From e8a681b2dc9bba5ffa0044fd37f3528038f8e383 Mon Sep 17 00:00:00 2001
From: aheinri5 <Anna@netzkritzler.de>
Date: Wed, 16 Dec 2020 17:16:07 +0100
Subject: [PATCH] [base] Modified run_simulation so it can be used by ensembles
later
---
R/sim_utils.R | 118 +++++++++++++++++++++++++++++++-------------------
1 file changed, 74 insertions(+), 44 deletions(-)
diff --git a/R/sim_utils.R b/R/sim_utils.R
index 835a6ae..8588a27 100644
--- a/R/sim_utils.R
+++ b/R/sim_utils.R
@@ -6,76 +6,105 @@
#'@description Calls OGS6 object validator functions, exports all necessary
#' files and starts OpenGeoSys6
#'@param ogs6_obj OGS6: Simulation object
-#'@param iter_n number: Number of iterations (for simulation chains)
#'@param output_to_log_file flag: Should output be written to a log file?
#'@export
-run_simulation <- function(ogs6_obj, iter_n = 1, output_to_log_file = TRUE) {
+run_simulation <- function(ogs6_obj, output_to_log_file = TRUE) {
- assertthat::assert_that(inherits(ogs6_obj, "OGS6"))
- assertthat::assert_that(assertthat::is.number(iter_n),
- iter_n > 0, iter_n < 500)
+ assertthat::assert_that(inherits(ogs6_obj), "OGS6")
assertthat::assert_that(assertthat::is.flag(output_to_log_file))
- #Call all validators
+ # Call all validators
validate_all(ogs6_obj)
- #Export the simulation files
+ # Create the simulation folder
+ if (!dir.exists(ogs6_obj$sim_path)) {
+ dir.create(ogs6_obj$sim_path)
+ } else{
+ if (length(dir(ogs6_obj$sim_path, all.files = TRUE)) != 0) {
+ warning(
+ paste0(
+ "The defined sim_path directory '",
+ ogs6_obj$sim_path,
+ "' is not empty. Files may be overwritten."
+ ),
+ call. = FALSE
+ )
+ }
+ }
+
+ # Export the simulation files
export_gml(ogs6_obj)
export_prj(ogs6_obj)
- #Construct the system call
- ogs6_call <- paste0(ogs6_obj$ogs_bin_path,
- "ogs.exe ",
- ogs6_obj$sim_path,
- ogs6_obj$sim_name,
- ".prj -o ",
- ogs6_obj$sim_path)
+ # Construct the system call
+ ogs6_call <- paste0(
+ ogs6_obj$ogs_bin_path,
+ "ogs.exe ",
+ ogs6_obj$sim_path,
+ ogs6_obj$sim_name,
+ ".prj -o ",
+ ogs6_obj$sim_path
+ )
+
+ # Finally, make the system call to start the simulation
+ if (output_to_log_file) {
+ system(command = setup_logging(ogs6_obj$sim_name,
+ ogs6_obj$sim_path,
+ ogs6_call))
+ } else{
+ system(command = ogs6_call)
+ }
- system_call <- ogs6_call
+ closeAllConnections()
+}
- #Direct simulation output to log file
- if(output_to_log_file){
- # Create logfile directory
- logfile_dir <- paste0(ogs6$sim_path, "logfiles/")
+#===== LOGGING UTILITY =====
- if(!dir.exists(logfile_dir)){
- dir.create(logfile_dir)
- }else{
- warning("Logfile directory already exists", call. = FALSE)
- }
- for(i in seq_len(iter_n)){
+#'setup_logging
+#'@description Sets up logging.
+#'@param sim_name string: Simulation name
+#'@param sim_path string: Simulation path
+#'@param ogs6_call string: Corresponding OGS6 call
+setup_logging <- function(sim_name, sim_path, ogs6_call){
- logfile_path <- paste0(logfile_dir,
- ogs6_obj$sim_name,
- "_log_", iter_n, ".txt")
+ assertthat::assert_that(assertthat::is.string(sim_name))
+ assertthat::assert_that(assertthat::is.string(sim_path))
+ sim_path <- validate_is_dir_path(sim_path)
- #Call OGS6
- system(command = paste("R CMD BATCH --no-echo",
- script_path,
- logfile_path))
+ assertthat::assert_that(assertthat::is.string(ogs6_call))
- # read_in_output(ogs6_obj)
- }
+ # Create logfile directory
+ logfile_dir <- paste0(sim_path, "logfiles/")
- #Write to file...
+ if(!dir.exists(logfile_dir)){
+ dir.create(logfile_dir)
}
- #Run simulations (and read in output as input)
- for(i in seq_len(iter_n)){
-
- #Call OGS6
- system(command = ogs6_call)
+ # Create initialization script
+ script_path <- paste0(logfile_dir, "sim_init.R")
- # read_in_output(ogs6_obj)
+ if(!file.exists(script_path)){
+ file.create(script_path)
}
- closeAllConnections()
+ cmd_str <- paste0("system(command = \"", ogs6_call, "\")")
+
+ file_conn <- file(script_path)
+ writeLines(c(cmd_str), file_conn)
+ close(file_conn)
+
+ # Return string for calling R CMD BATCH
+ batch_call <- paste0("R CMD BATCH --no-echo ",
+ script_path, " ",
+ sim_name, "_log.txt")
+
+ return(invisible(batch_call))
}
-#===== VALIDATION UTILITY =====
+#===== Validation utility =====
#'validate_all
@@ -103,7 +132,7 @@ validate_all <- function(ogs6_obj) {
}
-#===== CHAINING UTILITY (WIP) =====
+#===== Chaining utility (WIP) =====
#'read_in_output
@@ -118,3 +147,4 @@ read_in_output <- function(ogs6_obj) {
+
--
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