diff --git a/.Rbuildignore b/.Rbuildignore
index 2b3cefdb354fa876267d1450bda440e250c96f42..77187af248b9c45aca63b68bc1a4746165da0d6a 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -5,6 +5,7 @@
^inst/examples/Theis_problem
^inst/examples/Theis_well_pumping
^LICENSE.md
+^config.yml
^doc$
^Meta$
^data-raw$
diff --git a/DESCRIPTION b/DESCRIPTION
index 1e50751378bc7010f172c78c4f501efe10e4601a..00aee868dec700d47d7531ad8e66ba106dcfa8ff 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,13 +2,16 @@ Package: r2ogs6
Type: Package
Title: An API to the multi-physics simulator OpenGeoSys-v6
Version: 0.1.0
-Author: person(given = "Johannes",
- family = "Boog",
- role = c("aut", "cre"),
- email = "johannesboog@yahoo.de",
- comment = structure("https://orcid.org/0000-0003-1094-9255",
- .Names = "ORCID"))
-Maintainer: Johannes Boog <johannesboog@yahoo.de>
+Authors@R: c(person(given = "Anna",
+ family = "Heinrich",
+ role = c("aut"),
+ email = "aheinri5@web.de"),
+ person(given = "Johannes",
+ family = "Boog",
+ role = c("aut", "cre"),
+ email = "johannesboog@yahoo.de",
+ comment = structure("https://orcid.org/0000-0003-1094-9255",
+ .Names = "ORCID")))
Description: Define and manage simulations using OpenGeoSys-v6.
License: file LICENSE
Encoding: UTF-8
@@ -32,7 +35,9 @@ Imports:
dplyr,
rlang,
doParallel,
- reticulate
+ reticulate,
+ config,
+ sticky
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Depends:
diff --git a/NAMESPACE b/NAMESPACE
index 503a2aae0cfcc7ce3d6581738b4b52c526e5f4b0..c832e9ff2dc63b61c7737e39002999319467ed5e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,11 +7,14 @@ export(OGS6_gml)
export(OGS6_pvd)
export(OGS6_vtu)
export(ogs6_call_ogs6)
+export(ogs6_download_ogs6)
export(ogs6_export_sim_files)
export(ogs6_generate_benchmark_script)
+export(ogs6_generate_benchmark_scripts)
export(ogs6_generate_structured_mesh)
export(ogs6_get_combinations)
export(ogs6_get_medium_property)
+export(ogs6_prj_top_level_classes)
export(ogs6_read_output_files)
export(ogs6_run_simulation)
export(prj_borehole_heat_exchanger)
diff --git a/R/analyse_xml.R b/R/analyse_xml.R
index 262304b0e21a1ac6f5f7749871f3cefa1ee1dede..80b4eeaa9ecd82e42333e82296e947e4f857c361 100644
--- a/R/analyse_xml.R
+++ b/R/analyse_xml.R
@@ -1,21 +1,20 @@
-#This is a helper function which can be used to combat missing documentation.
-#Benchmark HydroMechanics:
-# analyse_xml("D:\\Programme\\OpenGeoSys\\ogs-master-Tests-Data/",
-# "\\.vtu$",
-# "VTKFile")
+#===== analyse_xml =====
-#'analyse_xml
-#'@description This is a helper function which can be used to combat missing
+
+#' analyse_xml
+#' @description
+#' This is a helper function which can be used to combat missing
#' documentation. It looks for files in a path which match the given pattern
#' and then attempts to parse them as XML. For each occurence of the specified
#' element, it documents its attributes and direct children and prints a little
#' summary of its findings at the end.
-#'@param path string: A path
-#'@param pattern string: A regex pattern
-#'@param xpath string: An XPath expression. WARNING: Only works for expressions
-#' that return nodesets, use it to look up tag names.
-#'@param print_findings Optional: Should the results be printed to the console?
+#' @param path string: A path
+#' @param pattern string: A regex pattern
+#' @param xpath string: An XPath expression. WARNING: Only works for expressions
+#' that return nodesets, use it to look up tag names.
+#' @param print_findings Optional: Should the results be printed to the console?
+#' @noRd
analyse_xml <- function(path,
pattern,
xpath,
@@ -259,11 +258,13 @@ print_analysis_findings <- function(invalid_files_count,
#===== get_required =====
-#'get_required
-#'@description Helper function to mark required attributes or children from a
+#' get_required
+#' @description
+#' Helper function to mark required attributes or children from a
#' vector of names and a vector of occurrence probabilities
-#'@param names A vector of names
-#'@param occurence_probabilities A vector of occurrence probabilities
+#' @param names A vector of names
+#' @param occurence_probabilities A vector of occurrence probabilities
+#' @noRd
get_required <- function(names, occurence_probabilities){
required <- logical()
diff --git a/R/compare_xml.R b/R/compare_xml.R
deleted file mode 100644
index 115a4be61eedce965d10ba9e36e70d7e25e2d9e1..0000000000000000000000000000000000000000
--- a/R/compare_xml.R
+++ /dev/null
@@ -1,122 +0,0 @@
-
-
-#'compare_xml
-#'@description Helper function to check if 2 XML documents have the same
-#' content. This is a recursive function. Strictly WIP!
-#'@param xml_node_x xml2::xml_node: Node to compare
-#'@param xml_node_y xml2::xml_node: Node to compare to
-compare_xml <- function(xml_node_x, xml_node_y){
-
- assertthat::assert_that("xml_node" %in% class(xml_node_x))
- assertthat::assert_that("xml_node" %in% class(xml_node_y))
-
- x_node_name <- xml2::xml_name(xml_node_x)
- y_node_name <- xml2::xml_name(xml_node_y)
-
- ret_str <- ""
-
- # Recursion stops here
- if(length(xml2::xml_children(xml_node_x)) == 0 ||
- length(xml2::xml_children(xml_node_y)) == 0 ){
-
- if(length(xml2::xml_children(xml_node_x)) !=
- length(xml2::xml_children(xml_node_y))){
- ret_str <- paste0("Child mismatch: <",
- x_node_name, "> in x has ",
- length(xml2::xml_children(xml_node_x)),
- " children while <",
- y_node_name, " in y has ",
- length(xml2::xml_children(xml_node_y)), ".\n")
- }
-
- if(x_node_name != y_node_name){
- ret_str <- paste0(ret_str,
- "Name mismatch: <", x_node_name, "> in x, <",
- y_node_name, " in y.\n")
- }
-
- if(xml2::xml_text(xml_node_x) != xml2::xml_text(xml_node_y)){
- ret_str <- paste0(ret_str,
- "Text mismatch: \"", xml2::xml_text(xml_node_x),
- "\" in x, \"",
- xml2::xml_text(xml_node_x), "\" in y.\n")
- }
-
- if(xml2::xml_attrs(xml_node_x) != xml2::xml_attrs(xml_node_y)){
-
- x_node_attrs <- paste(names(xml2::xml_attrs(xml_node_x)),
- xml2::xml_attrs(xml_node_x),
- sep = " = ", collapse = ",\n")
-
- y_node_attrs <- paste(names(xml2::xml_attrs(xml_node_y)),
- xml2::xml_attrs(xml_node_y),
- sep = " = ", collapse = ",\n")
-
- ret_str <- paste0(ret_str,
- "Attribute mismatch: (", x_node_attrs,
- ") in x, (",
- y_node_attrs, ") in y.\n")
- }
-
- return(invisible(ret_str))
- }
-
- y_children_ordered <- xml2::xml_children(xml_node_y)
- y_child_names <- get_nodeset_names(y_children_ordered)
-
- x_children_ordered <- xml2::xml_children(xml_node_x)
-
- if(0){
- cat("Children of <", x_node_name, "> tags are not the same ",
- "for x and y. compare_xml() may not yield all differences. ",
- "Continuing iteration based on first parameter (x).", sep = "")
- }
-
- for(i in seq_len(length(x_children_ordered))){
-
- x_child <- x_children_ordered[[i]]
-
- # If x has a child y doesn't have
- if(xml2::xml_name(x_child) %in% y_child_names){
-
-
- ret_str <- paste0(ret_str, compare_xml(x_child))
-
- }else{
- ret_str <- paste0(ret_str,
- "<", xml2::xml_name(x_child),
- "> is a child of <",
- x_node_name,
- "> in x but not of <",
- y_node_name, "> in y.")
- }
- }
-
- return(invisible(ret_str))
-}
-
-
-# order_nodeset <- function(nodeset){
-#
-# nodeset_names <- sort(get_nodeset_names(nodeset))
-# ordered_nodeset <- rep(NULL, length(nodeset_names))
-#
-# for(){
-#
-# }
-#
-#
-# }
-
-
-get_nodeset_names <- function(nodeset){
-
- nodeset_names <- c()
-
- for(i in seq_along(nodeset)){
- nodeset_names <- c(nodeset_names, xml2::xml_name(nodeset[[i]]))
- }
-
- return(invisible(nodeset_names))
-}
-
diff --git a/R/download_ogs6.R b/R/download_ogs6.R
new file mode 100644
index 0000000000000000000000000000000000000000..019c5f8483da4ebe72b711459c6bd5a250adfa23
--- /dev/null
+++ b/R/download_ogs6.R
@@ -0,0 +1,93 @@
+
+
+#' Download OpenGeoSys 6
+#'
+#' Downloads latest prebuilt OpenGeoSys 6 version
+#'
+#' @param path String: Download path. Defaults to ...
+#' @param os String: Operating System.
+#' @param set_as_default_bin_path flag: Defaults to `TRUE`
+#' @export
+ogs6_download_ogs6 <- function(path,
+ os,
+ set_as_default_bin_path = TRUE){
+
+ default_installation_paths <-
+ list(
+ Windows = c("C:/Program Files/",
+ "D:/Program Files/"),
+ Darwin = c("/Applications/"),
+ Linux = c("~/software/",
+ "~/opt/")
+ )
+
+ if(missing(os)){
+ os <- Sys.info()["sysname"]
+ }
+
+ assertthat::assert_that(assertthat::is.string(os))
+ assertthat::assert_that(os %in% names(default_installation_paths))
+ assertthat::assert_that(assertthat::is.flag(set_as_default_bin_path))
+
+ if(missing(path)){
+
+ path <- NULL
+
+ for(i in default_installation_paths[[os]]){
+ if(dir.exists(i)){
+ path <- i
+ break
+ }
+ }
+
+ if(is.null(path)){
+ stop(
+ paste0(
+ "Did not find any default path for OpenGeoSys 6 ",
+ "on your System. I checked the following paths:\n",
+ paste(default_installation_paths[[os]], collapse = "\n"),
+ "\nPlease specify a path manually instead."
+ ),
+ call. = FALSE
+ )
+ }
+ }
+
+ path <- as_dir_path(path)
+
+ if(os == "Windows"){
+
+ url_path <-
+ paste0(
+ "https://ogsstorage.blob.core.windows.net/binaries/ogs6/",
+ "6.3.3/ogs-6.3.3-Windows-10.0.14393-python-3.7.2-utils.zip"
+ )
+
+ ogs_zip_folder <- paste0(path, basename(url_path))
+ utils::download.file(url_path, ogs_zip_folder)
+
+ ogs_folder <- gsub("\\.zip$", "", ogs_zip_folder)
+ utils::unzip(ogs_zip_folder, exdir = ogs_folder)
+ unlink(ogs_zip_folder)
+
+ }else{
+ url_path <-
+ paste0(
+ "https://ogsstorage.blob.core.windows.net/binaries/ogs6/",
+ "6.3.3/ogs-6.3.3-Windows-10.0.14393-python-3.7.2-utils.zip"
+ )
+
+ ogs_folder <- "/scif/apps/ogs"
+
+ sif_path <- paste0(path, "ogs-6.3.3-serial.sif")
+ utils::download.file(url_path, sif_path)
+ }
+
+ bin_path <- paste0(ogs_folder, "/bin")
+
+ if(set_as_default_bin_path){
+ options(r2ogs6.default_ogs6_bin_path = bin_path)
+ }
+
+ return(invisible())
+}
diff --git a/R/export_gml.R b/R/export_gml.R
index d758f2f4506c159d1f6fcab3e49d48ca1909b111..ac91882d6e3b79c67c74699e2ec4df59d8c43375 100644
--- a/R/export_gml.R
+++ b/R/export_gml.R
@@ -6,6 +6,7 @@
#' @description Creates a .gml XML document based on user input data
#' @param gml OGS6_gml:
#' @param path string:
+#' @noRd
export_gml <- function(gml, path) {
assertthat::assert_that(assertthat::is.string(path))
diff --git a/R/export_prj.R b/R/export_prj.R
index a9453d8882049e72265cd6be3145a9e07b19738c..8f3aa5969136c943d366926f8ba334574b90e3ca 100644
--- a/R/export_prj.R
+++ b/R/export_prj.R
@@ -3,9 +3,11 @@
#' export_prj
-#' @description Wrapper function to create a \code{.prj} XML document based on
-#' the user input data
+#' @description
+#' Wrapper function to create a \code{.prj} XML document based on the user
+#' input data
#' @param ogs6_obj OGS6: Simulation object
+#' @noRd
export_prj <- function(ogs6_obj) {
prj_xml <- xml2::xml_new_root(
@@ -18,20 +20,19 @@ export_prj <- function(ogs6_obj) {
#If there is a .gml defined, add "mesh" node, else add "meshes" node
if(is.null(ogs6_obj$geometry)) {
- basenames <- lapply(ogs6_obj$meshes, function(x){basename(x)})
- meshes_node <- to_node(basenames, "meshes")
+ meshes_node <- meshes_to_xml(ogs6_obj$meshes)
}else{
xml2::xml_add_child(
prj_xml,
xml2::as_xml_document(to_node(ogs6_obj$geometry)))
- meshes_node <- to_node(basename(ogs6_obj$meshes[[1]]), "mesh")
+ meshes_node <- meshes_to_xml(ogs6_obj$meshes)
}
xml2::xml_add_child(prj_xml,
- xml2::as_xml_document(meshes_node))
+ meshes_node)
#Get implemented classes
- prj_components <- prj_top_level_classes()
+ prj_components <- ogs6_prj_top_level_classes()
# Include file reference
if(names(ogs6_obj$processes)[[1]] == "include"){
diff --git a/R/export_utils.R b/R/export_utils.R
index b625847acb73a879493adf2b3b03470fbd86b31e..ef1d2c1ee8bc411051bd83cfe22202a7be9d956f 100644
--- a/R/export_utils.R
+++ b/R/export_utils.R
@@ -15,6 +15,7 @@
#' flattened to a string in XML
#' @param unwrap_on_exp character: Optional: This is for lists which will not
#' be exported to XML
+#' @noRd
to_node <- function(object, object_name = "",
attribute_names = character(),
flatten_on_exp = character(),
@@ -173,3 +174,38 @@ to_node <- function(object, object_name = "",
return(invisible(object_node))
}
}
+
+
+#===== meshes_to_xml =====
+
+
+#' meshes_to_xml
+#' @description
+#' Helper function for a mesh element of a .prj file.
+#' @param meshes list: List of meshes
+#' @noRd
+meshes_to_xml <- function(meshes){
+
+ meshes_doc <- xml2::read_xml("<meshes/>")
+
+ xml_children <- lapply(meshes, function(x){
+ if(x[["axially_symmetric"]]){
+ xml2::as_xml_document(
+ list(mesh = structure(list(basename(x[["path"]])),
+ axially_symmetric = "true")))
+ }else{
+ xml2::as_xml_document(
+ list(mesh = list(basename(x[["path"]]))))
+ }
+ })
+
+ if(length(meshes) == 1){
+ return(xml_children[[1]])
+ }else{
+ for(i in seq_len(length(xml_children))){
+ xml2::xml_add_child(meshes_doc, xml_children[[i]])
+ }
+ return(meshes_doc)
+ }
+}
+
diff --git a/R/generate_benchmark_script.R b/R/generate_benchmark_script.R
index adbe432d8fea2c12880fbe4ed1d40ef5851f7186..e5538307297dfed92a57428252031ce1516c3baf 100644
--- a/R/generate_benchmark_script.R
+++ b/R/generate_benchmark_script.R
@@ -1,25 +1,22 @@
-#===== generate_all_benchmarks =====
+#===== ogs6_generate_benchmark_scripts =====
-#' generate_all_benchmark_scripts
-#' @description Wrapper function to generate benchmark scripts from all
-#' \code{.prj} files in a directory
+#' Generate benchmark scripts
+#'
+#' This is a wrapper function for `ogs6_generate_benchmark_script()`.
+#'
#' @param path string: Path to a benchmark directory to generate scripts from
-#' @param sim_path string: Path where all simulation files will be saved
-#' @param scripts_path string: Path where benchmark scripts will be saved
-#' @param read_in_gmls flag: Optional: Should \code{.gml} files just be copied
-#' or read in too?
-#' @param read_in_vtus flag: Optional: Should \code{.vtu} files just be copied
-#' or read in too?
