R/run_simstrat.R

In aemon-j/SimstratR: Work with Simstrat in R

#'@title Run the Simstrat model
#'
#'@description
#'This runs the Simstrat model on the specific simulation stored in \code{sim_folder}.
#'The specified \code{sim_folder} must contain a valid .par file.
#'
#'@param sim_folder the directory where simulation files are contained
#'@param par_file the parameter file that needs to be run
#'@param verbose Save output as character vector. Defaults to FALSE
#'@keywords methods
#'@author
#'Jorrit Mesman, Tadhg Moore
#'@examples
#'sim_folder <- system.file("extdata", package = "SimstratR")
#'run_simstrat(sim_folder, par_file = "simstrat.par")
#'@export
#'@importFrom utils packageName

run_simstrat <- function (sim_folder = ".", par_file = "simstrat.par", verbose = FALSE)
{
  ### Windows
  if(.Platform$pkgType == "win.binary"){
    return(run_simstratWin(sim_folder, par_file, verbose))
  }

  ### UNIX
  if(.Platform$pkgType == "source"){
    return(run_simstratNIX(sim_folder, par_file, verbose))
  }


  ### macOS ###
  if(grepl("mac.binary",.Platform$pkgType)){
    maj_v_number <- as.numeric(strsplit(
      Sys.info()["release"][[1]], ".", fixed = TRUE)[[1]][1])

    if(maj_v_number < 13.0){
      stop("pre-mavericks mac OSX is not supported. Consider upgrading")
    }

    return(run_simstratOSx(sim_folder, par_file, verbose))

  }
}

run_simstratWin <- function(sim_folder,par_file="simstrat.par",verbose=verbose){

  if(.Platform$r_arch == "x64"){
    simstrat_path <- system.file("extbin/win/simstrat_windows_301.exe", package = packageName())
  }else{
    stop("No Simstrat executable available for your machine yet...")
  }

  origin <- getwd()
  setwd(sim_folder)

  tryCatch({
    if(verbose){
      out <- system2(simstrat_path, wait = TRUE, stdout = TRUE,
                     stderr = "", args = par_file)
    }else{
      out <- system2(simstrat_path, wait = TRUE, stdout = NULL,
                     stderr = NULL, args = par_file)
    }
    setwd(origin)
    return(out)
  }, error = function(err){
    print(paste("Simstrat_ERROR:  ", err))
    setwd(origin)
  })
}

# run_simstratOSx <- function(sim_folder, par_file = "simstrat.par", verbose=verbose){
#
#   # simstrat_path <- system.file("extbinmac/simstrat.exe", package = "SimstratR")
#   # # File to the folder with the mac-executable for simstrat
#
#   # ship gotm and libs to sim_folder
#   #Sys.setenv(DYLD_FALLBACK_LIBRARY_PATH = lib_path) #Libraries?
#
#
#   origin <- getwd()
#   setwd(sim_folder)
#
#   tryCatch({
#     if(verbose){
#       out <- system2(simstrat_path, wait = TRUE, stdout = "",
#                      stderr = "", args = par_file)
#
#     }else{
#       out <- system2(simstrat_path, wait = TRUE, stdout = NULL,
#                      stderr = NULL, args = par_file)
#     }
#
#     setwd(origin)
# 	return(out)
#   }, error = function(err){
#     print(paste("GOTM_ERROR:  ", err))
#
#     setwd(origin)
#   })
# }

run_simstratNIX <- function(sim_folder, par_file = "simstrat.par", verbose = verbose){
  simstrat_path <- system.file("exec/simstrat_linux_301", package = packageName())

  # Sys.setenv(LD_LIBRARY_PATH = paste(system.file("extbin/nix",
  #                                                package = packageName()),
  #                                  Sys.getenv("LD_LIBRARY_PATH"),
  #                                  sep = ":"))
  origin <- getwd()
  setwd(sim_folder)

  tryCatch({
    if(verbose){
      out <- system2(simstrat_path, wait = TRUE, stdout = TRUE,
                     stderr = "", args = par_file, env = paste0("LD_LIBRARY_PATH=", simstrat_path))
    }else{
      out <- system2(simstrat_path, wait = TRUE, stdout = NULL,
                     stderr = NULL, args = par_file, env = paste0("LD_LIBRARY_PATH=", simstrat_path))
    }
    setwd(origin)
    return(out)
  }, error = function(err){
    print(paste("Simstrat_ERROR:  ", err))
    setwd(origin)
  })
}

run_simstratOSx <- function(sim_folder, par_file = "simstrat.par", verbose = verbose){
  simstrat_path <- system.file("exec/simstrat_mac_301", package = packageName())


  origin <- getwd()
  setwd(sim_folder)

  tryCatch({
    if(verbose){
      out <- system2(simstrat_path, wait = TRUE, stdout = TRUE,
                     stderr = "", args = par_file)
    }else{
      out <- system2(simstrat_path, wait = TRUE, stdout = NULL,
                     stderr = NULL, args = par_file)
    }
    setwd(origin)
    return(out)
  }, error = function(err){
    print(paste("Simstrat_ERROR:  ", err))
    setwd(origin)
  })
}
#
# ### From GLEON/gotm3r
simstrat.systemcall <- function(sim_folder, simstrat_path, verbose, system.args){
  origin <- getwd()
  setwd(sim_folder)

  tryCatch({
    if (verbose){
      out <- system2(simstrat_path, wait = TRUE, stdout = "",
                     stderr = "", args = system.args)
    }else{
      out <- system2(simstrat_path, wait = TRUE, stdout = NULL,
                     stderr = NULL, args = system.args)
    }
    setwd(origin)
    return(out)
  }, error = function(err){
    print(paste("simstrat_ERROR:  ", err))
    setwd(origin)
  })
}

# ### macOS ###
# run_gotmOSx <- function(sim_folder, verbose, system.args){
#   gotm_path <- system.file("exec/macgotm", package = "GOTMr")
#   gotm.systemcall(sim_folder = sim_folder, gotm_path = gotm_path, verbose = verbose, system.args = system.args)
# }