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Commit 57e6d53e authored by Marco De Lucia's avatar Marco De Lucia
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preparing demos and included files (db, dataset, ...)

parent 131808cd
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demo/00Index 0 → 100644
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demo-equilibrium 1D reactive transport with equilibrium chemistry
demo-kinetics 1D reactive transport with kinetic chemistry
demo/demo-equilibrium.R 0 → 100644
View file @ 57e6d53e
### Licence: LGPL version 2.1
### Time-stamp: "Last modified 2016-04-15 17:17:41 delucia"
library(RedModRphree)
Matplot <- function(sample, sur, sim, head=FALSE, ...) {
rs <- sur[[sample]]$C
rn <- sim[[sample]]$C
if(head){
cat("Surrogate:\n")
print(head(rs))
cat("Simulation:\n")
print(head(rn))
}
matplot(rn[,c("Ca","Mg","Calcite","Dolomite")], type="l", lwd=2, lty="solid", col=c("red", "black","blue","olivedrab3"), ...)
matplot(rs[,c("Ca","Mg","Calcite","Dolomite")], type="l", lwd=2, lty="dashed",col=c("red", "black","blue","olivedrab3"), add=TRUE)
legend("topright", c("Ca","Mg","Calcite","Dolomite"), text.col=c("red", "black","blue","olivedrab3"), bty="n")
}
base <- c(
"SOLUTION 1",
"units mol/kgw",
"temp 25.0",
"water 1",
"pH 9.91 charge",
"pe 4.0",
"C 1.2279E-04",
"Ca 1.2279E-04",
"Mg 0.001",
"Cl 0.002",
"PURE 1",
"O2g -0.1675 10",
"KINETICS 1",
"-steps 100",
"-bad_step_max 1000",
"Calcite",
"-m 0.000207",
"-parms 3.20",
"Dolomite",
"-m 0.0",
"-parms 0.32",
"END")
initsim <- c(
"SELECTED_OUTPUT",
"-high_precision true",
"-reset false",
"USER_PUNCH",
"-head C Ca Cl Mg H e O2g Calcite Dolomite",
"10 PUNCH TOT(\"C\"), TOT(\"Ca\"), TOT(\"Cl\"), TOT(\"Mg\"), ACT(\"H+\"), ACT(\"e-\"), EQUI(\"O2g\"), EQUI(\"Calcite\"), EQUI(\"Dolomite\")",
"SOLUTION 1",
"units mol/kgw",
"temp 25.0",
"water 1",
"pH 9.91 charge",
"pe 4.0",
"C 1.2279E-04",
"Ca 1.2279E-04",
"Cl 1E-12",
"Mg 1E-12",
"PURE 1",
"O2g -0.6788 10.0",
"Calcite 0.0 2.07E-3",
"Dolomite 0.0 0.0",
"END")
db <- RPhreeFile( "db/pqc_strip_kin.dat", is.db=TRUE )
phrLoadDatabaseString(db)
selout <- c(
"SELECTED_OUTPUT",
"-high_precision true",
"-reset false",
"-time",
"-soln",
"-temperature true",
"-water true",
"-pH",
"-pe",
"-totals C Ca Cl Mg",
"-kinetic_reactants Calcite Dolomite",
"-equilibrium O2g")
prop <- c("C","Ca","Cl","Mg","pH","pe","O2g", "Calcite","Dolomite")
maxsim <- 20 ## minimum number of single chemical simulations in each time step to spawn parallelization
grid <- 50 ## grid discretization (number of elements)
L <- 0.5 ## total system length [m]
U <- 9.375e-6 ## imposed (constant) Darcy velocity [m3/s]
Cf <- 0.9 ## Courant number to add some numerical dispersion
## boundary conditions (concentration of the injected fluid entering into the 1D column)
bound <- c(H=1E-7, e=1E-4, Mg=0.001, Cl=0.002)