-#' @param starting_from_prj_path string: Optional:
-#' @param skip_prj_paths character: Optional: \code{.prj} paths to skip
-generate_all_benchmark_scripts <-
+#' @inheritParams ogs6_generate_benchmark_script
+#' @param starting_from_prj_path string: Optional: `.prj` path to start from
+#' @param skip_prj_paths character: Optional: `.prj` paths to skip
+#' @export
+ogs6_generate_benchmark_scripts <-
function(path,
sim_path,
- scripts_path,
- read_in_gmls,
- read_in_vtus = FALSE,
+ script_path,
+ read_in_gml,
+ read_in_vtu = FALSE,
starting_from_prj_path = "",
skip_prj_paths = character()){
@@ -31,23 +28,32 @@ generate_all_benchmark_scripts <-
sim_path <- unlist(options("r2ogs6.default_sim_path"))
}
- if(missing(scripts_path)){
- scripts_path <- unlist(options("r2ogs6.default_script_path"))
+ if(missing(script_path)){
+ script_path <- unlist(options("r2ogs6.default_script_path"))
}
- missing_read_in_gmls <- missing(read_in_gmls)
+ if(missing(read_in_gml)){
+ read_in_gml <- substitute()
+ }
path <- as_dir_path(path)
- scripts_path <- as_dir_path(scripts_path)
+ script_path <- as_dir_path(script_path)
assertthat::assert_that(assertthat::is.string(starting_from_prj_path))
assertthat::assert_that(is.character(skip_prj_paths))
- assertthat::assert_that(assertthat::is.flag(read_in_vtus))
prj_paths <- list.files(path = path,
pattern = "\\.prj$",
recursive = TRUE,
full.names = TRUE)
+ script_paths_rel <- lapply(list.files(
+ path = path,
+ pattern = "\\.prj$",
+ recursive = T,
+ full.names = F
+ ),
+ dirname)
+
# If we know the benchmarks up to a specific file are working, skip them
if(starting_from_prj_path != ""){
@@ -75,26 +81,28 @@ generate_all_benchmark_scripts <-
# cat("\nGenerating script from path", prj_paths[[i]])
# Put simulations in their own subfolders under sim_path
- sim_subdir <-
- paste0(sim_path,
- basename(dirname(prj_paths[[i]])), "_",
- tools::file_path_sans_ext(basename(prj_paths[[i]])))
+ sim_subfolder_path <- paste0(
+ sim_path,
+ script_paths_rel[[i]],
+ "/",
+ tools::file_path_sans_ext(basename(prj_paths[[i]])))
+
+ script_subfolder_path <- paste0(script_path, script_paths_rel[[i]])
+
+ if(!dir.exists(script_subfolder_path)){
+ dir.create(script_subfolder_path,
+ recursive = TRUE)
+ }
out<- tryCatch(
{
- if(missing_read_in_gmls){
- ogs6_generate_benchmark_script(prj_path = prj_paths[[i]],
- sim_path = sim_subdir,
- script_path = scripts_path,
- read_in_vtu = read_in_vtus)
- }else{
- ogs6_generate_benchmark_script(prj_path = prj_paths[[i]],
- sim_path = sim_subdir,
- script_path = scripts_path,
- read_in_gml = read_in_gmls,
- read_in_vtu = read_in_vtus)
- }
-
+ ogs6_generate_benchmark_script(
+ prj_path = prj_paths[[i]],
+ sim_path = sim_subfolder_path,
+ script_path = script_subfolder_path,
+ read_in_gml = read_in_gml,
+ read_in_vtu = read_in_vtu
+ )
},
error = function(cond){
message(paste("\nogs6_generate_benchmark_script() failed for",
@@ -113,16 +121,18 @@ generate_all_benchmark_scripts <-
#===== ogs6_generate_benchmark_script =====
-#' ogs6_generate_benchmark_script
-#' @description Generates a benchmark script from an existing \code{.prj} file.
-#' @param prj_path string: \code{.prj} file the script will be based on
+#' Generate benchmark script
+#'
+#' Generates an R script from an existing `.prj` benchmark file.
+#'
+#' @param prj_path string: `.prj` file the script will be based on
#' @param sim_path string: Path where all simulation files will be saved
#' @param ogs6_bin_path string: Path to OpenGeoSys executable. Defaults to
#' options("r2ogs6.default_ogs6_bin_path").
#' @param script_path string: Path where benchmark script will be saved
-#' @param read_in_gml flag: Optional: Should \code{.gml} file just be copied or
+#' @param read_in_gml flag: Optional: Should `.gml` file just be copied or
#' read in too?
-#' @param read_in_vtu flag: Optional: Should \code{.vtu} file(s) just be copied
+#' @param read_in_vtu flag: Optional: Should `.vtu` file(s) just be copied
#' or read in too?
#' @export
ogs6_generate_benchmark_script <- function(prj_path,
@@ -159,7 +169,7 @@ ogs6_generate_benchmark_script <- function(prj_path,
read_in_vtu,
read_in_gml = FALSE)
- prj_components = prj_top_level_classes()
+ prj_components = ogs6_prj_top_level_classes()
sim_name <- tools::file_path_sans_ext(basename(prj_path))
@@ -239,7 +249,7 @@ ogs6_generate_benchmark_script <- function(prj_path,
dir.create(script_path, showWarnings = FALSE)
}
- filename <- paste0(script_path, sim_name, ".R")
+ filename <- paste0(script_path, "/", sim_name, ".R")
if(file.exists(filename)){
filename <- paste0(script_path,
@@ -263,15 +273,18 @@ ogs6_generate_benchmark_script <- function(prj_path,
}
-#' construct_add_call
-#' @description Constructs a call based on an \code{OGS6} component. This is a
-#' recursive function, handle with care.
-#' @param object An object (numeric, character, list, NULL, \code{OGS6} or
-#' \code{r2ogs6} class object)
+#' Construct a call for `OGS6$add()`
+#'
+#' This is a recursive function.
+#'
+#' @param object An object (numeric, character, list, NULL, `OGS6` or
+#' r2ogs6 class object)
#' @param nested_call Optional: For recursion purposes, you should leave this as
-#' it is.
-#' @return A string representing the code with which the component would be
-#' added to an \code{OGS6} object
+#' it is.
+#' @return
+#' A string representing the code with which the component would be
+#' added to an `OGS6` object
+#' @noRd
construct_add_call <- function(object, nested_call = FALSE) {
#For values of type numeric or character, dput will give us usable output
@@ -351,7 +364,7 @@ construct_add_call <- function(object, nested_call = FALSE) {
regexp_2 <- "[\\w_]* = ((NULL)|(list\\(\\)))(,[:space:])"
ret_str <- stringr::str_remove_all(ret_str, regexp_1)
ret_str <- stringr::str_remove_all(ret_str, regexp_2)
- ret_str <- delete_keywords_from_str(ret_str)
+ ret_str <- stringr::str_remove_all(ret_str, "repeat = ")
ret_str <- stringr::str_replace_all(ret_str,
" = [A-Za-z_]* = ", " = ")
@@ -384,17 +397,3 @@ construct_add_call <- function(object, nested_call = FALSE) {
return(invisible(ret_str))
}
}
-
-
-#' delete_keywords_from_str
-#' @description Utility function to delete keywords from a string,
-#' this is important because there is a <repeat> tag in <time_loop> and
-#' "repeat" is a reserved word in R (extend this function if you find more
-#' reserved words)
-#' @param string string
-delete_keywords_from_str <- function(string){
-
- string <- stringr::str_remove_all(string, "repeat = ")
-
- return(invisible(string))
-}
diff --git a/R/generate_class.R b/R/generate_class.R
index 68a9d2769bc3b804a0d9af790ffb02cb4525ff12..0cf59a656de412cc757372019e4dfe4ac4277f5f 100644
--- a/R/generate_class.R
+++ b/R/generate_class.R
@@ -1,5 +1,4 @@
-
#===== S3 class generation =====
#===== generate_constructor =====
@@ -13,6 +12,7 @@
#' the same tag name as an element for which a class was already specified,
#' a prefix must be appended to the class name
#' @param print_result flag: Should the result be printed to the console?
+#' @noRd
generate_constructor <- function(params,
prefix = "",
print_result = FALSE){
@@ -26,11 +26,16 @@ generate_constructor <- function(params,
attr_flags <- params[[3]]
param_flags <- params[[4]]
+ assertthat::assert_that(is.logical(param_flags))
class_name <- paste0("prj_", prefix, tag_name)
param_str <- flags_to_con_str(param_flags)
- assign_str <- flags_to_assign_str(param_flags)
+
+ assign_str <- paste(names(param_flags),
+ names(param_flags),
+ sep = " = ",
+ collapse = ",\n")
con_str <- paste0("new_", class_name, " <- function(", param_str, ") {\n")
@@ -74,6 +79,7 @@ generate_constructor <- function(params,
#' the same tag name as an element for which a class was already specified,
#' a prefix must be appended to the class name
#' @param print_result flag: Should the result be printed to the console?
+#' @noRd
generate_helper <- function(params,
prefix = "",
print_result = FALSE){
@@ -86,12 +92,12 @@ generate_helper <- function(params,
tag_name <- get_tag_from_xpath(xpath)
param_flags <- params[[4]]
+ assertthat::assert_that(is.logical(param_flags))
class_name <- paste0("prj_", prefix, tag_name)
doc_str <- flags_to_doc_str(param_flags)
con_str <- flags_to_con_str(param_flags)
- con_call_str <- flags_to_con_call_str(param_flags)
helper_str <- paste0("#'", class_name, "\n",
"#'@description tag: ", tag_name, "\n",
@@ -100,7 +106,9 @@ generate_helper <- function(params,
"#'@export\n",
class_name, " <- function(", con_str, ") {\n",
"\n# Add coercing utility here\n\n",
- "new_", class_name, "(", con_call_str, ")\n",
+ "new_", class_name, "(",
+ paste(names(param_flags), collapse = ",\n"),
+ ")\n",
"}\n")
if(print_result){
@@ -111,16 +119,14 @@ generate_helper <- function(params,
}
-#===== get parameter lists (for use in class constructor / helper) =====
+#===== flags_to_con_str =====
#' flags_to_con_str
#' @description Helper function to generate a string out of a flag vector
#' @param flags vector: Flags
-#' @param print_result flag: Should the result be printed to the console?
-flags_to_con_str <- function(flags, print_result = FALSE) {
-
- assertthat::assert_that(is.logical(flags))
+#' @noRd
+flags_to_con_str <- function(flags) {
flag_strs <- character()
@@ -134,71 +140,7 @@ flags_to_con_str <- function(flags, print_result = FALSE) {
flag_str <- paste(flag_strs, collapse = ",\n")
- if(print_result){
- cat(flag_str, "\n")
- }
-
- return(invisible(flag_str))
-}
-
-
-#' flags_to_con_call_str
-#' @description Helper function to generate a string out of a flag vector
-#' @param flags vector: Flags
-#' @param print_result flag: Should the result be printed to the console?
-flags_to_con_call_str <- function(flags, print_result = FALSE) {
-
- assertthat::assert_that(is.logical(flags))
-
- flag_str <- paste(names(flags), collapse = ",\n")
-
- if(print_result){
- cat(flag_str, "\n")
- }
-
- return(invisible(flag_str))
-}
-
-
-#' flags_to_name_str
-#' @description Helper function to generate a name string out of a flag vector
-#' @param flags vector: Flags
-#' @param print_result flag: Should the result be printed to the console?
-flags_to_name_str <- function(flags, print_result = FALSE) {
-
- assertthat::assert_that(is.logical(flags))
-
- flag_str <- paste0("\"", paste(names(flags), collapse = "\",\n\""), "\"")
-
- if(print_result){
- cat(flag_str, "\n")
- }
-
- return(invisible(flag_str))
-}
-
-
-#===== get class parameter list (for use in class constructor) =====
-
-
-#' flags_to_assign_str
-#' @description Helper function to generate a string out of a flag vector
-#' @param flags vector: Flags
-#' @param print_result flag: Should the result be printed to the console?
-flags_to_assign_str <- function(flags, print_result = FALSE){
-
- assertthat::assert_that(is.logical(flags))
-
- flag_str <- paste(names(flags),
- names(flags),
- sep = " = ",
- collapse = ",\n")
-
- if(print_result){
- cat(flag_str, "\n")
- }
-
- return(invisible(flag_str))
+ return(flag_str)
}
@@ -209,6 +151,7 @@ flags_to_assign_str <- function(flags, print_result = FALSE){
#' @description Helper function to generate a string out of a flag vector
#' @param flags vector: Flags
#' @param print_result flag: Should the result be printed to the console?
+#' @noRd
flags_to_doc_str <- function(flags, print_result = FALSE){
assertthat::assert_that(is.logical(flags))
@@ -250,6 +193,7 @@ flags_to_doc_str <- function(flags, print_result = FALSE){
#' the same tag name as an element for which a class was already specified,
#' a prefix must be appended to the class name
#' @param print_result flag: Should the result be printed to the console?
+#' @noRd
generate_R6 <- function(params,
prefix = "",
print_result = TRUE){
@@ -321,6 +265,7 @@ generate_R6 <- function(params,
#' @description Helper function to generate a string out of a flag vector
#' @param flags vector: Flags
#' @param print_result flag: Should the result be printed to the console?
+#' @noRd
flags_to_r6_init_str <- function(flags, print_result = FALSE){
assertthat::assert_that(is.logical(flags))
@@ -352,6 +297,7 @@ flags_to_r6_init_str <- function(flags, print_result = FALSE){
#' @param flags vector: Flags
#' @param mutable flag: On per default, turn off if parameters are static
#' @param print_result flag: Should the result be printed to the console?
+#' @noRd
flags_to_r6_active_field_str <- function(flags,
mutable = TRUE,
print_result = FALSE){
@@ -402,6 +348,7 @@ flags_to_r6_active_field_str <- function(flags,
#' @description Helper function to generate a string out of a flag vector
#' @param flags vector: Flags
#' @param print_result flag: Should the result be printed to the console?
+#' @noRd
flags_to_r6_private_str <- function(flags, print_result = FALSE){
assertthat::assert_that(is.logical(flags))
@@ -428,12 +375,14 @@ flags_to_r6_private_str <- function(flags, print_result = FALSE){
#' generate_add_method
-#' @description Helper function to generate an R6 \code{add_*} method for a
-#' r2ogs6 class object
-#' @param tag_name The tag name of the XML element represented by the class
+#' @description
+#' Helper function to generate an R6 \code{add_*} method for a r2ogs6 class
#' object
-#' @param parent_tag_name The tag name of the parent of the XML element
-#' represented by the class object
+#' @param tag_name
+#' The tag name of the XML element represented by the class object
+#' @param parent_tag_name
+#' The tag name of the parent of the XML element represented by the class object
+#' @noRd
generate_add_method <- function(tag_name, parent_tag_name) {
has_wrapper <- (tag_name != parent_tag_name)
@@ -462,9 +411,10 @@ generate_add_method <- function(tag_name, parent_tag_name) {
#' generate_active_field
-#' @description Helper function to generate an R6 active field for a OGS6 class
-#' parameter
+#' @description
+#' Helper function to generate an R6 active field for a OGS6 class parameter
#' @param parameter_name The name of the OGS6 class parameter
+#' @noRd
generate_active_field <- function(parameter_name){
af_str <- paste0(parameter_name, " = function(value) {\n",
diff --git a/R/generate_xml.R b/R/generate_xml.R
index 264f180feff7ad7626efce0f10cd7a3a31014242..2fa4f084a2c19c3bb1c38f50e0958cf0f41c8854 100644
--- a/R/generate_xml.R
+++ b/R/generate_xml.R
@@ -10,6 +10,7 @@
#' @param pattern string: See \code{?analyse_xml}
#' @param xpath string: See \code{?analyse_xml}
#' @param export_path string: Path to export the XML document to
+#' @noRd
build_redux_doc <- function(path,
pattern,
xpath,
@@ -53,6 +54,7 @@ build_redux_doc <- function(path,
#' @param pattern string: See \code{?analyse_xml}
#' @param xpath string: See \code{?analyse_xml}
#' @param required flag: Recursion utility
+#' @noRd
build_redux_tree <- function(path,
pattern,
xpath,
diff --git a/R/ogs6.R b/R/ogs6.R
index 9c0d9efd25f18e996462aed487de89a6aef5d3df..c053455f3be05662efc00e3d5c67f012161a0907 100644
--- a/R/ogs6.R
+++ b/R/ogs6.R
@@ -37,11 +37,11 @@ OGS6 <- R6::R6Class("OGS6",
#' @param x An object of any .prj `prj` class
#' @examples
#' ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
- #' ogs6_obj$add(prj_parameter$new(name = "foo", type = "bar"))
+ #' ogs6_obj$add(prj_parameter(name = "foo", type = "bar"))
add = function(x){
# Assert that class name is in implemented .prj classes for OGS6
- ogs6_prj_classes <- prj_top_level_classes()
+ ogs6_prj_classes <- ogs6_prj_top_level_classes()
assertthat::assert_that(class(x) %in% ogs6_prj_classes)
# Get name of corresponding OGS6 component
@@ -98,6 +98,7 @@ OGS6 <- R6::R6Class("OGS6",
#' Adds a reference to a \code{.vtu} file and optionally, a \code{OGS6_vtu}
#' object
#' @param path string: A path
+ #' @param axisym flag: Is the mesh axially symmetrical?
