Add rotations and the filedister for the maize scenario

Grendel/rotations/UserDefinedFarm19.rot

+1
+0
+0
+100
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+SpringBarleyCloverGrass
+SeedGrass1
+SpringBarley
+WinterWheat
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+WinterWheat
+WinterRye
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+MaizeSilage
+SpringBarley
+WinterWheat
+MaizeSilage
+SpringBarley
+WinterWheat
+MaizeSilage
+SpringBarley
+WinterWheat
+WinterBarley
+WinterRape
+MaizeSilage
+SpringBarley
+Oats
+WinterWheat
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+SpringBarleySilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+WinterWheat
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+SpringBarleySilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+WinterWheat
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+SpringBarleySilage
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+MaizeSilage
+SpringBarleySilage
+WinterBarley
+WinterRape
+MaizeSilage
+SpringBarleySilage
+WinterWheat
+WinterRye
+SpringBarleySilage
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+CloverGrassGrazed2

Grendel/rotations/UserDefinedFarm191.rot

+1
+0
+0
+100
+MaizeSilage
+CloverGrassGrazed1
+CloverGrassGrazed2
+SpringBarleyCloverGrass
+SeedGrass1
+SpringBarley
+WinterWheat
+MaizeSilage
+SpringBarleyCloverGrass
+MaizeSilage
+CloverGrassGrazed2
+MaizeSilage
+CloverGrassGrazed1
+MaizeSilage
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+WinterWheat
+WinterRye
+SpringBarleyCloverGrass
+MaizeSilage
+CloverGrassGrazed2
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+MaizeSilage
+MaizeSilage
+SpringBarley
+WinterWheat
+MaizeSilage
+SpringBarley
+WinterWheat
+MaizeSilage
+SpringBarley
+WinterWheat
+WinterBarley
+WinterRape
+MaizeSilage
+SpringBarley
+Oats
+WinterWheat
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed1
+MaizeSilage
+SpringBarleySilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+WinterWheat
+SpringBarleyCloverGrass
+MaizeSilage
+CloverGrassGrazed2
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed1
+MaizeSilage
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+SpringBarleySilage
+SpringBarleyCloverGrass
+MaizeSilage
+CloverGrassGrazed2
+WinterWheat
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed1
+MaizeSilage
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+SpringBarleySilage
+MaizeSilage
+SpringBarleyCloverGrass
+MaizeSilage
+CloverGrassGrazed2
+MaizeSilage
+SpringBarleySilage
+WinterBarley
+WinterRape
+MaizeSilage
+SpringBarleySilage
+WinterWheat
+WinterRye
+SpringBarleySilage
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+MaizeSilage
+CloverGrassGrazed2

Grendel/rotations/UserDefinedFarm192.rot

+1
+0
+0
+100
+MaizeSilage
+CloverGrassGrazed1
+CloverGrassGrazed2
+MaizeSilage
+SeedGrass1
+SpringBarley
+WinterWheat
+MaizeSilage
+SpringBarleyCloverGrass
+MaizeSilage
+CloverGrassGrazed2
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed1
+MaizeSilage
+WinterWheat
+WinterRye
+SpringBarleyCloverGrass
+MaizeSilage
+CloverGrassGrazed2
+SpringBarleyCloverGrass
+MaizeSilage
+MaizeSilage
+MaizeSilage
+SpringBarley
+WinterWheat
+MaizeSilage
+SpringBarley
+WinterWheat
+MaizeSilage
+SpringBarley
+WinterWheat
+WinterBarley
+WinterRape
+MaizeSilage
+SpringBarley
+Oats
+WinterWheat
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed1
+MaizeSilage
+SpringBarleyCloverGrass
+MaizeSilage
+CloverGrassGrazed2
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+SpringBarleySilage
+MaizeSilage
+CloverGrassGrazed1
+MaizeSilage
+WinterWheat
+SpringBarleyCloverGrass
+MaizeSilage
+CloverGrassGrazed2
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed1
+MaizeSilage
+SpringBarleySilage
+SpringBarleyCloverGrass
+MaizeSilage
+CloverGrassGrazed2
+WinterWheat
+MaizeSilage
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed2
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed1
+MaizeSilage
+SpringBarleySilage
+MaizeSilage
+SpringBarleyCloverGrass
+CloverGrassGrazed1
+CloverGrassGrazed2
+MaizeSilage
+SpringBarleySilage
+WinterBarley
+WinterRape
+MaizeSilage
+SpringBarleySilage
+WinterWheat
+WinterRye
+SpringBarleySilage
+MaizeSilage
+SpringBarleyCloverGrass
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed2
+
+
+

Grendel/rotations/UserDefinedFarm193.rot

+1
+0
+0
+100
+SpringBarleyCloverGrass
+MaizeSilage
+MaizeSilage
+MaizeSilage
+SeedGrass1
+SpringBarley
+WinterWheat
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed1
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed2
+WinterWheat
+WinterRye
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+SpringBarley
+WinterWheat
+MaizeSilage
+SpringBarley
+WinterWheat
+MaizeSilage
+SpringBarley
+WinterWheat
+WinterBarley
+WinterRape
+MaizeSilage
+SpringBarley
+Oats
+WinterWheat
+MaizeSilage
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed2
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+SpringBarleySilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+WinterWheat
+MaizeSilage
+CloverGrassGrazed1
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+SpringBarleySilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+WinterWheat
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+SpringBarleyCloverGrass
+MaizeSilage
+MaizeSilage
+SpringBarleySilage
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed1
+MaizeSilage
+MaizeSilage
+SpringBarleySilage
+WinterBarley
+WinterRape
+MaizeSilage
+SpringBarleySilage
+WinterWheat
+WinterRye
+SpringBarleySilage
+MaizeSilage
+MaizeSilage
+MaizeSilage
+CloverGrassGrazed2
+MaizeSilage