setup <- list(n=50, len=L, U=U, base=base, first=selout, Cf=Cf, bound=bound, dt=210,
prop=prop, immobile=c(7,8,9), kin=c(8,9), ann=list(O2g=-0.1675), initsim=initsim)
oo <- ReactTranspBalanceKin(setup=setup, db=db, step="fix_dt", maxtime=2100,
procs=4, maxsim=maxsim, writeout=FALSE,
reduce=TRUE, surrogate=FALSE)
of <- ReactTranspBalanceKin(setup=setup, db=db, step="fix_dt", maxtime=2100,
procs=4, maxsim=maxsim, writeout=FALSE,
reduce=FALSE, surrogate=FALSE)
Matplot(101, sur=oo, sim=of, xlab="Domain element", ylab="Ca, Mg [molal], Calcite, Dolomite [mol]" ,main="RandomForest surrogate")
load(file="Rdata/20180411_CalcKin_Surr_EGU.Rdata")
MySurr <- function(state, model){
require(caret)
excl <- which(colnames(state)=="O2g")
remember_state_names <- colnames(state)
des <- state[,-excl]
if (NA %in% des) {
print(des)
stop("Mysurr: NA in data")
}
if (NaN %in% des) {
print(des)
stop("Mysurr: NaN in data")
}
order_for_surrogate <- c("C","Ca","Cl","Mg","pH","pe","Calcite","Dolomite")
rem_attr <- attr(state,"immobile")
ss <- des[, order_for_surrogate]
pred <- lapply(names(model), function(x) predict.train(model[[x]], ss))
out <- cbind(as.data.frame(pred), state[,excl])
colnames(out) <- c(names(model),"O2g")
## order back to how it is expected in "state"
out <- out[,remember_state_names]
attr(out,"immobile") <- rem_attr
return(out)
}
so <- ReactTranspBalanceKin(setup=setup, db=db, step="fix_dt", maxtime=21000,
procs=4, maxsim=maxsim, writeout=FALSE,
reduce=TRUE, surrogate=TRUE, surrogate.FUN=MySurr,
model=mods, baleq=baleq, tol=1E-5, call_pqc=TRUE)
sf <- ReactTranspBalanceKin(setup=setup, db=db, step="fix_dt", maxtime=21000,
procs=4, maxsim=maxsim, writeout=FALSE,
reduce=FALSE, surrogate=TRUE, surrogate.FUN=MySurr,
model=mods, baleq=baleq, tol=1E-5, call_pqc=TRUE)
par(mfrow=c(2,1))
Matplot(101, sur=so, sim=oo, xlab="Domain element", ylab="Ca, Mg [molal], Calcite, Dolomite [mol]" ,main="RandomForest surrogate")
Matplot(101, sur=sf, sim=of, xlab="Domain element", ylab="Ca, Mg [molal], Calcite, Dolomite [mol]" ,main="RandomForest surrogate")
##### test equilibrium
prop <- c("C(4)","Ca","Cl","Mg","pH","pe","Calcite","Dolomite")
## PHREEQC mojo to output selection
sel <- RPhreeCheckSel(c(punch=TRUE))
selec <- c("SELECTED_OUTPUT",
"-high_precision true",
"-reset false",
"USER_PUNCH",
"-head C Ca Cl Mg pH pe Calcite Dolomite",
"10 PUNCH TOT(\"C(4)\"), TOT(\"Ca\"), TOT(\"Cl\"), TOT(\"Mg\"), -LA(\"H+\"), -LA(\"e-\"), EQUI(\"Calcite\"), EQUI(\"Dolomite\")")
## load the initial phreeqc script, which also defines initial conditions
geoinp <- RPhreeFile("Surrogates/calcite_pqc2.pqc")
db2 <- RPhreeFile( "Peter/phreeqc.dat", is.db=TRUE)
phrLoadDatabaseString(db2)
maxsim <- 50 ## minimum number of single chemical simulations in each time step to spawn parallelization
grid <- 100 ## grid discretization (number of elements)