#' @param read_in_vtu flag: Optional: Should \code{.vtu} file just be
#' copied or read in too?
#' @examples
@@ -105,12 +106,16 @@ OGS6 <- R6::R6Class("OGS6",
#' ogs6_obj$add_vtu("this_works.vtu")
#' \dontrun{ogs6_obj$add_vtu("this_doesnt.oops")}
add_vtu = function(path,
+ axisym = FALSE,
read_in_vtu = FALSE){
assertthat::assert_that(assertthat::is.string(path))
assertthat::assert_that(grepl("\\.vtu$", path))
+ assertthat::assert_that(assertthat::is.flag(axisym))
assertthat::assert_that(assertthat::is.flag(read_in_vtu))
- self$meshes <- c(self$meshes, mesh = path)
+ self$meshes <- c(self$meshes,
+ list(mesh = list(path = path,
+ axially_symmetric = axisym)))
if(read_in_vtu){
private$.vtus <- c(private$.vtus, list(OGS6_vtu$new(path)))
@@ -230,14 +235,14 @@ OGS6 <- R6::R6Class("OGS6",
#' Clears components from the \code{OGS6} object
#' @param which character: The names of the components (all by default).
#' If you want to delete only some components, run
- #' \code{names(prj_top_level_classes())} for the available options.
+ #' \code{names(ogs6_prj_top_level_classes())} for the available options.
clear = function(which){
if(missing(which)){
- which <- names(prj_top_level_classes())
+ which <- names(ogs6_prj_top_level_classes())
}
- valid_input = names(prj_top_level_classes())
+ valid_input = names(ogs6_prj_top_level_classes())
null_it <- c("geometry", "time_loop")
@@ -328,12 +333,15 @@ OGS6 <- R6::R6Class("OGS6",
}else{
assertthat::assert_that(is.list(value))
lapply(value, function(x){
- assertthat::assert_that(assertthat::is.string(x))
+ assertthat::assert_that(is.list(x), length(x) == 2)
+ assertthat::assert_that(assertthat::is.string(x[[1]]))
+ assertthat::assert_that(assertthat::is.flag(x[[2]]))
})
private$.meshes <- value
}
},
+
#' @field vtus
#' \code{.vtu}s. \code{value} must be list of \code{OGS6_vtu} objects
vtus = function(value) {
@@ -341,7 +349,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.vtus
}else{
is_wrapper_list(value,
- prj_top_level_classes()[["vtus"]])
+ ogs6_prj_top_level_classes()[["vtus"]])
private$.vtus <- value
}
},
@@ -365,7 +373,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.search_length_algorithm
}else{
assertthat::assert_that(
- prj_top_level_classes()[["search_length_algorithm"]] %in%
+ ogs6_prj_top_level_classes()[["search_length_algorithm"]] %in%
class(value))
private$.search_length_algorithm <- value
}
@@ -380,10 +388,10 @@ OGS6 <- R6::R6Class("OGS6",
}else{
# If there already is a process element
if(length(private$.processes) > 0){
- if(prj_top_level_classes()[["processes"]] %in%
+ if(ogs6_prj_top_level_classes()[["processes"]] %in%
class(private$.processes[[1]])){
is_wrapper_list(value,
- prj_top_level_classes()[["processes"]])
+ ogs6_prj_top_level_classes()[["processes"]])
}else{
assertthat::assert_that(assertthat::is.string(value))
value <- list(include = c(file = value))
@@ -394,7 +402,7 @@ OGS6 <- R6::R6Class("OGS6",
value <- list(include = c(file = value))
}else{
is_wrapper_list(value,
- prj_top_level_classes()[["processes"]])
+ ogs6_prj_top_level_classes()[["processes"]])
}
}
@@ -410,7 +418,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.time_loop
}else{
assertthat::assert_that(
- prj_top_level_classes()[["time_loop"]] %in%
+ ogs6_prj_top_level_classes()[["time_loop"]] %in%
class(value))
private$.time_loop <- value
}
@@ -424,7 +432,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.local_coordinate_system
}else{
assertthat::assert_that(
- prj_top_level_classes()[["local_coordinate_system"]] %in%
+ ogs6_prj_top_level_classes()[["local_coordinate_system"]] %in%
class(value))
private$.local_coordinate_system <- value
}
@@ -438,7 +446,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.media
}else{
is_wrapper_list(value,
- prj_top_level_classes()[["media"]])
+ ogs6_prj_top_level_classes()[["media"]])
private$.media <- value
}
},
@@ -451,7 +459,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.parameters
}else{
is_wrapper_list(value,
- prj_top_level_classes()[["parameters"]])
+ ogs6_prj_top_level_classes()[["parameters"]])
private$.parameters <- value
}
},
@@ -464,7 +472,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.chemical_system
}else{
assertthat::assert_that(
- prj_top_level_classes()[["chemical_system"]] %in%
+ ogs6_prj_top_level_classes()[["chemical_system"]] %in%
class(value))
private$.chemical_system <- value
}
@@ -478,7 +486,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.curves
}else{
is_wrapper_list(value,
- prj_top_level_classes()[["curves"]])
+ ogs6_prj_top_level_classes()[["curves"]])
private$.curves <- value
}
},
@@ -492,7 +500,7 @@ OGS6 <- R6::R6Class("OGS6",
}else{
is_wrapper_list(
value,
- prj_top_level_classes()[["process_variables"]])
+ ogs6_prj_top_level_classes()[["process_variables"]])
private$.process_variables <- value
}
},
@@ -506,7 +514,7 @@ OGS6 <- R6::R6Class("OGS6",
}else{
is_wrapper_list(
value,
- prj_top_level_classes()[["nonlinear_solvers"]])
+ ogs6_prj_top_level_classes()[["nonlinear_solvers"]])
private$.nonlinear_solvers <- value
}
},
@@ -519,7 +527,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.linear_solvers
}else{
is_wrapper_list(value,
- prj_top_level_classes()[["linear_solvers"]])
+ ogs6_prj_top_level_classes()[["linear_solvers"]])
private$.linear_solvers <- value
}
},
@@ -532,7 +540,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.test_definition
}else{
is_wrapper_list(value,
- prj_top_level_classes()[["test_definition"]])
+ ogs6_prj_top_level_classes()[["test_definition"]])
private$.test_definition <- value
}
},
@@ -545,7 +553,7 @@ OGS6 <- R6::R6Class("OGS6",
private$.insitu
}else{
assertthat::assert_that(
- prj_top_level_classes()[["insitu"]] %in%
+ ogs6_prj_top_level_classes()[["insitu"]] %in%
class(value))
private$.insitu <- value
}
@@ -605,3 +613,47 @@ OGS6 <- R6::R6Class("OGS6",
.pvds = NULL
)
)
+
+
+#===== ogs6_prj_top_level_classes =====
+
+
+#' ogs6_prj_top_level_classes
+#' @description Returns named character vector of \code{OGS6} top level
+#' \code{.prj} tags (names) represented by \code{r2ogs6} classes along with
+#' their class names (values).
+#' @return character
+#' @export
+ogs6_prj_top_level_classes <- function(){
+
+ xpaths_for_classes <- xpaths_for_classes
+
+ flattened_xpaths <- unlist(xpaths_for_classes)
+ names(flattened_xpaths) <- NULL
+
+ prj_components <- character()
+ seen <- character()
+
+ for(i in seq_len(length(flattened_xpaths))){
+
+ split_xpath <-
+ unlist(strsplit(flattened_xpaths[[i]], "/", fixed = TRUE))
+
+ if(!split_xpath[[1]] %in% seen){
+ if(!is.null(get_class_from_xpath(split_xpath[[1]]))){
+ prj_components <- c(prj_components,
+ get_class_from_xpath(split_xpath[[1]]))
+
+ }else{
+ xpath <- paste(split_xpath[[1]], split_xpath[[2]], sep = "/")
+ prj_components <- c(prj_components,
+ get_class_from_xpath(xpath))
+ }
+
+ names(prj_components)[[length(prj_components)]] <- split_xpath[[1]]
+ seen <- c(seen, split_xpath[[1]])
+ }
+ }
+
+ return(prj_components)
+}
diff --git a/R/ogs6_ensemble.R b/R/ogs6_ensemble.R
index 5bb6b2b32618b3a0eb65ef0bdb15636ce2494efb..ce51aad54355f68e470da513d008d59b53c29a94 100644
--- a/R/ogs6_ensemble.R
+++ b/R/ogs6_ensemble.R
@@ -34,13 +34,16 @@ OGS6_Ensemble <- R6::R6Class(
dp_str <- stringr::str_remove_all(
dp_str,
- "(^list\\()|(\\)$)|[:space:]|([A-Za-z_]*\\s*=\\s*)")
+ "(^list\\()|(\\)$)|[:space:]|([A-Za-z_0-9]*\\s*=\\s*)")
dp_strs <- unlist(strsplit(dp_str, "list\\("))
dp_strs <- dp_strs[dp_strs != ""]
private$.dp_parameters <- lapply(dp_strs, function(x){
- unlist(strsplit(x, ","))[[1]]
+ dp_p <- unlist(strsplit(x, ","))[[1]]
+ dp_p <- gsub("^[A-Za-z_0-9]*\\$", "ogs6_obj$", dp_p)
+ #cat("after:", dp_p, "\n")
+ return(dp_p)
})
assertthat::assert_that(is.list(parameters))
@@ -217,7 +220,7 @@ OGS6_Ensemble <- R6::R6Class(
sim_tbls <- c(sim_tbls, list(sim_tbl))
}
- return(bind_rows(sim_tbls))
+ return(dplyr::bind_rows(sim_tbls))
}
),
@@ -307,8 +310,7 @@ OGS6_Ensemble <- R6::R6Class(
sequential_mode,
percentages_mode) {
- orig_sim_name <- ogs6_obj$sim_name
- orig_sim_path <- ogs6_obj$sim_path
+ orig_ogs6 <- ogs6_obj$clone(deep = T)
parameter_values <- self$parameter_values
@@ -326,20 +328,23 @@ OGS6_Ensemble <- R6::R6Class(
for(j in seq_len(length(parameter_values[[i]]))){
- # Modify parameter reference of original object
+ # Clone object
+ ogs6_obj <- private$copy_and_modify(
+ orig_ogs6,
+ orig_ogs6$sim_name,
+ sim_id,
+ orig_ogs6$sim_path)
+
+ # Modify parameter
set_param_call <-
paste0(self$dp_parameters[[i]],
" <- parameter_values[[i]][[j]]")
eval(parse(text = set_param_call))
- # Clone object
- new_ogs6_obj <- private$copy_and_modify(ogs6_obj,
- orig_sim_name,
- sim_id,
- orig_sim_path)
+
private$.ensemble <-
- c(private$.ensemble, list(new_ogs6_obj))
+ c(private$.ensemble, list(ogs6_obj))
sim_id <- sim_id + 1
}
@@ -357,7 +362,13 @@ OGS6_Ensemble <- R6::R6Class(
# n iterations in first loop == n objects to create
for (i in seq_len(length(parameter_values[[1]]))) {
- # Modify parameter reference of original object
+ # Clone object
+ ogs6_obj <- private$copy_and_modify(orig_ogs6,
+ orig_ogs6$sim_name,
+ (i + 1),
+ orig_ogs6$sim_path)
+
+ # Modify parameter
for (j in seq_len(length(self$dp_parameters))) {
set_param_call <-
paste0(self$dp_parameters[[j]],
@@ -365,15 +376,9 @@ OGS6_Ensemble <- R6::R6Class(
eval(parse(text = set_param_call))
}
- # Clone object
- new_ogs6_obj <- private$copy_and_modify(ogs6_obj,
- orig_sim_name,
- i,
- orig_sim_path)
-
# Add clone to list of simulation objects
private$.ensemble <- c(private$.ensemble,
- list(new_ogs6_obj))
+ list(ogs6_obj))
}
}
},
diff --git a/R/ogs6_gml.R b/R/ogs6_gml.R
index 1dd40a99dd11150e24945914286266f713c4cd5f..48ffb801170437a1ce91b989a753368ffb3b9a9a 100644
--- a/R/ogs6_gml.R
+++ b/R/ogs6_gml.R
@@ -146,12 +146,6 @@ OGS6_gml <- R6::R6Class(
}
},
- #'@field is_subclass
- #'Getter for private parameter '.is_subclass'
- is_subclass = function(value) {
- private$.is_subclass
- },
-
#'@field attr_names
#'Getter for private parameter '.attr_names'
attr_names = function(value) {
@@ -197,7 +191,6 @@ OGS6_gml <- R6::R6Class(
.points = NULL,
.polylines = NULL,
.surfaces = NULL,
- .is_subclass = TRUE,
.attr_names = c("point", "name", "id", "element"),
.flatten_on_exp = character()
)
@@ -207,12 +200,14 @@ OGS6_gml <- R6::R6Class(
#===== Validation utility =====
-#'validate_points
-#'@description Checks if the input is a tibble, if this tibble has the right
-#' number of elements, if those elements are named correctly and if there are
+#' validate_points
+#' @description
+#' Checks if the input is a tibble, if this tibble has the right number of
+#' elements, if those elements are named correctly and if there are
#' any overlapping points or duplicate point names
-#'@param points tibble: Must have 3 vectors named 'x', 'y' and 'z', may have
-#' optional 'name' vector
+#' @param points tibble: Must have 3 vectors named 'x', 'y' and 'z', may have
+#' optional 'name' vector
+#' @noRd
validate_points <- function(points) {
assertthat::assert_that(inherits(points, "tbl_df"))
@@ -256,11 +251,13 @@ validate_points <- function(points) {
}
-#'validate_polylines
-#'@description Checks if the input is a list, if this list consists of other
+#' validate_polylines
+#' @description
+#' Checks if the input is a list, if this list consists of other
#' lists and if those lists have the correct structure (length of 2, first
#' element is a string named 'name', second element is a numeric vector)
-#'@param polylines list(list("foo", c(1, 2))):
+#' @param polylines list(list("foo", c(1, 2))):
+#' @noRd
validate_polylines <- function(polylines) {
assertthat::assert_that(is.list(polylines))
@@ -280,12 +277,14 @@ validate_polylines <- function(polylines) {
}
-#'validate_surfaces
-#'@description Checks if the input is a list, if this list consists of other
+#' validate_surfaces
+#' @description
+#' Checks if the input is a list, if this list consists of other
#' lists and if those lists have the correct structure (length of 2 or 3, first
#' element is a string named 'name', second and third element are numeric
#' vectors)
-#'@param surfaces list(list("foo", c(1, 2, 3), c(2, 3, 4))):
+#' @param surfaces list(list("foo", c(1, 2, 3), c(2, 3, 4))):
+#' @noRd
validate_surfaces <- function(surfaces) {
assertthat::assert_that(is.list(surfaces))
@@ -320,13 +319,15 @@ validate_surfaces <- function(surfaces) {
}
-#'validate_pnt_values
-#'@description Checks if two numerical vectors of length 3
+#' validate_pnt_values
+#' @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.
