[[i]]))
par(new = TRUE)
plot(ae$delta_mass_titrant, prot2, type = "l", col = "green",
xlim = c(0,0.5), ylab = "", xlab = "", yaxt = "n",
ylim = c(-0.015,0.015))
abline(v = (ae$TA[[1]]*100/3))
abline(v = ((ae$TA[[1]] - ae$SumCO2[[1]])*100/3))
abline(h = 0)
###################################################
### code chunk number 77: TAfit4
###################################################
initial_ae <- aquaenv(S = 35, t = 15, SumCO2 = 0.002, TA = 0.0022)
ae <- titration(initial_ae, mass_sample = 0.01, mass_titrant = 0.003,
conc_titrant = 0.01, S_titrant = 0.5, steps = 20)
###################################################
### code chunk number 78: TAfit5
###################################################
titcurve <- cbind(ae$delta_mass_titrant, ae$pH)
###################################################
### code chunk number 79: TAfit6
###################################################
fit1 <- TAfit(initial_ae, titcurve, conc_titrant = 0.01,
mass_sample = 0.01, S_titrant = 0.5)
fit1
###################################################
### code chunk number 80: TAfit6a (eval = FALSE)
###################################################
## initial_ae_ <- aquaenv(S = 35, t = 15, SumCO2 = 0.002, TA = 0.0022,
## k1k2 = "lueker", khf = "perez")
## ae_ <- titration(initial_ae_, mass_sample = 0.01, mass_titrant = 0.003,
## conc_titrant = 0.01,
## S_titrant = 0.5, steps = 20, k1k2 = "roy",
## khf = "perez")
## titcurve_ <- cbind(ae_$delta_mass_titrant, ae_$pH)
## fit1_ <- TAfit(initial_ae_, titcurve_, conc_titrant = 0.01,
## mass_sample = 0.01, S_titrant = 0.5, k1k2 = "roy",
## khf = "perez", verbose = TRUE)
## fit1_
###################################################
### code chunk number 81: TAfit7 (eval = FALSE)
###################################################
## ae <- titration(initial_ae, mass_sample = 0.01, mass_titrant = 0.003,
## conc_titrant = 0.01, steps = 20, seawater_titrant = TRUE)
## titcurve <- cbind(ae$delta_mass_titrant, ae$pH)
## tottitcurve <- cbind(ae$pH, convert(ae$pH, "pHscale", "free2tot", S = 35, t = 15))
## Etitcurve <- cbind(ae$delta_mass_titrant,
## (0.4 - ((PhysChemConst$R/10)*initial_ae$T/PhysChemConst$F)*
## log(10^-tottitcurve[,2])))
###################################################
### code chunk number 82: TAfit8 (eval = FALSE)
###################################################
## fit2 <- TAfit(initial_ae, Etitcurve, conc_titrant = 0.01, mass_sample = 0.01,
## Evals = TRUE, verbose = TRUE, seawater_titrant = TRUE)
## fit2
###################################################
### code chunk number 83: TAfit9
###################################################
fit3 <- TAfit(initial_ae, titcurve, conc_titrant = 0.01, mass_sample = 0.01,
S_titrant = 0.5, K_CO2fit = TRUE)
fit3
initial_ae$K_CO2
###################################################
### code chunk number 84: TAfit10
###################################################
ae <- titration(initial_ae, mass_sample = 0.01, mass_titrant = 0.003,
conc_titrant = 0.01, steps = 20, seawater_titrant = TRUE)
titcurve <- cbind(ae$delta_mass_titrant, ae$pH)
fit4 <- TAfit(initial_ae, titcurve, conc_titrant = 0.01, mass_sample = 0.01,
K_CO2fit = TRUE, seawater_titrant = TRUE)
fit4
###################################################
### code chunk number 85: TAfit11 (eval = FALSE)
###################################################
## Etitcurve <- cbind(titcurve[,1], (0.4 - ((PhysChemConst$R/10)*initial_ae$T/
## PhysChemConst$F)*log(10^-titcurve[,2])))
## fit5 <- TAfit(initial_ae, Etitcurve, conc_titrant = 0.01, mass_sample = 0.01,
## K_CO2fit = TRUE, seawater_titrant = TRUE, Evals = TRUE)
## fit5
###################################################
### code chunk number 86: TAfit12 (eval = FALSE)
###################################################
## neqsptitcurve <- rbind(titcurve[1:9,], titcurve[11:20,])
## fit6 <- TAfit(initial_ae, neqsptitcurve, conc_titrant = 0.01,
## mass_sample = 0.01, seawater_titrant = TRUE, equalspaced = FALSE,
## verbose = TRUE, debug = TRUE)
## fit6
###################################################
### code chunk number 87: TAfit13
###################################################
noisetitcurve <- titcurve * rnorm(length(titcurve), mean = 1, sd = 0.01) #one percent error possible
fit7 <- TAfit(initial_ae, noisetitcurve, conc_titrant = 0.01, mass_sample = 0.01,
seawater_titrant = TRUE, verbose = FALSE, debug = TRUE)