L <- 0.5 ## total system length [m]
U <- 9.375e-6 ## imposed (constant) Darcy velocity [m3/s]
Cf <- 0.8 ## Courant number to add some numerical dispersion
## boundary conditions (concentration of the injected fluid entering into the 1D column)
bound <- c(H=1E-7, e=1E-4, Mg=0.001, Cl=0.002) #, "O(0)"=0.04,
grid <- 50 ## grid discretization (number of elements)
setup <- list(n=grid, len=L, U=U, base=geoinp, first=selec, Cf=Cf, bound=bound, prop=prop, immobile=c(7,8), initsim=c(selec, geoinp))
source("RedModRphree/R/Rphree_ReactTrans.R")
source("RedModRphree/R/Rphree_Kinetics.R")
eo <- ReactTranspBalanceEq(setup=setup, db=db2, step="time", maxtime=21000,
procs=4, maxsim=maxsim, writeout=FALSE,
reduce=TRUE, surrogate=FALSE)
ef <- ReactTranspBalanceEq(setup=setup, db=db2, step="time", maxtime=21000,
procs=4, maxsim=maxsim, writeout=FALSE,
reduce=FALSE, surrogate=FALSE)
load(file="Rdata/20180314_calcite_pqc_4.Rdata")
load(file="Surrogates/20180316_calcite_pqc_parRF.Rdata")
MySurr <- function(state, model){
order_for_surrogate <- c("C","Ca","Cl","Mg","Calcite","Dolomite","pH","pe")
remember_names <- colnames(state)
rem_attr <- attr(state,"immobile")
ss <- state[, order_for_surrogate]
pred <- lapply(names(model), function(x) as.numeric(predict(model[[x]], ss)))
names(pred) <- names(model)
out <- data.matrix(as.data.frame(pred))
## order back to how it is expected in "state"
out <- out[,remember_names]
attr(out,"immobile") <- rem_attr
return(out)
}
ro <- ReactTranspBalanceEq(setup=setup, db=db2, step="time", maxtime=21000,
procs=4, maxsim=maxsim, writeout=FALSE,
reduce=TRUE, surrogate=TRUE, surrogate.FUN=MySurr, model=mods, baleq=baleq, tol=1E-5, call_pqc=TRUE)
rf <- ReactTranspBalanceEq(setup=setup, db=db2, step="time", maxtime=21000,
procs=4, maxsim=maxsim, writeout=FALSE,
reduce=FALSE, surrogate=TRUE, surrogate.FUN=MySurr, model=mods, baleq=baleq, tol=1E-5, call_pqc=TRUE)
Matplot(25, sur=otr, sim=sr, xlab="Domain element", ylab="Ca, Mg [molal], Calcite, Dolomite [mol]" ,main="RandomForest surrogate")
s1 <- AdvectionPQC(state_T, inflow=bound, dx=L/50, dt=853.3333)
prop <- c("C","Ca","Cl","Mg","pH","pe","O2g", "Calcite","Dolomite")
distprop <- c("C","Ca","Cl","Mg","pH","pe","O2g", "Calcite","Dolomite")
maxsim <- 20 ## minimum number of single chemical simulations in each time step to spawn parallelization
grid <- 50 ## grid discretization (number of elements)
L <- 0.5 ## total system length [m]
U <- 9.375e-6 ## imposed (constant) Darcy velocity [m3/s]
Cf <- 0.9 ## Courant number to add some numerical dispersion
## boundary conditions (concentration of the injected fluid entering into the 1D column)
bound <- c(H=1E-7, e=1E-4, Mg=0.001, Cl=0.002) #, "O(0)"=0.04,
exper <- expand.grid(grid=c(50, 100, 200), tol=c(1E-6, 1E-5, 1E-4))
simsur <- vector(mode="list",length=nrow(exper))
