Added full chemistry case

cases/icon-art-full-chem/config.yaml

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+# Configuration file for the 'icon-art-full-chem-test' case with ICON
+
+workflow: icon-art-full-chem
+constraint: mc
+run_on: cpu
+compute_queue: normal
+ntasks_per_node: 36
+restart_step: PT6H
+startdate: 2019-02-12T00:00:00Z
+enddate: 2019-02-26T00:00:00Z
+
+eccodes_dir: /users/icontest/pool/data/ICON/mch/eccodes_definitions
+latbc_filename: LBC_<y><m><d><h>.nc
+inidata_prefix: IC_
+inidata_nameformat: '%Y%m%d%H'
+inidata_filename_suffix: .nc
+lbcdata_prefix: LBC_
+lbcdata_nameformat: '%Y%m%d%H'
+lbcdata_filename_suffix: .nc
+output_filename: icon-full-chem-test
+filename_format: <output_filename>_<ddhhmmss>
+lateral_boundary_grid_order: lateral_boundary
+art_input_folder: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/art
+
+walltime:
+    prepare_icon: '00:10:00'
+    prepare_art_full_chem: '01:00:00'
+    icon: '02:00:00'
+
+meteo:
+    dir: /scratch/snx3000/ckeller/proc_chain_data/input/meteo
+    prefix: era5_
+    nameformat: '%Y%m%d%H'
+    suffix: .grb
+    inc: 3
+
+chem:
+    dir: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/chem
+    prefix: camchem_
+    nameformat: '%Y%m%d%H'
+    suffix: .nc
+    inc: 3
+    icbc_filename: camchem-20190212-20190226.nc
+    ref_date: '2000-03-01 00:00:00'
+
+
+input_files:
+    radiation_grid_filename: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/grid/base_grid.nc
+    #radiation_grid_filename: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/grid/icon_R03B07_DOM01.nc
+    dynamics_grid_filename: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/grid/icon_R03B07_DOM01.nc
+    #dynamics_grid_filename: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/grid/icon_R03B08_DOM02.nc
+    map_file_latbc: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/grid/map_file.latbc
+    lateral_boundary_grid: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/grid/lateral_boundary_DOM01.grid.nc
+    #lateral_boundary_grid: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/grid/lateral_boundary_DOM02.grid.nc
+    extpar_filename: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/grid/extpar_DOM01.nc
+    #extpar_filename: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/grid/extpar_DOM02.nc
+    cldopt_filename: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/rad/rrtm_cldopt.nc
+    lrtm_filename: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/rad/rrtmg_lw.nc
+    map_file_ana: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/mapping/map_file.ana
+    meccatracer_xml_filename: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/xml/mecca_tracers.xml
+    oem_gridded_emissions_nc: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/oem/oem_gridded_emissions.nc
+    oem_vertical_profiles_nc: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/oem/vertical_profiles.nc
+    oem_hourofday_nc: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/oem/hourofday.nc
+    oem_dayofweek_nc: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/oem/dayofweek.nc
+    oem_monthofyear_nc: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/oem/monthofyear.nc
+    #oem_gridded_emissions_nc: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/oem/oem_gridded_emissions_DOM02.nc
+    #oem_vertical_profiles_nc: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/oem/vertical_profiles_DOM02.nc
+    #oem_hourofday_nc: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/oem/hourofday_DOM02.nc
+    #oem_dayofweek_nc: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/oem/dayofweek_DOM02.nc
+    #oem_monthofyear_nc: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/oem/monthofyear_DOM02.nc
+    aerodyn_tracers: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/aerodyn/tracers_aerosol.xml
+    aerodyn_modes: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/aerodyn/modes.xml
+    aerodyn_coag: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/aerodyn/coagulate.xml
+    aerodyn_emiss: /scratch/snx3000/ckeller/proc_chain_data/input/icon-art-full-chem/aerodyn/emiss.xml
+
+
+icon:
+    binary_file: /scratch/snx3000/ckeller/proc_chain_data/ext/icon-art/bin/icon
+    runjob_filename: icon_runjob.cfg
+    era5_icjob: icon_era5_ic.sh
+    era5_lbcjob: icon_era5_lbc.sh
+    chem_icjob: icon_camchem_ic.sh
+    chem_lbcjob: icon_camchem_lbc.sh
+    compute_queue: normal
+    walltime: '02:00:00'
+    np_tot: 32
+    np_io: 3
+    np_restart: 1
+    np_prefetch: 1
+    timestep: 120.
+

