[docs] updated documentation

NAMESPACE

@@ -8,7 +8,12 @@ export(OGS6_pvd)
 export(OGS6_vtu)
 export(generate_benchmark_script)
 export(generate_structured_mesh)
+export(ogs_call_ogs6)
+export(ogs_export_sim_files)
+export(ogs_get_combinations)
 export(ogs_get_medium_property)
+export(ogs_read_output_files)
+export(ogs_run_simulation)
 export(r2ogs6_borehole_heat_exchanger)
 export(r2ogs6_boundary_condition)
 export(r2ogs6_capillary_pressure)
@@ -52,5 +57,4 @@ export(r2ogs6_time_stepping)
 export(r2ogs6_tl_process)
 export(r2ogs6_vtkdiff)
 export(read_in_prj)
-export(run_simulation)
 importFrom(foreach,"%dopar%")

man/OGS6_Ensemble.Rd

@@ -25,7 +25,8 @@ Constructor for the OGS6_Ensemble base class
 \subsection{Public methods}{
 \itemize{
 \item \href{#method-new}{\code{OGS6_Ensemble$new()}}
-\item \href{#method-ogs_run_simulation}{\code{OGS6_Ensemble$ogs_run_simulation()}}
+\item \href{#method-print}{\code{OGS6_Ensemble$print()}}
+\item \href{#method-run_simulation}{\code{OGS6_Ensemble$run_simulation()}}
 \item \href{#method-relevant_parameter_at}{\code{OGS6_Ensemble$relevant_parameter_at()}}
 \item \href{#method-clone}{\code{OGS6_Ensemble$clone()}}
 }
@@ -62,13 +63,23 @@ have the same length.}
 }
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-ogs_run_simulation"></a>}}
-\if{latex}{\out{\hypertarget{method-ogs_run_simulation}{}}}
-\subsection{Method \code{ogs_run_simulation()}}{
-Runs the simulation. This calls r2ogs6::ogs_run_simulation() internally.
-For ensembles, output will be written to logfiles.
+\if{html}{\out{<a id="method-print"></a>}}
+\if{latex}{\out{\hypertarget{method-print}{}}}
+\subsection{Method \code{print()}}{
+Overrides default printing behaviour
 \subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$ogs_run_simulation(parallel = FALSE, verbose = F)}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$print()}\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::ogs_run_simulation()
+internally. For ensembles, output will always be written to logfiles.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$run_simulation(parallel = FALSE, verbose = F)}\if{html}{\out{</div>}}
 }
 
 \subsection{Arguments}{

man/export_all_sim_files.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/sim_utils.R
-\name{export_all_sim_files}
-\alias{export_all_sim_files}
-\title{export_all_sim_files}
-\usage{
-export_all_sim_files(ogs6_obj)
-}
-\arguments{
-\item{ogs6_obj}{OGS6: Simulation object}
-}
-\description{
-Exports and / or copies all simulation files to
-`ogs6_obj$sim_path`
-}

man/run_simulation.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/sim_utils.R
-\name{run_simulation}
-\alias{run_simulation}
-\title{run_simulation}
-\usage{
-run_simulation(ogs6_obj, write_logfile = TRUE, ogs_bin_path)
-}
-\arguments{
-\item{ogs6_obj}{OGS6: Simulation object}
-
-\item{write_logfile}{flag: Should output be written to a logfile?}
-
-\item{ogs_bin_path}{string: Optional: OpenGeoSys 6 bin folder path. Defaults
-to `options("r2ogs6.default_ogs_bin_path")`}
-}
-\description{
-Calls OGS6 object validator functions, exports all necessary
-files and starts OpenGeoSys6
-}