timesur <- vector(mode="list",length=nrow(exper))
outbalsur <- vector(mode="list",length=nrow(exper))
source("Rphree_SurrogateKin.R")
for (i in seq(nrow(exper))) {
setup <- list(n=exper$grid[i], len=L, U=U, base=base, first=selout, Cf=Cf, bound=bound, dt=500,
prop=prop, distprop=distprop, immobile=c(7,8,9), kin=c(8,9), sel=sel, ann=list(O2g=-0.1675), initsim=initsim, init_npunch=9)
timesur[[i]] <- system.time( simsur[[i]] <- ReactTranspCompleteOutputBalKin(setup=setup, db=db, step="fix_dt", maxtime=2100,
procs=4, maxsim=maxsim, writeout=FALSE,
reduce=TRUE, surrogate=TRUE, surrogate.FUN=MySurr,
model=mods, baleq=baleq, tol=exper$tol[i], call_pqc=TRUE) )
outbalsur[[i]] <- out_bal
}
save(list=c("des", "res", "samp", "design", "result", "timesur","outbalsur","simsur","mods","MySurr","baleq"), file="Rdata/20180411_CalcKin_Surr_EGU.Rdata")
load(file="Rdata/20180411_CalcKin_Surr_EGU.Rdata")
data.table::fwrite(design, file = "TestCalcitePQC_Kinetic_design.csv", append = FALSE, quote = "auto",
sep = ",", eol = "\n", na = "NA", dec = ".", row.names = FALSE, col.names = TRUE)
data.table::fwrite(result, file = "TestCalcitePQC_Kinetic_result.csv", append = FALSE, quote = "auto",
sep = ",", eol = "\n", na = "NA", dec = ".", row.names = FALSE, col.names = TRUE)
## data.table::fwrite(design, file = "TestCalcitePQC_3_design.csv", append = FALSE, quote = "auto",
## sep = ",", eol = "\n", na = "NA", dec = ".", row.names = FALSE, col.names = TRUE)
data.table::fwrite(result, file = "TestCalcitePQC_3_results.csv", append = FALSE, quote = "auto",
sep = ",", eol = "\n", na = "NA", dec = ".", row.names = FALSE, col.names = TRUE)
subexp1 <- subset(exper, grid==50 | grid == 100 | grid == 200)
toto <- rep(c(1, 2, 3), 3)
par(mfrow=c(3,3))
for (i in seq(nrow(subexp1))) {
Matplot(11, sur=simsur[[i]], sim=expsim[[ toto[i] ]], xlab="Domain element", ylab="Ca, Mg [molal], Calcite, Dolomite [mol]", main=paste("RandomForest surrogate, tol=", subexp1$tol[i]))
}
###################################### for debug and development
load(file="Rdata/20180411_CalcKin_Surr_EGU.Rdata")
base <- RPhreeFile("Surrogates/stub_kin.pqc")
initsim <- RPhreeFile("Surrogates/stub_kin_init.pqc")
sel <- RPhreeCheckSel(c(punch=TRUE))
db <- RPhreeFile( "db/pqc_strip_kin.dat", is.db=TRUE )
selout <- c(
"SELECTED_OUTPUT",
"-high_precision true",
"-reset false",
"-time",
"-soln",
"-temperature true",
"-water true",
"-pH",
"-pe",
"-totals C Ca Cl Mg",
"-kinetic_reactants Calcite Dolomite",
"-equilibrium O2g")
prop <- c("C","Ca","Cl","Mg","pH","pe","O2g", "Calcite","Dolomite")
distprop <- c("C","Ca","Cl","Mg","pH","pe","O2g", "Calcite","Dolomite")
maxsim <- 10 ## minimum number of single chemical simulations in each time step to spawn parallelization
grid <- 50 ## grid discretization (number of elements)
L <- 0.5 ## total system length [m]
U <- 9.375e-6 ## imposed (constant) Darcy velocity [m3/s]
