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Commit 20ed513a authored by Johannes Boog's avatar Johannes Boog
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[doc] update for OGS6_msh class support 

    update namespace
    add and update examples, function descriptions
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NAMESPACE
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− 0
View file @ 20ed513a
......@@ -5,6 +5,7 @@ export(OGS6_Chain)
export(OGS6_Ensemble)
export(OGS6_gml)
export(OGS6_h5)
export(OGS6_msh)
export(OGS6_pvd)
export(OGS6_vtu)
export(ogs6_call_ogs6)
......
man/OGS6.Rd
+ 39
− 37
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......@@ -30,12 +30,12 @@ ogs6_obj$add_gml("this_works.gml")
\dontrun{ogs6_obj$add_gml("this_doesnt.oops")}
## ------------------------------------------------
## Method `OGS6$add_vtu`
## Method `OGS6$add_mesh`
## ------------------------------------------------
ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
ogs6_obj$add_vtu("this_works.vtu")
\dontrun{ogs6_obj$add_vtu("this_doesnt.oops")}
ogs6_obj$add_mesh("this_works.vtu")
\dontrun{ogs6_obj$add_mesh("this_doesnt.oops")}
## ------------------------------------------------
## Method `OGS6$update_component`
......@@ -115,27 +115,29 @@ ogs6_obj$get_status()
\item{\code{h5s}}{\code{h5s} \code{value} must be of class \code{H5IdComponent}
as returned by \code{rhdf5::h5read()}.}
\item{\code{mshs}}{\code{mshs} \code{value} must be an object of class \code{OGS6_msh}.}
}
\if{html}{\out{</div>}}
}
\section{Methods}{
\subsection{Public methods}{
\itemize{
\item \href{#method-new}{\code{OGS6$new()}}
\item \href{#method-add}{\code{OGS6$add()}}
\item \href{#method-add_gml}{\code{OGS6$add_gml()}}
\item \href{#method-add_vtu}{\code{OGS6$add_vtu()}}
\item \href{#method-update_component}{\code{OGS6$update_component()}}
\item \href{#method-get_status}{\code{OGS6$get_status()}}
\item \href{#method-print}{\code{OGS6$print()}}
\item \href{#method-print_log}{\code{OGS6$print_log()}}
\item \href{#method-clear}{\code{OGS6$clear()}}
\item \href{#method-clone}{\code{OGS6$clone()}}
\item \href{#method-OGS6-new}{\code{OGS6$new()}}
\item \href{#method-OGS6-add}{\code{OGS6$add()}}
\item \href{#method-OGS6-add_gml}{\code{OGS6$add_gml()}}
\item \href{#method-OGS6-add_mesh}{\code{OGS6$add_mesh()}}
\item \href{#method-OGS6-update_component}{\code{OGS6$update_component()}}
\item \href{#method-OGS6-get_status}{\code{OGS6$get_status()}}
\item \href{#method-OGS6-print}{\code{OGS6$print()}}
\item \href{#method-OGS6-print_log}{\code{OGS6$print_log()}}
\item \href{#method-OGS6-clear}{\code{OGS6$clear()}}
\item \href{#method-OGS6-clone}{\code{OGS6$clone()}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-new"></a>}}
\if{latex}{\out{\hypertarget{method-new}{}}}
\if{html}{\out{<a id="method-OGS6-new"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6-new}{}}}
\subsection{Method \code{new()}}{
Creates new OGS6 object
\subsection{Usage}{
......@@ -162,8 +164,8 @@ saved}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-add"></a>}}
\if{latex}{\out{\hypertarget{method-add}{}}}
\if{html}{\out{<a id="method-OGS6-add"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6-add}{}}}
\subsection{Method \code{add()}}{
Adds a .prj simulation component
\subsection{Usage}{
......@@ -188,8 +190,8 @@ ogs6_obj$add(prj_parameter(name = "foo", type = "bar"))
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-add_gml"></a>}}
\if{latex}{\out{\hypertarget{method-add_gml}{}}}
\if{html}{\out{<a id="method-OGS6-add_gml"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6-add_gml}{}}}
\subsection{Method \code{add_gml()}}{
Adds a reference to a file with ending .gml and optionally, a
\code{OGS6_gml} object
......@@ -217,13 +219,13 @@ ogs6_obj$add_gml("this_works.gml")
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-add_vtu"></a>}}
\if{latex}{\out{\hypertarget{method-add_vtu}{}}}
\subsection{Method \code{add_vtu()}}{
\if{html}{\out{<a id="method-OGS6-add_mesh"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6-add_mesh}{}}}
\subsection{Method \code{add_mesh()}}{
Adds a reference to a \code{.vtu} file and optionally, a \code{OGS6_vtu}
object
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_vtu(path, axisym = FALSE, read_in_vtu = FALSE)}\if{html}{\out{</div>}}
\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_mesh(path, axisym = FALSE, read_in_vtu = FALSE)}\if{html}{\out{</div>}}
}
\subsection{Arguments}{
......@@ -241,8 +243,8 @@ copied or read in too?}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
\preformatted{ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
ogs6_obj$add_vtu("this_works.vtu")
\dontrun{ogs6_obj$add_vtu("this_doesnt.oops")}
ogs6_obj$add_mesh("this_works.vtu")
\dontrun{ogs6_obj$add_mesh("this_doesnt.oops")}
}
\if{html}{\out{</div>}}
......@@ -250,8 +252,8 @@ ogs6_obj$add_vtu("this_works.vtu")
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-update_component"></a>}}
\if{latex}{\out{\hypertarget{method-update_component}{}}}
\if{html}{\out{<a id="method-OGS6-update_component"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6-update_component}{}}}
\subsection{Method \code{update_component()}}{
Update a component of the \code{OGS6} object.
