scripts/generate_SoilSens_test.R
In femeunier/SoilSensitivity:
rm(list = ls())
library(dplyr)
library(tidyr)
library(PEcAnRTM)
library(purrr)
library(rrtm)
library(ED2scenarios)
library(PEcAn.ED2)
library(purrr)
library(ggplot2)
library(ggridges)
library(cowplot)
library(pracma)
library(BayesianTools)
library(raster)
# library(rnaturalearth)
# library(rnaturalearthdata)
# library(lattice)
ED_REG_LATMIN = -10.5
ED_REG_LATMAX = -0.5
ED_REG_LONMIN = -60.5
ED_REG_LONMAX = -50.5
GRID_RES = 1
X = seq(ED_REG_LONMIN,ED_REG_LONMAX,GRID_RES)
Y = seq(ED_REG_LATMIN,ED_REG_LATMAX,GRID_RES)
ref_dir <- "/data/gent/vo/000/gvo00074/pecan/output/other_runs/SoilSensitivity/run"
rundir <- "/data/gent/vo/000/gvo00074/pecan/output/other_runs/SoilSensitivity/run/grid"
ICdir <- "/data/gent/vo/000/gvo00074/pecan/output/other_runs/LSliana/IC/"
outdir <- "/kyukon/scratch/gent/vo/000/gvo00074/felicien/SoilSensitivity/out"
ed2in <- read_ed2in(file.path(ref_dir,"ED2IN"))
ed2in$IMONTHA = 1
ed2in$IDATEA = 1
ed2in$IYEARA = 2000
ed2in$IMONTHZ = 2
ed2in$IDATEZ = 1
ed2in$IYEARZ = 2005
list_dir <- list()
# load landmask here
land <- readRDS("landmask.RDS")
land_IC <- readRDS("land_IC.RDS")
cssfile_base <- "Amazon"
Nsimuperjob = 3
isimu = 0
defaults <- list()
PREFIX_XML <- "<?xml version=\"1.0\"?>\n<!DOCTYPE config SYSTEM \"ed.dtd\">\n"
# Default settings
settings <- list(model = list(revision = "git",
config.header = NULL),
pfts = list(pft = list(num = 1,
ed2_pft_number = 1,
name = "saccharum"),
pft = list(num = 2,
ed2_pft_number = 2,
name = "Early"),
pft = list(num = 3,
ed2_pft_number = 3,
name = "Mid"),
pft = list(num = 4,
ed2_pft_number = 4,
name = "Late")))
# Config
config <- list()
config[["saccharum"]] <- unlist(list(num = 1))
config[["Early"]] <- unlist(list(num = 2))
config[["Mid"]] <- unlist(list(num = 3))
config[["Late"]] <- unlist(list(num = 4,
wood_Kmax = 0.01))
# scenars <- c("ref","hydro","clay")
# scenars <- c("ref_nohydro","silt_nohydro","clay_nohydro")
# scenars <- c("soilgrids_ref","soilgrids_SD","soilgrids")
scenars <- c("HWSD_ref","HWSD_SD","HWSD")
HWSD <- brick(file.path(".","HWSD_all.grd"))
soilgrids <- brick(file.path(".","soilgrid_all.grd"))
depths <- c(-Inf,-1,-0.6,-0.3,-0.15,Inf)
all_depths <- c(-8,-7,-6.2,-5.5,-4.9,-4.3,-3.8,-3.3,-2.8,-2.3,-1.8,-1.3,-1,-0.6,-0.3,-0.15)
all_depths_SD <- c(-2,-1.9,-1.8,-1.7,-1.6,-1.5,-1.4,-1.3,-1.15,-1,-0.9,-0.75,-0.6,-0.45,-0.3,-0.15)
for(ix in seq(1,length(X))){
for(iy in seq(1,length(Y))){
clat = Y[iy]; clon = X[ix]
if (land[which(rownames(land_IC)==clat),
which(colnames(land_IC)==clon)]){
for (iscenar in seq(1,length(scenars))){
run_name <- paste0("SoilSens_Amazon_",scenars[iscenar],"_X_",abs(X[ix]),ifelse(X[ix]<0,"W","E"),
"_Y_",abs(Y[iy]),ifelse(Y[iy]<0,"S","N"))
isimu = isimu + 1
run_ref <- file.path(rundir,run_name)
out_ref <- file.path(outdir,run_name)
if(!dir.exists(run_ref)) dir.create(run_ref)
if(!dir.exists(out_ref)) dir.create(out_ref)