-#'@param element_1 numeric, length = 3
-#'@param element_2 numeric, length = 3
+#' @param element_1 numeric, length = 3
+#' @param element_2 numeric, length = 3
+#' @noRd
validate_pnt_values = function (element_1, element_2) {
if(element_1[[1]] == element_1[[2]] ||
diff --git a/R/prj_medium.R b/R/prj_medium.R
index d7edbacebea1b2326b2cea1acfd616023b5381a3..8f8308a9e73667275166fb05bd72104e8dd8f02d 100644
--- a/R/prj_medium.R
+++ b/R/prj_medium.R
@@ -306,7 +306,7 @@ ogs6_get_medium_property <- function(medium, name){
assertthat::assert_that(assertthat::is.string(name))
properties_names <- lapply(medium$properties, `[[`, "name")
- property <- properties[properties_names == name][[1]]
+ property <- medium$properties[properties_names == name][[1]]
return(invisible(property))
}
diff --git a/R/prj_vtkdiff.R b/R/prj_vtkdiff.R
index 79c3b0d620291846e79643b51962258d57860e3d..e3986ea4c3bb6ecdba4ef7b220a0e3d846d76258 100644
--- a/R/prj_vtkdiff.R
+++ b/R/prj_vtkdiff.R
@@ -13,28 +13,28 @@
#' @example man/examples/ex_prj_vtkdiff.R
#' @export
prj_vtkdiff <- function(field,
- absolute_tolerance,
- relative_tolerance,
- file = NULL,
- regex = NULL) {
+ absolute_tolerance,
+ relative_tolerance,
+ file = NULL,
+ regex = NULL) {
#Coerce input
absolute_tolerance <- coerce_string_to_numeric(absolute_tolerance)
relative_tolerance <- coerce_string_to_numeric(relative_tolerance)
new_prj_vtkdiff(field,
- absolute_tolerance,
- relative_tolerance,
- file,
- regex)
+ absolute_tolerance,
+ relative_tolerance,
+ file,
+ regex)
}
new_prj_vtkdiff <- function(field,
- absolute_tolerance,
- relative_tolerance,
- file = NULL,
- regex = NULL) {
+ absolute_tolerance,
+ relative_tolerance,
+ file = NULL,
+ regex = NULL) {
assertthat::assert_that(assertthat::is.string(field))
diff --git a/R/read_in_gml.R b/R/read_in_gml.R
index f96eb2c4d59084c043a5b363744ffb9458f7ed07..ad04c8fc91c205bd9c0047f896f1d56f7b40bb7f 100644
--- a/R/read_in_gml.R
+++ b/R/read_in_gml.R
@@ -5,6 +5,7 @@
#' read_in_points
#' @description Reads points from a \code{.gml} file
#' @param xml_doc A parsed XML document (of class \code{xml2::xml_document})
+#' @noRd
read_in_points <- function(xml_doc) {
points_tibble <- tibble::tibble(x = c(),
@@ -40,6 +41,7 @@ read_in_points <- function(xml_doc) {
#' read_in_polylines
#' @description Reads polylines from a \code{.gml} file
#' @param xml_doc A parsed XML document (of class \code{xml2::xml_document})
+#' @noRd
read_in_polylines <- function(xml_doc) {
polylines_list <- list()
@@ -74,6 +76,7 @@ read_in_polylines <- function(xml_doc) {
#' read_in_surfaces
#' @description Reads surfaces from a \code{.gml} file
#' @param xml_doc A parsed XML document (of class \code{xml2::xml_document})
+#' @noRd
read_in_surfaces <- function(xml_doc) {
surfaces_list <- list()
diff --git a/R/read_in_prj.R b/R/read_in_prj.R
index 4fbaaf02cdfe90fbd9e6de5c86fdd24ec98ba64b..ed6b67af032a8776c319e75ed5ae951a6991c2f8 100644
--- a/R/read_in_prj.R
+++ b/R/read_in_prj.R
@@ -58,12 +58,21 @@ read_in_prj <- function(ogs6_obj,
vtu_ref <- xml2::xml_text(vtu_ref_nodes[[i]])
vtu_path <- paste0(dirname(prj_path), "/", vtu_ref)
+ axisym_val <- xml2::xml_attr(vtu_ref_nodes[[i]], "axially_symmetric")
+
+ if(!is.na(axisym_val) && axisym_val == "true"){
+ axisym_val <- TRUE
+ }else{
+ axisym_val <- FALSE
+ }
+
# Read in .vtu file(s) or just save their path
ogs6_obj$add_vtu(path = vtu_path,
+ axisym = axisym_val,
read_in_vtu = read_in_vtu)
}
- prj_components <- prj_top_level_classes()
+ prj_components <- ogs6_prj_top_level_classes()
# Include file reference
processes_include_node <-
diff --git a/R/read_in_utils.R b/R/read_in_utils.R
index 7263d8b75ecb7badff0d4813cc3534c71ce26b8d..11add850e852058ed7335a3ac1f2219b6a998792 100644
--- a/R/read_in_utils.R
+++ b/R/read_in_utils.R
@@ -8,6 +8,7 @@
#' @param path string: A file to be parsed as XML
#' @return The parsed XML file (as class object of type
#' \code{xml2::xml_document})
+#' @noRd
validate_read_in_xml <- function(path){
assertthat::assert_that(assertthat::is.string(path))
@@ -34,6 +35,7 @@ validate_read_in_xml <- function(path){
#' @param ogs6_obj A OGS6 class object
#' @param path string: Path to file XML elements should be read from
#' @param xpath string: An XPath expression (should be absolute!)
+#' @noRd
read_in <- function(ogs6_obj,
path,
xpath){
@@ -75,6 +77,7 @@ read_in <- function(ogs6_obj,
#' @description Takes an XML node and turns it into a class object
#' @param xml_node xml2::xml_node: XML node
#' @param xpath string: XPath expression (for subclass differentiation)
+#' @noRd
node_to_prj_class_object <- function(xml_node,
xpath){
@@ -158,6 +161,7 @@ node_to_prj_class_object <- function(xml_node,
#' 3) Parent nodes whose children have no children are represented as lists
#' @param xml_node xml2::xml_node: XML node
#' @param xpath string: XPath expression (for subclass differentiation)
+#' @noRd
node_to_object <- function(xml_node,
xpath = ""){
@@ -225,6 +229,7 @@ node_to_object <- function(xml_node,
#' @description Gets class arguments
#' @param class_name string: The name of a class
#' @return character: Named vector of class arguments
+#' @noRd
get_class_args <- function(class_name){
assertthat::assert_that(assertthat::is.string(class_name))
@@ -246,6 +251,7 @@ get_class_args <- function(class_name){
#' @param parameters list: Parameters
#' @param class_name string: The name of a class
#' @return list: Parameters ordered by argument order of class
+#' @noRd
order_parameters <- function(parameters, class_name){
assertthat::assert_that(is.list(parameters))
diff --git a/R/sim_utils.R b/R/sim_utils.R
index d559ddf8307ebca1d06a8c28a3d0a817ca4af085..6e7e56a170368fbff610da3f09812ac6e2cf15b0 100644
--- a/R/sim_utils.R
+++ b/R/sim_utils.R
@@ -32,7 +32,7 @@ ogs6_run_simulation <- function(ogs6_obj,
ogs6_read_output_files(ogs6_obj = ogs6_obj)
- return(invisible(exit_code))
+ return(exit_code)
}
@@ -96,7 +96,7 @@ ogs6_export_sim_files <- function(ogs6_obj,
# Copy all referenced .vtu files to ogs6_obj$sim_path
lapply(ogs6_obj$meshes, function(x){
- file.copy(x, ogs6_obj$sim_path)
+ file.copy(x[["path"]], ogs6_obj$sim_path)
})
if(!is.null(ogs6_obj$python_script)){
@@ -187,7 +187,7 @@ ogs6_call_ogs6 <- function(ogs6_obj,
args = ogs6_args)
}
- return(invisible(exit_code))
+ return(exit_code)
}
@@ -256,11 +256,14 @@ ogs6_read_output_files <- function(ogs6_obj){
#===== Test benchmarks =====
-#' run_benchmark
-#' @description Utility function for quick benchmark runs
+#' Run benchmark
+#'
+#' Utility function for quick benchmark runs
+#'
#' @param prj_path string:
#' @param ogs6_bin_path string:
#' @param sim_path string: Path where simulation files will be saved
+#' @noRd
run_benchmark <- function(prj_path,
ogs6_bin_path,
sim_path){
@@ -280,7 +283,6 @@ run_benchmark <- function(prj_path,
sim_name <- tools::file_path_sans_ext(basename(prj_path))
ogs6_obj <- OGS6$new(sim_name = sim_name,
- sim_id = 1,
sim_path = sim_path)
read_in_prj(ogs6_obj = ogs6_obj,
@@ -291,16 +293,18 @@ run_benchmark <- function(prj_path,
}
-#' run_all_benchmarks
-#' @description Utility function, for quick benchmark runs. Calls
-#' run_benchmark internally.
+#' Run benchmarks
+#'
+#' This is a wrapper function for `run_benchmark()`.
+#'
#' @param path string: Path to benchmark folder
#' @param ogs6_processlib_path string: Path to OpenGeoSys 6 ProcessLib folder
#' which contains relevant Tests.cmake files
#' @param ogs6_bin_path string:
#' @param sim_path string: Path where simulation files will be saved
-#' @param starting_from_prj_path string: \code{.prj} path to start from
+#' @param starting_from_prj_path string: `.prj` path to start from
#' @param print_results flag: Print results in the end?
+#' @noRd
run_all_benchmarks <- function(path,
ogs6_processlib_path,
ogs6_bin_path,
@@ -449,10 +453,13 @@ print_run_all_benchmarks <- function(nonexisting_prj_paths,
}
-#' get_benchmark_paths
-#' @description Gets paths to all benchmarks that should work
+#' Get benchmark paths
+#'
+#' Gets paths to all benchmarks that should work from `Tests.cmake` files
+#'
#' @param ogs6_processlib_path string: Path to OpenGeoSys 6 ProcessLib folder
-#' which contains relevant Tests.cmake files
+#' which contains relevant `Tests.cmake` files
+#' @noRd
get_benchmark_paths <- function(ogs6_processlib_path){
tests_cmake_files <- list.files(path = ogs6_processlib_path,
diff --git a/R/utils.R b/R/utils.R
index 0b291685b0015ebfe7febac95c22055f43197b86..99ec0330358fbdf569585988ce818d5e04456750 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -6,8 +6,7 @@
#' @description Gets r2ogs6 class name from an xpath-like expression
#' @param xpath string: An xpath expression. Works for path-like xpaths only
#' @return string: The class name.
-#' @examples
-#' get_class_from_xpath("processes/process")
+#' @noRd
get_class_from_xpath <- function(xpath){
assertthat::assert_that(assertthat::is.string(xpath))
@@ -31,8 +30,7 @@ get_class_from_xpath <- function(xpath){
#' @description Utility function, returns the tag name of a r2ogs6 class
#' @param class_name string: The name of a r2ogs6 class
#' @return string: The tag name corresponding to \code{class_name}
-#' @examples
-#' get_tag_from_class("prj_process")
+#' @noRd
get_tag_from_class <- function(class_name) {
assertthat::assert_that(assertthat::is.string(class_name))
@@ -51,8 +49,7 @@ get_tag_from_class <- function(class_name) {
#' @description Gets the XML tag name from an xpath expression
#' @param xpath string: An xpath expression. Works for path-like xpaths only
#' @return string: The XML tag name
-#' @examples
-#' get_tag_from_xpath("processes/process")
+#' @noRd
get_tag_from_xpath <- function(xpath){
xpath_split <- unlist(strsplit(xpath, "/", fixed = TRUE))
@@ -65,6 +62,7 @@ get_tag_from_xpath <- function(xpath){
#' get_prj_top_level_tags
#' @description Gets top level .prj tags along with info if they are required.
#' @return list: List of lists.
+#' @noRd
get_prj_top_level_tags <- function(){
prj_reduxml <- system.file("extdata/xml_redux/", "prj_redu.xml",
@@ -81,46 +79,6 @@ get_prj_top_level_tags <- function(){
}
-#' prj_top_level_classes
-#' @description Returns named character vector of \code{OGS6} top level
-#' \code{.prj} tags (names) represented by \code{r2ogs6} classes along with their
-#' class names (values).
-#' @return character
-prj_top_level_classes <- function(){
-
- xpaths_for_classes <- xpaths_for_classes
-
- flattened_xpaths <- unlist(xpaths_for_classes)
- names(flattened_xpaths) <- NULL
-
- prj_components <- character()
- seen <- character()
-
- for(i in seq_len(length(flattened_xpaths))){
-
- split_xpath <-
- unlist(strsplit(flattened_xpaths[[i]], "/", fixed = TRUE))
-
- if(!split_xpath[[1]] %in% seen){
- if(!is.null(get_class_from_xpath(split_xpath[[1]]))){
- prj_components <- c(prj_components,
- get_class_from_xpath(split_xpath[[1]]))
-
- }else{
- xpath <- paste(split_xpath[[1]], split_xpath[[2]], sep = "/")
- prj_components <- c(prj_components,
- get_class_from_xpath(xpath))
- }
-
- names(prj_components)[[length(prj_components)]] <- split_xpath[[1]]
- seen <- c(seen, split_xpath[[1]])
- }
- }
-
- return(prj_components)
-}
-
-
#===== Coercion utility =====
@@ -128,8 +86,7 @@ prj_top_level_classes <- function(){
#' @description If an object is of type string, coerces it to a numeric type
#' @param obj object: Any object
#' @return numeric if \code{obj} was a string, else unchanged \code{obj}
-#' @examples
-#' coerce_string_to_numeric("12 54 2 \n 2")
+#' @noRd
coerce_string_to_numeric <- function(obj){
if(assertthat::is.string(obj)){
@@ -147,6 +104,7 @@ coerce_string_to_numeric <- function(obj){
#' @param names character: How the vector elements will be named as
#' per default
#' @return vector: Named vector where the names correspond to \code{names}
+#' @noRd
coerce_names <- function(vector, names) {
assertthat::assert_that(is.vector(vector))
@@ -178,6 +136,7 @@ coerce_names <- function(vector, names) {
#' @description Validator function for a parameter list or vector or \code{NULL}
#' @param obj A list (or vector) of parameters
#' @param names How the list elements will be named as per default
+#' @noRd
is_null_or_coerce_names <- function(obj, names){
if(!is.null(obj)){
@@ -192,6 +151,7 @@ is_null_or_coerce_names <- function(obj, names){
#' @description Cleans an imported list because sometimes strings containing
#' only newline characters and spaces get imported in
#' @param list list: A list
+#' @noRd
clean_imported_list <- function(list){
assertthat::assert_that(is.list(list))
@@ -214,6 +174,7 @@ clean_imported_list <- function(list){
#' as_dir_path
#' @description Checks if a given path ends on \code{/}
#' @param path string: A path
+#' @noRd
as_dir_path <- function(path){
assertthat::assert_that(assertthat::is.string(path))
@@ -237,6 +198,7 @@ as_dir_path <- function(path){
#' @param print_messages flag: Optional: Print error messages? Defaults to
#' \code{TRUE}
#' @return character: Vector of invalid XML paths
+#' @noRd
filter_invalid_xml <- function(paths,
encoding = "ISO-8859-1",
print_messages = TRUE){
@@ -270,6 +232,7 @@ filter_invalid_xml <- function(paths,
#' are_numbers
#' @description Checks if objects are numbers
#' @param ... Ellipsis
+#' @noRd
are_numbers <- function(...){
lapply(list(...), function(x){
@@ -283,6 +246,7 @@ are_numbers <- function(...){
#' are_null_or_numbers
#' @description Checks if objects are either \code{NULL} or numbers
#' @param ... Ellipsis
+#' @noRd
are_null_or_numbers <- function(...){
lapply(list(...), function(x){
@@ -298,6 +262,7 @@ are_null_or_numbers <- function(...){
#' are_numeric
#' @description Checks if objects are numeric
#' @param ... Ellipsis
+#' @noRd
are_numeric <- function(...){
lapply(list(...), function(x){
@@ -311,6 +276,7 @@ are_numeric <- function(...){
#' are_null_or_numeric
#' @description Checks if objects are either \code{NULL} or numeric
#' @param ... Ellipsis
+#' @noRd
are_null_or_numeric <- function(...){
lapply(list(...), function(x){
@@ -326,6 +292,7 @@ are_null_or_numeric <- function(...){
#' are_strings
#' @description Checks if objects are strings
#' @param ... Ellipsis
+#' @noRd
are_strings <- function(...){
lapply(list(...), function(x){
@@ -339,6 +306,7 @@ are_strings <- function(...){
#' are_null_or_strings
#' @description Checks if objects are either \code{NULL} or strings
#' @param ... Ellipsis
+#' @noRd
are_null_or_strings <- function(...){
lapply(list(...), function(x){
@@ -354,6 +322,7 @@ are_null_or_strings <- function(...){
#' are_string_flags
#' @description Checks if objects are strings reading either "true" or "false"
#' @param ... Ellipsis
+#' @noRd
are_string_flags <- function(...){
lapply(list(...), function(x){
@@ -369,6 +338,7 @@ are_string_flags <- function(...){
#' @description Checks if objects are either \code{NULL} or strings reading
#' either "true" or "false"
#' @param ... Ellipsis
+#' @noRd
are_null_or_string_flags <- function(...){
lapply(list(...), function(x){
@@ -386,6 +356,7 @@ are_null_or_string_flags <- function(...){
#' \code{element_class}
#' @param list list: List to check
#' @param element_class string: Class each element of \code{list} should have
+#' @noRd
is_wrapper_list <- function(list, element_class) {
assertthat::assert_that(is.list(list))
@@ -403,6 +374,7 @@ is_wrapper_list <- function(list, element_class) {
#' of class \code{element_class}
#' @param obj list | NULL: Object to check
#' @param element_class string: Class each element of \code{obj} should have
+#' @noRd
is_null_or_wrapper_list <- function(obj, element_class) {
if(!is.null(obj)){
@@ -422,6 +394,7 @@ is_null_or_wrapper_list <- function(obj, element_class) {
#' class \code{class_name}
#' @param obj The object to check
#' @param class_name The name of the expected class
+#' @noRd
is_null_or_has_class <- function(obj, class_name){
if(!is.null(obj)){
diff --git a/R/zzz.R b/R/zzz.R
index 3db11061130c50af8a88e7cb11b3b1a0313356b0..240be700d88b023dca18971f6a63065bb5529d9b 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -9,56 +9,29 @@ vtk <- NULL
op <- options()
op.r2ogs6 <- list(
# Default paths
- r2ogs6.default_sim_path = "",
- r2ogs6.default_script_path = "",
- r2ogs6.default_benchmark_path = "",
- r2ogs6.default_ogs6_processlib_path = "",
- r2ogs6.default_ogs6_utils_path = "",
- r2ogs6.default_ogs6_bin_path = "",
- r2ogs6.max_lines_gml = 300,
-
- # External file reference tags
-
- # Reticulate setting for reading in VTK
- r2ogs6.use_python = ""
+ r2ogs6.default_sim_path = NULL,
+ r2ogs6.default_script_path = NULL,
+ r2ogs6.default_benchmark_path = NULL,
+ r2ogs6.default_ogs6_processlib_path = NULL,
+ r2ogs6.default_ogs6_bin_path = NULL,
+ r2ogs6.max_lines_gml = 300
)
toset <- !(names(op.r2ogs6) %in% names(op))
if (any(toset)) options(op.r2ogs6[toset])
- # use superassignments to update global Python references
- vtk <<- reticulate::import("vtk", delay_load = TRUE)
-
- test_config <- TRUE
+ if(file.exists("config.yml")){
+ cfg <- config::get()
- if (test_config) {
- options(
- r2ogs6.default_sim_path = "D:/OGS_sims/",
- r2ogs6.default_script_path = "D:/OGS_scripts/",
- r2ogs6.default_benchmark_path =
- "D:/Programme/OpenGeoSys/ogs-master/Tests/Data/",
- r2ogs6.default_ogs6_processlib_path =
- "D:/Programme/OpenGeoSys/ogs-master/ProcessLib/",
- r2ogs6.default_ogs6_utils_path =
- paste0(
- "D:/Programme/OpenGeoSys/",
- "ogs-6.3.2-Windows-10.0.14393-x64-python-3.7.2-de-utils",
- "/bin/"
- ),
- r2ogs6.default_ogs6_bin_path =
- paste0(
- "D:/Programme/OpenGeoSys/",
- "ogs-6.3.2-Windows-10.0.14393-x64-python-3.7.2-de-utils",
- "/bin/ogs.exe"
- ),
- r2ogs6.max_lines_gml = 300,
- r2ogs6.use_python = "D:/Programme/anaconda3/envs/rtest/python.exe"
- )
-
- reticulate::use_virtualenv(unlist(options("r2ogs6.use_python")))
+ for(i in names(op.r2ogs6)){
+ eval(parse(text = paste0("options(", i, " = cfg$", i, ")")))
+ }
}
- invisible()
+ # use superassignments to update global Python references
+ vtk <<- reticulate::import("vtk", delay_load = TRUE)
+
+ return(invisible())
}
@@ -67,7 +40,7 @@ vtk <- NULL
packageStartupMessage(
paste("r2ogs6 works best with its options set :)\nFor",
"an overview, use the command",
- "'options()[grepl(\"r2ogs6.\",",
- "names(options()), fixed = TRUE)]'\nTo set an option, use the",
+ "'options()[grepl(\"^r2ogs6\",",
+ "names(options()))]'\nTo set an option, use the",
"command 'options(\"<option_name>\" = <option_value>)'\n"))
}
diff --git a/data/xpaths_for_classes.rda b/data/xpaths_for_classes.rda
index 03d04f8f8f88fa252cdf6898aead797c96224390..2abd4f9f3ce8a1bd79cce42b6854a6bf9df5390b 100644
Binary files a/data/xpaths_for_classes.rda and b/data/xpaths_for_classes.rda differ
diff --git a/man/OGS6.Rd b/man/OGS6.Rd
index 02a07ae3388d40a4912cadccfbdc49ec5fd4abe6..8ef7607947e580f0909f57859b65a8a057b386ae 100644
--- a/man/OGS6.Rd
+++ b/man/OGS6.Rd
@@ -19,7 +19,7 @@ ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
## ------------------------------------------------
ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
-ogs6_obj$add(prj_parameter$new(name = "foo", type = "bar"))
+ogs6_obj$add(prj_parameter(name = "foo", type = "bar"))
## ------------------------------------------------
## Method `OGS6$add_gml`
@@ -167,7 +167,7 @@ Adds a .prj simulation component
\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(prj_parameter$new(name = "foo", type = "bar"))
+ogs6_obj$add(prj_parameter(name = "foo", type = "bar"))
}
\if{html}{\out{</div>}}
@@ -210,7 +210,7 @@ ogs6_obj$add_gml("this_works.gml")
Adds a reference to a \code{.vtu} file and optionally, a \code{OGS6_vtu}
object
\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_vtu(path, read_in_vtu = FALSE)}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_vtu(path, axisym = FALSE, read_in_vtu = FALSE)}\if{html}{\out{</div>}}
}
\subsection{Arguments}{
@@ -218,6 +218,8 @@ object
\describe{
\item{\code{path}}{string: A path}
+\item{\code{axisym}}{flag: Is the mesh axially symmetrical?}
+
\item{\code{read_in_vtu}}{flag: Optional: Should \code{.vtu} file just be
copied or read in too?}
}
@@ -296,7 +298,7 @@ Clears components from the \code{OGS6} object
\describe{
\item{\code{which}}{character: The names of the components (all by default).
