[base] docs and NAMESPACE cleanup

DESCRIPTION

@@ -38,7 +38,8 @@ Imports:
     dplyr,
     rlang,
     doParallel,
-    stats
+    stats,
+    reticulate
 RoxygenNote: 7.1.1
 VignetteBuilder: knitr
 Depends: 

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(OGS6)
+export(OGS6_Chain)
+export(OGS6_Ensemble)
+export(OGS6_gml)
+export(OGS6_pvd)
+export(OGS6_vtu)
+export(generate_benchmark_script)
+export(generate_structured_mesh)
+export(r2ogs6_borehole_heat_exchanger)
+export(r2ogs6_boundary_condition)
+export(r2ogs6_capillary_pressure)
+export(r2ogs6_chemical_system)
+export(r2ogs6_com_property)
+export(r2ogs6_component)
+export(r2ogs6_convergence_criterion)
+export(r2ogs6_curve)
+export(r2ogs6_deactivated_subdomain)
+export(r2ogs6_eigen)
+export(r2ogs6_flow_and_temperature_control)
+export(r2ogs6_fluid)
+export(r2ogs6_fracture_model)
+export(r2ogs6_fracture_properties)
+export(r2ogs6_global_process_coupling)
+export(r2ogs6_insitu)
+export(r2ogs6_jacobian_assembler)
+export(r2ogs6_kinetic_reactant)
+export(r2ogs6_linear_solver)
+export(r2ogs6_local_coordinate_system)
+export(r2ogs6_material_property)
+export(r2ogs6_medium)
+export(r2ogs6_nonlinear_solver)
+export(r2ogs6_output)
+export(r2ogs6_parameter)
+export(r2ogs6_ph_property)
+export(r2ogs6_phase)
+export(r2ogs6_phase_component)
+export(r2ogs6_phasefield_parameters)
+export(r2ogs6_pipes)
+export(r2ogs6_porous_medium)
+export(r2ogs6_process)
+export(r2ogs6_process_variable)
+export(r2ogs6_rate)
+export(r2ogs6_search_length_algorithm)
+export(r2ogs6_solution)
+export(r2ogs6_source_term)
+export(r2ogs6_time_loop)
+export(r2ogs6_time_stepping)
+export(r2ogs6_tl_process)
+export(r2ogs6_vtkdiff)
+export(read_in_prj)
+export(run_simulation)
+importFrom(foreach,"%dopar%")

R/utils.R

@@ -205,18 +205,17 @@ get_nonstandard_tag_names <- function(){
 }
 
 
-#'get_implemented_classes
-#'@description Returns class names (and variable names) of `OGS6` variables.
-#' Change this if you implement new `OGS6` variables or delete old ones!
-#' If you implement a new variable, you add the following the `class_names`
-#' vector: `name_of_OGS6_variable = "name_of_your_class"`
-#'@return character: Named vector containing class names of `OGS6` variables
-#' and their corresponding variable name
-get_implemented_classes <- function(){
-
-  class_names <- c(vtus = "OGS6_vtu",
-                   gml = "r2ogs6_gml",
-                   search_length_algorithm = "r2ogs6_search_length_algorithm",
+#'addable_prj_components
+#'@description Returns all possible `OGS6` top level .prj components (names)
+#' along with their respective class names (values).
+#' Change this if you implement new `OGS6` .prj components or delete old ones!
+#' If you implement a new components, you add the following to the `class_names`
+#' vector: `name_of_prj_component = "name_of_your_class"`
+#'@return character: Named vector of `OGS6` top level .prj components (names)
+#' along with their respective class names (values)
+addable_prj_components <- function(){
+
+  class_names <- c(search_length_algorithm = "r2ogs6_search_length_algorithm",
                    processes = "r2ogs6_process",
                    media = "r2ogs6_medium",
                    time_loop = "r2ogs6_time_loop",
@@ -297,15 +296,15 @@ get_obj_status <- function(flag, obj){
 #'@param ogs6_parameter_name string: Name of a OGS6 parameter
 is_optional_sim_component <- function(ogs6_parameter_name){
 