Cf <- 0.9 ## Courant number to add some numerical dispersion
## boundary conditions (concentration of the injected fluid entering into the 1D column)
bound <- c(H=1E-7, e=1E-4, Mg=0.001, Cl=0.002) #, "O(0)"=0.04,
source("Rphree_SurrogateKin.R")
setup <- list(n=grid, len=L, U=U, base=base, first=selout, Cf=Cf, bound=bound,
prop=prop, distprop=distprop, immobile=c(7,8,9), kin=c(8,9), sel=sel, ann=list(O2g=-0.1675), initsim=initsim, init_npunch=9)
library(profvis)
profvis({
gc()
tracemem(Res_C)
sim <- ReactTranspCompleteOutputBalKin(setup=setup, db=db, step="time", maxtime=21000,procs=1, maxsim=maxsim, writeout=FALSE, reduce=FALSE, surrogate=FALSE)
})
library(caret)
MySurr <- function(state, model){
excl <- which(colnames(state)=="O2g")
remember_state_names <- colnames(state)
des <- state[,-excl]
if (NA %in% des) {
print(des)
stop("Mysurr: NA in data")
}
if (NaN %in% des) {
print(des)
stop("Mysurr: NaN in data")
}
order_for_surrogate <- c("C","Ca","Cl","Mg","pH","pe","Calcite","Dolomite")
rem_attr <- attr(state,"immobile")
ss <- des[, order_for_surrogate]
pred <- parallel::mclapply(names(model), function(x) predict.train(model[[x]], ss), mc.cores=4)
out <- cbind(as.data.frame(pred), state[,excl])
colnames(out) <- c(names(model),"O2g")
out <- out[,remember_state_names]
attr(out,"immobile") <- rem_attr
return(out)
}
setup <- list(n=20, len=L, U=U, base=base, first=selout, Cf=Cf, bound=bound,
prop=prop, distprop=distprop, immobile=c(7,8,9), kin=c(8,9), sel=sel, ann=list(O2g=-0.1675), initsim=initsim, init_npunch=9)
Rprof(tmp <- tempfile()) ##, memory.profiling = TRUE, gc.profiling = TRUE)
sim <- ReactTranspCompleteOutputBalKin(setup=setup, db=db, step="time", maxtime=4200,
procs=1, maxsim=maxsim, writeout=FALSE, tol=1E-5,
reduce=FALSE, surrogate=TRUE, surrogate.FUN=MySurr, model=mods, baleq=baleq, call_pqc=TRUE)
Rprof()
proftools::plotProfileCallGraph(readProfileData(tmp), score="total")
proftools::plotProfileCallGraph(readProfileData(tmp), style=plain.style, score="total")
library(profvis)
profvis({
sim <- ReactTranspCompleteOutputBalKin(setup=setup, db=db, step="time", maxtime=4200,
procs=1, maxsim=maxsim, writeout=FALSE, tol=1E-5,
reduce=FALSE, surrogate=TRUE, surrogate.FUN=MySurr, model=mods, baleq=baleq, call_pqc=TRUE)
})
demo/demo-kinetics.R 0 → 100644
View file @ 57e6d53e
### Licence: LGPL version 2.1
### Time-stamp: "Last modified 2016-04-15 17:17:41 delucia"
library(RedModRphree)
db <- RPhreeFile(system.file("extdata", "phreeqc_kin.dat", package="RedModRphree"), is.db=TRUE)
Matplot <- function(sample, sur, sim, head=FALSE, ...) {
rs <- sur[[sample]]$C
rn <- sim[[sample]]$C
if(head){
cat("Surrogate:\n")
print(head(rs))
cat("Simulation:\n")
print(head(rn))
}
matplot(rn[,c("Ca","Mg","Calcite","Dolomite")], type="l", lwd=2, lty="solid", col=c("red", "black","blue","olivedrab3"), ...)