if(!dir.exists(file.path(out_ref,"analy"))) dir.create(file.path(out_ref,"analy"))
if(!dir.exists(file.path(out_ref,"histo"))) dir.create(file.path(out_ref,"histo"))
# ED2IN
ed2in_scenar <- ed2in
ed2in_scenar$IEDCNFGF <- file.path(run_ref,"config.xml")
ed2in_scenar$FFILOUT = file.path(out_ref,"analy","analysis")
ed2in_scenar$SFILOUT = file.path(out_ref,"histo","history")
ed2in_scenar$POI_LAT <- Y[iy]
ed2in_scenar$POI_LON <- X[ix]
ed2in_scenar$SFILIN <- file.path(ICdir,
paste0(cssfile_base,".lat",sprintf("%.4f",Y[iy]),"lon",sprintf("%.4f",X[ix])))
if (file.exists(paste0(ed2in_scenar$SFILIN,".css"))){
css <- read.table(paste0(ed2in_scenar$SFILIN,".css"),header = TRUE)
ed2in_scenar$INCLUDE_THESE_PFT <- sort(unique(css[,6]))
}
if (!land_IC[which(rownames(land_IC)==clat),
which(colnames(land_IC)==clon)]){
ed2in_scenar$IED_INIT_MODE = 0
ed2in_scenar$INCLUDE_THESE_PFT <- 1
}
## Scenars
# Soil properties
if (scenars[iscenar] != "ref"){
if (scenars[iscenar] == "silt"){
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872"
ed2in_scenar$ISOILFLG <- 2
ed2in_scenar$SLXCLAY = 0.053
ed2in_scenar$SLXSAND = 0.073
} else if (scenars[iscenar] == "clay"){
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872"
ed2in_scenar$ISOILFLG <- 2
ed2in_scenar$SLXCLAY = 0.629
ed2in_scenar$SLXSAND = 0.195
} else if (scenars[iscenar] == "ref_nohydro"){
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872"
ed2in_scenar$PLANT_HYDRO_SCHEME <- 0
ed2in_scenar$H2O_PLANT_LIM <- 2
} else if (scenars[iscenar] == "silt_nohydro"){
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872"
ed2in_scenar$PLANT_HYDRO_SCHEME <- 0
ed2in_scenar$H2O_PLANT_LIM <- 2
ed2in_scenar$ISOILFLG <- 2
ed2in_scenar$SLXCLAY = 0.053
ed2in_scenar$SLXSAND = 0.073
} else if (scenars[iscenar] == "clay_nohydro"){
ed2in_scenar$PLANT_HYDRO_SCHEME <- 0
ed2in_scenar$H2O_PLANT_LIM <- 2
ed2in_scenar$ISOILFLG <- 2
ed2in_scenar$SLXCLAY = 0.629
ed2in_scenar$SLXSAND = 0.195
} else if (scenars[iscenar] == "HWSD_ref") {
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872_soil"
soil.textfile <- file.path(run_ref,"soil.txt")
e <- extent(clon-0.05,clon+0.05,clat-0.05,clat+0.05)
ed2in_scenar$SLZ <- all_depths
subsoil <- raster::extract(HWSD[[2]], e)
soil <- rep(subsoil,16)
writeLines(con = soil.textfile, text = as.character(soil))
} else if (scenars[iscenar] == "HWSD") {
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872_soil"
soil.textfile <- file.path(run_ref,"soil.txt")
e <- extent(clon-0.05,clon+0.05,clat-0.05,clat+0.05)
ed2in_scenar$SLZ <- all_depths
topsoil <- raster::extract(HWSD[[1]], e)
subsoil <- raster::extract(HWSD[[2]], e)
soil <- rep(1,16)
soil[ed2in_scenar$SLZ < -1] <- subsoil
soil[ed2in_scenar$SLZ >= -1] <- topsoil
writeLines(con = soil.textfile, text = as.character(soil))
} else if (scenars[iscenar] == "HWSD_SD") {
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872_soil"
soil.textfile <- file.path(run_ref,"soil.txt")
e <- extent(clon-0.05,clon+0.05,clat-0.05,clat+0.05)
ed2in_scenar$SLZ <- all_depths_SD
