Commit a19d2d34 authored by Marco De Lucia's avatar Marco De Lucia
Browse files

Added stub and tracked some missed files

parent 7b53474e
# RedModRphree #
This package serves as test bed for the developments about surrogate
models and reactive transport in the framework of the RedMod project.
### Installation ###
In R, the quickest way is to install the package `devtools` and
install RedModRphree directly from this repository:
To install in a specific directory (which R must know about, e.g.,
specifying the variable R_LIBS_USER in the file `$HOME/.Renviron`:
devtools::install_git("", lib="~/MyRPackageDir")
This should take care of (mostly) all dependencies.
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Rphree_Kinetics.R
\title{Distribute all values from a matrix into a buffer, EQUILIBRIUM case}
DistributeMatrix(input, prop, values, minerals, SI = FALSE)
\item{input}{The input buffer to manipulate}
\item{prop}{The names of properties to distribute}
\item{values}{matrix or data.frame containing the values to distribute}
\item{minerals}{indeces of the EQUILIBRIUM minerals}
\item{SI}{logical, defaults to FALSE. Should we paste SI before value of a mineral?}
input buffer with the values in correct places
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Rphree_ReactTrans.R
\title{1D Reactive transport simulations using phreeqc or a
surrogate, equilibrium simulations}
ReactTranspBalanceEq(setup, init, maxtime, step = c("time", "iter", "fix_dt"),
db = "phreeqc.dat", procs = 1, maxsim = 150, reduce = TRUE,
ebreak = FALSE, writeout = FALSE, surrogate = FALSE, surrogate.FUN,
model, baleq, tol = 1e-09, call_pqc = TRUE)
\item{setup}{a list with several input parameters}
\item{init}{optional, initial state of the simulation}
\item{maxtime}{depending on \code{step}, the simulation time}
\item{step}{one of c("time","iter","fix_dt"), defines the time
\item{db}{the chemical database}
\item{procs}{number of processors to be used in parallel execution}
\item{maxsim}{number of simulations above which parallelization is
\item{reduce}{logical, defaults to TRUE. Should we find the unique
occurences of a geochemical problem?}
\item{ebreak}{logical, defaults to FALSE. If TRUE, an early break
is invoked}
\item{writeout}{logical, defaults to FALSE.}
\item{surrogate}{logical, defaults to FALSE. Should we use
surrogates instead of phreeqc?}
\item{surrogate.FUN}{The function which calls the surrogate}
\item{model}{The list of surrogate models, one element per
\item{baleq}{data structure containing the balance equations}
\item{tol}{absolute tolerance on the mass balance}
\item{call_pqc}{logical, defaults to TRUE: if TRUE, calls phreeqc
on the surrogate simulations which trespass the tolerance}
a list containing lots of stuff
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