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Commit c9b0ebad authored by Ruben Heinrich's avatar Ruben Heinrich
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[docs] OGS6 class is now properly documented

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R/ogs6.R
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#===== OGS6 documentation =====
#'OGS6
#'
#'The OpenGeoSys6 simulation class, core of the r2ogs6 package
#'
#'@docType class
#'
#'
NULL
#===== OGS6 =====
#'OGS6
#'@description Constructor for the OGS6 base class
#'@param sim_name The name of the simulation
#'@param sim_id The ID of the simulation
#'@param sim_path The path where all relevant files for the simulation will be
#' saved
#'@param ogs_bin_path Path to OpenGeoSys6 /bin directory
#'@param test_mode In test mode, sim_path and ogs_bin_path will not be
#' validated. If you're not a developer, please leave this variable as it is :)
#'@export
OGS6 <- R6::R6Class("OGS6",
public = list(
#'@description
#'Creates new OGS6 object
#'@param sim_name string: Simulation name
#'@param sim_id double: Simulation ID
#'@param sim_path string: Path where all files for the simulation will be
#' saved
#'@param ogs_bin_path string: Path to OpenGeoSys6 /bin directory
#'@param test_mode In test mode, sim_path and ogs_bin_path will not be
#' validated. If you're not a developer, please leave this as it is :)
initialize = function(sim_name,
sim_id,
sim_path,
......@@ -50,15 +41,29 @@ OGS6 <- R6::R6Class("OGS6",
private$.ogs_bin_path <- ogs_bin_path
},
#===== ADDING COMPONENTS =====
#'@description
#'... (WIP)
#'@param name ...
#'@param value ...
add_sim_output = function(name, value) {
private$.sim_output[[name]] <- value
},
#'@description
#'Adds a r2ogs6_mesh object
#'@param mesh r2ogs6_mesh
add_mesh = function(mesh){
assertthat::assert_that(class(mesh) == "r2ogs6_mesh")
private$.meshes <- c(private$.meshes, list(mesh))
},
#'@description
#'Adds a r2ogs6_gml object
#'@param gml r2ogs6_gml
add_gml = function(gml){
assertthat::assert_that(class(gml) == "r2ogs6_gml")
if(!is.null(private$.gml)){
......@@ -70,6 +75,9 @@ OGS6 <- R6::R6Class("OGS6",
private$.geometry <- paste0(gml$name, ".gml")
},
#'@description
#'Adds a python script
#'@param python_script string: File name of python script
add_python_script = function(python_script){
assertthat::assert_that(assertthat::is.string(python_script))
if(!is.null(private$.python_script)){
......@@ -80,11 +88,17 @@ OGS6 <- R6::R6Class("OGS6",
private$.python_script <- python_script
},
#'@description
#'Adds a r2ogs6_process object
#'@param process r2ogs6_process
add_process = function(process){
assertthat::assert_that(class(process) == "r2ogs6_process")
private$.processes <- c(private$.processes, list(process))
},
#'@description
#'Adds a r2ogs6_time_loop object
#'@param time_loop r2ogs6_time_loop
add_time_loop = function(time_loop){
assertthat::assert_that(class(time_loop) == "r2ogs6_time_loop")
if(!is.null(private$.time_loop)){
......@@ -93,6 +107,9 @@ OGS6 <- R6::R6Class("OGS6",
private$.time_loop <- time_loop
},
#'@description
#'Adds a r2ogs6_local_coordinate_system object
#'@param local_coordinate_system r2ogs6_local_coordinate_system
add_local_coordinate_system = function(local_coordinate_system){
assertthat::assert_that(class(local_coordinate_system) ==
"r2ogs6_local_coordinate_system")
......@@ -103,21 +120,33 @@ OGS6 <- R6::R6Class("OGS6",
private$.local_coordinate_system <- local_coordinate_system
},
#'@description
#'Adds a r2ogs6_medium object
#'@param medium r2ogs6_medium
add_medium = function(medium){
assertthat::assert_that(class(medium) == "r2ogs6_medium")
private$.media <- c(private$.media, list(medium))
},
#'@description
#'Adds a r2ogs6_parameter object
#'@param parameter r2ogs6_parameter
add_parameter = function(parameter){
assertthat::assert_that(class(parameter) == "r2ogs6_parameter")
private$.parameters <- c(private$.parameters, list(parameter))