-  optional_sim_components <- c("gml",
-                               "vtus",
-                               "local_coordinate_system",
-                               "curves",
-                               "search_length_algorithm",
-                               "test_definition",
-                               "insitu")
+  mandatory_components <- c("meshes",
+                            "processes",
+                            "time_loop",
+                            "nonlinear_solvers",
+                            "linear_solvers",
+                            "parameters",
+                            "process_variables")
 
-  return(invisible(ogs6_parameter_name %in% optional_sim_components))
+  return(invisible(!ogs6_parameter_name %in% mandatory_components))
 }
 
 
@@ -313,23 +312,15 @@ is_optional_sim_component <- function(ogs6_parameter_name){
 
 
 #'coerce_string_to_numeric
-#'@description If an object is of type string, coerces it to a numeric type:
-#' A double if 'split' is FALSE as per default, a numeric vector otherwise.
-#' If 'split' is set to true the string will be split at ' ' (whitespace)
-#' characters.
+#'@description If an object is of type string, coerces it to a numeric type
 #'@param obj An object to check
-#'@param split flag: Should object be split at ' ' (whitespace) if it is a
-#' string?
 #'@return The object as a numeric type (if 'obj' was a string, else the
 #' unchanged 'obj')
-coerce_string_to_numeric <- function(obj, split = FALSE){
+coerce_string_to_numeric <- function(obj){
 
   if(assertthat::is.string(obj)){
-    if(split){
-      obj <- as.double(unlist(strsplit(obj, " ")))
-    }else{
-      obj <- as.double(obj)
-    }
+    obj <- trimws(gsub("\r?\n|\r|\\s+", " ", obj))
+    obj <- as.double(unlist(strsplit(obj, " ")))
   }
 
   return(invisible(obj))

man/OGS6_Piece.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/vtu.R
-\name{OGS6_Piece}
-\alias{OGS6_Piece}
-\title{OGS6_Piece}
-\description{
-Constructor for the OGS6_Piece base class
-}
-\section{Active bindings}{
-\if{html}{\out{<div class="r6-active-bindings">}}
-\describe{
-\item{\code{NumberOfPoints}}{Access to private parameter '.NumberOfPoints'}
-
-\item{\code{NumberOfCells}}{Access to private parameter '.NumberOfCells'}
-
-\item{\code{PointData}}{Access to private parameter '.PointData'}
-
-\item{\code{Points}}{Access to private parameter '.Points'}
-
-\item{\code{Cells}}{Access to private parameter '.Cells'}
-
-\item{\code{CellData}}{Access to private parameter '.CellData'}
-
-\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_Piece$new()}}
-\item \href{#method-clone}{\code{OGS6_Piece$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_Piece object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6_Piece$new(
-  NumberOfPoints,
-  NumberOfCells,
-  PointData,
-  Points,
-  Cells,
-  CellData = NULL
-)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{NumberOfPoints}}{string | number:}
-
-\item{\code{NumberOfCells}}{string | number:}
-
-\item{\code{PointData}}{list, :}
-
-\item{\code{Points}}{list, :}
-
-\item{\code{Cells}}{list, :}
-
-\item{\code{CellData}}{list, : Optional:}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-clone"></a>}}
-\if{latex}{\out{\hypertarget{method-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6_Piece$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_UnstructuredGrid.Rd

-% 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{attr_names}}{Access to private parameter '.attr_names'}
-
-\item{\code{flatten_on_exp}}{Access to private parameter '.flatten_on_exp'}
-}
-\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$new(Piece, FieldData = NULL)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{Piece}}{OGS6_Piece:}
-
-\item{\code{FieldData}}{character, length == 2: Optional:}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-clone"></a>}}
-\if{latex}{\out{\hypertarget{method-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6_UnstructuredGrid$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>}}
-}
-}
-}

man/check_file_extension.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_utils.R
-\name{check_file_extension}
-\alias{check_file_extension}
-\title{check_file_extension}
-\usage{
-check_file_extension(file, expected_extension)
-}
-\arguments{
-\item{file}{A file}
-
-\item{expected_extension}{The expected file extension}
-}
-\description{
-Helper function to check the extension of a file
-}

