diff --git a/R/generate_benchmark_script.R b/R/generate_benchmark_script.R
index 588dd5d7db5ab024b4f715671d41545a499524f2..adbe432d8fea2c12880fbe4ed1d40ef5851f7186 100644
--- a/R/generate_benchmark_script.R
+++ b/R/generate_benchmark_script.R
@@ -117,7 +117,8 @@ generate_all_benchmark_scripts <-
#' @description Generates a benchmark script from an existing \code{.prj} file.
#' @param prj_path string: \code{.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: OpenGeoSys bin folder path
+#' @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
#' read in too?
diff --git a/R/ogs6_vtu.R b/R/ogs6_vtu.R
index 78060dd36e08d7bab22ac4d14faa4b3914274259..9b6f5309d96f90a901e12f1cdf97945fde830110 100644
--- a/R/ogs6_vtu.R
+++ b/R/ogs6_vtu.R
@@ -334,18 +334,18 @@ validate_coordinates <- function(coordinates){
#' (VTK mesh generator). For full documentation see
#' https://www.opengeosys.org/docs/tools/meshing/structured-mesh-generation/
#' @param args_str string: The arguments the script will be called with
-#' @param ogs6_bin_path string: Optional: Path to OpenGeoSys6 bin folder.
-#' Defaults to options("r2ogs6.default_ogs6_bin_path")
+#' @param ogs6_utils_path string: Optional: Path to OpenGeoSys6 utils folder.
+#' Defaults to options("r2ogs6.default_ogs6_utils_path")
#' @return string: .vtu file path
#' @export
ogs6_generate_structured_mesh = function(args_str,
- ogs6_bin_path) {
+ ogs6_utils_path) {
- if(missing(ogs6_bin_path)){
- ogs6_bin_path <- unlist(options("r2ogs6.default_ogs6_bin_path"))
+ if(missing(ogs6_utils_path)){
+ ogs6_utils_path <- unlist(options("r2ogs6.default_ogs6_utils_path"))
}
- assertthat::assert_that(assertthat::is.string(ogs6_bin_path))
+ assertthat::assert_that(assertthat::is.string(ogs6_utils_path))
assertthat::assert_that(assertthat::is.string(args_str))
@@ -353,7 +353,7 @@ ogs6_generate_structured_mesh = function(args_str,
vtu_path <- stringr::str_extract(args_str, "-o [^ ]*")
vtu_path <- stringr::str_remove(vtu_path, "-o ")
- system(command = paste0(ogs6_bin_path,
+ system(command = paste0(ogs6_utils_path,
"generateStructuredMesh.exe ",
args_str))
diff --git a/R/sim_utils.R b/R/sim_utils.R
index d39682cd928043be0002f241c8c67d77469bf1ec..5b05e0041327edaf70caf612e525bc2138a7edc6 100644
--- a/R/sim_utils.R
+++ b/R/sim_utils.R
@@ -9,7 +9,7 @@
#' @param write_logfile flag: Should output be written to a logfile? If
#' \code{FALSE}, output will be written to console. If \code{TRUE}, logfile
#' directory will be created in \code{ogs6$sim_path} directory
-#' @param ogs6_bin_path string: Optional: OpenGeoSys 6 bin folder path. Defaults
+#' @param ogs6_bin_path string: Optional: OpenGeoSys 6 executable path. Defaults
#' to \code{options("r2ogs6.default_ogs6_bin_path")}
#' @param verbose flag
#' @export
@@ -117,7 +117,8 @@ ogs6_export_sim_files <- function(ogs6_obj,
#' @param write_logfile flag: Should output be written to a logfile? If
#' \code{FALSE}, output will be written to console. If \code{TRUE}, logfile
#' directory will be created in \code{ogs6$sim_path} directory
-#' @param ogs6_bin_path string: Optional: OpenGeoSys 6 bin folder path. Defaults
+#' @param ogs6_bin_path string: Optional: Path to OpenGeoSys 6 executable or
+#' OpenGeoSys container (singularity image) file. Defaults
#' to \code{options("r2ogs6.default_ogs6_bin_path")}
#' @param verbose flag
#' @export
@@ -136,16 +137,20 @@ ogs6_call_ogs6 <- function(ogs6_obj,
assertthat::assert_that(assertthat::is.string(ogs6_bin_path))
assertthat::assert_that(assertthat::is.flag(verbose))
- # Construct the call
- exe_str <- ifelse(Sys.info()["sysname"] == "Windows",
- "ogs.exe",
- "ogs")
-
- ogs6_command_str <- paste0(ogs6_bin_path, exe_str)
- sim_path_full <- paste0(ogs6_obj$sim_path,
+ # construt call to os
+ prj_path_full <- paste0(ogs6_obj$sim_path,
ogs6_obj$sim_name,
".prj")
- ogs6_args <- c(sim_path_full, "-o", ogs6_obj$sim_path)
+ ogs6_args <- c(prj_path_full, "-o", ogs6_obj$sim_path)
+ ogs6_command <- construct_ogs_command(ogs6_bin_path)
+
+ # reorder for using 'system2()'
+ if (length(ogs6_command)>1) {
+ ogs6_command_str <- ogs6_command[1]
+ ogs6_args <- c(ogs6_command[-1], ogs6_args)
+ } else {
+ ogs6_command_str <- ogs6_command
+ }
exit_code <- 0
@@ -181,6 +186,44 @@ ogs6_call_ogs6 <- function(ogs6_obj,
}
+
+#' construct_ogs_command
+#' @description Constructs the call string to for 'system2()'.
+#' @param ogs6_bin_path string: Optional: Path to OpenGeoSys 6 executable or
+#' OpenGeoSys container (singularity image) file. Defaults
+#' to \code{options("r2ogs6.default_ogs6_bin_path")}
+#'
+#' @return string: Call object.
+construct_ogs_command <- function(ogs6_bin_path){
+
+ assertthat::assert_that(assertthat::is.string(ogs6_bin_path))
+
+ # check if existent
+ if (dir.exists(ogs6_bin_path)) {
+ stop("'ogs6_bin_path' has to be an executable or container image file.",
+ call. = FALSE)
+ }
+ else if (!(file.exists(ogs6_bin_path))) {
+ stop("'ogs6_bin_path' does not exist.'",
+ call. = FALSE)
+ }
+
+ # Construct the call wether ogs6_bin_path is executable or
+ # container image file
+ if (stringr::str_sub(ogs6_bin_path, -4) == ".sif"){
+
+ assertthat::assert_that(file.exists(ogs6_bin_path))
+ ogs6_command <- c("singularity","exec", "--app ogs",
+ ogs6_bin_path, "ogs")
+ }
+ else {
+ ogs6_command <- paste0(ogs6_bin_path)
+ assertthat::assert_that(file.exists(ogs6_command))
+ }
+
+ return(ogs6_command)
+}
+
#===== ogs6_read_output_files =====
diff --git a/R/zzz.R b/R/zzz.R
index 8b70e3c21673b8268d3f21c54144869df99bf9c2..3db11061130c50af8a88e7cb11b3b1a0313356b0 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -13,6 +13,7 @@ vtk <- NULL
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,
@@ -38,12 +39,18 @@ vtk <- NULL
"D:/Programme/OpenGeoSys/ogs-master/Tests/Data/",
r2ogs6.default_ogs6_processlib_path =
"D:/Programme/OpenGeoSys/ogs-master/ProcessLib/",
- r2ogs6.default_ogs6_bin_path =
+ 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"
)