},
#'@description
#'Adds a r2ogs6_curve object
#'@param curve r2ogs6_curve
add_curve = function(curve){
assertthat::assert_that(class(curve) == "r2ogs6_curve")
private$.curves <- c(private$.curves, list(curve))
},
#'@description
#'Adds a r2ogs6_process_variable object
#'@param process_variable r2ogs6_process_variable
add_process_variable = function(process_variable){
assertthat::assert_that(class(process_variable) ==
"r2ogs6_process_variable")
......@@ -125,6 +154,9 @@ OGS6 <- R6::R6Class("OGS6",
list(process_variable))
},
#'@description
#'Adds a r2ogs6_nonlinear_solver object
#'@param nonlinear_solver r2ogs6_nonlinear_solver
add_nonlinear_solver = function(nonlinear_solver){
assertthat::assert_that(class(nonlinear_solver) ==
"r2ogs6_nonlinear_solver")
......@@ -132,16 +164,25 @@ OGS6 <- R6::R6Class("OGS6",
list(nonlinear_solver))
},
#'@description
#'Adds a r2ogs6_linear_solver object
#'@param linear_solver r2ogs6_linear_solver
add_linear_solver = function(linear_solver){
assertthat::assert_that(class(linear_solver) == "r2ogs6_linear_solver")
private$.linear_solvers <- c(private$.linear_solvers, list(linear_solver))
},
#'@description
#'Adds a r2ogs6_vtkdiff object
#'@param vtkdiff r2ogs6_vtkdiff
add_vtkdiff = function(vtkdiff){
assertthat::assert_that(class(vtkdiff) == "r2ogs6_vtkdiff")
private$.test_definition <- c(private$.test_definition, list(vtkdiff))
},
#'@description
#'Adds a r2ogs6_insitu object
#'@param insitu r2ogs6_insitu
add_insitu = function(insitu){
assertthat::assert_that(class(insitu) == "r2ogs6_insitu")
......@@ -151,6 +192,13 @@ OGS6 <- R6::R6Class("OGS6",
private$.insitu <- insitu
},
#===== UTILITY FUNCTIONS =====
#'@description
#'Checks if the OGS6 object has all necessary parameters for
#' starting a simulation
get_status = function(){
flag <- TRUE
......@@ -191,6 +239,11 @@ OGS6 <- R6::R6Class("OGS6",
return(invisible(flag))
},
#'@description
#'Clears components from the OGS6 object
#'@param which character: The names of the components (all by default).
#' If you want to delete only some components, run
#' names(get_implemented_classes()) for the available options.
clear = function(which = names(get_implemented_classes())){
assertthat::assert_that(is.character(which))
......@@ -221,171 +274,130 @@ OGS6 <- R6::R6Class("OGS6",
),
#===== ACTIVE FIELDS =====
active = list(
#'@field sim_output
#'Getter for OGS6 private parameter '.sim_output'
sim_output = function(value) {
if (missing(value)) {
private$.sim_output
} else {
stop("To modify `$sim_output`, use set_sim_output().", call. = FALSE)
}
private$.sim_output
},
sim_name = function(value) {
if (missing(value)) {
private$.sim_name
} else {
stop("`$sim_name` is read only", call. = FALSE)
}
#'@field sim_name
#'Getter for OGS6 private parameter '.sim_name'
sim_name = function() {
private$.sim_name
},
sim_id = function(value) {
if (missing(value)) {
private$.sim_id
} else {
stop("`$sim_id` is read only", call. = FALSE)
}
#'@field sim_id
#'Getter for OGS6 private parameter '.sim_id'
sim_id = function() {
private$.sim_id
},
sim_path = function(value) {
if (missing(value)) {
private$.sim_path
} else {
stop("`$sim_path` is read only", call. = FALSE)
}
#'@field sim_path
#'Getter for OGS6 private parameter '.sim_path'
sim_path = function() {
private$.sim_path
},
ogs_bin_path = function(value) {
if (missing(value)) {
private$.ogs_bin_path
} else {
stop("`$ogs_bin_path` is read only", call. = FALSE)
}
#'@field ogs_bin_path
#'Getter for OGS6 private parameter '.ogs_bin_path'
ogs_bin_path = function() {
private$.ogs_bin_path
},
gml = function(value) {
if (missing(value)) {
private$.gml
} else {
stop("`To modify `$gml`, use add_gml().", call. = FALSE)
}
#'@field gml
#'Getter for OGS6 private parameter '.gml'
gml = function() {
private$.gml
},
meshes = function(value) {
if (missing(value)) {
private$.meshes
} else {
stop("`$meshes` is read only", call. = FALSE)
}