matplot(rs[,c("Ca","Mg","Calcite","Dolomite")], type="l", lwd=2, lty="dashed",col=c("red", "black","blue","olivedrab3"), add=TRUE)
legend("topright", c("Ca","Mg","Calcite","Dolomite"), text.col=c("red", "black","blue","olivedrab3"), bty="n")
}
base <- c(
"SOLUTION 1",
"units mol/kgw",
"temp 25.0",
"water 1",
"pH 9.91 charge",
"pe 4.0",
"C 1.2279E-04",
"Ca 1.2279E-04",
"Mg 0.001",
"Cl 0.002",
"PURE 1",
"O2g -0.1675 10",
"KINETICS 1",
"-steps 100",
"-bad_step_max 1000",
"Calcite",
"-m 0.000207",
"-parms 3.20",
"Dolomite",
"-m 0.0",
"-parms 0.32",
"END")
initsim <- c(
"SELECTED_OUTPUT",
"-high_precision true",
"-reset false",
"USER_PUNCH",
"-head C Ca Cl Mg H e O2g Calcite Dolomite",
"10 PUNCH TOT(\"C\"), TOT(\"Ca\"), TOT(\"Cl\"), TOT(\"Mg\"), ACT(\"H+\"), ACT(\"e-\"), EQUI(\"O2g\"), EQUI(\"Calcite\"), EQUI(\"Dolomite\")",
"SOLUTION 1",
"units mol/kgw",
"temp 25.0",
"water 1",
"pH 9.91 charge",
"pe 4.0",
"C 1.2279E-04",
"Ca 1.2279E-04",
"Cl 1E-12",
"Mg 1E-12",
"PURE 1",
"O2g -0.6788 10.0",
"Calcite 0.0 2.07E-3",
"Dolomite 0.0 0.0",
"END")
db <- RPhreeFile( "db/pqc_strip_kin.dat", is.db=TRUE )
phrLoadDatabaseString(db)
selout <- c(
"SELECTED_OUTPUT",
"-high_precision true",
"-reset false",
"-time",
"-soln",
"-temperature true",
"-water true",
"-pH",
"-pe",
"-totals C Ca Cl Mg",
"-kinetic_reactants Calcite Dolomite",
"-equilibrium O2g")
prop <- c("C","Ca","Cl","Mg","pH","pe","O2g", "Calcite","Dolomite")
maxsim <- 20 ## minimum number of single chemical simulations in each time step to spawn parallelization
grid <- 50 ## grid discretization (number of elements)
L <- 0.5 ## total system length [m]
U <- 9.375e-6 ## imposed (constant) Darcy velocity [m3/s]
Cf <- 0.9 ## Courant number to add some numerical dispersion
## boundary conditions (concentration of the injected fluid entering into the 1D column)
bound <- c(H=1E-7, e=1E-4, Mg=0.001, Cl=0.002)
## pack all together in a "setup" list
setup <- list(n=50, len=L, U=U, base=base, first=selout, Cf=Cf, bound=bound, dt=210,
prop=prop, immobile=c(7,8,9), kin=c(8,9), ann=list(O2g=-0.1675), initsim=initsim)
oo <- ReactTranspBalanceKin(setup=setup, db=db, step="fix_dt", maxtime=2100,
procs=4, maxsim=maxsim, writeout=FALSE,
reduce=TRUE, surrogate=FALSE)
of <- ReactTranspBalanceKin(setup=setup, db=db, step="fix_dt", maxtime=2100,
procs=4, maxsim=maxsim, writeout=FALSE,
reduce=FALSE, surrogate=FALSE)
Matplot(101, sur=oo, sim=of, xlab="Domain element", ylab="Ca, Mg [molal], Calcite, Dolomite [mol]" ,main="RandomForest surrogate")
load(file="Rdata/20180411_CalcKin_Surr_EGU.Rdata")
MySurr <- function(state, model){
require(caret)
excl <- which(colnames(state)=="O2g")
