[docs] Updating documentation

man/OGS6.Rd

@@ -52,6 +52,8 @@ Constructor for the OGS6 base class
 \item{\code{test_definition}}{Access to private parameter '.test_definition'}
 
 \item{\code{insitu}}{Access to private parameter '.insitu'}
+
+\item{\code{pvd}}{Access to private parameter '.pvd'}
 }
 \if{html}{\out{</div>}}
 }
@@ -124,6 +126,9 @@ Adds a simulation component (WIP)
 not of a proprietary `r2ogs6` class, `component_name` must be
 supplied. E.g. If you're adding a `python_script` which is a string, you
 would call `your_ogs6_obj$add("some_script.py", "python_script")`}
+
+\item{\code{component_name}}{string: Optional: The name of the component to be
+added}
 }
 \if{html}{\out{</div>}}
 }

man/OGS6_Ensemble.Rd

@@ -43,6 +43,8 @@ Creates new OGS6_Ensemble object
 of a sublist references an OGS6 parameter, the second one is a list or
 vector of values. Note that the second elements of the sublists must
 have the same length.}
+
+\item{\code{ens_dir_name}}{string: Name of ensemble directory}
 }
 \if{html}{\out{</div>}}
 }

man/OGS6_gml.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/gml.R
+\name{OGS6_gml}
+\alias{OGS6_gml}
+\title{OGS6_gml}
+\description{
+Constructor for the OGS6_gml base class
+}
+\section{Active bindings}{
+\if{html}{\out{<div class="r6-active-bindings">}}
+\describe{
+\item{\code{gml_path}}{Getter for private parameter '.gml_path'}
+
+\item{\code{name}}{Access to private parameter '.name'}
+
+\item{\code{points}}{Access to private parameter '.points'}
+
+\item{\code{polylines}}{Access to private parameter '.polylines'}
+
+\item{\code{surfaces}}{Access to private parameter '.surfaces'}
+
+\item{\code{is_subclass}}{Getter for private parameter '.is_subclass'}
+
+\item{\code{attr_names}}{Getter for private parameter '.attr_names'}
+
+\item{\code{flatten_on_exp}}{Getter for private parameter '.flatten_on_exp'}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{OGS6_gml$new()}}
+\item \href{#method-clone}{\code{OGS6_gml$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_gml object
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_gml$new(
+  gml_path = NULL,
+  name = NULL,
+  points = NULL,
+  polylines = NULL,
+  surfaces = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{gml_path}}{string: Optional: Path to .gml file}
+
+\item{\code{name}}{string: Geometry name}
+
+\item{\code{points}}{tibble: Must have 3 vectors named 'x', 'y' and 'z', may
+have optional 'name' vector}
+
+\item{\code{polylines}}{list(list("foo", c(1, 2))):}
+
+\item{\code{surfaces}}{list(list("foo", c(1, 2, 3), c(2, 3, 4))):}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_gml$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_pvd.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vtu.R
+\name{OGS6_pvd}
+\alias{OGS6_pvd}
+\title{OGS6_pvd}
+\description{
+Constructor for the OGS6_pvd base class
+}
+\section{Active bindings}{
+\if{html}{\out{<div class="r6-active-bindings">}}
+\describe{
+\item{\code{pvd_path}}{Getter for private parameter '.pvd_path'}
+
+\item{\code{datasets}}{Getter for private parameter '.datasets'}
+
+\item{\code{vtu_paths}}{Getter for `datasets` `file`}
+
+\item{\code{abs_vtu_paths}}{Gets absolute .vtu paths, e.g. `dirname(pvd_path)` + `datasets` `file`}
+
+\item{\code{timesteps}}{Gets timesteps from private parameter '.datasets'}
+
+\item{\code{OGS6_vtus}}{Getter for private parameter '.OGS6_vtus'}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{OGS6_pvd$new()}}
+\item \href{#method-get_vtu_path_by_timestep}{\code{OGS6_pvd$get_vtu_path_by_timestep()}}
+\item \href{#method-get_timestep_by_vtu_path}{\code{OGS6_pvd$get_timestep_by_vtu_path()}}
+\item \href{#method-get_PointData_time_tibble}{\code{OGS6_pvd$get_PointData_time_tibble()}}
+\item \href{#method-get_PointData_at_timestep}{\code{OGS6_pvd$get_PointData_at_timestep()}}
+\item \href{#method-clone}{\code{OGS6_pvd$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_pvd object
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_pvd$new(pvd_path)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{pvd_path}}{string: Path to .pvd file}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_vtu_path_by_timestep"></a>}}
+\if{latex}{\out{\hypertarget{method-get_vtu_path_by_timestep}{}}}
+\subsection{Method \code{get_vtu_path_by_timestep()}}{
+Returns .vtu path for specified timestep
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_pvd$get_vtu_path_by_timestep(timestep)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{timestep}}{string: Timestep}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_timestep_by_vtu_path"></a>}}
+\if{latex}{\out{\hypertarget{method-get_timestep_by_vtu_path}{}}}
+\subsection{Method \code{get_timestep_by_vtu_path()}}{
+Returns timestep for specified .vtu path
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_pvd$get_timestep_by_vtu_path(vtu_path)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{vtu_path}}{string: .vtu path}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_PointData_time_tibble"></a>}}
+\if{latex}{\out{\hypertarget{method-get_PointData_time_tibble}{}}}
+\subsection{Method \code{get_PointData_time_tibble()}}{
+Creates a tibble object from PointData
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_pvd$get_PointData_time_tibble(
+  point_ids,
+  Names,
+  start_at_timestep,
+  end_at_timestep
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{point_ids}}{numeric: Optional: IDs of the points of interest.
+Will default to all point IDs if not defined.}
+
+\item{\code{Names}}{character: `Name` attributes of `DataArray` elements}
+
+\item{\code{start_at_timestep}}{number: Timestep to start at}
+
+\item{\code{end_at_timestep}}{number: Timestep to end at}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_PointData_at_timestep"></a>}}
+\if{latex}{\out{\hypertarget{method-get_PointData_at_timestep}{}}}
+\subsection{Method \code{get_PointData_at_timestep()}}{
+Gets PointData at specified timestep. Calls
+`get_PointData_time_tibble` internally with `start_at_timestep` and
+`end_at_timestep` both being `timestep`
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_pvd$get_PointData_at_timestep(point_ids, Names, timestep)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{point_ids}}{number: Point IDs}
+
+\item{\code{Names}}{character: `Name` attributes of `DataArray` elements}
+
+\item{\code{timestep}}{string: Timestep}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_pvd$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_vtu.Rd

