Replacement scripts for TSMP2 (domain-file, globecover, topography)

mksurfdata/README_replace.md

@@ -4,4 +4,30 @@ The script `replace_clm5_with_clm3_5_data.sh` replaces variables in the CLM5 sur
 The changed mapping for CLM3_5 can be found here:
 https://icg4geo.icg.kfa-juelich.de/Configurations/TSMP_statfiles_IBG3/TSMP_EUR-0275/-/tree/main/static.resource/08_LandCover
 
+# Replacement of CLM5 data with ICON data
+
+** work in progress, on the long-run to be implemented in the static file generation process **
+
+This section assumes that CLM performs on the icosahedral grid.
+
+For running R-script on JSC machine, load `ml Stages/2025  GCCcore R` in advance, R-package `ncdf4` needs to be installed.
+
+This script unifies the CLM5/eCLM domain file and surface file.
+
+Replacement of domain file:
+`Rscript replace_domfile2tsmp.r`
+This script can be also used to modify the OASIS mask (optional).
+
+Replacement of surface file:
+`Rscript replace_surdat2tsmp.r`
+
+Replacement of topography file:
+`Rscript replace_topo2tsmp.r`
+
+Cut out lateral boundary grid points in static fields with mean of NCO:
+At JSC machines, load environment `ml Stages/2025  Intel/2024.2.0-CUDA-12  ParaStationMPI/5.10.0-1 NCO/5.3.0`
+
+Use `ncks` to cut the domain, e.g. for 
+`ncks -d gridcell,9944,199919 <file-in> <file-out>`
+`chmod 755 <file-out>`
 