Grendel/scenario_02_maize-availability_file-dist.R

+#!/usr/local/bin/r
+# Copy run directories and setup parameters
+# Author: Lars Dalby
+
+# Set the local R package library (if not done already)
+if(!"/home/ldalby/R/packages" %in% .libPaths()) {
+	.libPaths("/home/ldalby/R/packages")
+}
+
+suppressWarnings(library(ralmass))
+suppressMessages(library(tidyverse))
+library(fs)
+# Get the slurm job-id (is being passed in from the shell script calling this R script)
+args <- commandArgs(trailingOnly=TRUE)
+
+# Make sure we don"t write any e"s in extreme numbers. 
+options(scipen = 99)
+
+# The base directory with all input files except ParameterValues.txt (ParameterValues.txt file is written further down):
+basedir <- "/home/ldalby/workspace/Goose/RunDirectory"
+# The parent directory of all the work directories
+pathtodirs <- path("/scratch", args)
+# Setup the directories
+npar <- 4  # Specifies the number of run directories
+years <- 3  # the number of seasons to run (goose sims run over the year boundary)
+basename <- "WD"  # The prefix to the directories
+# Make the directories and copy the files:
+for (i in 1:npar) {
+  index <- stringr::str_pad(as.character(1:npar), width = 2, pad = "0")
+	dir_create(path(pathtodirs, paste0(basename,index[i])))
+  	file_copy(path = path(basedir, dir(basedir)),
+	          new_path = path(pathtodirs, paste0(basename,index[i])),
+	          overwrite = TRUE)
+}
+
+dirs <- dir(pathtodirs) 
+# Edit the scripts to reflect the correct paths:
+for (i in seq_along(dirs)) {
+	wd <- path(pathtodirs, dirs[i])
+	AppendWorkDir(WorkDir = wd, InScript = path(wd, "scenario_01_goose-numbers.R"), OutScript = "batchr.r") 
+	AppendWorkDir(WorkDir = wd, InScript = path(wd, "PreRunSetup.r"), OutScript = "PreRunSetup.r") 
+}
+# Read in the config so we can get the default values: 
+cfg <- readLines("/home/ldalby/workspace/Goose/RunDirectory/TIALMaSSConfig.cfg")
+
+# Ditribute the different parameters ----
+nsteps <- 10  # the number of intervals to split the parameter in
+
+replace_rotation <- function(new_rot, old_rot, wd_path) {
+  rot_paths <- "/home/ldalby/ALMaSS_all/almass/Grendel/rotations/"
+  focal_rot <- path(rot_paths, new_rot)
+  file_copy(focal_rot,
+            new_path = path(wd_path, old_rot), 
+            overwrite = TRUE)
+}
+old_rot <- "UserDefinedFarm19.rot"
+rot_path <- "/home/ldalby/ALMaSS_all/almass/Grendel/rotations"
+# Startno scaler - maize rotation 191 ----
+wdpath <- path(pathtodirs, dirs[1])
+seq(1, 10, length.out = nsteps) %>% 
+  round() %>% 
+  GenerateParams("GOOSE_STARTNO_SCALER" = ., write = TRUE, path = wdpath)
+replace_rotation(new_rot = path(rot_path, "UserDefinedFarm191.rot"),
+                 old_rot = old_rot,
+                 wd_path <- wdpath)
+
+# Startno scaler - maize rotation 192 ----
+wdpath <- path(pathtodirs, dirs[1])
+seq(1, 10, length.out = nsteps) %>% 
+  round() %>% 
+  GenerateParams("GOOSE_STARTNO_SCALER" = ., write = TRUE, path = wdpath)
+replace_rotation(new_rot = path(rot_path, "UserDefinedFarm192.rot"),
+                 old_rot = old_rot,
+                 wd_path <- wdpath)
+
+# Startno scaler - maize rotation 193 ----
+wdpath <- path(pathtodirs, dirs[1])
+seq(1, 10, length.out = nsteps) %>% 
+  round() %>% 
+  GenerateParams("GOOSE_STARTNO_SCALER" = ., write = TRUE, path = wdpath)
+replace_rotation(new_rot = path(rot_path, "UserDefinedFarm193.rot"),
+                 old_rot = old_rot,
+                 wd_path <- wdpath)
+
+# Edit the bat, ini and cfg files to match the parameters set above:
+for (i in seq_along(dirs)) {
+	wd <- path(pathtodirs, dirs[i])
+	edit_bat(wd, "_01_BatchLoop.sh")
+	EditIni(WorkDir = wd, Model = "goose", NYear = years + 1)
+	EditConfig(file = path(wd, "TIALMaSSConfig.cfg"), config = "GOOSE_MODELEXITDAY", value = 31 + years*365)
+	EditConfig(file = path(wd, "TIALMaSSConfig.cfg"), config = "MAP_WEATHER_FILE", value = "Vejlerne2011-2014.pre")
+}