@@ -9,25 +9,11 @@ Constructor for the OGS6_vtu base class
 \section{Active bindings}{
 \if{html}{\out{<div class="r6-active-bindings">}}
 \describe{
-\item{\code{type}}{Access to private parameter '.type'}
+\item{\code{vtu_path}}{Getter for private parameter '.vtu_path'}
 
-\item{\code{version}}{Access to private parameter '.version'}
+\item{\code{vtkUnstructuredGrid}}{Access to private parameter '.vtkUnstructuredGrid'}
 
-\item{\code{byte_order}}{Access to private parameter '.byte_order'}
-
-\item{\code{UnstructuredGrid}}{Access to private parameter '.UnstructuredGrid'}
-
-\item{\code{header_type}}{Access to private parameter '.header_type'}
-
-\item{\code{compressor}}{Access to private parameter '.compressor'}
-
-\item{\code{AppendedData}}{Access to private parameter '.AppendedData '}
-
-\item{\code{is_subclass}}{Access to private parameter '.is_subclass'}
-
-\item{\code{attr_names}}{Access to private parameter '.attr_names'}
-
-\item{\code{flatten_on_exp}}{Access to private parameter '.flatten_on_exp'}
+\item{\code{dsa_wrapped_vtkUnstructuredGrid}}{Getter for private parameter '.dsa_wrapped_vtkUnstructuredGrid'}
 }
 \if{html}{\out{</div>}}
 }
@@ -35,7 +21,9 @@ Constructor for the OGS6_vtu base class
 \subsection{Public methods}{
 \itemize{
 \item \href{#method-new}{\code{OGS6_vtu$new()}}
-\item \href{#method-get_data_arrays}{\code{OGS6_vtu$get_data_arrays()}}
+\item \href{#method-get_PointData_for_point}{\code{OGS6_vtu$get_PointData_for_point()}}
+\item \href{#method-get_PointData}{\code{OGS6_vtu$get_PointData()}}
+\item \href{#method-get_number_of_points}{\code{OGS6_vtu$get_number_of_points()}}
 \item \href{#method-clone}{\code{OGS6_vtu$clone()}}
 }
 }
@@ -45,58 +33,69 @@ Constructor for the OGS6_vtu base class
 \subsection{Method \code{new()}}{
 Creates new OGS6_vtu object
 \subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6_vtu$new(
-  type,
-  version,
-  byte_order,
-  UnstructuredGrid,
-  header_type = NULL,
-  compressor = NULL,
-  AppendedData = NULL
-)}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_vtu$new(vtu_path)}\if{html}{\out{</div>}}
 }
 