mksurfdata/replace_domfile2tsmp.r

@@ -0,0 +1,156 @@
+## Program to CLM5/eCLM domain file
+##
+##
+
+## Load libs
+require(ncdf4)
+
+########
+## Settings
+########
+
+dirname <- "/p/scratch/cslts/poll1/sim/euro-cordex/tsmp2_workflow-engine/dta/geo/"
+
+# Reference eCLM domainfile 
+fnameraw <- paste0(dirname,"eclm/static/domain.lnd.ICON-11_ICON-11.230302.nc")
+#fnameraw <- "/p/scratch/cslts/poll1/sim/euro-cordex/eur-0275_icon-eclm_testcase/eur-0275_icon-eclm_testcase/geo/static/eclm/domain.lnd.R13B07_R13B07.240419.nc"
+
+# New/Modified eCLM domainfile
+fnamenew <- paste0(dirname,"eclm/static/domain.lnd.ICON-11_ICON-11.230302_landlake.nc")
+#fnamenew <- "/p/scratch/cslts/poll1/sim/euro-cordex/eur-0275_icon-eclm_testcase/eur-0275_icon-eclm_testcase/geo/static/eclm/domain.lnd.R13B07_R13B07.240419_land.nc"
+
+
+# Reference files (ICON grid and external pareameter)
+l_hom <- F # all grid points active (reference needed)
+fnameref <- paste0(dirname,"icon/static/europe011_DOM01.nc")
+fnamerefext <-  paste0(dirname,"icon/static/external_parameter_icon_europe011_DOM01_tiles.nc")
+#fnameref <- "/p/scratch/cslts/poll1/sim/euro-cordex/eur-0275_icon-eclm_testcase/eur-0275_icon-eclm_testcase/geo/static/icon/EUR-R13B07_2473796_grid_inclbrz_v1.nc"
+#fnamerefext <- "/p/scratch/cslts/poll1/sim/euro-cordex/eur-0275_icon-eclm_testcase/eur-0275_icon-eclm_testcase/geo/static/icon/external_parameter_icon_EUR-R13B07_2473796_grid_inclbrz_v1.nc"
+
+# 
+l_rm_iconlake <- F
+fnamenewext <-  paste0(dirname,"icon/static/external_parameter_icon_europe011_DOM01_tiles_nolakes.nc")
+#fnamenewext <- "/p/scratch/cslts/poll1/sim/euro-cordex/eur-0275_icon-eclm_testcase/eur-0275_icon-eclm_testcase/geo/static/icon/external_parameter_icon_EUR-R13B07_2473796_grid_inclbrz_v1_allland.nc"
+
+# 
+l_oas_mask <- F
+fnameoasmask <-  paste0(dirname,"oasis/static/masks_lakes_rev.nc")
+#fnameoasmask <- "/p/scratch/cslts/poll1/sim/euro-cordex/tsmp2_workflow-engine/dta/geo/oasis/static/masks_lakes_rev.nc"
+
+########
+## Start of Program
+########
+
+# const
+r_earth <- 6371000 # can vary with lon/lat
+
+## Read in actual grid
+
+ff <- nc_open(fnameraw)
+mask_raw <- ncvar_get(ff,"mask")
+frac_raw <- ncvar_get(ff,"frac")
+area_raw <- ncvar_get(ff,"area")
+lonc_raw <- ncvar_get(ff,"xc")
+lonv_raw <- ncvar_get(ff,"xv")
+nc_close(ff)
+
+if (l_hom){
+
+ # all land
+ mask_new <- array(1,dim(mask_raw))
+ frac_new <- array(1,dim(frac_raw))
+
+} else {
+
+ ##
+ ff <- nc_open(fnameref)
+ area_ref <- ncvar_get(ff,"cell_area")
+ nc_close(ff)
+
+ ff <- nc_open(fnamerefext)
+ frland_ref <- ncvar_get(ff,"FR_LAND")
+ frlake_ref <- ncvar_get(ff,"FR_LAKE")
+ soiltyp_ref <- ncvar_get(ff,"SOILTYP")
+ luclass_ref <- ncvar_get(ff,"LU_CLASS_FRACTION")
+ nc_close(ff)
+
+ mask_new <- array(1,dim(mask_raw))
+
+ ## Calculate new mask
+ mask_new <- frac_new <- array(1,dim(mask_raw))
+ frland_new <- frland_ref+frlake_ref
+ mask_new[frland_new<0.5] <- 0 # water points but no lakes
+ frac_new[frland_new<0.5] <- 0
+
+} # l_hom
+
+## Remove lake soil type from ICON
+if (l_rm_iconlake){
+ soiltyp_new <- soiltyp_ref
+ ind_frland <- which(frland_new>=0.5)
+ for (ii in 1:length(ind_frland)){
+   if (soiltyp_ref[ind_frland[ii]]==8 | soiltyp_ref[ind_frland[ii]]==9){
+     soiltyp_new[ind_frland[ii]] <- 3 # change to sandy soil
+   } # if soiltyp
+ } # for ii
+ luclass_new <- luclass_ref
+ #ind_frlake <- which(frlake_ref>=0.5)
+ ind_frlake <- which(frlake_ref>0.)
+ for (ii in 1:length(ind_frlake)){
+   # take water point lu to vegetation
+   luclass_new[ind_frlake[ii],21] <- luclass_ref[ind_frlake[ii],21]-frlake_ref[ind_frlake[ii]]
+   luclass_new[ind_frlake[ii],4] <- luclass_ref[ind_frlake[ii],4]+frlake_ref[ind_frlake[ii]]
+ } # for ii
+
+ # to check LU_CLASS_FRACTION, NDVIRATIO, NDVI_MAX
+} # l_rm_iconlake
+
+# transform all negative longitudes
+lonc_new <- lonc_raw
+lonc_new[lonc_new< 0] = lonc_new[lonc_new< 0]+360
+lonv_new <- lonv_raw
+lonv_new[lonv_new< 0] = lonv_new[lonv_new< 0]+360
+
+# transform to radian
+area_new <- area_ref/r_earth
+
+frlake_new <- array(0,dim(frlake_ref))
+
+## Overwrite eCLM grid
+
+if (!file.exists(fnamenew))
+    system(paste0("cp ",fnameraw," ",fnamenew))
+
+filename <- paste0(fnamenew)
+ff <- nc_open(filename,write=TRUE)
+ncvar_put(ff,"mask",mask_new)
+ncvar_put(ff,"frac",frac_new)
+ncvar_put(ff,"area",area_new)
+ncvar_put(ff,"xc",lonc_new)
+ncvar_put(ff,"xv",lonv_new)
+nc_close(ff)
+
+print(paste("Write new CLM domain file ",fnamenew))
+
+## Overwrite ICON extpar
+if (l_rm_iconlake){
+ if (!file.exists(fnamenewext))
+    system(paste0("cp ",fnamerefext," ",fnamenewext))
+
+ ff <- nc_open(fnamenewext,write=TRUE)
+ ncvar_put(ff,"FR_LAKE",frlake_new)
+ ncvar_put(ff,"SOILTYP",soiltyp_new)
+ ncvar_put(ff,"LU_CLASS_FRACTION",luclass_new)
+ nc_close(ff) 
+
+ print(paste("Write new ICON external parameter",fnamenewext)) 
+} # l_rm_iconlake
+
+## rewrite mask.nc
+if (l_oas_mask){
+ mask_oas <- array(0,dim(mask_raw))
+ mask_oas[mask_new==0] <- 1 # inverse mask
+ ff <- nc_open(fnameoasmask,write=TRUE)
+ ncvar_put(ff,"gclm.msk",mask_oas)
+ nc_close(ff)  
+} # l_oas_mask