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Commit 3ecc6623 authored by Ruben Heinrich's avatar Ruben Heinrich
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[base] default paths called from options() now

parent 8557e3e6
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1 merge request!6Merge branch 7 fixed functionality into master
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R/generate_benchmark_script.R
+ 13
− 24
View file @ 3ecc6623
......@@ -14,8 +14,6 @@
#' in too?
#'@param read_in_gmls flag: Optional: Should .gml files just be copied or read
#' in too?
#'@param test_mode flag: Optional: In test mode, if `path` is missing,
#' internal function `get_default_benchmark_path()` will be called
generate_all_benchmark_scripts <-
function(path,
sim_path,
......@@ -23,21 +21,18 @@ generate_all_benchmark_scripts <-
starting_from_prj_path = "",
skip_prj_paths = character(),
read_in_vtus = FALSE,
read_in_gmls = TRUE,
test_mode = FALSE){
read_in_gmls = TRUE){
assertthat::assert_that(assertthat::is.flag(test_mode))
if(missing(path) && test_mode){
path <- get_default_benchmark_path()
if(missing(path)){
path <- options("r2ogs6.default_benchmark_path")
}
if(missing(sim_path) && test_mode){
sim_path <- get_default_sim_path()
if(missing(sim_path)){
sim_path <- options("r2ogs6.default_sim_path")
}
if(missing(scripts_path) && test_mode){
scripts_path <- get_default_script_path()
if(missing(scripts_path)){
scripts_path <- options("r2ogs6.default_script_path")
}
path <- validate_is_dir_path(path)
......@@ -95,8 +90,7 @@ generate_all_benchmark_scripts <-
sim_path = sim_subdir,
script_path = scripts_path,
read_in_vtu = read_in_vtus,
read_in_gml = read_in_gmls,
test_mode = test_mode)
read_in_gml = read_in_gmls)
}
cat("\nFailed parsing the following files:")
......@@ -119,25 +113,20 @@ generate_all_benchmark_scripts <-
#' in too?
#'@param read_in_gml flag: Optional: Should .gml file just be copied or read
#' in too?
#'@param test_mode flag: Optional: In test mode, if `ogs_bin_path` is missing,
#' internal function `get_default_ogs_bin_path()` will be called
#'@export
generate_benchmark_script <- function(prj_path,
sim_path,
ogs_bin_path,
script_path,
read_in_vtu = FALSE,
read_in_gml = TRUE,
test_mode = FALSE) {
assertthat::assert_that(assertthat::is.flag(test_mode))
read_in_gml = TRUE) {
if(missing(ogs_bin_path) && test_mode){
ogs_bin_path <- get_default_ogs_bin_path()
if(missing(ogs_bin_path)){
ogs_bin_path <- options("r2ogs6.default_bin_path")
}
if(missing(script_path) && test_mode){
script_path <- get_default_script_path()
if(missing(script_path)){
script_path <- options("r2ogs6.default_script_path")
}
assertthat::assert_that(assertthat::is.string(prj_path))
......
R/ogs6.R
+ 9
− 2
View file @ 3ecc6623
......@@ -27,7 +27,14 @@ OGS6 <- R6::R6Class("OGS6",
assertthat::assert_that(assertthat::is.number(sim_id))
self$sim_name <- sim_name
self$sim_path <- sim_path
if(missing(sim_path)){
sim_path <- options("r2ogs6.default_sim_path")
}
if(missing(ogs_bin_path)){
ogs_bin_path <- options("r2ogs6.default_ogs_bin_path")
}
if(!test_mode){
if(!file.exists(paste0(ogs_bin_path, "generateStructuredMesh.exe"))) {
......@@ -37,8 +44,8 @@ OGS6 <- R6::R6Class("OGS6",
}
}
private$.sim_name <- sim_name
private$.sim_id <- sim_id
self$sim_path <- sim_path
private$.ogs_bin_path <- validate_is_dir_path(ogs_bin_path)
},
......
R/read_in_utils.R
+ 3
− 3
View file @ 3ecc6623
......@@ -107,7 +107,7 @@ read_in <- function(ogs6_obj,
add_call <- paste0("ogs6_obj$add_", child_name, "(r2ogs6_obj)")
#Parse all children
for (i in seq_along(nodes)) {
for (i in seq_len(length(nodes))) {
r2ogs6_obj <- node_to_r2ogs6_obj(nodes[[i]],
xpath_expr,
......@@ -144,7 +144,7 @@ node_to_r2ogs6_obj <- function(xml_node,
parameters <- c(parameters, xml2::xml_attrs(xml_node))
}
for(i in seq_along(parameter_nodes)){
for(i in seq_len(length(parameter_nodes))){
new_xpath_expr <- paste0(xpath_expr,
"/",
......@@ -324,7 +324,7 @@ guess_structure <- function(xml_node,
wrapper_list <- list()
for (i in seq_along(xml2::xml_children(xml_node))) {
for (i in seq_len(length((xml2::xml_children(xml_node))))) {
child_node <- xml2::xml_children(xml_node)[[i]]
child_name <- xml2::xml_name(child_node)
......