 \subsection{Arguments}{
 \if{html}{\out{<div class="arguments">}}
 \describe{
-\item{\code{type}}{string:}
-
-\item{\code{version}}{string:}
-
-\item{\code{byte_order}}{string:}
-
-\item{\code{UnstructuredGrid}}{OGS6_UnstructuredGrid:}
-
-\item{\code{header_type}}{string: Optional:}
+\item{\code{vtu_path}}{string: Path to .vtu file}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_PointData_for_point"></a>}}
+\if{latex}{\out{\hypertarget{method-get_PointData_for_point}{}}}
+\subsection{Method \code{get_PointData_for_point()}}{
+Gets PointData for point with ID `point_id`
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_vtu$get_PointData_for_point(point_id, Names)}\if{html}{\out{</div>}}
+}
 
-\item{\code{compressor}}{string: Optional:}
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{point_id}}{number: Point ID}
 
-\item{\code{AppendedData}}{string: Optional:}
+\item{\code{Names}}{character: Optional: `Name` attributes of `DataArray`
+elements, defaults to all in `PointData`}
 }
 \if{html}{\out{</div>}}
 }
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-get_data_arrays"></a>}}
-\if{latex}{\out{\hypertarget{method-get_data_arrays}{}}}
-\subsection{Method \code{get_data_arrays()}}{
-Gets specified DataArrays
+\if{html}{\out{<a id="method-get_PointData"></a>}}
+\if{latex}{\out{\hypertarget{method-get_PointData}{}}}
+\subsection{Method \code{get_PointData()}}{
+Gets PointData of `DataArray` element with `Name` attribute
 \subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6_vtu$get_data_arrays(Names = character(), categories = character())}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_vtu$get_PointData(Name)}\if{html}{\out{</div>}}
 }
 
 \subsection{Arguments}{
 \if{html}{\out{<div class="arguments">}}
 \describe{
-\item{\code{Names}}{character: Optional: Select `DataArray` by `Name`}
-
-\item{\code{categories}}{character: Optional: One or more of
-`get_valid_vtu_categories()`}
+\item{\code{Name}}{string: Optional: `Name` attribute of `DataArray`
+elements, defaults to all in `PointData`}
 }
 \if{html}{\out{</div>}}
 }
 }
 \if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_number_of_points"></a>}}
+\if{latex}{\out{\hypertarget{method-get_number_of_points}{}}}
+\subsection{Method \code{get_number_of_points()}}{
+Gets number of points
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{OGS6_vtu$get_number_of_points()}\if{html}{\out{</div>}}
+}
+
+\subsection{Returns}{
+number: The number of points
+}
+}
+\if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-clone"></a>}}
 \if{latex}{\out{\hypertarget{method-clone}{}}}
 \subsection{Method \code{clone()}}{

man/generate_structured_mesh.Rd

@@ -4,15 +4,13 @@
 \alias{generate_structured_mesh}
 \title{generate_structured_mesh}
 \usage{
-generate_structured_mesh(ogs6_obj, call_str, read_in_vtu)
+generate_structured_mesh(args_str, ogs_bin_path)
 }
 \arguments{
-\item{ogs6_obj}{OGS6: Simulation object}
+\item{args_str}{string: The arguments the script will be called with}
 
-\item{call_str}{string: The arguments the script will be called with
-(EXCEPT -o output_file_name, this will be generated automatically!)}
-
-\item{read_in_vtu}{flag: Should .vtu file just be copied or read in too?}
+\item{ogs_bin_path}{string: Optional: Path to OpenGeoSys6 bin folder.
+Defaults to options("r2ogs6.default_ogs_bin_path").}
 }
 \value{
 string: .vtu file path

man/validate_pnt_values.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/gml.R
+\name{validate_pnt_values}
+\alias{validate_pnt_values}
+\title{validate_pnt_values}
+\usage{
+validate_pnt_values(element_1, element_2)
+}
+\arguments{
+\item{element_1}{numeric, length = 3}
+
+\item{element_2}{numeric, length = 3}
+}
+\description{
+Checks if two numerical vectors of length 3
+(two surface elements) each consist of 3 different elements and have
+exactly 2 matching elements between them. Think of the two vectors as
+triangles, and the triangles together form a square which is our surface.
+}