remember_state_names <- colnames(state)
des <- state[,-excl]
if (NA %in% des) {
print(des)
stop("Mysurr: NA in data")
}
if (NaN %in% des) {
print(des)
stop("Mysurr: NaN in data")
}
order_for_surrogate <- c("C","Ca","Cl","Mg","pH","pe","Calcite","Dolomite")
rem_attr <- attr(state,"immobile")
ss <- des[, order_for_surrogate]
pred <- lapply(names(model), function(x) predict.train(model[[x]], ss))
out <- cbind(as.data.frame(pred), state[,excl])
colnames(out) <- c(names(model),"O2g")
## order back to how it is expected in "state"
out <- out[,remember_state_names]
attr(out,"immobile") <- rem_attr
return(out)
}
so <- ReactTranspBalanceKin(setup=setup, db=db, step="fix_dt", maxtime=21000,
procs=4, maxsim=maxsim, writeout=FALSE,
reduce=TRUE, surrogate=TRUE, surrogate.FUN=MySurr,
model=mods, baleq=baleq, tol=1E-5, call_pqc=TRUE)
sf <- ReactTranspBalanceKin(setup=setup, db=db, step="fix_dt", maxtime=21000,
procs=4, maxsim=maxsim, writeout=FALSE,
reduce=FALSE, surrogate=TRUE, surrogate.FUN=MySurr,
model=mods, baleq=baleq, tol=1E-5, call_pqc=TRUE)
par(mfrow=c(2,1))
Matplot(101, sur=so, sim=oo, xlab="Domain element", ylab="Ca, Mg [molal], Calcite, Dolomite [mol]" ,main="RandomForest surrogate")
Matplot(101, sur=sf, sim=of, xlab="Domain element", ylab="Ca, Mg [molal], Calcite, Dolomite [mol]" ,main="RandomForest surrogate")
inst/extdata/phreeqc_kin.dat 0 → 100644
View file @ 57e6d53e
### This is the standard "phreeqc.dat" stripped of EXCHANGE and
### SURFACE and with the RATES for Calcite and Dolomite to use with
### RedModRphree
### Time-stamp: "Last modified 2018-05-06 14:36:23 delucia"
# PHREEQC.DAT for calculating pressure dependence of reactions, with
# molal volumina of aqueous species and of minerals, and
# critical temperatures and pressures of gases used in Peng-Robinson's EOS.
# Details are given at the end of this file.
SOLUTION_MASTER_SPECIES
#
#element species alk gfw_formula element_gfw
#
H H+ -1.0 H 1.008
H(0) H2 0 H
H(1) H+ -1.0 0
E e- 0 0.0 0
O H2O 0 O 16.0
O(0) O2 0 O
O(-2) H2O 0 0
Ca Ca+2 0 Ca 40.08
Mg Mg+2 0 Mg 24.312
Na Na+ 0 Na 22.9898
K K+ 0 K 39.102
Fe Fe+2 0 Fe 55.847
Fe(+2) Fe+2 0 Fe
Fe(+3) Fe+3 -2.0 Fe
Mn Mn+2 0 Mn 54.938
Mn(+2) Mn+2 0 Mn
Mn(+3) Mn+3 0 Mn
Al Al+3 0 Al 26.9815
Ba Ba+2 0 Ba 137.34
Sr Sr+2 0 Sr 87.62
Si H4SiO4 0 SiO2 28.0843
Cl Cl- 0 Cl 35.453
C CO3-2 2.0 HCO3 12.0111
C(+4) CO3-2 2.0 HCO3
C(-4) CH4 0 CH4
Alkalinity CO3-2 1.0 Ca0.5(CO3)0.5 50.05
S SO4-2 0 SO4 32.064
S(6) SO4-2 0 SO4
S(-2) HS- 1.0 S
N NO3- 0 N 14.0067
N(+5) NO3- 0 N
N(+3) NO2- 0 N
N(0) N2 0 N
N(-3) NH4+ 0 N 14.0067
#Amm AmmH+ 0 AmmH 17.0
B H3BO3 0 B 10.81
P PO4-3 2.0 P 30.9738