From f6fa74d6bc9d22d26f4647a48b8548f7285d9850 Mon Sep 17 00:00:00 2001
From: aheinri5 <Anna@netzkritzler.de>
Date: Fri, 18 Dec 2020 22:40:56 +0100
Subject: [PATCH] [docs] Updated documentation
---
man/OGS6_Ensemble.Rd | 2 +-
man/OGS6_UnstructuredGrid.Rd | 67 +++++++++++++++++++++++++++++++++
man/OGS6_mesh.Rd | 65 ++++++++++++++++++++++++++++++++
man/construct_add_call.Rd | 2 +-
man/generate_structured_mesh.Rd | 11 +++---
man/pick_vtu_file.Rd | 5 ++-
man/read_in_prj.Rd | 4 +-
man/read_in_vtu.Rd | 2 +-
8 files changed, 147 insertions(+), 11 deletions(-)
create mode 100644 man/OGS6_UnstructuredGrid.Rd
create mode 100644 man/OGS6_mesh.Rd
diff --git a/man/OGS6_Ensemble.Rd b/man/OGS6_Ensemble.Rd
index 772713a..34a5bef 100644
--- a/man/OGS6_Ensemble.Rd
+++ b/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}{
diff --git a/man/OGS6_UnstructuredGrid.Rd b/man/OGS6_UnstructuredGrid.Rd
new file mode 100644
index 0000000..ae30a4c
--- /dev/null
+++ b/man/OGS6_UnstructuredGrid.Rd
@@ -0,0 +1,67 @@
+% 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>}}
+}
+}
+}
diff --git a/man/OGS6_mesh.Rd b/man/OGS6_mesh.Rd
new file mode 100644
index 0000000..b4149f3
--- /dev/null
+++ b/man/OGS6_mesh.Rd
@@ -0,0 +1,65 @@
+% 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>}}
+}
+}
+}
diff --git a/man/construct_add_call.Rd b/man/construct_add_call.Rd
index a9727df..fb98e19 100644
--- a/man/construct_add_call.Rd
+++ b/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
diff --git a/man/generate_structured_mesh.Rd b/man/generate_structured_mesh.Rd
index 9cfb90d..e16d4e6 100644
--- a/man/generate_structured_mesh.Rd
+++ b/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/
}
diff --git a/man/pick_vtu_file.Rd b/man/pick_vtu_file.Rd
index 1360afd..6c26251 100644
--- a/man/pick_vtu_file.Rd
+++ b/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
}
diff --git a/man/read_in_prj.Rd b/man/read_in_prj.Rd
index 3bda7d9..5902d1e 100644
--- a/man/read_in_prj.Rd
+++ b/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
diff --git a/man/read_in_vtu.Rd b/man/read_in_vtu.Rd
index 7de06c7..93dac6e 100644
--- a/man/read_in_vtu.Rd
+++ b/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}
}
--
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