If you want to delete only some components, run
-\code{names(prj_top_level_classes())} for the available options.}
+\code{names(ogs6_prj_top_level_classes())} for the available options.}
}
\if{html}{\out{</div>}}
}
diff --git a/man/OGS6_gml.Rd b/man/OGS6_gml.Rd
index 48aad92508f8439a3ce953d3e51b7147e639198d..a377808a6f5b6291ac3ace8e5845b75e5fc73059 100644
--- a/man/OGS6_gml.Rd
+++ b/man/OGS6_gml.Rd
@@ -39,8 +39,6 @@ OGS6_gml$new(
\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'}
diff --git a/man/analyse_xml.Rd b/man/analyse_xml.Rd
deleted file mode 100644
index 547750eb187f67c302eb30cfe5452094d7a0db50..0000000000000000000000000000000000000000
--- a/man/analyse_xml.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/analyse_xml.R
-\name{analyse_xml}
-\alias{analyse_xml}
-\title{analyse_xml}
-\usage{
-analyse_xml(path, pattern, xpath, print_findings = TRUE)
-}
-\arguments{
-\item{path}{string: A path}
-
-\item{pattern}{string: A regex pattern}
-
-\item{xpath}{string: An XPath expression. WARNING: Only works for expressions
-that return nodesets, use it to look up tag names.}
-
-\item{print_findings}{Optional: Should the results be printed to the console?}
-}
-\description{
-This is a helper function which can be used to combat missing
-documentation. It looks for files in a path which match the given pattern
-and then attempts to parse them as XML. For each occurence of the specified
-element, it documents its attributes and direct children and prints a little
-summary of its findings at the end.
-}
diff --git a/man/are_null_or_numbers.Rd b/man/are_null_or_numbers.Rd
deleted file mode 100644
index a646d8c38c459e29f8024965596693c5749d96d1..0000000000000000000000000000000000000000
--- a/man/are_null_or_numbers.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{are_null_or_numbers}
-\alias{are_null_or_numbers}
-\title{are_null_or_numbers}
-\usage{
-are_null_or_numbers(...)
-}
-\arguments{
-\item{...}{Ellipsis}
-}
-\description{
-Checks if objects are either \code{NULL} or numbers
-}
diff --git a/man/are_null_or_numeric.Rd b/man/are_null_or_numeric.Rd
deleted file mode 100644
index d6f3c7b7e0a3f9fc36d79d17343f747b4020b60f..0000000000000000000000000000000000000000
--- a/man/are_null_or_numeric.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{are_null_or_numeric}
-\alias{are_null_or_numeric}
-\title{are_null_or_numeric}
-\usage{
-are_null_or_numeric(...)
-}
-\arguments{
-\item{...}{Ellipsis}
-}
-\description{
-Checks if objects are either \code{NULL} or numeric
-}
diff --git a/man/are_null_or_string_flags.Rd b/man/are_null_or_string_flags.Rd
deleted file mode 100644
index 31b05fdeef2f14a2fdec1b9f5c0908a02931ccb2..0000000000000000000000000000000000000000
--- a/man/are_null_or_string_flags.Rd
+++ /dev/null
@@ -1,15 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{are_null_or_string_flags}
-\alias{are_null_or_string_flags}
-\title{are_null_or_string_flags}
-\usage{
-are_null_or_string_flags(...)
-}
-\arguments{
-\item{...}{Ellipsis}
-}
-\description{
-Checks if objects are either \code{NULL} or strings reading
-either "true" or "false"
-}
diff --git a/man/are_null_or_strings.Rd b/man/are_null_or_strings.Rd
deleted file mode 100644
index c9c67f0df76c7a298fa01d1eb72530094be6df54..0000000000000000000000000000000000000000
--- a/man/are_null_or_strings.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{are_null_or_strings}
-\alias{are_null_or_strings}
-\title{are_null_or_strings}
-\usage{
-are_null_or_strings(...)
-}
-\arguments{
-\item{...}{Ellipsis}
-}
-\description{
-Checks if objects are either \code{NULL} or strings
-}
diff --git a/man/are_numbers.Rd b/man/are_numbers.Rd
deleted file mode 100644
index 680aee69d9a903518e408500e6233331dd25a742..0000000000000000000000000000000000000000
--- a/man/are_numbers.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{are_numbers}
-\alias{are_numbers}
-\title{are_numbers}
-\usage{
-are_numbers(...)
-}
-\arguments{
-\item{...}{Ellipsis}
-}
-\description{
-Checks if objects are numbers
-}
diff --git a/man/are_numeric.Rd b/man/are_numeric.Rd
deleted file mode 100644
index a9de7949a592be64a24aaf0983b1bdb19b2eaaaa..0000000000000000000000000000000000000000
--- a/man/are_numeric.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{are_numeric}
-\alias{are_numeric}
-\title{are_numeric}
-\usage{
-are_numeric(...)
-}
-\arguments{
-\item{...}{Ellipsis}
-}
-\description{
-Checks if objects are numeric
-}
diff --git a/man/are_string_flags.Rd b/man/are_string_flags.Rd
deleted file mode 100644
index cbcae8d8e4819cccdb31f50fa77eefa1b60cb6ef..0000000000000000000000000000000000000000
--- a/man/are_string_flags.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{are_string_flags}
-\alias{are_string_flags}
-\title{are_string_flags}
-\usage{
-are_string_flags(...)
-}
-\arguments{
-\item{...}{Ellipsis}
-}
-\description{
-Checks if objects are strings reading either "true" or "false"
-}
diff --git a/man/are_strings.Rd b/man/are_strings.Rd
deleted file mode 100644
index 0fe8bc5e80bea020a14944dbf7ebcf6984069393..0000000000000000000000000000000000000000
--- a/man/are_strings.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{are_strings}
-\alias{are_strings}
-\title{are_strings}
-\usage{
-are_strings(...)
-}
-\arguments{
-\item{...}{Ellipsis}
-}
-\description{
-Checks if objects are strings
-}
diff --git a/man/as_dir_path.Rd b/man/as_dir_path.Rd
deleted file mode 100644
index 47b0dc6ed94582cc19e38593865b065fca955df1..0000000000000000000000000000000000000000
--- a/man/as_dir_path.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{as_dir_path}
-\alias{as_dir_path}
-\title{as_dir_path}
-\usage{
-as_dir_path(path)
-}
-\arguments{
-\item{path}{string: A path}
-}
-\description{
-Checks if a given path ends on \code{/}
-}
diff --git a/man/build_redux_doc.Rd b/man/build_redux_doc.Rd
deleted file mode 100644
index 85e005c088c3eec2f9ad7a86291511eed47db4f4..0000000000000000000000000000000000000000
--- a/man/build_redux_doc.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_xml.R
-\name{build_redux_doc}
-\alias{build_redux_doc}
-\title{build_redux_doc}
-\usage{
-build_redux_doc(path, pattern, xpath, export_path)
-}
-\arguments{
-\item{path}{string: See \code{?analyse_xml}}
-
-\item{pattern}{string: See \code{?analyse_xml}}
-
-\item{xpath}{string: See \code{?analyse_xml}}
-
-\item{export_path}{string: Path to export the XML document to}
-}
-\description{
-Builds an XML document based on the findings of
-\code{analyse_xml()}. Calls recursive function \code{build_redux_tree()}
-internally.
-}
diff --git a/man/build_redux_tree.Rd b/man/build_redux_tree.Rd
deleted file mode 100644
index 11f2cc7ecc0d692234617cb7530f8903431596f9..0000000000000000000000000000000000000000
--- a/man/build_redux_tree.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_xml.R
-\name{build_redux_tree}
-\alias{build_redux_tree}
-\title{build_redux_tree}
-\usage{
-build_redux_tree(path, pattern, xpath, required)
-}
-\arguments{
-\item{path}{string: See \code{?analyse_xml}}
-
-\item{pattern}{string: See \code{?analyse_xml}}
-
-\item{xpath}{string: See \code{?analyse_xml}}
-
-\item{required}{flag: Recursion utility}
-}
-\description{
-Builds an XML tree based on the findings of
-\code{analyse_xml()}. This is a recursive function.
-}
diff --git a/man/clean_imported_list.Rd b/man/clean_imported_list.Rd
deleted file mode 100644
index a8e0644c5d8a0240a81c9419caab37df98ce2677..0000000000000000000000000000000000000000
--- a/man/clean_imported_list.Rd
+++ /dev/null
@@ -1,15 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{clean_imported_list}
-\alias{clean_imported_list}
-\title{clean_imported_list}
-\usage{
-clean_imported_list(list)
-}
-\arguments{
-\item{list}{list: A list}
-}
-\description{
-Cleans an imported list because sometimes strings containing
-only newline characters and spaces get imported in
-}
diff --git a/man/coerce_names.Rd b/man/coerce_names.Rd
deleted file mode 100644
index be60541341a4930832171abc851ac402db62b686..0000000000000000000000000000000000000000
--- a/man/coerce_names.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{coerce_names}
-\alias{coerce_names}
-\title{coerce_names}
-\usage{
-coerce_names(vector, names)
-}
-\arguments{
-\item{vector}{vector: Vector of parameters}
-
-\item{names}{character: How the vector elements will be named as
-per default}
-}
-\value{
-vector: Named vector where the names correspond to \code{names}
-}
-\description{
-Validator function for a parameter vector
-}
diff --git a/man/coerce_string_to_numeric.Rd b/man/coerce_string_to_numeric.Rd
deleted file mode 100644
index 4061da8a4305c77485bf9295d927195a3545f2c4..0000000000000000000000000000000000000000
--- a/man/coerce_string_to_numeric.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{coerce_string_to_numeric}
-\alias{coerce_string_to_numeric}
-\title{coerce_string_to_numeric}
-\usage{
-coerce_string_to_numeric(obj)
-}
-\arguments{
-\item{obj}{object: Any object}
-}
-\value{
-numeric if \code{obj} was a string, else unchanged \code{obj}
-}
-\description{
-If an object is of type string, coerces it to a numeric type
-}
-\examples{
- coerce_string_to_numeric("12 54 2 \n 2")
-}
diff --git a/man/compare_xml.Rd b/man/compare_xml.Rd
deleted file mode 100644
index 205de120b9fd6d1529176311bb06211b3fe0b4b2..0000000000000000000000000000000000000000
--- a/man/compare_xml.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/compare_xml.R
-\name{compare_xml}
-\alias{compare_xml}
-\title{compare_xml}
-\usage{
-compare_xml(xml_node_x, xml_node_y)
-}
-\arguments{
-\item{xml_node_x}{xml2::xml_node: Node to compare}
-
-\item{xml_node_y}{xml2::xml_node: Node to compare to}
-}
-\description{
-Helper function to check if 2 XML documents have the same
-content. This is a recursive function. Strictly WIP!
-}
diff --git a/man/construct_add_call.Rd b/man/construct_add_call.Rd
deleted file mode 100644
index 3753914b929358ba876859776d1eac2790b9320b..0000000000000000000000000000000000000000
--- a/man/construct_add_call.Rd
+++ /dev/null
@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_benchmark_script.R
-\name{construct_add_call}
-\alias{construct_add_call}
-\title{construct_add_call}
-\usage{
-construct_add_call(object, nested_call = FALSE)
-}
-\arguments{
-\item{object}{An object (numeric, character, list, NULL, \code{OGS6} or
-\code{r2ogs6} class object)}
-
-\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 \code{OGS6} object
-}
-\description{
-Constructs a call based on an \code{OGS6} component. This is a
-recursive function, handle with care.
