[docs] Updated documentation

man/OGS6_Ensemble.Rd

@@ -31,7 +31,7 @@ Constructor for the OGS6_Ensemble base class
 \subsection{Method \code{new()}}{
 Creates new OGS6_Ensemble object
 \subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$new(ogs6_obj, parameters)}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_Ensemble$new(ogs6_obj, parameters, ens_dir_name = "Ensemble")}\if{html}{\out{</div>}}
 }
 
 \subsection{Arguments}{

man/OGS6_UnstructuredGrid.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vtu.R
+\name{OGS6_UnstructuredGrid}
+\alias{OGS6_UnstructuredGrid}
+\title{OGS6_UnstructuredGrid}
+\description{
+Constructor for the OGS6_UnstructuredGrid base class
+}
+\section{Active bindings}{
+\if{html}{\out{<div class="r6-active-bindings">}}
+\describe{
+\item{\code{Piece}}{Access to private parameter '.Piece'}
+
+\item{\code{FieldData}}{Access to private parameter '.FieldData'}
+
+\item{\code{is_subclass}}{Access to private parameter '.is_subclass'}
+
+\item{\code{subclasses_names}}{Access to private parameter '.subclasses_names'}
+
+\item{\code{attr_names}}{Access to private parameter '.attr_names'}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{OGS6_UnstructuredGrid$new()}}
+\item \href{#method-clone}{\code{OGS6_UnstructuredGrid$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_UnstructuredGrid object
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_UnstructuredGrid$new(Piece, FieldData = NULL)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{Piece}}{OGS6_Piece:}
+
+\item{\code{FieldData}}{character, length == 2:}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_UnstructuredGrid$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>}}
+}
+}
+}

man/OGS6_mesh.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vtu.R
+\name{OGS6_mesh}
+\alias{OGS6_mesh}
+\title{OGS6_mesh}
+\description{
+Constructor for the OGS6_mesh base class
+}
+\section{Active bindings}{
+\if{html}{\out{<div class="r6-active-bindings">}}
+\describe{
+\item{\code{mesh_path}}{Access to private parameter '.mesh_path'}
+
+\item{\code{mesh_filename}}{Access to private parameter '.mesh_filename'}
+
+\item{\code{is_subclass}}{Access to private parameter '.is_subclass'}
+
+\item{\code{subclasses_names}}{Access to private parameter '.subclasses_names'}
+
+\item{\code{attr_names}}{Access to private parameter '.attr_names'}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{OGS6_mesh$new()}}
+\item \href{#method-clone}{\code{OGS6_mesh$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_mesh object
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_mesh$new(mesh_path)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{mesh_path}}{string:}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_mesh$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>}}
+}
+}
+}

man/construct_add_call.Rd

@@ -7,7 +7,7 @@
 construct_add_call(object, nested_call = FALSE)
 }
 \arguments{
-\item{object}{An object (numeric, character, list, NULL, or r2ogs6 class
+\item{object}{An object (numeric, character, list, NULL, OGS6 or r2ogs6 class
 object)}
 
 \item{nested_call}{Optional: For recursion purposes, you should leave this as

man/generate_structured_mesh.Rd

@@ -7,15 +7,16 @@
 generate_structured_mesh(ogs6_obj, call_str)
 }
 \arguments{
-\item{ogs6_obj}{A OGS6 class object (containing the path to the ogs6 bin/ folder)}
+\item{ogs6_obj}{OGS6: Simulation object}
 
-\item{call_str}{The arguments the script will be called with (EXCEPT -o output_file_name, this will
-be generated automatically!)}
+\item{call_str}{The arguments the script will be called with
+(EXCEPT -o output_file_name, this will be generated automatically!)}
 }
 \value{
 The newly generated .vtu file path
 }
 \description{
-Wrapper function to call generateStructuredMesh.exe (VTK mesh generator).
-For full documentation see https://www.opengeosys.org/docs/tools/meshing/structured-mesh-generation/
+Wrapper function to call generateStructuredMesh.exe
+(VTK mesh generator). For full documentation see
+https://www.opengeosys.org/docs/tools/meshing/structured-mesh-generation/
 }

man/pick_vtu_file.Rd

@@ -7,8 +7,9 @@
 pick_vtu_file(ogs6_obj)
 }
 \arguments{
-\item{ogs6_obj}{A OGS6 class object}
+\item{ogs6_obj}{OGS6: Simulation object}
 }
 \description{
-Lets the user pick a .vtu file and adds it to the specified OGS6 class object
+Lets the user pick a .vtu file and adds it to the specified OGS6
+class object
 }

man/read_in_prj.Rd

@@ -4,12 +4,14 @@
 \alias{read_in_prj}
 \title{read_in_prj}
 \usage{
-read_in_prj(ogs6_obj, prj_path)
+read_in_prj(ogs6_obj, prj_path, read_in_vtu = FALSE)
 }
 \arguments{
 \item{ogs6_obj}{A OGS6 class object}
 
 \item{prj_path}{The path to the project file that should be read in}
+
+\item{read_in_vtu}{flag: Should .vtu file be copied or read in?}
 }
 \description{
 Wrapper function to read in a whole .prj file

man/read_in_vtu.Rd

@@ -7,7 +7,7 @@
 read_in_vtu(ogs6_obj, vtu_path)
 }
 \arguments{
-\item{ogs6_obj}{A OGS6 class object}
+\item{ogs6_obj}{OGS6: Simulation object}
 
 \item{vtu_path}{The path to the mesh file that should be read in}
 }