fit7
###################################################
### code chunk number 88: TAfit14
###################################################
ylim <- range(noisetitcurve[,2], calc)
xlim <- range(tit$delta_mass_titrant, noisetitcurve[,1])
plot(noisetitcurve[,1], noisetitcurve[,2], xlim = xlim, ylim = ylim,
type = "l", xlab = "delta mass titrant", ylab = "pH (free scale)")
par(new = TRUE)
plot(tit$delta_mass_titrant, calc, xlim = xlim, ylim = ylim, type = "l",
col = "red", xlab = "", ylab = "")
###################################################
### code chunk number 89: TAfit15
###################################################
conc_titrant <- 0.3 # mol/kg-soln
mass_sample <- 0.2 # kg
S_titrant <- 14.835 # is aequivalent to the ionic strength of 0.3 mol/kg-soln
SumBOH3 <- 0.00042 # mol/kg-soln
SumH2SO4 <- 0.02824 # mol/kg-soln
SumHF <- 0.00007 # mol/kg-soln
###################################################
### code chunk number 90: TAfit16
###################################################
sam <- cbind(sample_dickson1981[,1]/1000, sample_dickson1981[,2]) # convert mass of titrant from g to kg
###################################################
### code chunk number 91: TAfit17
###################################################
dicksonfit <- TAfit(aquaenv(S = 35, t = 25, SumBOH3 = SumBOH3,
SumH2SO4 = SumH2SO4, SumHF=SumHF), sam, conc_titrant,
mass_sample, S_titrant = S_titrant, debug = TRUE)
dicksonfit
###################################################
### code chunk number 92: TAfit18
###################################################
dicksontitration1 <- titration(aquaenv(S = 35, t = 25, SumCO2 = 0.00220,
SumBOH3 = SumBOH3, SumH2SO4 = SumH2SO4, SumHF = SumHF, TA = 0.00245),
mass_sample = mass_sample, mass_titrant = 0.0025,
conc_titrant = conc_titrant, steps = 50, type = "HCl")
###################################################
### code chunk number 93: TAfit19
###################################################
dicksontitration2 <- titration(aquaenv(S = 35, t = 25, SumCO2 = 0.00220,
SumBOH3 = SumBOH3, SumH2SO4 = SumH2SO4, SumHF = SumHF, TA = 0.00245),
mass_sample = mass_sample, mass_titrant = 0.0025,
conc_titrant = conc_titrant, S_titrant = S_titrant, steps = 50, type = "HCl")
###################################################
### code chunk number 94: TAfit20
###################################################
plot(dicksontitration1, xval = dicksontitration1$delta_mass_titrant,
what = "pH", xlim = c(0,0.0025), ylim = c(3,8.2), col = "red",
xlab = "delta mass titrant")
par(new = TRUE)
plot(dicksontitration2, xval = dicksontitration2$delta_mass_titrant,
what = "pH", xlim = c(0,0.0025), ylim = c(3,8.2), col = "blue", xlab = "")
par(new = TRUE)
plot(sam[,1], sam[,2], type = "l", xlim = c(0,0.0025),
ylim = c(3,8.2), xlab = "", ylab = "")
###################################################
### code chunk number 95: TAfit21
###################################################
plot(dicksontitration2$pH - sam[,2])
###################################################
### code chunk number 96: TAfit22
###################################################
dicksonfit2 <- TAfit(aquaenv(S = 35, t = 25, SumBOH3 = SumBOH3,
SumH2SO4 = SumH2SO4, SumHF = SumHF), sam, conc_titrant,
mass_sample, S_titrant = S_titrant, debug = TRUE, K_CO2fit = TRUE)
dicksonfit2
###################################################
### code chunk number 97: AquaEnv.rnw:1763-1764
###################################################
###################################################
### code chunk number 98: TAfit23
###################################################
dicksontitration3 <- titration(aquaenv(S = 35, t = 25, SumCO2 = 0.00220,
SumBOH3 = SumBOH3, SumH2SO4 = SumH2SO4, SumHF = SumHF, TA = 0.00245,
k_w = 4.32e-14, k_co2 = 1e-6, k_hco3 = 8.20e-10, k_boh3 = 1.78e-9,
k_hso4 = (1/1.23e1), k_hf = (1/4.08e2)),
mass_sample = mass_sample, mass_titrant = 0.0025, conc_titrant = conc_titrant,
steps = 50, type = "HCl", S_titrant = S_titrant,
k_w = 4.32e-14, k_co2 = 1e-6, k_hco3 = 8.20e-10, k_boh3 = 1.78e-9,
k_hso4 = (1/1.23e1), k_hf = (1/4.08e2))
plot(dicksontitration3, xval = dicksontitration3$delta_mass_titrant,
what = "pH", xlim = c(0,0.0025), ylim = c(3,8.2), col = "blue",
xlab = "delta mass titrant")
par(new = TRUE)
plot(sam[,1], sam[,2], type = "l", xlim = c(0,0.0025), ylim = c(3,8.2),
xlab = "", ylab = "")