#'@field meshes
#'Getter for OGS6 private parameter '.meshes'
meshes = function() {
private$.meshes
},
geometry = function(value) {
if (missing(value)) {
private$.geometry
} else {
stop("`$geometry` is read only", call. = FALSE)
}
#'@field geometry
#'Getter for OGS6 private parameter '.geometry'
geometry = function() {
private$.geometry
},
python_script = function(value) {
if (missing(value)) {
private$.python_script
} else {
stop("`$python_script` is read only", call. = FALSE)
}
#'@field python_script
#'Getter for OGS6 private parameter '.python_script'
python_script = function() {
private$.python_script
},
processes = function(value) {
if (missing(value)) {
private$.processes
} else {
stop("`To modify `$processes`, use add_process().", call. = FALSE)
}
#'@field processes
#'Getter for OGS6 private parameter '.processes'
processes = function() {
private$.processes
},
time_loop = function(value) {
if (missing(value)) {
private$.time_loop
} else {
stop("`To modify `$time_loop`, use add_time_loop().", call. = FALSE)
}
#'@field time_loop
#'Getter for OGS6 private parameter '.time_loop'
time_loop = function() {
private$.time_loop
},
local_coordinate_system = function(value) {
if (missing(value)) {
private$.local_coordinate_system
} else {
stop(paste("`To modify `$local_coordinate_system`,",
"use add_local_coordinate_system()."),
call. = FALSE)
}
#'@field local_coordinate_system
#'Getter for OGS6 private parameter '.local_coordinate_system'
local_coordinate_system = function() {
private$.local_coordinate_system
},
media = function(value) {
if (missing(value)) {
private$.media
} else {
stop("`To modify `$media`, use add_medium().", call. = FALSE)
}
#'@field media
#'Getter for OGS6 private parameter '.media'
media = function() {
private$.media
},
parameters = function(value) {
if (missing(value)) {
private$.parameters
} else {
stop("`To modify `$parameters`, use add_parameter().", call. = FALSE)
}
#'@field parameters
#'Getter for OGS6 private parameter '.parameters'
parameters = function() {
private$.parameters
},
curves = function(value) {
if (missing(value)) {
private$.curves
} else {
stop("`To modify `$curves`, use add_curve().", call. = FALSE)
}
#'@field curves
#'Getter for OGS6 private parameter '.curves'
curves = function() {
private$.curves
},
process_variables = function(value) {
if (missing(value)) {
private$.process_variables
} else {
stop("`To modify `$process_variables`, use add_process_variable().",
call. = FALSE)
}
#'@field process_variables
#'Getter for OGS6 private parameter '.process_variables'
process_variables = function() {
private$.process_variables
},
nonlinear_solvers = function(value) {
if (missing(value)) {
private$.nonlinear_solvers
} else {
stop("`To modify `$nonlinear_solvers`, use add_nonlinear_solver().",
call. = FALSE)
}
#'@field nonlinear_solvers
#'Getter for OGS6 private parameter '.nonlinear_solvers'
nonlinear_solvers = function() {
private$.nonlinear_solvers
},
linear_solvers = function(value) {
if (missing(value)) {
private$.linear_solvers
} else {
stop("`To modify `$linear_solvers`, use add_linear_solver().",
call. = FALSE)
}
#'@field linear_solvers
#'Getter for OGS6 private parameter '.linear_solvers'
linear_solvers = function() {
private$.linear_solvers
},
test_definition = function(value) {
if (missing(value)) {
private$.test_definition
} else {
stop("`To modify `$test_definition`, use add_vtkdiff().",
call. = FALSE)
}
#'@field test_definition
#'Getter for OGS6 private parameter '.test_definition'
test_definition = function() {
private$.test_definition
},
insitu = function(value) {
if (missing(value)) {
private$.insitu
} else {
stop("`To modify `$insitu`, use add_insitu().", call. = FALSE)
}
#'@field insitu
#'Getter for OGS6 private parameter '.insitu'
insitu = function() {
private$.insitu
}
),
......@@ -417,4 +429,3 @@ OGS6 <- R6::R6Class("OGS6",
.insitu = NULL
)
)
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