[docs] updated documentation

man/export_all_sim_files.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sim_utils.R
+\name{export_all_sim_files}
+\alias{export_all_sim_files}
+\title{export_all_sim_files}
+\usage{
+export_all_sim_files(ogs6_obj)
+}
+\arguments{
+\item{ogs6_obj}{OGS6: Simulation object}
+}
+\description{
+Exports and / or copies all simulation files to
+`ogs6_obj$sim_path`
+}

man/generate_all_benchmark_scripts.Rd

@@ -6,28 +6,30 @@
 \usage{
 generate_all_benchmark_scripts(
   path,
-  scripts_path = "D:/OGS_scripts/",
+  sim_path,
+  scripts_path,
   starting_from_prj_path = "",
   skip_prj_paths = character(),
-  read_in_vtus = TRUE,
-  test_mode = FALSE
+  read_in_vtus = FALSE,
+  read_in_gmls = TRUE
 )
 }
 \arguments{
 \item{path}{string: Path to a benchmark directory to generate scripts from}
 
-\item{scripts_path}{string: Optional: Path where benchmark scripts will be
-saved. Change this to fit your system!}
+\item{sim_path}{string: Path where all simulation files will be saved}
+
+\item{scripts_path}{string: Path where benchmark scripts will be saved}
 
 \item{starting_from_prj_path}{string: Optional:}
 
 \item{skip_prj_paths}{character: Optional: .prj paths to skip}
 
-\item{read_in_vtus}{flag: Optional: Should .vtu file just be copied or read
+\item{read_in_vtus}{flag: Optional: Should .vtu files just be copied or read
 in too?}
 
-\item{test_mode}{flag: Optional: In test mode, if `path` is missing,
-internal function `get_default_benchmark_path()` will be called}
+\item{read_in_gmls}{flag: Optional: Should .gml files just be copied or read
+in too?}
 }
 \description{
 Wrapper function to generate benchmark scripts from all .prj

man/generate_benchmark_script.Rd

@@ -6,16 +6,21 @@
 \usage{
 generate_benchmark_script(
   prj_path,
-  script_path = "D:/OGS_scripts/",
+  sim_path,
+  ogs_bin_path,
+  script_path,
   read_in_vtu = FALSE,
   read_in_gml = TRUE
 )
 }
 \arguments{
-\item{prj_path}{The path to the project file the script will be based on}
+\item{prj_path}{string: .prj file the script will be based on}
 
-\item{script_path}{string: Optional: Path where benchmark script will be
-saved. Change this to fit your system!}
+\item{sim_path}{string: Path where all simulation files will be saved}
+
+\item{ogs_bin_path}{string: OpenGeoSys bin folder path}
+
+\item{script_path}{string: Path where benchmark script will be saved}
 
 \item{read_in_vtu}{flag: Optional: Should .vtu file(s) just be copied or read
 in too?}

man/run_all_benchmarks.Rd

@@ -7,7 +7,7 @@
 run_all_benchmarks(
   path,
   ogs_bin_path,
-  sim_path = "D:/OGS_all_simulations/",
+  sim_path,
   starting_from_prj_path = "",
   print_failed_prj_paths = TRUE
 )
@@ -19,9 +19,9 @@ run_all_benchmarks(
 
 \item{sim_path}{string:}
 
-\item{starting_from_prj_path}{string:}
+\item{starting_from_prj_path}{string: .prj path to start from}
 
-\item{print_failed_prj_paths}{flag:}
+\item{print_failed_prj_paths}{flag: Output paths where `read_in_prj()` failed?}
 }
 \description{
 Utility function, for quick benchmark runs. Calls

man/run_benchmark.Rd

@@ -4,15 +4,14 @@
 \alias{run_benchmark}
 \title{run_benchmark}
 \usage{
-run_benchmark(prj_path, ogs_bin_path, sim_path = "D:/OGS_all_simulations/")
+run_benchmark(prj_path, ogs_bin_path, sim_path)
 }
 \arguments{
 \item{prj_path}{string:}
 
 \item{ogs_bin_path}{string:}
 
-\item{sim_path}{string: Optional: Path where simulation files will be saved.
-Change this to fit your system!}
+\item{sim_path}{string: Path where simulation files will be saved.}
 }
 \description{
 Utility function for quick benchmark runs

man/validate_all.Rd

@@ -7,7 +7,7 @@
 validate_all(ogs6_obj)
 }
 \arguments{
-\item{ogs6_obj}{A OGS6 class object}
+\item{ogs6_obj}{OGS6: Simulation object}
 }
 \description{
 Validates all necessary parameters