topsoil <- raster::extract(HWSD[[1]], e)
subsoil <- raster::extract(HWSD[[2]], e)
soil <- rep(1,16)
soil[ed2in_scenar$SLZ < -1] <- subsoil
soil[ed2in_scenar$SLZ >= -1] <- topsoil
writeLines(con = soil.textfile, text = as.character(soil))
} else if (scenars[iscenar] == "soilgrids_ref") {
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872_soil"
soil.textfile <- file.path(run_ref,"soil.txt")
e <- extent(clon-0.05,clon+0.05,clat-0.05,clat+0.05)
ed2in_scenar$SLZ <- all_depths
subsoil <- raster::extract(soilgrids[[6]], e)
soil <- rep(subsoil,16)
writeLines(con = soil.textfile, text = as.character(soil))
} else if (scenars[iscenar] == "soilgrids") {
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872_soil"
soil.textfile <- file.path(run_ref,"soil.txt")
e <- extent(clon-0.05,clon+0.05,clat-0.05,clat+0.05)
ed2in_scenar$SLZ <- all_depths
soil <- rep(1,16)
for (idepth in seq(1,length(depths)-1)){
tempsoil <- raster::extract(soilgrids[[6+1-idepth]], e)
soil[ed2in_scenar$SLZ >= depths[idepth] & ed2in_scenar$SLZ < depths[idepth+1]] <- tempsoil
}
writeLines(con = soil.textfile, text = as.character(soil))
} else if (scenars[iscenar] == "soilgrids_SD") {
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872_soil"
soil.textfile <- file.path(run_ref,"soil.txt")
e <- extent(clon-0.05,clon+0.05,clat-0.05,clat+0.05)
ed2in_scenar$SLZ <- all_depths_SD
soil <- rep(1,16)
# print("----")
for (idepth in seq(1,length(depths)-1)){
tempsoil <- raster::extract(soilgrids[[6+1-idepth]], e)
# print(tempsoil)
soil[ed2in_scenar$SLZ >= depths[idepth] & ed2in_scenar$SLZ < depths[idepth+1]] <- tempsoil
}
writeLines(con = soil.textfile, text = as.character(soil))
}
}
write_ed2in(ed2in_scenar,filename = file.path(run_ref,"ED2IN"))
# config
config_simu <- config
# Modify config if needed
for (ipft in seq(1,length(config_simu))){
if (!(config[[ipft]]["num"] %in% ed2in_scenar$INCLUDE_THESE_PFT)){
config_simu[[names(config)[ipft]]] <- NULL
}
}
xml <- write.config.xml.ED2(defaults = defaults,
settings = settings,
trait.values = config_simu)
XML::saveXML(xml, file = file.path(run_ref,"config.xml"), indent = TRUE,
prefix = PREFIX_XML)
if (isimu == 1){
isfirstjob = TRUE
dir_joblauncher = run_ref
list_dir[[run_name]] = run_ref
} else{
isfirstjob = FALSE
}
# job.sh
write_joblauncher_noR(file = file.path(dir_joblauncher,"job.sh"),
nodes = 1,ppn = 1,mem = 16,walltime = 12,
prerun = "ml purge ; ml UDUNITS/2.2.26-intel-2018a R/3.4.4-intel-2018a-X11-20180131 HDF5/1.10.1-intel-2018a; ulimit -s unlimited",
CD = run_ref,
ed_exec = ed_exec,
ED2IN = "ED2IN",
firstjob = isfirstjob)
if (isimu == Nsimuperjob){
isimu = 0
}
}
}
}
}
dumb <- write_bash_submission(file = file.path(rundir,"all_jobs.sh"),
list_files = list_dir,
job_name = "job.sh")
# scp /home/femeunier/Documents/projects/SoilSensitivity/scripts/generate_SoilSens_test.R hpc:/data/gent/vo/000/gvo00074/felicien/R
femeunier/SoilSensitivity documentation built on March 30, 2022, 10:23 a.m.
