diff --git a/man/OGS6.Rd b/man/OGS6.Rd index 9db04259727910a9551f7b292c015eaeea36de37..f99e587e129bd7752e3670e20756bb092c1be9fc 100644 --- a/man/OGS6.Rd +++ b/man/OGS6.Rd @@ -9,12 +9,14 @@ Constructor for the OGS6 base class \section{Active bindings}{ \if{html}{\out{<div class="r6-active-bindings">}} \describe{ -\item{\code{sim_name}}{Getter for OGS6 private parameter '.sim_name'} +\item{\code{sim_name}}{Access to private parameter '.sim_name'} \item{\code{sim_id}}{Getter for OGS6 private parameter '.sim_id'} \item{\code{sim_path}}{Access to private parameter '.sim_path'} +\item{\code{logfile}}{Access to private parameter '.logfile'} + \item{\code{ogs_bin_path}}{Getter for OGS6 private parameter '.ogs_bin_path'} \item{\code{geometry}}{Getter for OGS6 private parameter '.geometry'} @@ -68,6 +70,7 @@ Constructor for the OGS6 base class \item \href{#method-add_vtkdiff}{\code{OGS6$add_vtkdiff()}} \item \href{#method-add_insitu}{\code{OGS6$add_insitu()}} \item \href{#method-get_status}{\code{OGS6$get_status()}} +\item \href{#method-print_log}{\code{OGS6$print_log()}} \item \href{#method-clear}{\code{OGS6$clear()}} \item \href{#method-clone}{\code{OGS6$clone()}} } @@ -343,10 +346,21 @@ Adds a r2ogs6_insitu object \subsection{Method \code{get_status()}}{ Checks if the OGS6 object has all necessary parameters for starting a simulation +print_log \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$get_status()}\if{html}{\out{</div>}} } +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-print_log"></a>}} +\if{latex}{\out{\hypertarget{method-print_log}{}}} +\subsection{Method \code{print_log()}}{ +Prints logfile to console (if it exists) +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{OGS6$print_log()}\if{html}{\out{</div>}} +} + } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-clear"></a>}} diff --git a/man/OGS6_Chain.Rd b/man/OGS6_Chain.Rd new file mode 100644 index 0000000000000000000000000000000000000000..c0c4bd5bd4e08e9f82c334d00e95842e8d77500c --- /dev/null +++ b/man/OGS6_Chain.Rd @@ -0,0 +1,84 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/ogs6_chain.R +\name{OGS6_Chain} +\alias{OGS6_Chain} +\title{OGS6_Chain} +\description{ +Constructor for the OGS6_Chain base class +} +\section{Methods}{ +\subsection{Public methods}{ +\itemize{ +\item \href{#method-new}{\code{OGS6_Chain$new()}} +\item \href{#method-run_simulation}{\code{OGS6_Chain$run_simulation()}} +\item \href{#method-print_log}{\code{OGS6_Chain$print_log()}} +\item \href{#method-clone}{\code{OGS6_Chain$clone()}} +} +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-new"></a>}} +\if{latex}{\out{\hypertarget{method-new}{}}} +\subsection{Method \code{new()}}{ +Creates new OGS6_Chain object +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{OGS6_Chain$new(ogs6_obj, iter_n)}\if{html}{\out{</div>}} +} + +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{ogs6_obj}}{OGS6: A simulation object.} + +\item{\code{iter_n}}{number: Number of iterations (length of the chain)} +} +\if{html}{\out{</div>}} +} +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-run_simulation"></a>}} +\if{latex}{\out{\hypertarget{method-run_simulation}{}}} +\subsection{Method \code{run_simulation()}}{ +Runs the simulation. This calls r2ogs6::run_simulation() internally. +For chains, output will be written to logfiles. +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{OGS6_Chain$run_simulation()}\if{html}{\out{</div>}} +} + +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-print_log"></a>}} +\if{latex}{\out{\hypertarget{method-print_log}{}}} +\subsection{Method \code{print_log()}}{ +Reads in logfile of simulation and prints it to the console. +This calls print_log internally. If no index is specified, this will +print the logfile of the last object in the chain. +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{OGS6_Chain$print_log(index)}\if{html}{\out{</div>}} +} + +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{index}}{number: chain index of a OGS6 object} +} +\if{html}{\out{</div>}} +} +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-clone"></a>}} +\if{latex}{\out{\hypertarget{method-clone}{}}} +\subsection{Method \code{clone()}}{ +The objects of this class are cloneable with this method. +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{OGS6_Chain$clone(deep = FALSE)}\if{html}{\out{</div>}} +} + +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{deep}}{Whether to make a deep clone.