-}
diff --git a/man/delete_keywords_from_str.Rd b/man/delete_keywords_from_str.Rd
deleted file mode 100644
index 0da3be3be5cbab070dfef905baed9147cfc73afc..0000000000000000000000000000000000000000
--- a/man/delete_keywords_from_str.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_benchmark_script.R
-\name{delete_keywords_from_str}
-\alias{delete_keywords_from_str}
-\title{delete_keywords_from_str}
-\usage{
-delete_keywords_from_str(string)
-}
-\arguments{
-\item{string}{string}
-}
-\description{
-Utility function to delete keywords from a string,
-this is important because there is a <repeat> tag in <time_loop> and
-"repeat" is a reserved word in R (extend this function if you find more
-reserved words)
-}
diff --git a/man/export_gml.Rd b/man/export_gml.Rd
deleted file mode 100644
index b98610b8e14079f57ce3d444a43049f2e79faf8f..0000000000000000000000000000000000000000
--- a/man/export_gml.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/export_gml.R
-\name{export_gml}
-\alias{export_gml}
-\title{export_gml}
-\usage{
-export_gml(gml, path)
-}
-\arguments{
-\item{gml}{OGS6_gml:}
-
-\item{path}{string:}
-}
-\description{
-Creates a .gml XML document based on user input data
-}
diff --git a/man/export_prj.Rd b/man/export_prj.Rd
deleted file mode 100644
index 6aabeb8da266cb9dc9b090a39dbecf7cea647a48..0000000000000000000000000000000000000000
--- a/man/export_prj.Rd
+++ /dev/null
@@ -1,15 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/export_prj.R
-\name{export_prj}
-\alias{export_prj}
-\title{export_prj}
-\usage{
-export_prj(ogs6_obj)
-}
-\arguments{
-\item{ogs6_obj}{OGS6: Simulation object}
-}
-\description{
-Wrapper function to create a \code{.prj} XML document based on
-the user input data
-}
diff --git a/man/filter_invalid_xml.Rd b/man/filter_invalid_xml.Rd
deleted file mode 100644
index 512b64458afecef2f05bac5407aced522c20ca1c..0000000000000000000000000000000000000000
--- a/man/filter_invalid_xml.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{filter_invalid_xml}
-\alias{filter_invalid_xml}
-\title{filter_invalid_xml}
-\usage{
-filter_invalid_xml(paths, encoding = "ISO-8859-1", print_messages = TRUE)
-}
-\arguments{
-\item{paths}{character: Vector of (maybe-)XML paths}
-
-\item{encoding}{string: Optional: XML encoding. Defaults to ISO-8859-1}
-
-\item{print_messages}{flag: Optional: Print error messages? Defaults to
-\code{TRUE}}
-}
-\value{
-character: Vector of invalid XML paths
-}
-\description{
-Filters invalid XML paths out of a vector
-}
diff --git a/man/flags_to_assign_str.Rd b/man/flags_to_assign_str.Rd
deleted file mode 100644
index 80172d6355169dfba66a577308890ecc476b53e6..0000000000000000000000000000000000000000
--- a/man/flags_to_assign_str.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_class.R
-\name{flags_to_assign_str}
-\alias{flags_to_assign_str}
-\title{flags_to_assign_str}
-\usage{
-flags_to_assign_str(flags, print_result = FALSE)
-}
-\arguments{
-\item{flags}{vector: Flags}
-
-\item{print_result}{flag: Should the result be printed to the console?}
-}
-\description{
-Helper function to generate a string out of a flag vector
-}
diff --git a/man/flags_to_con_call_str.Rd b/man/flags_to_con_call_str.Rd
deleted file mode 100644
index 42b7ae74e9c2574c448895e3cc95a62d26a13f2c..0000000000000000000000000000000000000000
--- a/man/flags_to_con_call_str.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_class.R
-\name{flags_to_con_call_str}
-\alias{flags_to_con_call_str}
-\title{flags_to_con_call_str}
-\usage{
-flags_to_con_call_str(flags, print_result = FALSE)
-}
-\arguments{
-\item{flags}{vector: Flags}
-
-\item{print_result}{flag: Should the result be printed to the console?}
-}
-\description{
-Helper function to generate a string out of a flag vector
-}
diff --git a/man/flags_to_con_str.Rd b/man/flags_to_con_str.Rd
deleted file mode 100644
index 551edc77a45820f4db84f3c4b343b42ebf16baaa..0000000000000000000000000000000000000000
--- a/man/flags_to_con_str.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_class.R
-\name{flags_to_con_str}
-\alias{flags_to_con_str}
-\title{flags_to_con_str}
-\usage{
-flags_to_con_str(flags, print_result = FALSE)
-}
-\arguments{
-\item{flags}{vector: Flags}
-
-\item{print_result}{flag: Should the result be printed to the console?}
-}
-\description{
-Helper function to generate a string out of a flag vector
-}
diff --git a/man/flags_to_doc_str.Rd b/man/flags_to_doc_str.Rd
deleted file mode 100644
index 99f41e18c7c5906ffe15dae81b7b56effe717fca..0000000000000000000000000000000000000000
--- a/man/flags_to_doc_str.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_class.R
-\name{flags_to_doc_str}
-\alias{flags_to_doc_str}
-\title{flags_to_doc_str}
-\usage{
-flags_to_doc_str(flags, print_result = FALSE)
-}
-\arguments{
-\item{flags}{vector: Flags}
-
-\item{print_result}{flag: Should the result be printed to the console?}
-}
-\description{
-Helper function to generate a string out of a flag vector
-}
diff --git a/man/flags_to_name_str.Rd b/man/flags_to_name_str.Rd
deleted file mode 100644
index 87600c60789a5b8a026f87e13ee2c721495255d1..0000000000000000000000000000000000000000
--- a/man/flags_to_name_str.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_class.R
-\name{flags_to_name_str}
-\alias{flags_to_name_str}
-\title{flags_to_name_str}
-\usage{
-flags_to_name_str(flags, print_result = FALSE)
-}
-\arguments{
-\item{flags}{vector: Flags}
-
-\item{print_result}{flag: Should the result be printed to the console?}
-}
-\description{
-Helper function to generate a name string out of a flag vector
-}
diff --git a/man/flags_to_r6_active_field_str.Rd b/man/flags_to_r6_active_field_str.Rd
deleted file mode 100644
index 86b1d4a897380586bb8cdf0626ed1ecb777bb001..0000000000000000000000000000000000000000
--- a/man/flags_to_r6_active_field_str.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_class.R
-\name{flags_to_r6_active_field_str}
-\alias{flags_to_r6_active_field_str}
-\title{flags_to_r6_active_field_str}
-\usage{
-flags_to_r6_active_field_str(flags, mutable = TRUE, print_result = FALSE)
-}
-\arguments{
-\item{flags}{vector: Flags}
-
-\item{mutable}{flag: On per default, turn off if parameters are static}
-
-\item{print_result}{flag: Should the result be printed to the console?}
-}
-\description{
-Helper function to generate a string out of a flag vector
-}
diff --git a/man/flags_to_r6_init_str.Rd b/man/flags_to_r6_init_str.Rd
deleted file mode 100644
index ffe0431a1cc39d95543d8507541b5ed35e9a4b6b..0000000000000000000000000000000000000000
--- a/man/flags_to_r6_init_str.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_class.R
-\name{flags_to_r6_init_str}
-\alias{flags_to_r6_init_str}
-\title{flags_to_r6_init_str}
-\usage{
-flags_to_r6_init_str(flags, print_result = FALSE)
-}
-\arguments{
-\item{flags}{vector: Flags}
-
-\item{print_result}{flag: Should the result be printed to the console?}
-}
-\description{
-Helper function to generate a string out of a flag vector
-}
diff --git a/man/flags_to_r6_private_str.Rd b/man/flags_to_r6_private_str.Rd
deleted file mode 100644
index bf76a854a5295b1ae6894cc7bace31b27501b10b..0000000000000000000000000000000000000000
--- a/man/flags_to_r6_private_str.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_class.R
-\name{flags_to_r6_private_str}
-\alias{flags_to_r6_private_str}
-\title{flags_to_r6_private_str}
-\usage{
-flags_to_r6_private_str(flags, print_result = FALSE)
-}
-\arguments{
-\item{flags}{vector: Flags}
-
-\item{print_result}{flag: Should the result be printed to the console?}
-}
-\description{
-Helper function to generate a string out of a flag vector
-}
diff --git a/man/generate_R6.Rd b/man/generate_R6.Rd
deleted file mode 100644
index 664e8232b49d006d0eaa744d1cabc95340fc9a86..0000000000000000000000000000000000000000
--- a/man/generate_R6.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_class.R
-\name{generate_R6}
-\alias{generate_R6}
-\title{generate_R6}
-\usage{
-generate_R6(params, prefix = "", print_result = TRUE)
-}
-\arguments{
-\item{params}{list: (Return value of \code{analyse_xml()})}
-
-\item{prefix}{Optional: For subclasses whose represented elements have
-the same tag name as an element for which a class was already specified,
-a prefix must be appended to the class name}
-
-\item{print_result}{flag: Should the result be printed to the console?}
-}
-\description{
-Helper function to generate a R6 class out of a tag name
-and a flag vector
-}
diff --git a/man/generate_active_field.Rd b/man/generate_active_field.Rd
deleted file mode 100644
index b9603567c95fbd760018e806fc7e0fd6d4b3ab61..0000000000000000000000000000000000000000
--- a/man/generate_active_field.Rd
+++ /dev/null
@@ -1,15 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_class.R
-\name{generate_active_field}
-\alias{generate_active_field}
-\title{generate_active_field}
-\usage{
-generate_active_field(parameter_name)
-}
-\arguments{
-\item{parameter_name}{The name of the OGS6 class parameter}
-}
-\description{
-Helper function to generate an R6 active field for a OGS6 class
-parameter
-}
diff --git a/man/generate_add_method.Rd b/man/generate_add_method.Rd
deleted file mode 100644
index 9957c8e1f195b87069276ba371ed5c60eb5eb903..0000000000000000000000000000000000000000
--- a/man/generate_add_method.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_class.R
-\name{generate_add_method}
-\alias{generate_add_method}
-\title{generate_add_method}
-\usage{
-generate_add_method(tag_name, parent_tag_name)
-}
-\arguments{
-\item{tag_name}{The tag name of the XML element represented by the class
-object}
-
-\item{parent_tag_name}{The tag name of the parent of the XML element
-represented by the class object}
-}
-\description{
-Helper function to generate an R6 \code{add_*} method for a
-r2ogs6 class object
-}
diff --git a/man/generate_all_benchmark_scripts.Rd b/man/generate_all_benchmark_scripts.Rd
deleted file mode 100644
index 3832caf0aadc4f3b15b19e5db9e067e3709fe7e0..0000000000000000000000000000000000000000
--- a/man/generate_all_benchmark_scripts.Rd
+++ /dev/null
@@ -1,37 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_benchmark_script.R
-\name{generate_all_benchmark_scripts}
-\alias{generate_all_benchmark_scripts}
-\title{generate_all_benchmark_scripts}
-\usage{
-generate_all_benchmark_scripts(
- path,
- sim_path,
- scripts_path,
- read_in_gmls,
- read_in_vtus = FALSE,
- starting_from_prj_path = "",
- skip_prj_paths = character()
-)
-}
-\arguments{
-\item{path}{string: Path to a benchmark directory to generate scripts from}
-
-\item{sim_path}{string: Path where all simulation files will be saved}
-
-\item{scripts_path}{string: Path where benchmark scripts will be saved}
-
-\item{read_in_gmls}{flag: Optional: Should \code{.gml} files just be copied
-or read in too?}
-
-\item{read_in_vtus}{flag: Optional: Should \code{.vtu} files just be copied
-or read in too?}
-
-\item{starting_from_prj_path}{string: Optional:}
-
-\item{skip_prj_paths}{character: Optional: \code{.prj} paths to skip}
-}
-\description{
-Wrapper function to generate benchmark scripts from all
-\code{.prj} files in a directory
-}
diff --git a/man/generate_constructor.Rd b/man/generate_constructor.Rd
deleted file mode 100644
index e4709eba899f055184af40317b1ec6da1cb6a239..0000000000000000000000000000000000000000
--- a/man/generate_constructor.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_class.R
-\name{generate_constructor}
-\alias{generate_constructor}
-\title{generate_constructor}
-\usage{
-generate_constructor(params, prefix = "", print_result = FALSE)
-}
-\arguments{
-\item{params}{list: (Return value of \code{analyse_xml()})}
-
-\item{prefix}{Optional: For subclasses whose represented elements have
-the same tag name as an element for which a class was already specified,
-a prefix must be appended to the class name}
-
-\item{print_result}{flag: Should the result be printed to the console?}
-}
-\description{
-Helper function to generate a constructor out of a tag name
-and a flag vector
-}
diff --git a/man/generate_helper.Rd b/man/generate_helper.Rd
deleted file mode 100644
index 92a6b422c229e57ef453cb2d24e5a2af0bc9c021..0000000000000000000000000000000000000000
--- a/man/generate_helper.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_class.R
-\name{generate_helper}
-\alias{generate_helper}
-\title{generate_helper}
-\usage{
-generate_helper(params, prefix = "", print_result = FALSE)
-}
-\arguments{
-\item{params}{list: (Return value of \code{analyse_xml()})}
-
-\item{prefix}{Optional: For subclasses whose represented elements have
-the same tag name as an element for which a class was already specified,
-a prefix must be appended to the class name}
-
-\item{print_result}{flag: Should the result be printed to the console?}
-}
-\description{
-Helper function to generate a helper out of a tag name
-and a flag vector
-}
diff --git a/man/get_benchmark_paths.Rd b/man/get_benchmark_paths.Rd
deleted file mode 100644
index 112419dbbc57ae8896ee43913fa0544a73c20d1b..0000000000000000000000000000000000000000
--- a/man/get_benchmark_paths.Rd
+++ /dev/null
@@ -1,15 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/sim_utils.R
-\name{get_benchmark_paths}
-\alias{get_benchmark_paths}
-\title{get_benchmark_paths}
-\usage{
-get_benchmark_paths(ogs6_processlib_path)
-}
-\arguments{
-\item{ogs6_processlib_path}{string: Path to OpenGeoSys 6 ProcessLib folder
-which contains relevant Tests.cmake files}
-}
-\description{
-Gets paths to all benchmarks that should work
-}
diff --git a/man/get_class_args.Rd b/man/get_class_args.Rd
deleted file mode 100644
index 82debcba03ce2a6143a6185d2aa0bd3cec85e3e3..0000000000000000000000000000000000000000
--- a/man/get_class_args.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_utils.R
-\name{get_class_args}
-\alias{get_class_args}
-\title{get_class_args}
-\usage{
-get_class_args(class_name)
-}
-\arguments{
-\item{class_name}{string: The name of a class}
-}
-\value{
-character: Named vector of class arguments
-}
-\description{
-Gets class arguments
-}
diff --git a/man/get_class_from_xpath.Rd b/man/get_class_from_xpath.Rd
deleted file mode 100644
index c064a55df381e43d94dfa61ae370864a402ee5d8..0000000000000000000000000000000000000000
--- a/man/get_class_from_xpath.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_class_from_xpath}
-\alias{get_class_from_xpath}
-\title{get_class_from_xpath}
-\usage{
-get_class_from_xpath(xpath)
-}
-\arguments{
-\item{xpath}{string: An xpath expression. Works for path-like xpaths only}
-}
-\value{
-string: The class name.
-}
-\description{
-Gets r2ogs6 class name from an xpath-like expression
-}
-\examples{
- get_class_from_xpath("processes/process")
-}
diff --git a/man/get_prj_top_level_tags.Rd b/man/get_prj_top_level_tags.Rd
deleted file mode 100644
index 4c8ea40df834abb6c6670a6d24014ad8877c6c0f..0000000000000000000000000000000000000000
--- a/man/get_prj_top_level_tags.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_prj_top_level_tags}
-\alias{get_prj_top_level_tags}
-\title{get_prj_top_level_tags}
-\usage{
-get_prj_top_level_tags()
-}
-\value{
-list: List of lists.
-}
-\description{
-Gets top level .prj tags along with info if they are required.