R Package Documentation
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rm(list = ls())
library(dplyr)
library(tidyr)
library(PEcAnRTM)
library(purrr)
library(rrtm)
library(ED2scenarios)
library(PEcAn.ED2)
library(purrr)
library(ggplot2)
library(ggridges)
library(cowplot)
library(pracma)
library(BayesianTools)
library(raster)
# library(rnaturalearth)
# library(rnaturalearthdata)
# library(lattice)
ED_REG_LATMIN = -10.5
ED_REG_LATMAX = -0.5
ED_REG_LONMIN = -60.5
ED_REG_LONMAX = -50.5
GRID_RES = 1
X = seq(ED_REG_LONMIN,ED_REG_LONMAX,GRID_RES)
Y = seq(ED_REG_LATMIN,ED_REG_LATMAX,GRID_RES)
ref_dir <- "/data/gent/vo/000/gvo00074/pecan/output/other_runs/SoilSensitivity/run"
rundir <- "/data/gent/vo/000/gvo00074/pecan/output/other_runs/SoilSensitivity/run/grid"
ICdir <- "/data/gent/vo/000/gvo00074/pecan/output/other_runs/LSliana/IC/"
outdir <- "/kyukon/scratch/gent/vo/000/gvo00074/felicien/SoilSensitivity/out"
ed2in <- read_ed2in(file.path(ref_dir,"ED2IN"))
ed2in$IMONTHA = 1
ed2in$IDATEA = 1
ed2in$IYEARA = 2000
ed2in$IMONTHZ = 2
ed2in$IDATEZ = 1
ed2in$IYEARZ = 2005
list_dir <- list()
# load landmask here
land <- readRDS("landmask.RDS")
land_IC <- readRDS("land_IC.RDS")
cssfile_base <- "Amazon"
Nsimuperjob = 3
isimu = 0
defaults <- list()
PREFIX_XML <- "<?xml version=\"1.0\"?>\n<!DOCTYPE config SYSTEM \"ed.dtd\">\n"
# Default settings
settings <- list(model = list(revision = "git",
config.header = NULL),
pfts = list(pft = list(num = 1,
ed2_pft_number = 1,
name = "saccharum"),
pft = list(num = 2,
ed2_pft_number = 2,
name = "Early"),
pft = list(num = 3,
ed2_pft_number = 3,
name = "Mid"),
pft = list(num = 4,
ed2_pft_number = 4,
name = "Late")))
# Config
config <- list()
config[["saccharum"]] <- unlist(list(num = 1))
config[["Early"]] <- unlist(list(num = 2))
config[["Mid"]] <- unlist(list(num = 3))
config[["Late"]] <- unlist(list(num = 4,
wood_Kmax = 0.01))
# scenars <- c("ref","hydro","clay")
# scenars <- c("ref_nohydro","silt_nohydro","clay_nohydro")
# scenars <- c("soilgrids_ref","soilgrids_SD","soilgrids")
scenars <- c("HWSD_ref","HWSD_SD","HWSD")
HWSD <- brick(file.path(".","HWSD_all.grd"))
soilgrids <- brick(file.path(".","soilgrid_all.grd"))
depths <- c(-Inf,-1,-0.6,-0.3,-0.15,Inf)
all_depths <- c(-8,-7,-6.2,-5.5,-4.9,-4.3,-3.8,-3.3,-2.8,-2.3,-1.8,-1.3,-1,-0.6,-0.3,-0.15)
all_depths_SD <- c(-2,-1.9,-1.8,-1.7,-1.6,-1.5,-1.4,-1.3,-1.15,-1,-0.9,-0.75,-0.6,-0.45,-0.3,-0.15)
for(ix in seq(1,length(X))){
for(iy in seq(1,length(Y))){
clat = Y[iy]; clon = X[ix]
if (land[which(rownames(land_IC)==clat),
which(colnames(land_IC)==clon)]){
for (iscenar in seq(1,length(scenars))){
run_name <- paste0("SoilSens_Amazon_",scenars[iscenar],"_X_",abs(X[ix]),ifelse(X[ix]<0,"W","E"),
"_Y_",abs(Y[iy]),ifelse(Y[iy]<0,"S","N"))
isimu = isimu + 1
run_ref <- file.path(rundir,run_name)
out_ref <- file.path(outdir,run_name)
if(!dir.exists(run_ref)) dir.create(run_ref)
if(!dir.exists(out_ref)) dir.create(out_ref)