man/decode_appended_data.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_vtu.R
-\name{decode_appended_data}
-\alias{decode_appended_data}
-\title{decode_appended_data}
-\usage{
-decode_appended_data(appended_data, compressor = "")
-}
-\arguments{
-\item{appended_data}{character: AppendedData}
-
-\item{compressor}{string: Optional: How the data was compressed, this is the
-`compressor` attribute of *VTKFile*}
-}
-\value{
-list: DataArrays with `data` element which is the decoded data
-}
-\description{
-Decodes AppendedData
-}

man/get_implemented_classes.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_implemented_classes}
-\alias{get_implemented_classes}
-\title{get_implemented_classes}
-\usage{
-get_implemented_classes()
-}
-\description{
-Utility function, returns the names of all classes implemented
-so far. Change this if you implement new classes or delete old ones!
-If you implement a new class, you add the following to the character vector:
-<name_of_corresponding_OGS6_parameter> = <name_of_your_class>
-}

man/get_valid_vtu_categories.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_valid_vtu_categories}
-\alias{get_valid_vtu_categories}
-\title{get_valid_vtu_categories}
-\usage{
-get_valid_vtu_categories()
-}
-\value{
-character: `OGS6_vtu` categories
-}
-\description{
-Returns all valid `OGS6_vtu` categories.
-}

man/get_vtu_data_arrays_from_file.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_vtu.R
-\name{get_vtu_data_arrays_from_file}
-\alias{get_vtu_data_arrays_from_file}
-\title{get_vtu_data_arrays_from_file}
-\usage{
-get_vtu_data_arrays_from_file(
-  vtu_path,
-  Names = character(),
-  categories = character()
-)
-}
-\arguments{
-\item{vtu_path}{string: .vtu file path}
-
-\item{Names}{character: Optional: Select `DataArray` elements by `Name`
-attribute}
-
-\item{categories}{character: Optional: One or more of `FieldData`, `PointData`,
-`CellData`, `Points` or `Cells`. If left empty, will get `DataArray`
-elements from whole XML document.}
-}
-\description{
-Reads DataArray elements from a .vtu file
-}

man/guess_structure.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_utils.R
-\name{guess_structure}
-\alias{guess_structure}
-\title{guess_structure}
-\usage{
-guess_structure(xml_node, xpath_expr, subclasses_names = character())
-}
-\arguments{
-\item{xml_node}{xml2::xml_node: XML node}
-
-\item{xpath_expr}{string: XPath expression (for subclass differentiation)}
-
-\item{subclasses_names}{Optional: character: Names of r2ogs6 subclasses
-(r2ogs6 classes without a OGS6$add method)}
-}
-\description{
-Guesses the R representation of an XML node and adds it to
-parameter list. This is a recursive function.
-ASSUMPTIONS:
-1) Leaf nodes will have EITHER a value OR attributes (and will not be missing
-both, e.g. '<a/>').
-2) Leaf nodes will never be r2ogs6_* objects
-3) If there are multiple occurrences of r2ogs6_* class (and subclass)
-elements on the same level, they have a wrapper node as their parent
-(e.g. <processes>, <properties>) which  will contain ONLY elements of this
-type
-4) Wrapper nodes are represented as lists
-5) Parent nodes whose children have no children are represented as lists
-}

man/new_r2ogs6_gml.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gml.R
-\name{new_r2ogs6_gml}
-\alias{new_r2ogs6_gml}
-\title{new_r2ogs6_gml}
-\usage{
-new_r2ogs6_gml(name, points, polylines = NULL, surfaces = NULL)
-}
-\arguments{
-\item{name}{The name of the geometry}
-
-\item{points}{A tibble of points}
-
-\item{polylines}{Optional: A list of polylines}
-
-\item{surfaces}{Optional: A list of surfaces}
-}
-\description{
-Constructor for S3 class new_r2ogs6_gml
-}

