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Add support for mesh files in MSH format

Merged Add support for mesh files in MSH format
67-feat_msh-file-support into master
Merged Johannes Boog requested to merge 67-feat_msh-file-support into master
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man/OGS6.Rd
+ 39
− 37
@@ -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}{