} +} +\if{html}{\out{</div>}} +} +} +} diff --git a/man/OGS6_Ensemble.Rd b/man/OGS6_Ensemble.Rd index 55cfa5d5f8c046ab1a9ccd25563671a42e9439c4..772713a4f2800d3a2aad17093743befc66287486 100644 --- a/man/OGS6_Ensemble.Rd +++ b/man/OGS6_Ensemble.Rd @@ -9,9 +9,7 @@ Constructor for the OGS6_Ensemble base class \section{Active bindings}{ \if{html}{\out{<div class="r6-active-bindings">}} \describe{ -\item{\code{parameters}}{Access to private parameter '.parameters'} - -\item{\code{sim_name}}{Getter for private parameter '.sim_name'} +\item{\code{parameters}}{Getter for private parameter '.parameters'} \item{\code{ens_path}}{Getter for private parameter '.ens_path'} @@ -23,7 +21,6 @@ Constructor for the OGS6_Ensemble base class \subsection{Public methods}{ \itemize{ \item \href{#method-new}{\code{OGS6_Ensemble$new()}} -\item \href{#method-add_parameter}{\code{OGS6_Ensemble$add_parameter()}} \item \href{#method-run_simulation}{\code{OGS6_Ensemble$run_simulation()}} \item \href{#method-clone}{\code{OGS6_Ensemble$clone()}} } @@ -51,36 +48,23 @@ have the same length.} } } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-add_parameter"></a>}} -\if{latex}{\out{\hypertarget{method-add_parameter}{}}} -\subsection{Method \code{add_parameter()}}{ -Adds a parameter. +\if{html}{\out{<a id="method-run_simulation"></a>}} +\if{latex}{\out{\hypertarget{method-run_simulation}{}}} +\subsection{Method \code{run_simulation()}}{ +Runs the simulation. This calls r2ogs6::run_simulation() internally. +For ensembles, output will be written to logfiles. \subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$add_parameter(parameter)}\if{html}{\out{</div>}} +\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$run_simulation(parallel = FALSE)}\if{html}{\out{</div>}} } \subsection{Arguments}{ \if{html}{\out{<div class="arguments">}} \describe{ -\item{\code{parameter}}{list, length == 2: The first element references an -OGS6 parameter, the second one is a list or vector of values. -To find out how many values you need to supply, call ensemble_size -on this object.} +\item{\code{parallel}}{flag: Should the function be run in parallel? +This is implementented via the 'parallel' package.} } \if{html}{\out{</div>}} } -} -\if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-run_simulation"></a>}} -\if{latex}{\out{\hypertarget{method-run_simulation}{}}} -\subsection{Method \code{run_simulation()}}{ -Runs the simulation. This calls run_simulation() internally. For -ensembles, logfiles will never be written to console. This function -should be suited for parallelization. -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$run_simulation()}\if{html}{\out{</div>}} -} - } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-clone"></a>}} diff --git a/man/run_simulation.Rd b/man/run_simulation.Rd index f5eefb60b92d118f6f4bdd2ccbe1eddb508f9197..05865c410baabc5caa9d2bf5a5a25dade16529de 100644 --- a/man/run_simulation.Rd +++ b/man/run_simulation.Rd @@ -4,12 +4,12 @@ \alias{run_simulation} \title{run_simulation} \usage{ -run_simulation(ogs6_obj, output_to_log_file = TRUE) +run_simulation(ogs6_obj, write_logfile = TRUE) } \arguments{ \item{ogs6_obj}{OGS6: Simulation object} -\item{output_to_log_file}{flag: Should output be written to a log file?} +\item{write_logfile}{flag: Should output be written to a logfile?} } \description{ Calls OGS6 object validator functions, exports all necessary