From 938a29f9f646c6239b670557845f1528d5c7fd7e Mon Sep 17 00:00:00 2001
From: "nicolas.forquet" <nicolas.forquet@irstea.fr>
Date: Thu, 22 Oct 2020 18:01:23 +0200
Subject: [PATCH] * re-organizing code (turn it into function) * add HP1
support
---
hydrus/{file_manip.R => file_manip_fcn.R} | 61 +++++++++++------
hydrus/main_script.R | 83 ++++++++++++++++++-----
hydrus/simulation_fcn.R | 13 +++-
3 files changed, 118 insertions(+), 39 deletions(-)
rename hydrus/{file_manip.R => file_manip_fcn.R} (78%)
diff --git a/hydrus/file_manip.R b/hydrus/file_manip_fcn.R
similarity index 78%
rename from hydrus/file_manip.R
rename to hydrus/file_manip_fcn.R
index c26d655..e76c162 100644
--- a/hydrus/file_manip.R
+++ b/hydrus/file_manip_fcn.R
@@ -1,22 +1,22 @@
# Nicolas Forquet, 2015
-new.hydrus.subfolder = function(new.name,reference.folder,hydrus.folder.path){
- # new.name : name of the new hydrus subfolder
- # reference.folder : folder containing all new hydrus subfolder
- # hydrus.folder : folder containing the reference model obtained with the GUI
- # NOTE: the reference folder must contain a copy of the Hydrus batch executable file : H2D_Calc.exe
-
- # get the content list from the reference folder
- files2copy <- list.files(path = hydrus.folder.path)
- # create a new folder into the reference folder
- setwd(reference.folder)
- dir.create(new.name)
- # copy all input files
- file.copy(list.files(pattern = ".exe", ignore.case = TRUE),paste0(new.name,"/",list.files(pattern = ".exe", ignore.case = TRUE)))
- for (i in 1:length(files2copy)){
- file.copy(paste(hydrus.folder,files2copy[i],sep = "/"),paste(new.name,files2copy[i],sep = "/"))
- }
-}
+# new.hydrus.subfolder = function(new.name,reference.folder,hydrus.folder.path){
+# # new.name : name of the new hydrus subfolder
+# # reference.folder : folder containing all new hydrus subfolder
+# # hydrus.folder : folder containing the reference model obtained with the GUI
+# # NOTE: the reference folder must contain a copy of the Hydrus batch executable file : H2D_Calc.exe
+#
+# # get the content list from the reference folder
+# files2copy <- list.files(path = hydrus.folder.path)
+# # create a new folder into the reference folder
+# setwd(reference.folder)
+# dir.create(new.name)
+# # copy all input files
+# file.copy(list.files(pattern = ".exe", ignore.case = TRUE),paste0(new.name,"/",list.files(pattern = ".exe", ignore.case = TRUE)))
+# for (i in 1:length(files2copy)){
+# file.copy(paste(hydrus.folder,files2copy[i],sep = "/"),paste(new.name,files2copy[i],sep = "/"))
+# }
+# }
dummy.white.space = function(char.line){
temp = unlist(strsplit(char.line," ",fixed = TRUE))
@@ -109,13 +109,32 @@ write_domain = function(reference.folder, file.name.out = "empty", Axz = "empty"
return(new_linn)
}
-level_01.creator = function(new.subfolder.path){
- # new.name : name of the new hydrus subfolder
- # reference.folder : folder containing all new hydrus subfolder
+level_01.creator = function(new.subfolder.path, HP1 = FALSE){
+ # new.subfolder.path : the path to which create the level_01.dir file (and the path.dat file if HP1 is in use)
+ file.create(paste(new.subfolder.path,"/Level_01.dir",sep=""))
level01.file = file(paste(new.subfolder.path,"/Level_01.dir",sep=""),"w")
- #working.directory = paste(reference.folder,"/",new.name,sep="")
writeLines(new.subfolder.path,level01.file)
close(level01.file)
+ if (HP1 == TRUE){
+ file.create(paste(new.subfolder.path,"/path.dat",sep=""))
+ path.file = file(paste(new.subfolder.path,"/path.dat",sep=""),"w")
+ writeLines(new.subfolder.path,path.file)
+ close(path.file)
+ }
+}
+
+exe_copy = function(hydrus.path, new.subfolder.path, HP1 = FALSE){
+ path <- paste0(hydrus.path, "/H1D_CALC.EXE")
+ new.path <- paste0(new.subfolder.path, "/H1D_CALC.EXE")
+ file_copy(path, new.path, overwrite = TRUE)
+ if (HP1 == TRUE){
+ path <- paste0(hydrus.path, "/HP1.exe")
+ new.path <- paste0(new.subfolder.path, "/HP1.exe")
+ file_copy(path, new.path, overwrite = TRUE)
+ path <- paste0(hydrus.path, "/Phreeqc.dll")
+ new.path <- paste0(new.subfolder.path, "/Phreeqc.dll")
+ file_copy(path, new.path, overwrite = TRUE)
+ }
}
modify.selector = function(new.name,hydrus.folder,data,header.size = 24, end.size = 65){
diff --git a/hydrus/main_script.R b/hydrus/main_script.R
index d37eea0..9d012df 100644
--- a/hydrus/main_script.R
+++ b/hydrus/main_script.R
@@ -1,22 +1,73 @@
-# specify the location of the rhydrus folder:
-rhydrus.folder <- "C:/Users/forquet/Documents/script_R/rhydrus"
-# source the file with functions dedicated to file manipulation
-filename <- paste0(rhydrus.folder,"/file_manip.R")
-source(filename)
-
-# This function process the output of the script .bat that estimates processor usage.
