diff --git a/man/OGS6.Rd b/man/OGS6.Rd index 7f57ee26904451a8ada8183f9b42d4e58d4f4b79..d3a9656b184bebf2cba4796b4a6ee481cee48ec1 100644 --- a/man/OGS6.Rd +++ b/man/OGS6.Rd @@ -6,6 +6,51 @@ \description{ Constructor for the OGS6 base class } +\section{Active bindings}{ +\if{html}{\out{<div class="r6-active-bindings">}} +\describe{ +\item{\code{sim_output}}{Getter for OGS6 private parameter '.sim_output'} + +\item{\code{sim_name}}{Getter for OGS6 private parameter '.sim_name'} + +\item{\code{sim_id}}{Getter for OGS6 private parameter '.sim_id'} + +\item{\code{sim_path}}{Getter for OGS6 private parameter '.sim_path'} + +\item{\code{ogs_bin_path}}{Getter for OGS6 private parameter '.ogs_bin_path'} + +\item{\code{gml}}{Getter for OGS6 private parameter '.gml'} + +\item{\code{meshes}}{Getter for OGS6 private parameter '.meshes'} + +\item{\code{geometry}}{Getter for OGS6 private parameter '.geometry'} + +\item{\code{python_script}}{Getter for OGS6 private parameter '.python_script'} + +\item{\code{processes}}{Getter for OGS6 private parameter '.processes'} + +\item{\code{time_loop}}{Getter for OGS6 private parameter '.time_loop'} + +\item{\code{local_coordinate_system}}{Getter for OGS6 private parameter '.local_coordinate_system'} + +\item{\code{media}}{Getter for OGS6 private parameter '.media'} + +\item{\code{parameters}}{Getter for OGS6 private parameter '.parameters'} + +\item{\code{curves}}{Getter for OGS6 private parameter '.curves'} + +\item{\code{process_variables}}{Getter for OGS6 private parameter '.process_variables'} + +\item{\code{nonlinear_solvers}}{Getter for OGS6 private parameter '.nonlinear_solvers'} + +\item{\code{linear_solvers}}{Getter for OGS6 private parameter '.linear_solvers'} + +\item{\code{test_definition}}{Getter for OGS6 private parameter '.test_definition'} + +\item{\code{insitu}}{Getter for OGS6 private parameter '.insitu'} +} +\if{html}{\out{</div>}} +} \section{Methods}{ \subsection{Public methods}{ \itemize{ @@ -34,6 +79,7 @@ Constructor for the OGS6 base class \if{html}{\out{<a id="method-new"></a>}} \if{latex}{\out{\hypertarget{method-new}{}}} \subsection{Method \code{new()}}{ +Creates new OGS6 object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$new(sim_name, sim_id, sim_path, ogs_bin_path, test_mode = FALSE)}\if{html}{\out{</div>}} } @@ -41,17 +87,17 @@ Constructor for the OGS6 base class \subsection{Arguments}{ \if{html}{\out{<div class="arguments">}} \describe{ -\item{\code{sim_name}}{The name of the simulation} +\item{\code{sim_name}}{string: Simulation name} -\item{\code{sim_id}}{The ID of the simulation} +\item{\code{sim_id}}{double: Simulation ID} -\item{\code{sim_path}}{The path where all relevant files for the simulation will be +\item{\code{sim_path}}{string: Path where all files for the simulation will be saved} -\item{\code{ogs_bin_path}}{Path to OpenGeoSys6 /bin directory} +\item{\code{ogs_bin_path}}{string: Path to OpenGeoSys6 /bin directory} \item{\code{test_mode}}{In test mode, sim_path and ogs_bin_path will not be -validated. If you're not a developer, please leave this variable as it is :)} +validated. If you're not a developer, please leave this as it is :)} } \if{html}{\out{</div>}} } @@ -60,141 +106,265 @@ validated. If you're not a developer, please leave this variable as it is :)} \if{html}{\out{<a id="method-add_sim_output"></a>}} \if{latex}{\out{\hypertarget{method-add_sim_output}{}}} \subsection{Method \code{add_sim_output()}}{ +... (WIP) \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_sim_output(name, value)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{name}}{...} + +\item{\code{value}}{...} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_mesh"></a>}} \if{latex}{\out{\hypertarget{method-add_mesh}{}}} \subsection{Method \code{add_mesh()}}{ +Adds a r2ogs6_mesh object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_mesh(mesh)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{mesh}}{r2ogs6_mesh} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_gml"></a>}} \if{latex}{\out{\hypertarget{method-add_gml}{}}} \subsection{Method \code{add_gml()}}{ +Adds a r2ogs6_gml object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_gml(gml)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{gml}}{r2ogs6_gml} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_python_script"></a>}} \if{latex}{\out{\hypertarget{method-add_python_script}{}}} \subsection{Method \code{add_python_script()}}{ +Adds a python script \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_python_script(python_script)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{python_script}}{string: File name of python script} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_process"></a>}} \if{latex}{\out{\hypertarget{method-add_process}{}}} \subsection{Method \code{add_process()}}{ +Adds a r2ogs6_process