R/sim_utils.R
+ 65
− 40
View file @ 3ecc6623
......@@ -32,22 +32,8 @@ run_simulation <- function(ogs6_obj, write_logfile = TRUE) {
}
}
# Export the simulation files
if(!is.null(ogs6_obj$gml)){
export_gml(ogs6_obj$gml,
paste0(ogs6_obj$sim_path, basename(ogs6_obj$geometry)))
}else if(!is.null(ogs6_obj$geometry)){
file.copy(ogs6_obj$geometry, ogs6_obj$sim_path)
}
export_prj(ogs6_obj)
# Copy all referenced .vtu files to ogs6_obj$sim_path
lapply(ogs6_obj$meshes, function(x){
file.copy(x, ogs6_obj$sim_path)
})
# Copy referenced ...
# Export (and / or copy referenced) simulation files
export_all_sim_files(ogs6_obj)
# Construct the call
ogs6_command_str <- paste0(ogs6_obj$ogs_bin_path, "ogs.exe")
......@@ -74,6 +60,8 @@ run_simulation <- function(ogs6_obj, write_logfile = TRUE) {
assertthat::assert_that(!file.exists(ogs6_obj$logfile))
file.create(ogs6_obj$logfile)
cat("\nRunning sim...\n")
exit_code <- system2(command = ogs6_command_str,
args = ogs6_args,
stdout = ogs6_obj$logfile)
......@@ -88,12 +76,45 @@ run_simulation <- function(ogs6_obj, write_logfile = TRUE) {
}
#===== Export utility =====
#'export_all_sim_files
#'@description Exports and / or copies all simulation files to
#' `ogs6_obj$sim_path`
#'@param ogs6_obj OGS6: Simulation object
export_all_sim_files <- function(ogs6_obj){
assertthat::assert_that(inherits(ogs6_obj, "OGS6"))
if(!is.null(ogs6_obj$gml)){
export_gml(ogs6_obj$gml,
paste0(ogs6_obj$sim_path, basename(ogs6_obj$geometry)))
}else if(!is.null(ogs6_obj$geometry)){
file.copy(ogs6_obj$geometry, ogs6_obj$sim_path)
}
# Copy all referenced .vtu files to ogs6_obj$sim_path
lapply(ogs6_obj$meshes, function(x){
file.copy(x, ogs6_obj$sim_path)
})
if(!is.null(ogs6_obj$python_script)){
file.copy(ogs6_obj$python_script, ogs6_obj$sim_path)
}
export_prj(ogs6_obj)
return(invisible())
}
#===== Validation utility =====
#'validate_all
#'@description Validates all necessary parameters
#'@param ogs6_obj A OGS6 class object
#'@param ogs6_obj OGS6: Simulation object
validate_all <- function(ogs6_obj) {
if(!ogs6_obj$get_status(print_status = FALSE)){
......@@ -123,26 +144,26 @@ validate_all <- function(ogs6_obj) {
#'@description Utility function for quick benchmark runs
#'@param prj_path string:
#'@param ogs_bin_path string:
#'@param sim_path string: Optional: Path where simulation files will be saved.
#' Change this to fit your system!
#'@param sim_path string: Path where simulation files will be saved.
run_benchmark <- function(prj_path,
ogs_bin_path,
sim_path = "D:/OGS_all_simulations/"){
sim_path){
if(missing(ogs_bin_path)){
ogs_bin_path <- options("r2ogs6.default_ogs_bin_path")
}
if(missing(ogs_bin_path) ||
!assertthat::is.string(ogs_bin_path) ||
ogs_bin_path == ""){
ogs_bin_path <- get_default_ogs_bin_path()
if(missing(sim_path)){
sim_path <- options("r2ogs6.default_sim_path")
}
assertthat::assert_that(assertthat::is.string(prj_path))
assertthat::assert_that(assertthat::is.string(ogs_bin_path))
assertthat::assert_that(assertthat::is.string(sim_path))
sim_path <- validate_is_dir_path(sim_path)
sim_name <- substr(basename(prj_path),
start = 0,
stop = nchar(basename(prj_path)) - 4)
sim_name <- tools::file_path_sans_ext(basename(prj_path))
sim_subdir_path <- paste0(sim_path,
basename(dirname(prj_path)),
......@@ -156,7 +177,8 @@ run_benchmark <- function(prj_path,
read_in_prj(ogs6_obj = ogs6_obj,
prj_path = prj_path,
read_in_vtu = FALSE)
read_in_vtu = FALSE,
read_in_gml = TRUE)
return(invisible(run_simulation(ogs6_obj)))
}
......@@ -168,28 +190,31 @@ run_benchmark <- function(prj_path,
#'@param path string:
#'@param ogs_bin_path string:
#'@param sim_path string:
#'@param starting_from_prj_path string:
#'@param print_failed_prj_paths flag:
#'@param starting_from_prj_path string: .prj path to start from
#'@param print_failed_prj_paths flag: Output paths where `read_in_prj()` failed?
run_all_benchmarks <- function(path,
ogs_bin_path,
sim_path = "D:/OGS_all_simulations/",
sim_path,
starting_from_prj_path = "",
print_failed_prj_paths = TRUE){
if(missing(path) ||
!assertthat::is.string(path) ||
path == ""){
path <- get_default_benchmark_path()
if(missing(path)){
path <- options("r2ogs6.default_benchmark_path")
}
if(missing(ogs_bin_path) ||
!assertthat::is.string(ogs_bin_path) ||
ogs_bin_path == ""){
ogs_bin_path <- get_default_ogs_bin_path()
if(missing(ogs_bin_path)){
ogs_bin_path <- options("r2ogs6.default_ogs_bin_path")
}
assertthat::assert_that(assertthat::is.flag(print_failed_prj_paths))
if(missing(sim_path)){
sim_path <- options("r2ogs6.default_sim_path")
}
assertthat::assert_that(assertthat::is.string(path))
assertthat::assert_that(assertthat::is.string(ogs_bin_path))
assertthat::assert_that(assertthat::is.string(sim_path))
assertthat::assert_that(assertthat::is.string(starting_from_prj_path))
assertthat::assert_that(assertthat::is.flag(print_failed_prj_paths))
prj_paths <- list.files(path = path,
pattern = "\\.prj$",
......
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