* re-organizing code (turn it into function)

* add HP1 support

hydrus/file_manip.R → hydrus/file_manip_fcn.R

 # 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){

hydrus/main_script.R

-# 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)
 

hydrus/simulation_fcn.R

 # 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