###################################################
### code chunk number 99: TAfit24
###################################################
plot(dicksontitration3$pH - sam[,2])
###################################################
### code chunk number 100: TAfit25
###################################################
dicksonfit3 <- TAfit(aquaenv(S = 35, t = 25, SumBOH3 = SumBOH3, SumH2SO4 = SumH2SO4,
SumHF = SumHF, k_w = 4.32e-14, k_co2 = 1e-6, k_hco3 = 8.20e-10,
k_boh3 = 1.78e-9, k_hso4 = (1/1.23e1), k_hf = (1/4.08e2)),
sam, conc_titrant, mass_sample, S_titrant = S_titrant, debug = TRUE,
k_w = 4.32e-14, k_co2 = 1e-6, k_hco3 = 8.20e-10, k_boh3 = 1.78e-9,
k_hso4 = (1/1.23e1), k_hf = (1/4.08e2))
dicksonfit3
###################################################
### code chunk number 101: extend1
###################################################
simpletitration <- function(aquaenv, # an object of class aquaenv: minimal definition,
# contains all information about the system:
# T, S, d, total concentrations of nutrients etc
volume, # the volume of the (theoretical) titration vessel in l
amount, # the amount of titrant added in mol
steps, # the amount of steps the amount of titrant is added in
type) # the type of titrant: either "HCl" or "NaOH"
{
directionTAchange <- switch(type, HCl = -1, NaOH = +1)
TAconcchangeperstep <- convert(((amount/steps)/volume), "conc", "molar2molin", aquaenv$t, aquaenv$S)
aquaenvtemp <- aquaenv
for (i in 1:steps)
{
TA <- aquaenvtemp$TA + (directionTAchange * TAconcchangeperstep)
aquaenvtemp <- aquaenv(ae=aquaenvtemp, TA=TA)
aquaenv <- merge(aquaenv, aquaenvtemp)
}
aquaenv[["DeltaCTitrant"]] <- convert((amount/volume)/steps*(1:(steps+1)),
"conc", "molar2molin", aquaenv$t, aquaenv$S)
return(aquaenv) # object of class aquaenv which contains a titration simulation
}
###################################################
### code chunk number 102: extend2
###################################################
ae <- simpletitration(aquaenv(S = 35, t = 15, SumCO2 = 0.003500,
SumNH4 = 0.000020, pH = 11.3),
volume =100, amount = 1.5, steps = 100, type = "HCl")
what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "NH4", "NH3",
"H2SO4", "HSO4", "SO4", "HF", "F")
plot(ae, what = what, bjerrum = TRUE, log = TRUE, ylim = c(-6,-1),
legendinset = 0, lwd = 3, palette = c(1,3,4,5,6,colors()[seq(100,250,6)]))
###################################################
### code chunk number 103: extend3
###################################################
simpleTAfit <- function(ae, # an object of class aquaenv: minimal definition,
# contains all information about the system:
# T, S, d, total concentrations of nutrients etc
pHmeasurements, # a table containing the titration curve:
# basically a series of pH values (pH on free proton scale)
volume, # the volume of the titration vessel
amount, # the total amount of the titrant added
TAguess=0.0025, # a first guess for [TA] and [SumCO2] to be used as
# initial values for the optimization procedure
type="HCl") # the type of titrant: either "HCl" or "NaOH"
{
ae$Na <- NULL # make sure ae gets cloned as "skeleton": cloneaquaenv determines "skeleton"
# TRUE or FALSE from the presence of a value for Na
residuals <- function(state)
{
ae$SumCO2 <- state[[1]]
pHcalc <- simpletitration(aquaenv(ae=ae, TA=state[[2]]), volume=volume,
amount=amount, steps=(length(pHmeasurements)-1), type=type)$pH
residuals <- pHmeasurements-pHcalc
return(residuals)
}
require(minpack.lm)
out <- nls.lm(fn=residuals, par=c(TAguess, TAguess)) #guess for TA is also used as guess for SumCO2
result <- list(out$par[[2]], out$par[[1]], out$deviance)
attr(result[[1]], "unit") <- "mol/kg-soln"
attr(result[[2]], "unit") <- "mol/kg-soln"
names(result) <- c("TA", "SumCO2", "sumofsquares")
return(result) # a list of three values
# ([TA] in mol/kg-solution, [SumCO2] in mol/kg-solution, sum of the squared residuals)
}
###################################################
### code chunk number 104: extend4
###################################################
pHmeasurements <- ae$pH
fit <- simpleTAfit(aquaenv(S = 35, t = 15, SumNH4 = 0.00002),
pHmeasurements, volume = 100, amount = 1.5)
fit
###################################################
### code chunk number 105: CleaningUp
###################################################
graphics.off()
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