man/node_to_r2ogs6_obj.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_utils.R
-\name{node_to_r2ogs6_obj}
-\alias{node_to_r2ogs6_obj}
-\title{node_to_r2ogs6_obj}
-\usage{
-node_to_r2ogs6_obj(xml_node, xpath_expr, subclasses_names = character())
-}
-\arguments{
-\item{xml_node}{An XML node (of class xml2::xml_node)}
-
-\item{xpath_expr}{An XPath expression (for subclass differentiation)}
-
-\item{subclasses_names}{Optional: A character vector containing the names of
-r2ogs6 subclasses (r2ogs6 classes without a method for input_add)}
-}
-\description{
-Takes an XML node and turns it into a class object
-}

man/r2ogs6_gml.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gml.R
-\name{r2ogs6_gml}
-\alias{r2ogs6_gml}
-\title{r2ogs6_gml}
-\usage{
-r2ogs6_gml(name, points, polylines = NULL, surfaces = NULL)
-}
-\arguments{
-\item{name}{The name of the geometry}
-
-\item{points}{A tibble of points}
-
-\item{polylines}{Optional: A list of polylines}
-
-\item{surfaces}{Optional: A list of surfaces}
-}
-\description{
-S3 class describing the .gml file
-}

man/read_in_gml.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_gml.R
-\name{read_in_gml}
-\alias{read_in_gml}
-\title{read_in_gml}
-\usage{
-read_in_gml(gml_path)
-}
-\arguments{
-\item{gml_path}{The path to the geometry file that should be read in}
-}
-\description{
-Wrapper function to read in a whole .gml file
-}

man/read_in_output.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/sim_utils.R
-\name{read_in_output}
-\alias{read_in_output}
-\title{read_in_output}
-\usage{
-read_in_output(ogs6_obj)
-}
-\arguments{
-\item{ogs6_obj}{OGS6: Simulation object}
-}
-\description{
-After a OGS6 simulation was run, reads in the generated .vtu
-files as new input for
-the .prj file
-}

man/read_in_pvd.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_vtu.R
-\name{read_in_pvd}
-\alias{read_in_pvd}
-\title{read_in_pvd}
-\usage{
-read_in_pvd(pvd_path)
-}
-\arguments{
-\item{pvd_path}{string: Path to .pvd file that should be read in}
-}
-\value{
-character: Vector containing .vtu paths
-}
-\description{
-Function to read in a .pvd file
-}

man/read_in_vtu.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_vtu.R
-\name{read_in_vtu}
-\alias{read_in_vtu}
-\title{read_in_vtu}
-\usage{
-read_in_vtu(vtu_path)
-}
-\arguments{
-\item{vtu_path}{string: Path to .vtu file that should be read in}
-}
-\value{
-OGS6_vtu: Mesh object
-}
-\description{
-Wrapper function to read in a whole .vtu file as a OGS6_vtu
-class object
-}

man/validate_r2ogs6_gml.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gml.R
-\name{validate_r2ogs6_gml}
-\alias{validate_r2ogs6_gml}
-\title{validate_r2ogs6_gml}
-\usage{
-validate_r2ogs6_gml(r2ogs6_gml)
-}
-\arguments{
-\item{r2ogs6_gml}{r2ogs6_gml:}
-}
-\description{
-Validator for class r2ogs6_gml. Checks if the defined polylines
-and surfaces reference existing points.
-}

man/validate_surface_elements.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gml.R
-\name{validate_surface_elements}
-\alias{validate_surface_elements}
-\title{validate_surface_elements}
-\usage{
-validate_surface_elements(surface_element_1, surface_element_2)
-}
-\arguments{
-\item{surface_element_1}{numeric, length = 3}
-
-\item{surface_element_2}{numeric, length = 3}
-}
-\description{
-Helper function, checks if two numerical vectors of length 3
-(two surface elements) each consist of 3 different elements and also have
-exactly 2 matching elements between them which means they describe a valid
-surface. You can think of the two vectors as two triangles, and the two
-triangles together form a square which is our surface.
-}