-}
diff --git a/man/get_required.Rd b/man/get_required.Rd
deleted file mode 100644
index 19c7a0fad47298a02a1bd0569d5fe27218d6d280..0000000000000000000000000000000000000000
--- a/man/get_required.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/analyse_xml.R
-\name{get_required}
-\alias{get_required}
-\title{get_required}
-\usage{
-get_required(names, occurence_probabilities)
-}
-\arguments{
-\item{names}{A vector of names}
-
-\item{occurence_probabilities}{A vector of occurrence probabilities}
-}
-\description{
-Helper function to mark required attributes or children from a
-vector of names and a vector of occurrence probabilities
-}
diff --git a/man/get_tag_from_class.Rd b/man/get_tag_from_class.Rd
deleted file mode 100644
index e546c8a586cb27e78839aed0a3b604b77e967fab..0000000000000000000000000000000000000000
--- a/man/get_tag_from_class.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_tag_from_class}
-\alias{get_tag_from_class}
-\title{get_tag_from_class}
-\usage{
-get_tag_from_class(class_name)
-}
-\arguments{
-\item{class_name}{string: The name of a r2ogs6 class}
-}
-\value{
-string: The tag name corresponding to \code{class_name}
-}
-\description{
-Utility function, returns the tag name of a r2ogs6 class
-}
-\examples{
- get_tag_from_class("prj_process")
-}
diff --git a/man/get_tag_from_xpath.Rd b/man/get_tag_from_xpath.Rd
deleted file mode 100644
index 116a8885697ac7bc9b364533db0bcb78dd084689..0000000000000000000000000000000000000000
--- a/man/get_tag_from_xpath.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_tag_from_xpath}
-\alias{get_tag_from_xpath}
-\title{get_tag_from_xpath}
-\usage{
-get_tag_from_xpath(xpath)
-}
-\arguments{
-\item{xpath}{string: An xpath expression. Works for path-like xpaths only}
-}
-\value{
-string: The XML tag name
-}
-\description{
-Gets the XML tag name from an xpath expression
-}
-\examples{
- get_tag_from_xpath("processes/process")
-}
diff --git a/man/is_null_or_coerce_names.Rd b/man/is_null_or_coerce_names.Rd
deleted file mode 100644
index 8b49faf8895e77f2e6031c5d7cf53258855635da..0000000000000000000000000000000000000000
--- a/man/is_null_or_coerce_names.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{is_null_or_coerce_names}
-\alias{is_null_or_coerce_names}
-\title{is_null_or_coerce_names}
-\usage{
-is_null_or_coerce_names(obj, names)
-}
-\arguments{
-\item{obj}{A list (or vector) of parameters}
-
-\item{names}{How the list elements will be named as per default}
-}
-\description{
-Validator function for a parameter list or vector or \code{NULL}
-}
diff --git a/man/is_null_or_has_class.Rd b/man/is_null_or_has_class.Rd
deleted file mode 100644
index 42fc9c114e745f265697bc2fb8c7b1a3e840ca14..0000000000000000000000000000000000000000
--- a/man/is_null_or_has_class.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{is_null_or_has_class}
-\alias{is_null_or_has_class}
-\title{is_null_or_has_class}
-\usage{
-is_null_or_has_class(obj, class_name)
-}
-\arguments{
-\item{obj}{The object to check}
-
-\item{class_name}{The name of the expected class}
-}
-\description{
-Checks if an object is either \code{NULL} or a class object of
-class \code{class_name}
-}
diff --git a/man/is_null_or_wrapper_list.Rd b/man/is_null_or_wrapper_list.Rd
deleted file mode 100644
index 9c76eddf56a80ed99c153bea7b16c6cbfc9fef22..0000000000000000000000000000000000000000
--- a/man/is_null_or_wrapper_list.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{is_null_or_wrapper_list}
-\alias{is_null_or_wrapper_list}
-\title{is_null_or_wrapper_list}
-\usage{
-is_null_or_wrapper_list(obj, element_class)
-}
-\arguments{
-\item{obj}{list | NULL: Object to check}
-
-\item{element_class}{string: Class each element of \code{obj} should have}
-}
-\description{
-Checks if an object is either \code{NULL} or a list of elements
-of class \code{element_class}
-}
diff --git a/man/is_wrapper_list.Rd b/man/is_wrapper_list.Rd
deleted file mode 100644
index 379ef3e83f77996962b0295484e523e1b3222391..0000000000000000000000000000000000000000
--- a/man/is_wrapper_list.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{is_wrapper_list}
-\alias{is_wrapper_list}
-\title{is_wrapper_list}
-\usage{
-is_wrapper_list(list, element_class)
-}
-\arguments{
-\item{list}{list: List to check}
-
-\item{element_class}{string: Class each element of \code{list} should have}
-}
-\description{
-Checks if a list consists only of elements of class
-\code{element_class}
-}
diff --git a/man/node_to_object.Rd b/man/node_to_object.Rd
deleted file mode 100644
index 3a44763351b8dddc93369b23c11844d1c1f89635..0000000000000000000000000000000000000000
--- a/man/node_to_object.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_utils.R
-\name{node_to_object}
-\alias{node_to_object}
-\title{node_to_object}
-\usage{
-node_to_object(xml_node, xpath = "")
-}
-\arguments{
-\item{xml_node}{xml2::xml_node: XML node}
-
-\item{xpath}{string: XPath expression (for subclass differentiation)}
-}
-\description{
-Returns representation of an XML node. This is a recursive
-function.
-ASSUMPTIONS:
-1) Leaf nodes will never be prj_* objects
-2) Wrapper nodes are represented as lists
-3) Parent nodes whose children have no children are represented as lists
-}
diff --git a/man/node_to_prj_class_object.Rd b/man/node_to_prj_class_object.Rd
deleted file mode 100644
index 3e92a99094c6d3556d4c011fff7400a47a948a5b..0000000000000000000000000000000000000000
--- a/man/node_to_prj_class_object.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_utils.R
-\name{node_to_prj_class_object}
-\alias{node_to_prj_class_object}
-\title{node_to_prj_class_object}
-\usage{
-node_to_prj_class_object(xml_node, xpath)
-}
-\arguments{
-\item{xml_node}{xml2::xml_node: XML node}
-
-\item{xpath}{string: XPath expression (for subclass differentiation)}
-}
-\description{
-Takes an XML node and turns it into a class object
-}
diff --git a/man/ogs6_download_ogs6.Rd b/man/ogs6_download_ogs6.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..57c0017df17bfe5316175a16943326bc95a1d186
--- /dev/null
+++ b/man/ogs6_download_ogs6.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download_ogs6.R
+\name{ogs6_download_ogs6}
+\alias{ogs6_download_ogs6}
+\title{Download OpenGeoSys 6}
+\usage{
+ogs6_download_ogs6(path, os, set_as_default_bin_path = TRUE)
+}
+\arguments{
+\item{path}{String: Download path. Defaults to ...}
+
+\item{os}{String: Operating System.}
+
+\item{set_as_default_bin_path}{flag: Defaults to `TRUE`}
+}
+\description{
+Downloads latest prebuilt OpenGeoSys 6 version
+}
diff --git a/man/ogs6_generate_benchmark_script.Rd b/man/ogs6_generate_benchmark_script.Rd
index 1f2ea5d9b6ce686689af39ab54c2379de07934aa..6edfb199fd11423329b06d928eb327265662cb01 100644
--- a/man/ogs6_generate_benchmark_script.Rd
+++ b/man/ogs6_generate_benchmark_script.Rd
@@ -2,7 +2,7 @@
% Please edit documentation in R/generate_benchmark_script.R
\name{ogs6_generate_benchmark_script}
\alias{ogs6_generate_benchmark_script}
-\title{ogs6_generate_benchmark_script}
+\title{Generate benchmark script}
\usage{
ogs6_generate_benchmark_script(
prj_path,
@@ -14,7 +14,7 @@ ogs6_generate_benchmark_script(
)
}
\arguments{
-\item{prj_path}{string: \code{.prj} file the script will be based on}
+\item{prj_path}{string: `.prj` file the script will be based on}
\item{sim_path}{string: Path where all simulation files will be saved}
@@ -22,12 +22,12 @@ ogs6_generate_benchmark_script(
\item{script_path}{string: Path where benchmark script will be saved}
-\item{read_in_gml}{flag: Optional: Should \code{.gml} file just be copied or
+\item{read_in_gml}{flag: Optional: Should `.gml` file just be copied or
read in too?}
-\item{read_in_vtu}{flag: Optional: Should \code{.vtu} file(s) just be copied
+\item{read_in_vtu}{flag: Optional: Should `.vtu` file(s) just be copied
or read in too?}
}
\description{
-Generates a benchmark script from an existing \code{.prj} file.
+Generates an R script from an existing `.prj` benchmark file.
}
diff --git a/man/ogs6_generate_benchmark_scripts.Rd b/man/ogs6_generate_benchmark_scripts.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..c6eaee766257eee0f1660f478bed6a15b8c623b7
--- /dev/null
+++ b/man/ogs6_generate_benchmark_scripts.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generate_benchmark_script.R
+\name{ogs6_generate_benchmark_scripts}
+\alias{ogs6_generate_benchmark_scripts}
+\title{Generate benchmark scripts}
+\usage{
+ogs6_generate_benchmark_scripts(
+ path,
+ sim_path,
+ script_path,
+ read_in_gml,
+ read_in_vtu = FALSE,
+ starting_from_prj_path = "",
+ skip_prj_paths = character()
+)
+}
+\arguments{
+\item{path}{string: Path to a benchmark directory to generate scripts from}
+
+\item{sim_path}{string: Path where all simulation files will be saved}
+
+\item{script_path}{string: Path where benchmark script will be saved}
+
+\item{read_in_gml}{flag: Optional: Should `.gml` file just be copied or
+read in too?}
+
+\item{read_in_vtu}{flag: Optional: Should `.vtu` file(s) just be copied
+or read in too?}
+
+\item{starting_from_prj_path}{string: Optional: `.prj` path to start from}
+
+\item{skip_prj_paths}{character: Optional: `.prj` paths to skip}
+}
+\description{
+This is a wrapper function for `ogs6_generate_benchmark_script()`.
+}
diff --git a/man/prj_top_level_classes.Rd b/man/ogs6_prj_top_level_classes.Rd
similarity index 50%
rename from man/prj_top_level_classes.Rd
rename to man/ogs6_prj_top_level_classes.Rd
index e9e47962ceb633962bf1c1dd41f6b4f501965b2e..5a7e61c217860007fee8af7ddd25636b1beadbb4 100644
--- a/man/prj_top_level_classes.Rd
+++ b/man/ogs6_prj_top_level_classes.Rd
@@ -1,16 +1,16 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{prj_top_level_classes}
-\alias{prj_top_level_classes}
-\title{prj_top_level_classes}
+% Please edit documentation in R/ogs6.R
+\name{ogs6_prj_top_level_classes}
+\alias{ogs6_prj_top_level_classes}
+\title{ogs6_prj_top_level_classes}
\usage{
-prj_top_level_classes()
+ogs6_prj_top_level_classes()
}
\value{
character
}
\description{
Returns named character vector of \code{OGS6} top level
-\code{.prj} tags (names) represented by \code{r2ogs6} classes along with their
-class names (values).
+\code{.prj} tags (names) represented by \code{r2ogs6} classes along with
+their class names (values).
}
diff --git a/man/order_parameters.Rd b/man/order_parameters.Rd
deleted file mode 100644
index 8d18945c48dc4266482d8e82045c9c0488830a50..0000000000000000000000000000000000000000
--- a/man/order_parameters.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_utils.R
-\name{order_parameters}
-\alias{order_parameters}
-\title{order_parameters}
-\usage{
-order_parameters(parameters, class_name)
-}
-\arguments{
-\item{parameters}{list: Parameters}
-
-\item{class_name}{string: The name of a class}
-}
-\value{
-list: Parameters ordered by argument order of class
-}
-\description{
-Orders a list of parameters corresponding to the argument order
-of a class
-}
diff --git a/man/read_in.Rd b/man/read_in.Rd
deleted file mode 100644
index 14272311f9afe0e181ba936484d78a35c139f253..0000000000000000000000000000000000000000
--- a/man/read_in.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_utils.R
-\name{read_in}
-\alias{read_in}
-\title{read_in}
-\usage{
-read_in(ogs6_obj, path, xpath)
-}
-\arguments{
-\item{ogs6_obj}{A OGS6 class object}
-
-\item{path}{string: Path to file XML elements should be read from}
-
-\item{xpath}{string: An XPath expression (should be absolute!)}
-}
-\description{
-Reads in elements from a file
-}
diff --git a/man/read_in_points.Rd b/man/read_in_points.Rd
deleted file mode 100644
index 2b486cf2cf37efbdf536f7142640b60ba31ebc1b..0000000000000000000000000000000000000000
--- a/man/read_in_points.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_gml.R
-\name{read_in_points}
-\alias{read_in_points}
-\title{read_in_points}
-\usage{
-read_in_points(xml_doc)
-}
-\arguments{
-\item{xml_doc}{A parsed XML document (of class \code{xml2::xml_document})}
-}
-\description{
-Reads points from a \code{.gml} file
-}
diff --git a/man/read_in_polylines.Rd b/man/read_in_polylines.Rd
deleted file mode 100644
index 69b60ffc3521c4ab8310c698dc0ce63578e77489..0000000000000000000000000000000000000000
--- a/man/read_in_polylines.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_gml.R
-\name{read_in_polylines}
-\alias{read_in_polylines}
-\title{read_in_polylines}
-\usage{
-read_in_polylines(xml_doc)
-}
-\arguments{
-\item{xml_doc}{A parsed XML document (of class \code{xml2::xml_document})}
-}
-\description{
-Reads polylines from a \code{.gml} file
-}
diff --git a/man/read_in_surfaces.Rd b/man/read_in_surfaces.Rd
deleted file mode 100644
index ded5155738587b478b3c9f14a54a20fcc870fdcc..0000000000000000000000000000000000000000
--- a/man/read_in_surfaces.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_gml.R
-\name{read_in_surfaces}
-\alias{read_in_surfaces}
-\title{read_in_surfaces}
-\usage{
-read_in_surfaces(xml_doc)
-}
-\arguments{
-\item{xml_doc}{A parsed XML document (of class \code{xml2::xml_document})}
-}
-\description{
-Reads surfaces from a \code{.gml} file
-}
diff --git a/man/run_all_benchmarks.Rd b/man/run_all_benchmarks.Rd
deleted file mode 100644
index 67d157b1e8e06ba414021c32b9a6a7d28831d3f7..0000000000000000000000000000000000000000
--- a/man/run_all_benchmarks.Rd
+++ /dev/null
@@ -1,33 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/sim_utils.R
-\name{run_all_benchmarks}
-\alias{run_all_benchmarks}
-\title{run_all_benchmarks}
-\usage{
-run_all_benchmarks(
- path,
- ogs6_processlib_path,
- ogs6_bin_path,
- sim_path,
- starting_from_prj_path = "",
- print_results = TRUE
-)
-}
-\arguments{
-\item{path}{string: Path to benchmark folder}
-
-\item{ogs6_processlib_path}{string: Path to OpenGeoSys 6 ProcessLib folder
-which contains relevant Tests.cmake files}
-
-\item{ogs6_bin_path}{string:}
-
-\item{sim_path}{string: Path where simulation files will be saved}
-
-\item{starting_from_prj_path}{string: \code{.prj} path to start from}
-
-\item{print_results}{flag: Print results in the end?}
-}
-\description{
-Utility function, for quick benchmark runs. Calls
- run_benchmark internally.
-}
diff --git a/man/run_benchmark.Rd b/man/run_benchmark.Rd
deleted file mode 100644
index c05e53501806b0ec2f9bb5b32cbf0f836dce351d..0000000000000000000000000000000000000000
--- a/man/run_benchmark.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/sim_utils.R
-\name{run_benchmark}
-\alias{run_benchmark}
-\title{run_benchmark}
-\usage{
-run_benchmark(prj_path, ogs6_bin_path, sim_path)
-}
-\arguments{
-\item{prj_path}{string:}
-
-\item{ogs6_bin_path}{string:}
-
-\item{sim_path}{string: Path where simulation files will be saved}
-}
-\description{
-Utility function for quick benchmark runs
-}
diff --git a/man/to_node.Rd b/man/to_node.Rd
deleted file mode 100644
index 3c11db77bb07c3a84ea7a025c2f69231308effa3..0000000000000000000000000000000000000000
--- a/man/to_node.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/export_utils.R
-\name{to_node}
-\alias{to_node}
-\title{to_node}
-\usage{
-to_node(
- object,
- object_name = "",
- attribute_names = character(),
- flatten_on_exp = character(),
- unwrap_on_exp = character()
-)
-}
-\arguments{
-\item{object}{An object (so far works for r2ogs6 class objects, strings,
-numbers, lists and vectors)}
-
-\item{object_name}{string: Optional: The object name. If not supplied, this
-function tries 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{flatten_on_exp}{character: Optional: This is for vectors which will be
-flattened to a string in XML}
-
-\item{unwrap_on_exp}{character: Optional: This is for lists which will not
-be exported to XML}
-}
-\description{
-Recursive function to restructure objects so
-xml2::as_xml_document() function will convert them to the desired XML format
-}
diff --git a/man/validate_pnt_values.Rd b/man/validate_pnt_values.Rd
deleted file mode 100644
index e87a3a53925b7fc5e26661e6a6d427182910a12a..0000000000000000000000000000000000000000
--- a/man/validate_pnt_values.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ogs6_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.