if(!dir.exists(file.path(out_ref,"analy"))) dir.create(file.path(out_ref,"analy"))
if(!dir.exists(file.path(out_ref,"histo"))) dir.create(file.path(out_ref,"histo"))
# ED2IN
ed2in_scenar <- ed2in
ed2in_scenar$IEDCNFGF <- file.path(run_ref,"config.xml")
ed2in_scenar$FFILOUT = file.path(out_ref,"analy","analysis")
ed2in_scenar$SFILOUT = file.path(out_ref,"histo","history")
ed2in_scenar$POI_LAT <- Y[iy]
ed2in_scenar$POI_LON <- X[ix]
ed2in_scenar$SFILIN <- file.path(ICdir,
paste0(cssfile_base,".lat",sprintf("%.4f",Y[iy]),"lon",sprintf("%.4f",X[ix])))
if (file.exists(paste0(ed2in_scenar$SFILIN,".css"))){
css <- read.table(paste0(ed2in_scenar$SFILIN,".css"),header = TRUE)
ed2in_scenar$INCLUDE_THESE_PFT <- sort(unique(css[,6]))
}
if (!land_IC[which(rownames(land_IC)==clat),
which(colnames(land_IC)==clon)]){
ed2in_scenar$IED_INIT_MODE = 0
ed2in_scenar$INCLUDE_THESE_PFT <- 1
}
## Scenars
# Soil properties
if (scenars[iscenar] != "ref"){
if (scenars[iscenar] == "silt"){
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872"
ed2in_scenar$ISOILFLG <- 2
ed2in_scenar$SLXCLAY = 0.053
ed2in_scenar$SLXSAND = 0.073
} else if (scenars[iscenar] == "clay"){
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872"
ed2in_scenar$ISOILFLG <- 2
ed2in_scenar$SLXCLAY = 0.629
ed2in_scenar$SLXSAND = 0.195
} else if (scenars[iscenar] == "ref_nohydro"){
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872"
ed2in_scenar$PLANT_HYDRO_SCHEME <- 0
ed2in_scenar$H2O_PLANT_LIM <- 2
} else if (scenars[iscenar] == "silt_nohydro"){
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872"
ed2in_scenar$PLANT_HYDRO_SCHEME <- 0
ed2in_scenar$H2O_PLANT_LIM <- 2
ed2in_scenar$ISOILFLG <- 2
ed2in_scenar$SLXCLAY = 0.053
ed2in_scenar$SLXSAND = 0.073
} else if (scenars[iscenar] == "clay_nohydro"){
ed2in_scenar$PLANT_HYDRO_SCHEME <- 0
ed2in_scenar$H2O_PLANT_LIM <- 2
ed2in_scenar$ISOILFLG <- 2
ed2in_scenar$SLXCLAY = 0.629
ed2in_scenar$SLXSAND = 0.195
} else if (scenars[iscenar] == "HWSD_ref") {
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872_soil"
soil.textfile <- file.path(run_ref,"soil.txt")
e <- extent(clon-0.05,clon+0.05,clat-0.05,clat+0.05)
ed2in_scenar$SLZ <- all_depths
subsoil <- raster::extract(HWSD[[2]], e)
soil <- rep(subsoil,16)
writeLines(con = soil.textfile, text = as.character(soil))
} else if (scenars[iscenar] == "HWSD") {
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872_soil"
soil.textfile <- file.path(run_ref,"soil.txt")
e <- extent(clon-0.05,clon+0.05,clat-0.05,clat+0.05)
ed2in_scenar$SLZ <- all_depths
topsoil <- raster::extract(HWSD[[1]], e)
subsoil <- raster::extract(HWSD[[2]], e)
soil <- rep(1,16)
soil[ed2in_scenar$SLZ < -1] <- subsoil
soil[ed2in_scenar$SLZ >= -1] <- topsoil
writeLines(con = soil.textfile, text = as.character(soil))
} else if (scenars[iscenar] == "HWSD_SD") {
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872_soil"
soil.textfile <- file.path(run_ref,"soil.txt")
e <- extent(clon-0.05,clon+0.05,clat-0.05,clat+0.05)