object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_process(process)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{process}}{r2ogs6_process} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_time_loop"></a>}} \if{latex}{\out{\hypertarget{method-add_time_loop}{}}} \subsection{Method \code{add_time_loop()}}{ +Adds a r2ogs6_time_loop object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_time_loop(time_loop)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{time_loop}}{r2ogs6_time_loop} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_local_coordinate_system"></a>}} \if{latex}{\out{\hypertarget{method-add_local_coordinate_system}{}}} \subsection{Method \code{add_local_coordinate_system()}}{ +Adds a r2ogs6_local_coordinate_system object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_local_coordinate_system(local_coordinate_system)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{local_coordinate_system}}{r2ogs6_local_coordinate_system} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_medium"></a>}} \if{latex}{\out{\hypertarget{method-add_medium}{}}} \subsection{Method \code{add_medium()}}{ +Adds a r2ogs6_medium object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_medium(medium)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{medium}}{r2ogs6_medium} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_parameter"></a>}} \if{latex}{\out{\hypertarget{method-add_parameter}{}}} \subsection{Method \code{add_parameter()}}{ +Adds a r2ogs6_parameter object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_parameter(parameter)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{parameter}}{r2ogs6_parameter} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_curve"></a>}} \if{latex}{\out{\hypertarget{method-add_curve}{}}} \subsection{Method \code{add_curve()}}{ +Adds a r2ogs6_curve object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_curve(curve)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{curve}}{r2ogs6_curve} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_process_variable"></a>}} \if{latex}{\out{\hypertarget{method-add_process_variable}{}}} \subsection{Method \code{add_process_variable()}}{ +Adds a r2ogs6_process_variable object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_process_variable(process_variable)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{process_variable}}{r2ogs6_process_variable} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_nonlinear_solver"></a>}} \if{latex}{\out{\hypertarget{method-add_nonlinear_solver}{}}} \subsection{Method \code{add_nonlinear_solver()}}{ +Adds a r2ogs6_nonlinear_solver object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_nonlinear_solver(nonlinear_solver)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{nonlinear_solver}}{r2ogs6_nonlinear_solver} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_linear_solver"></a>}} \if{latex}{\out{\hypertarget{method-add_linear_solver}{}}} \subsection{Method \code{add_linear_solver()}}{ +Adds a r2ogs6_linear_solver object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_linear_solver(linear_solver)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{linear_solver}}{r2ogs6_linear_solver} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_vtkdiff"></a>}} \if{latex}{\out{\hypertarget{method-add_vtkdiff}{}}} \subsection{Method \code{add_vtkdiff()}}{ +Adds a r2ogs6_vtkdiff object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_vtkdiff(vtkdiff)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{vtkdiff}}{r2ogs6_vtkdiff} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-add_insitu"></a>}} \if{latex}{\out{\hypertarget{method-add_insitu}{}}} \subsection{Method \code{add_insitu()}}{ +Adds a r2ogs6_insitu object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$add_insitu(insitu)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{insitu}}{r2ogs6_insitu} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-get_status"></a>}} \if{latex}{\out{\hypertarget{method-get_status}{}}} \subsection{Method \code{get_status()}}{ +Checks if the OGS6 object has all necessary parameters for +starting a simulation \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$get_status()}\if{html}{\out{</div>}} } @@ -204,10 +374,20 @@ validated. If you're not a developer, please leave this variable as it is :)} \if{html}{\out{<a id="method-clear"></a>}} \if{latex}{\out{\hypertarget{method-clear}{}}} \subsection{Method \code{clear()}}{ +Clears components from the OGS6 object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{OGS6$clear(which = names(get_implemented_classes()))}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{which}}{character: The names of the components (all by default). +If you want to delete only some components, run +names(get_implemented_classes()) for the available options.} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-clone"></a>}} diff --git a/man/construct_add_call.Rd b/man/construct_add_call.Rd index 76831c74c112bb3326722c5888bd6d90982f5ee2..a9727df97b225d8abde74c7ff3cabbd42610c0e1 100644 --- a/man/construct_add_call.Rd +++ b/man/construct_add_call.Rd @@ -7,15 +7,17 @@ construct_add_call(object, nested_call = FALSE) } \arguments{ -\item{object}{An object (numeric, character, list, NULL, or r2ogs6 class object)} +\item{object}{An object (numeric, character, list, NULL, or r2ogs6 class +object)} -\item{nested_call}{Optional: For recursion purposes, you should leave this as it is.} +\item{nested_call}{Optional: For recursion purposes, you should leave this as +it is.} } \value{ A string representing the code with which the component would be added to an OGS6 object } \description{ -Constructs a call based on an OGS6 component. This is a recursive function -and its feelings are easily hurt. Please handle it with care. +Constructs a call based on an OGS6 component. This is a +recursive function, handle with care. } diff --git a/man/delete_nulls_from_str.Rd b/man/delete_nulls_from_str.Rd new file mode 100644 index 0000000000000000000000000000000000000000..1828713335490e4e0920838404f238215d504ca9 --- /dev/null +++ b/man/delete_nulls_from_str.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/generate_benchmark_script.R +\name{delete_nulls_from_str} +\alias{delete_nulls_from_str} +\title{delete_nulls_from_str} +\usage{ +delete_nulls_from_str(string) +} +\arguments{ +\item{string}{A string} +} +\description{ +Utility function to delete "param_name = NULL" from a string, +this isn't necessary for functionality of generate_benchmark_script but will +make generated scripts way more readable. +} diff --git a/man/generate_all_benchmarks.Rd b/man/generate_all_benchmarks.Rd index 9c82b4637e7ced8a19085ef0068f933f61c89d23..6f2b19ddac71f3179e34d9003ea016e15e0a8220 100644 --- a/man/generate_all_benchmarks.Rd +++ b/man/generate_all_benchmarks.Rd @@ -10,12 +10,13 @@ generate_all_benchmarks( ) } \arguments{ -\item{path}{Optional: A path to a benchmark directory to generate scripts from -(defaults to 'extdata/benchmarks' package folder)} +\item{path}{Optional: A path to a benchmark directory to generate scripts +from (defaults to 'extdata/benchmarks' package folder)} \item{dest_dir}{Optional: The directory to write the scripts to (defaults to 'extdata/benchmark_scripts' package folder)} } \description{ -Collector function to generate benchmarks from all .prj files in a directory +Collector function to generate benchmarks from all .prj files in +a directory } diff --git a/man/r2ogs6_parameter.Rd b/man/r2ogs6_parameter.Rd index 478806edd9cdd0826f78f258fb2564ec068031dc..470bb1b9c66d48fbaa3ac2e9ee6fdb598f0a64de 100644 --- a/man/r2ogs6_parameter.Rd +++ b/man/r2ogs6_parameter.Rd @@ -4,17 +4,49 @@ \alias{r2ogs6_parameter} \title{r2ogs6_parameter} \usage{ -r2ogs6_parameter(name, type, values = NULL, value = NULL) +r2ogs6_parameter( + name, + type, + value = NULL, + values = NULL, + curve = NULL, + parameter = NULL, + group_id_property = NULL, + index_values = NULL, + field_name = NULL, + mesh = NULL, + expression = NULL, + time_series = NULL, + use_local_coordinate_system = NULL +) } \arguments{ -\item{name}{The parameter name} +\item{name}{string:} -\item{type}{The parameter type} - -\item{values}{Optional: string | numeric: Parameter values} +\item{type}{string:} \item{value}{Optional: string | double: Parameter value} + +\item{values}{Optional: string | double: Parameter values} + +\item{curve}{Optional: string:} + +\item{parameter}{Optional: string:} + +\item{group_id_property}{Optional: string:} + +\item{index_values}{Optional: list:} + +\item{field_name}{Optional: string:} + +\item{mesh}{Optional: string:} + +\item{expression}{Optional: string:} + +\item{time_series}{Optional: list:} + +\item{use_local_coordinate_system}{Optional: string, "true" | "false":} } \description{ -S3 class describing a .prj parameter +tag: parameter } diff --git a/man/to_node.Rd b/man/to_node.Rd index 3d8685eb1d6562ca2350f38eb5e0eae7134d8d65..4ef5069ee441b56f3ebc958cd41781b200843a0a 100644 --- a/man/to_node.Rd +++ b/man/to_node.Rd @@ -12,17 +12,19 @@ to_node( ) } \arguments{ -\item{object}{An object (so far works for r2ogs6 class objects, strings, numbers, lists and vectors)} +\item{object}{An object (so far works for r2ogs6 class objects, strings, +numbers, lists and vectors)} \item{object_name}{Optional: The object name. If not supplied, this function will try to guess the tag name by deparsing the 'object' parameter} -\item{attribute_names}{Optional: A character vector containing names of attributes -or attribute nodes} +\item{attribute_names}{Optional: A character vector containing names of +attributes or attribute nodes} -\item{flatten_on_exp}{Optional: This is for vectors which will be flattened to a string in XML} +\item{flatten_on_exp}{Optional: This is for vectors which will be flattened +to a string in XML} } \description{ -Recursive function to restructure objects so xml2::as_xml_document() -function will convert them to the desired XML format +Recursive function to restructure objects so +xml2::as_xml_document() function will convert them to the desired XML format }