-}
diff --git a/man/validate_points.Rd b/man/validate_points.Rd
deleted file mode 100644
index 007e8df9f5271c11cfc0e2bba91e4d321da613f8..0000000000000000000000000000000000000000
--- a/man/validate_points.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ogs6_gml.R
-\name{validate_points}
-\alias{validate_points}
-\title{validate_points}
-\usage{
-validate_points(points)
-}
-\arguments{
-\item{points}{tibble: Must have 3 vectors named 'x', 'y' and 'z', may have
-optional 'name' vector}
-}
-\description{
-Checks if the input is a tibble, if this tibble has the right
-number of elements, if those elements are named correctly and if there are
-any overlapping points or duplicate point names
-}
diff --git a/man/validate_polylines.Rd b/man/validate_polylines.Rd
deleted file mode 100644
index 089d632ab373f05158b59ed8950c1b1cb607ad72..0000000000000000000000000000000000000000
--- a/man/validate_polylines.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ogs6_gml.R
-\name{validate_polylines}
-\alias{validate_polylines}
-\title{validate_polylines}
-\usage{
-validate_polylines(polylines)
-}
-\arguments{
-\item{polylines}{list(list("foo", c(1, 2))):}
-}
-\description{
-Checks if the input is a list, if this list consists of other
-lists and if those lists have the correct structure (length of 2, first
-element is a string named 'name', second element is a numeric vector)
-}
diff --git a/man/validate_read_in_xml.Rd b/man/validate_read_in_xml.Rd
deleted file mode 100644
index c97deee00c15d2e2fc3886b7d052f38eff18c3ac..0000000000000000000000000000000000000000
--- a/man/validate_read_in_xml.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_utils.R
-\name{validate_read_in_xml}
-\alias{validate_read_in_xml}
-\title{validate_read_in_xml}
-\usage{
-validate_read_in_xml(path)
-}
-\arguments{
-\item{path}{string: A file to be parsed as XML}
-}
-\value{
-The parsed XML file (as class object of type
-\code{xml2::xml_document})
-}
-\description{
-Utility function, tries parsing the provided file as an XML
-document
-}
diff --git a/man/validate_surfaces.Rd b/man/validate_surfaces.Rd
deleted file mode 100644
index 22c00a163038f144e7648a82a095a0ef033d8816..0000000000000000000000000000000000000000
--- a/man/validate_surfaces.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ogs6_gml.R
-\name{validate_surfaces}
-\alias{validate_surfaces}
-\title{validate_surfaces}
-\usage{
-validate_surfaces(surfaces)
-}
-\arguments{
-\item{surfaces}{list(list("foo", c(1, 2, 3), c(2, 3, 4))):}
-}
-\description{
-Checks if the input is a list, if this list consists of other
-lists and if those lists have the correct structure (length of 2 or 3, first
-element is a string named 'name', second and third element are numeric
-vectors)
-}
diff --git a/tests/testthat/test-export_utils.R b/tests/testthat/test-export_utils.R
index 1c152a509fc525a6c093ade94d8466a4de1a4d33..2223f177dd0235b808fd642608a3670960dc75ba 100644
--- a/tests/testthat/test-export_utils.R
+++ b/tests/testthat/test-export_utils.R
@@ -220,3 +220,27 @@ test_that("to_node works for prj_process class", {
expect_equal(attrs, c(internal_name = "sigma_xx", output_name = "sigma_xx"))
})
+
+
+
+test_that("meshes_to_node works for mesh / meshes elements", {
+
+ meshes <- list(mesh = list(path = "a", axially_symmetric = TRUE),
+ mesh = list(path = "b", axially_symmetric = FALSE))
+
+ test_xml_1 <- meshes_to_xml(meshes)
+
+ expect_equal(length(xml2::xml_find_all(test_xml_1,"/meshes/mesh")), 2)
+ expect_equal(xml2::xml_attrs(xml2::xml_find_first(test_xml_1,
+ "/meshes/mesh")),
+ c(axially_symmetric = "true"))
+
+
+ lone_mesh <- list(mesh = list(path = "a", axially_symmetric = TRUE))
+ test_xml_2 <- meshes_to_xml(lone_mesh)
+
+ expect_equal(length(xml2::xml_find_all(test_xml_2,"/mesh")), 1)
+ expect_equal(xml2::xml_attrs(xml2::xml_find_first(test_xml_2,
+ "/mesh")),
+ c(axially_symmetric = "true"))
+})
diff --git a/tests/testthat/test-generate_benchmark_script.R b/tests/testthat/test-generate_benchmark_script.R
index d5c6c126eb40816cae76517fac2aebae225d8702..4c40f5ec2d1c5370c360a5c1e519103e38d078d2 100644
--- a/tests/testthat/test-generate_benchmark_script.R
+++ b/tests/testthat/test-generate_benchmark_script.R
@@ -70,13 +70,3 @@ test_that("construct_add_call handles Ellipsis correctly", {
"list(index = 1,\nvalues = c(1, 2)),\n",
"index_values = list(index = 2,\nvalues = c(2, 3))))\n"))
})
-
-
-test_that("delete_keywords_from_str works", {
-
- test_str <- "prj_object(a = \"foo\", repeat = \"bar\")"
-
- test_str <- delete_keywords_from_str(test_str)
- expect_equal(test_str, "prj_object(a = \"foo\", \"bar\")")
-
-})
diff --git a/tests/testthat/test-ogs6_ensemble.R b/tests/testthat/test-ogs6_ensemble.R
index f57e2b16973f4a1920e39f6d52d6a93124789544..00b18816a17219221a16b3d58976d9aaece696ed 100644
--- a/tests/testthat/test-ogs6_ensemble.R
+++ b/tests/testthat/test-ogs6_ensemble.R
@@ -44,9 +44,21 @@ test_that("OGS6_Ensemble initialization works", {
)
expect_equal(length(ogs6_ens_seq_noper$ensemble), 4)
+
+ expect_equal(ogs6_ens_seq_noper$ensemble[[1]]$parameters[[1]]$value, 2)
+ expect_equal(ogs6_ens_seq_noper$ensemble[[1]]$parameters[[2]]$value, 4)
+
+ expect_equal(ogs6_ens_seq_noper$ensemble[[2]]$parameters[[1]]$value, 3)
+ expect_equal(ogs6_ens_seq_noper$ensemble[[2]]$parameters[[2]]$value, 4)
+
+ expect_equal(ogs6_ens_seq_noper$ensemble[[3]]$parameters[[1]]$value, 1)
+ expect_equal(ogs6_ens_seq_noper$ensemble[[3]]$parameters[[2]]$value, 5)
+
+ expect_equal(ogs6_ens_seq_noper$ensemble[[4]]$parameters[[1]]$value, 1)
expect_equal(ogs6_ens_seq_noper$ensemble[[4]]$parameters[[2]]$value, 6)
+
# Test with sequential_mode off and percentages_mode on
ogs6_ens_noseq_per <- OGS6_Ensemble$new(
ogs6_obj = ogs6_obj,
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index 1640ccc8a45132462cc2b0901703ea7411617161..2c179872d4d7a06a01a73c027bc98106060135a4 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -24,8 +24,8 @@ test_that("get_tag_from_xpath() works", {
})
-test_that("prj_top_level_classes() works", {
- expect_equal(prj_top_level_classes()[["processes"]], "prj_process")
+test_that("ogs6_prj_top_level_classes() works", {
+ expect_equal(ogs6_prj_top_level_classes()[["processes"]], "prj_process")
})
diff --git a/vignettes/ensemble_workflow_vignette.Rmd b/vignettes/ensemble_workflow_vignette.Rmd
index 40ba70782e1919eef6a4bc3943428b1b46f3312f..261206cf7b9432b2e91f2d67c53c6f06b3d7309a 100644
--- a/vignettes/ensemble_workflow_vignette.Rmd
+++ b/vignettes/ensemble_workflow_vignette.Rmd
@@ -1,5 +1,6 @@
---
title: "r2ogs6 Ensemble Guide"
+#output: pdf_document
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{r2ogs6 Ensemble Guide}
@@ -58,7 +59,7 @@ testdir_path <- tempdir()
sim_path <- paste0(testdir_path, "/axisym_theis_sim")
ogs6_obj <- OGS6$new(sim_name = "axisym_theis",
- sim_path = sim_path)
+ sim_path = "D:/ogs6_theis/axisym_theis_sim")
# Change this to fit your system
prj_path <- system.file("extdata/benchmarks/AxiSymTheis/",
@@ -83,10 +84,16 @@ ogs6_ens <-
parameters = list(list(ogs6_obj$media[[1]]$properties[[4]]$value,
percentages)),
percentages_mode = TRUE)
+```
+
+Now you can start the simulation.
-# Now we run the simulations
-exit_codes <- ogs6_ens$run_simulation()
-paste(exit_codes, collapse = " ")
+```{r, eval = FALSE}
+ogs6_ens$run_simulation()
+```
+
+```{r, include = FALSE}
+lapply(ogs6_ens$ensemble, ogs6_read_output_files)
```
#### Plot results for single simulation
@@ -176,9 +183,16 @@ ogs6_ens_big <-
sto = list(ogs6_obj$media[[1]]$properties[[4]]$value,
values = percentages)),
sequential_mode = TRUE)
+```
+
+Now you can start the simulation.
+
+```{r, eval = FALSE}
+ogs6_ens_big$run_simulation()
+```
-exit_codes <- ogs6_ens_big$run_simulation()
-paste(exit_codes)
+```{r, include = FALSE}
+lapply(ogs6_ens_big$ensemble, ogs6_read_output_files)
```
This will take a short time. As soon as the simulations are done, we can extract the point data much like we did before. This time we want to plot the point x coodinates on the x axis so we're leaving out `point_ids` to get all points. Also we just want the data from the last timestep.
@@ -197,16 +211,84 @@ Plotting time! Since we set `sequential_mode` to `TRUE`, the dataframe we just c
# Make plot
ggplot(per_por_sto_df,
aes(x = x,
- y = pressure,
+ y = -pressure, # Flip pressure because source term was positive
group = perc)) +
geom_point(aes(color = as.factor(perc))) +
- xlab("x point coordinate") +
+ xlab("Radius (m)") +
+ ylab("Head (m)") +
labs(color = "%") +
- facet_grid(cols = vars(name))
+ facet_grid(cols = vars(name),
+ labeller = as_labeller(c(per = "permeability",
+ por = "porosity",
+ sto = "storage")))
```
-Ta-Daa! We can see `permeability` has the most influence on the pressure. Though they may seem suspicious, `porosity` and `storage` are being plotted correctly - the points are just being placed right on top of each other. Since `porosity` can't go over the value `1` which was the original value, our value vector only went from -50% to 0% which is why the line colors of `porosity` and `storage` differ.
+Ta-Daa! We can see `permeability` has the most influence on the pressure. Though they may seem suspicious, `porosity` and `storage` are being plotted correctly - the points are just being placed right on top of each other. Since `porosity` can't go over the value `1` which was the original value, our value vector only went from -50% to 0% which is why the line colors of `porosity` and `storage` differ. Maybe we want to try and use a logarithmic approach for `storage`. This won't work with the built-in functionality of `OGS6_Ensemble` so we'll set up our Ensemble a little differently.
+```{r}
+# Calculate log value
+log_val <- log(as.numeric(
+ ogs6_obj$media[[1]]$properties[[4]]$value),
+ base = 10)
+
+# Apply changes to log value
+log_vals <- vapply(percentages, function(x){
+ log_val + (log_val * (x / 100))
+}, FUN.VALUE = numeric(1))
+
+# Transfer back to non-logarithmic scale
+back_transf_vals <- 10^log_vals
+
+# Change sim_path to fit your system
+ogs6_obj$sim_path <- "D:/ogs6_theis/axisym_theis_sim_log_storage"
+
+# Set up new ensemble
+ogs6_ens_sto <-
+ OGS6_Ensemble$new(
+ ogs6_obj = ogs6_obj,
+ parameters =
+ list(
+ sto = list(
+ ogs6_obj$media[[1]]$properties[[4]]$value,
+ values = back_transf_vals)
+ ),
+ percentages_mode = FALSE,
+ sequential_mode = TRUE
+ )
+```
+
+As before, we can run the simulation right away.
+
+```{r, eval = FALSE}
+ogs6_ens_sto$run_simulation()
+```
+
+```{r, include = FALSE}
+lapply(ogs6_ens_sto$ensemble, ogs6_read_output_files)
+```
+
+Let's check if we can observe any influence of `storage` on `pressure` now.
+
+```{r}
+# Get combined dataframe
+sto_df <-
+ ogs6_ens_sto$get_point_data(
+ keys = c("pressure"),
+ start_at_timestep = ogs6_ens_sto$ensemble[[1]]$pvds[[1]]$last_timestep)
+
+# Supply percentages manually since we couldn't use `percentages_mode`
+percs <- vapply(sto_df$sim_id,
+ function(x){percentages[[x]]},
+ FUN.VALUE = numeric(1))
+
+ggplot(sto_df,
+ aes(x = x,
+ y = -pressure)) +
+ geom_point(aes(color = as.factor(percs))) +
+ xlab("Radius (m)") +
+ ylab("Head (m)") +
+ labs(color = "%")
+```
## Theis solution for well pumping
@@ -228,7 +310,7 @@ First, we create a simulation object to base our ensemble on and read in the `.p
sim_path <- paste0(testdir_path, "/theis_sim")
ogs6_obj <- OGS6$new(sim_name = "theis",
- sim_path = sim_path)
+ sim_path = "D:/ogs6_theis/theis_sim")
# Change this to fit your system
prj_path <- system.file("extdata/benchmarks/theis_well_pumping/",
@@ -261,9 +343,16 @@ ogs6_ens_theis_2 <-
),
sequential_mode = TRUE
)
+```
+
+Now you can start the simulation.
-exit_codes <- ogs6_ens_theis_2$run_simulation()
-paste(exit_codes)
+```{r, eval = FALSE}
+ogs6_ens_theis_2$run_simulation()
+```
+
+```{r, include = FALSE}
+lapply(ogs6_ens_theis_2$ensemble, ogs6_read_output_files)
```
When the simulations have run, we can extract and plot the results like before. To avoid cluttering the plot, we only extract the `pressure` values for a single line. For this, we get the IDs of all points on the x axis.
@@ -297,12 +386,17 @@ per_por_slo_df <-
# Make plot
ggplot(per_por_slo_df,
aes(x = x,
- y = pressure,
+ y = pressure / 9806.65, # 1mH2O = 9806.65 kPa
group = perc)) +
geom_point(aes(color = as.factor(perc))) +
- xlab("x point coordinate") +
+ xlab("Radius (m)") +
+ ylab("Absenkung (m)") +
labs(color = "%") +
- facet_grid(cols = vars(name))
+ facet_grid(cols = vars(name),
+ labeller = as_labeller(c(per = "permeability",
+ por = "porosity",
+ slo = "slope"
+ )))
```
@@ -316,7 +410,8 @@ ggplot(per_df,
aes(x = x,
y = pressure)) +
geom_point(aes(color = as.factor(perc))) +
- xlab("x point coordinate") +
+ xlab("Radius (m)") +
+ ylab("Head (m)") +
labs(color = "%")
```
@@ -336,6 +431,9 @@ log_vals <- vapply(percentages, function(x){
# Transfer back to non-logarithmic scale
back_transf_vals <- 10^log_vals
+# Change sim_path to fit your system
+ogs6_obj$sim_path <- "D:/ogs6_theis/theis_sim_log_slope"
+
# Set up new ensemble
ogs6_ens_slo <-
OGS6_Ensemble$new(
@@ -349,8 +447,16 @@ ogs6_ens_slo <-
percentages_mode = FALSE,
sequential_mode = TRUE
)
+```
+
+As before, we can run the simulation right away.
+
+```{r, eval = FALSE}
+ogs6_ens_slo$run_simulation()
+```
-exit_codes <- ogs6_ens_slo$run_simulation()
+```{r, include = FALSE}
+lapply(ogs6_ens_slo$ensemble, ogs6_read_output_files)
```
Let's check if we can observe any influence of `slope` on `pressure` now.
@@ -374,9 +480,10 @@ percs <- vapply(slo_df$sim_id,
ggplot(slo_df,
aes(x = x,
- y = pressure)) +
+ y = pressure / 9806.65)) + # 1mH2O = 9806.65 kPa
geom_point(aes(color = as.factor(percs))) +
- xlab("x point coordinate") +
+ xlab("Radius (m)") +
+ ylab("Head (m)") +
labs(color = "%")
```
@@ -384,8 +491,3 @@ ggplot(slo_df,
## Summary
The `OGS6_Ensemble` class is a useful tool to set up ensemble runs for sensitivity analyses. In this vignette, we learned how to create `OGS6_Ensemble` objects. We looked at how the parameters `sequential_mode` and `percentages_mode` influence how our ensemble object is initialised. We started simulations via `OGS6_Ensemble$run_simulation()` and extracted information from the output files to plot them.
-
-```{r, include = FALSE}
-# Cleanup created folders
-do.call(file.remove, list(list.files(testdir_path, full.names = TRUE)))
-```
\ No newline at end of file
diff --git a/vignettes/user_workflow_vignette.Rmd b/vignettes/user_workflow_vignette.Rmd
index c441f380650ec2a7b52ccae1865d96f6c8903236..f88a809ce254e029d3fc20fa08b779bfb1f0347f 100644
--- a/vignettes/user_workflow_vignette.Rmd
+++ b/vignettes/user_workflow_vignette.Rmd
@@ -53,7 +53,6 @@ Usually, you will only ever define `sim_name`, `sim_path`.
```{r}
ogs6_obj <- OGS6$new(sim_name = "my_simulation",
- sim_id = 1,
sim_path = "my_sim_path")
```