ed2in_scenar$SLZ <- all_depths_SD
topsoil <- raster::extract(HWSD[[1]], e)
subsoil <- raster::extract(HWSD[[2]], e)
soil <- rep(1,16)
soil[ed2in_scenar$SLZ < -1] <- subsoil
soil[ed2in_scenar$SLZ >= -1] <- topsoil
writeLines(con = soil.textfile, text = as.character(soil))
} else if (scenars[iscenar] == "soilgrids_ref") {
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872_soil"
soil.textfile <- file.path(run_ref,"soil.txt")
e <- extent(clon-0.05,clon+0.05,clat-0.05,clat+0.05)
ed2in_scenar$SLZ <- all_depths
subsoil <- raster::extract(soilgrids[[6]], e)
soil <- rep(subsoil,16)
writeLines(con = soil.textfile, text = as.character(soil))
} else if (scenars[iscenar] == "soilgrids") {
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872_soil"
soil.textfile <- file.path(run_ref,"soil.txt")
e <- extent(clon-0.05,clon+0.05,clat-0.05,clat+0.05)
ed2in_scenar$SLZ <- all_depths
soil <- rep(1,16)
for (idepth in seq(1,length(depths)-1)){
tempsoil <- raster::extract(soilgrids[[6+1-idepth]], e)
soil[ed2in_scenar$SLZ >= depths[idepth] & ed2in_scenar$SLZ < depths[idepth+1]] <- tempsoil
}
writeLines(con = soil.textfile, text = as.character(soil))
} else if (scenars[iscenar] == "soilgrids_SD") {
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872_soil"
soil.textfile <- file.path(run_ref,"soil.txt")
e <- extent(clon-0.05,clon+0.05,clat-0.05,clat+0.05)
ed2in_scenar$SLZ <- all_depths_SD
soil <- rep(1,16)
# print("----")
for (idepth in seq(1,length(depths)-1)){
tempsoil <- raster::extract(soilgrids[[6+1-idepth]], e)
# print(tempsoil)
soil[ed2in_scenar$SLZ >= depths[idepth] & ed2in_scenar$SLZ < depths[idepth+1]] <- tempsoil
}
writeLines(con = soil.textfile, text = as.character(soil))
}
}
write_ed2in(ed2in_scenar,filename = file.path(run_ref,"ED2IN"))
# config
config_simu <- config
# Modify config if needed
for (ipft in seq(1,length(config_simu))){
if (!(config[[ipft]]["num"] %in% ed2in_scenar$INCLUDE_THESE_PFT)){
config_simu[[names(config)[ipft]]] <- NULL
}
}
xml <- write.config.xml.ED2(defaults = defaults,
settings = settings,
trait.values = config_simu)
XML::saveXML(xml, file = file.path(run_ref,"config.xml"), indent = TRUE,
prefix = PREFIX_XML)
if (isimu == 1){
isfirstjob = TRUE
dir_joblauncher = run_ref
list_dir[[run_name]] = run_ref
} else{
isfirstjob = FALSE
}
# job.sh
write_joblauncher_noR(file = file.path(dir_joblauncher,"job.sh"),
nodes = 1,ppn = 1,mem = 16,walltime = 12,
prerun = "ml purge ; ml UDUNITS/2.2.26-intel-2018a R/3.4.4-intel-2018a-X11-20180131 HDF5/1.10.1-intel-2018a; ulimit -s unlimited",
CD = run_ref,
ed_exec = ed_exec,
ED2IN = "ED2IN",
firstjob = isfirstjob)
if (isimu == Nsimuperjob){
isimu = 0
}
}
}
}
}
dumb <- write_bash_submission(file = file.path(rundir,"all_jobs.sh"),
list_files = list_dir,
job_name = "job.sh")
# scp /home/femeunier/Documents/projects/SoilSensitivity/scripts/generate_SoilSens_test.R hpc:/data/gent/vo/000/gvo00074/felicien/R
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