-output.bat <- function(output){
- usage <- rep(0,5)
- for (i in 1:5){
- usage[i] <- as.numeric(strsplit(output[4+i],split='"',fixed=TRUE)[[1]][4])
+hydrus.batch <- function(parameter.file, HP1 = FALSE){
+ #--------- load necessary libraries ----------#
+ library(fs)
+ library(rjson)
+ library(tidyverse)
+
+ #---- check if the parameter file exists ----#
+ if (file.exists(path = parameter.file) == FALSE){
+ stop("invalid parameter file path")
+ }
+
+ #----------- import parameters -------------#
+ parameter <- fromJSON(file = parameter.file)
+
+ #------------ Check parameter file ------------#
+
+ # check if the working folder is valid
+ if (dir.exists(path = parameter$working.folder) == FALSE){
+ stop("invalid working folder path")
+ }
+
+ # check if the rhydrus folder is valid
+ if (dir.exists(path = parameter$rhydrus.folder) == FALSE){
+ stop("invalid rhydrus folder path")
+ }
+
+ # check if the hydrus folder is valid
+ if (dir.exists(path = parameter$hydrus.folder) == FALSE){
+ stop("invalid hydrus folder path")
+ }
+
+ # check the reference model folder is valid:
+ if (dir.exists(path = parameter$reference.model.folder) == FALSE){
+ stop("invalid reference model path")
+ }
+
+ # convert simulation number to integer and check for valid output
+ parameter$simulation.number <- parse_integer(parameter$simulation.number)
+ if(is.na(parameter$simulation.number) == TRUE){
+ stop("invalid format for simulation.number")
+ }
+
+
+ #--------- load rhydrus functions --------#
+
+ # source the file with the functions dedicated to file manipulation
+ filename <- paste0(parameter$rhydrus.folder,"/file_manip_fcn.R")
+ source(filename)
+
+ # source the file with the functions dedicated to run simulations
+ filename <- paste0(parameter$rhydrus.folder,"/simulation_fcn.R")
+ source(filename)
+
+ #-------- create file tree --------#
+
+ for (i in 1:parameter$simulation.number){
+ # copy the reference model folder
+ dir_copy(path = parameter$reference.model.folder,
+ new_path = paste0(parameter$working.folder,"/","simulation","_",as.character(i)), overwrite = TRUE)
+
+ # modify input files
+
+ # create level_01.dir (and path.dat)
+ level_01.creator(paste0(parameter$working.folder,"/","simulation","_",as.character(i)), HP1 = HP1)
+ # and copy executable file(s)
+ exe_copy(parameter$hydrus.folder, paste0(parameter$working.folder,"/","simulation","_",as.character(i)), HP1 = HP1)
+
}
- mean_usage <- mean(usage)
- return(mean_usage)
}
-# repository that contains all Hydrus folders
-main.directory <- "C:/Users/forquet/Documents/script_R/rhydrus_demo/PF_1pulse"
-
# set the working directory to main.directory
setwd(main.directory)
diff --git a/hydrus/simulation_fcn.R b/hydrus/simulation_fcn.R
index 3b0863d..066b936 100644
--- a/hydrus/simulation_fcn.R
+++ b/hydrus/simulation_fcn.R
@@ -1,7 +1,16 @@
# This function process the output of the script .bat that estimates processor usage.
+#output.bat <- function(output){
+# usage <- as.numeric(trimws(strsplit(output[2],"\r")))
+# return(usage)
+#}
+# This function process the output of the script .bat that estimates processor usage.
output.bat <- function(output){
- usage <- as.numeric(trimws(strsplit(output[2],"\r")))
- return(usage)
+ usage <- rep(0,5)
+ for (i in 1:5){
+ usage[i] <- as.numeric(strsplit(output[4+i],split='"',fixed=TRUE)[[1]][4])
+ }
+ mean_usage <- mean(usage)
+ return(mean_usage)
}
# This function creates the file tree necessary to run simulation
--
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