\subsection{Usage}{
......@@ -280,8 +282,8 @@ second one is the corresponding value.}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-get_status"></a>}}
\if{latex}{\out{\hypertarget{method-get_status}{}}}
\if{html}{\out{<a id="method-OGS6-get_status"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6-get_status}{}}}
\subsection{Method \code{get_status()}}{
Checks if the \code{OGS6} object has all necessary parameters for
starting a simulation
......@@ -307,8 +309,8 @@ ogs6_obj$get_status()
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-print"></a>}}
\if{latex}{\out{\hypertarget{method-print}{}}}
\if{html}{\out{<a id="method-OGS6-print"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6-print}{}}}
\subsection{Method \code{print()}}{
Overrides default printing behaviour
print_log
......@@ -318,8 +320,8 @@ print_log
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-print_log"></a>}}
\if{latex}{\out{\hypertarget{method-print_log}{}}}
\if{html}{\out{<a id="method-OGS6-print_log"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6-print_log}{}}}
\subsection{Method \code{print_log()}}{
Prints logfile to console (if it exists)
\subsection{Usage}{
......@@ -328,8 +330,8 @@ Prints logfile to console (if it exists)
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-clear"></a>}}
\if{latex}{\out{\hypertarget{method-clear}{}}}
\if{html}{\out{<a id="method-OGS6-clear"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6-clear}{}}}
\subsection{Method \code{clear()}}{
Clears components from the \code{OGS6} object
\subsection{Usage}{
......@@ -347,8 +349,8 @@ If you want to delete only some components, run
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-clone"></a>}}
\if{latex}{\out{\hypertarget{method-clone}{}}}
\if{html}{\out{<a id="method-OGS6-clone"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6-clone}{}}}
\subsection{Method \code{clone()}}{
The objects of this class are cloneable with this method.
\subsection{Usage}{
......
man/OGS6_msh.Rd 0 → 100644
+ 70
− 0
View file @ 20ed513a
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ogs6_msh.R
\name{OGS6_msh}
\alias{OGS6_msh}
\title{OGS6_msh}
\description{
Small class to support \code{MSH} mesh files. Note that
MSH files are a legacy format from OGS5. It is recommended to switch to VTU
files.
}
\section{Active bindings}{
\if{html}{\out{<div class="r6-active-bindings">}}
\describe{
\item{\code{msh_path}}{Getter/setter for private parameter `.msh_path`}
}
\if{html}{\out{</div>}}
}
\section{Methods}{
\subsection{Public methods}{
\itemize{
\item \href{#method-OGS6_msh-new}{\code{OGS6_msh$new()}}
\item \href{#method-OGS6_msh-print}{\code{OGS6_msh$print()}}
\item \href{#method-OGS6_msh-clone}{\code{OGS6_msh$clone()}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-OGS6_msh-new"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6_msh-new}{}}}
\subsection{Method \code{new()}}{
reates new OGS6_vtu object..
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{OGS6_msh$new(msh_path)}\if{html}{\out{</div>}}
}
\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{msh_path}}{path to \code{*.msh} file.}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-OGS6_msh-print"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6_msh-print}{}}}
\subsection{Method \code{print()}}{
Overrides the default print method
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{OGS6_msh$print()}\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-OGS6_msh-clone"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6_msh-clone}{}}}
\subsection{Method \code{clone()}}{
The objects of this class are cloneable with this method.
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{OGS6_msh$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
+ 24
− 24
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......@@ -36,19 +36,19 @@ Constructor for the `OGS6_vtu` base class
\section{Methods}{
\subsection{Public methods}{
\itemize{
\item \href{#method-new}{\code{OGS6_vtu$new()}}
\item \href{#method-print}{\code{OGS6_vtu$print()}}
\item \href{#method-get_field_data}{\code{OGS6_vtu$get_field_data()}}
\item \href{#method-get_point_coords}{\code{OGS6_vtu$get_point_coords()}}
\item \href{#method-get_point_data_at}{\code{OGS6_vtu$get_point_data_at()}}
\item \href{#method-get_point_data}{\code{OGS6_vtu$get_point_data()}}
\item \href{#method-get_cell_data}{\code{OGS6_vtu$get_cell_data()}}
\item \href{#method-clone}{\code{OGS6_vtu$clone()}}
\item \href{#method-OGS6_vtu-new}{\code{OGS6_vtu$new()}}
\item \href{#method-OGS6_vtu-print}{\code{OGS6_vtu$print()}}
\item \href{#method-OGS6_vtu-get_field_data}{\code{OGS6_vtu$get_field_data()}}
\item \href{#method-OGS6_vtu-get_point_coords}{\code{OGS6_vtu$get_point_coords()}}
\item \href{#method-OGS6_vtu-get_point_data_at}{\code{OGS6_vtu$get_point_data_at()}}
\item \href{#method-OGS6_vtu-get_point_data}{\code{OGS6_vtu$get_point_data()}}
\item \href{#method-OGS6_vtu-get_cell_data}{\code{OGS6_vtu$get_cell_data()}}
\item \href{#method-OGS6_vtu-clone}{\code{OGS6_vtu$clone()}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-new"></a>}}
\if{latex}{\out{\hypertarget{method-new}{}}}
\if{html}{\out{<a id="method-OGS6_vtu-new"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6_vtu-new}{}}}
\subsection{Method \code{new()}}{
Creates new OGS6_vtu object.
\subsection{Usage}{
......@@ -64,8 +64,8 @@ Creates new OGS6_vtu object.
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-print"></a>}}
\if{latex}{\out{\hypertarget{method-print}{}}}
\if{html}{\out{<a id="method-OGS6_vtu-print"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6_vtu-print}{}}}
\subsection{Method \code{print()}}{
Overrides default printing behaviour.
\subsection{Usage}{
......@@ -74,8 +74,8 @@ Overrides default printing behaviour.
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-get_field_data"></a>}}
\if{latex}{\out{\hypertarget{method-get_field_data}{}}}
\if{html}{\out{<a id="method-OGS6_vtu-get_field_data"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6_vtu-get_field_data}{}}}
\subsection{Method \code{get_field_data()}}{
Gets FieldData.
\subsection{Usage}{
......@@ -97,8 +97,8 @@ elements.
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-get_point_coords"></a>}}
\if{latex}{\out{\hypertarget{method-get_point_coords}{}}}
\if{html}{\out{<a id="method-OGS6_vtu-get_point_coords"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6_vtu-get_point_coords}{}}}
\subsection{Method \code{get_point_coords()}}{
Gets coordinates of specific points by their IDs.
\subsection{Usage}{
......@@ -119,8 +119,8 @@ arrays.
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-get_point_data_at"></a>}}
\if{latex}{\out{\hypertarget{method-get_point_data_at}{}}}
\if{html}{\out{<a id="method-OGS6_vtu-get_point_data_at"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6_vtu-get_point_data_at}{}}}
\subsection{Method \code{get_point_data_at()}}{
Gets PointData at specified coordinates.
\subsection{Usage}{
......@@ -140,8 +140,8 @@ elements, defaults to all in `PointData`}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-get_point_data"></a>}}
\if{latex}{\out{\hypertarget{method-get_point_data}{}}}
\if{html}{\out{<a id="method-OGS6_vtu-get_point_data"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6_vtu-get_point_data}{}}}
\subsection{Method \code{get_point_data()}}{
Gets PointData for points with IDs in `point_ids`.
\subsection{Usage}{
......@@ -163,8 +163,8 @@ A tibble::tibble where each row represents a point.
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-get_cell_data"></a>}}
\if{latex}{\out{\hypertarget{method-get_cell_data}{}}}
\if{html}{\out{<a id="method-OGS6_vtu-get_cell_data"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6_vtu-get_cell_data}{}}}
\subsection{Method \code{get_cell_data()}}{
Gets CellData for cells with IDs in `cell_ids`.
\subsection{Usage}{
......@@ -186,8 +186,8 @@ A tibble::tibble where each row represents a cell.
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-clone"></a>}}
\if{latex}{\out{\hypertarget{method-clone}{}}}
\if{html}{\out{<a id="method-OGS6_vtu-clone"></a>}}
\if{latex}{\out{\hypertarget{method-OGS6_vtu-clone}{}}}
\subsection{Method \code{clone()}}{
The objects of this class are cloneable with this method.
\subsection{Usage}{
......
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