cases/icon-art-full-chem/icon_camchem_ic.sh

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+#!/bin/bash
+
+cd {cfg.icon_input_icbc}
+
+# ---------------------------------
+# -- Pre-processing
+# ---------------------------------
+
+rm -f {cfg.icon_input_icbc}/{cfg.chem_prefix}{cfg.startdate_sim_yyyymmddhh}_ic_icon{cfg.inidata_filename_suffix}
+
+# -- Change variable and coordinates names to be consistent with MECCA nomenclature
+cdo setpartabn,partab_chem,convert {cfg.icon_input_icbc}/{cfg.chem_prefix}{cfg.startdate_sim_yyyymmddhh}_ic{cfg.chem_suffix} data_in.nc
+
+# ---------------------------------
+# -- Re-mapping
+# ---------------------------------
+
+# -- Retrieve the triangular horizontal grid
+cdo -s selgrid,2 {cfg.input_files_scratch_dynamics_grid_filename} triangular-grid.nc
+
+# -- Create the weights for remapping CAM-Chem (lat,lon) grid onto the triangular grid
+echo "creating weights"
+cdo genbil,triangular-grid.nc data_in.nc weights.nc
+
+# -- Remap
+cdo -s remap,triangular-grid.nc,weights.nc data_in.nc chem_final.nc
+rm data_in.nc triangular-grid.nc
+
+# ---------------------------------
+# -- Post-processing
+# ---------------------------------
+
+# -- Rename dimensions and order alphabetically
+ncrename -h -d cell,ncells chem_final.nc
+ncrename -h -d nv,vertices chem_final.nc
+ncks chem_final.nc {cfg.icon_input_icbc}/{cfg.chem_prefix}{cfg.startdate_sim_yyyymmddhh}_ic_icon{cfg.inidata_filename_suffix} 
+rm chem_final.nc weights.nc 
+
+# -- Clean up
+rm {cfg.icon_input_icbc}/{cfg.chem_prefix}{cfg.startdate_sim_yyyymmddhh}_ic{cfg.chem_suffix}

cases/icon-art-full-chem/icon_camchem_lbc.sh

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+#!/bin/bash
+
+cd {cfg.icon_input_icbc}
+
+# -- Loop over file list
+i=0
+echo "DATAFILELIST is {datafile_list_chem}"
+for datafilename in {datafile_list_chem} ; do
+	datafile="${{datafilename##*/}}"  # get filename without path
+	outdatafile=${{datafile%.*}}      # get filename without suffix
+    ((i++))
+
+    # ---------------------------------
+    # -- Pre-processing
+    # ---------------------------------
+
+    rm -f {cfg.icon_input_icbc}/${{outdatafile}}_icon{cfg.inidata_filename_suffix}
+
+    # -- Change variable and coordinates names to be consistent with ICON nomenclature
+    cdo setpartabn,partab_chem,convert $datafilename data_in.nc
+
+    # ---------------------------------
+    # -- Re-mapping
+    # ---------------------------------
+
+    # -- Retrieve the lateral boundary grid 
+    cdo -s selgrid,2 {cfg.input_files_scratch_lateral_boundary_grid} triangular-grid.nc
+
+    # -- Create the weights for remapping CAM-Chem data from latlon grid onto the triangular grid
+    if [[ $i == "1" ]] ; then
+        echo "creating weights"
+        cdo genbil,triangular-grid.nc data_in.nc weights.nc
+    fi
+
+    # -- Remap
+    cdo -s remap,triangular-grid.nc,weights.nc data_in.nc chem_final.nc
+    rm data_in.nc triangular-grid.nc
+
+    # ---------------------------------
+    # -- Post-processing
+    # ---------------------------------
+
+    # -- Rename dimensions and order alphabetically
+    ncrename -h -d cell,ncells chem_final.nc
+    ncrename -h -d nv,vertices chem_final.nc
+    ncks chem_final.nc {cfg.icon_input_icbc}/${{outdatafile}}_icon{cfg.inidata_filename_suffix}
+    rm chem_final.nc 
+
+    # -- Clean up
+    rm $datafilename
+done
+# -- Clean up
+rm weights.nc

cases/icon-art-full-chem/icon_era5_ic.sh

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+#!/bin/bash
+
+cd {cfg.icon_input_icbc}
+
+# ---------------------------------
+# -- Pre-processing
+# ---------------------------------
+
+rm -f {cfg.icon_input_icbc}/{cfg.meteo_prefix}{cfg.startdate_sim_yyyymmddhh}_ic{cfg.inidata_filename_suffix}
+
+# -- Convert the GRIB files to NetCDF
+cdo -t ecmwf -f nc copy {cfg.meteo_dir}/{cfg.meteo_prefix}{cfg.startdate_sim_yyyymmddhh}{cfg.meteo_suffix} era5_ori.nc
+
+# -- Change variable and coordinates names to be consistent with ICON nomenclature
+cdo setpartabn,partab_meteo,convert era5_ori.nc tmp.nc
+
+# -- Order the variables alphabetically 
+ncks tmp.nc data_in.nc
+rm tmp.nc era5_ori.nc
+
+# ---------------------------------
+# -- Re-mapping
+# ---------------------------------
+
+# -- Retrieve the triangular grid
+cdo -s selgrid,2 {cfg.input_files_scratch_dynamics_grid_filename} triangular-grid.nc
+
+# -- Create the weights for remapping era5 latlon grid onto the triangular grid
+cdo gendis,triangular-grid.nc data_in.nc weights.nc
+
+# -- Extract the land-sea mask variable 
+cdo selname,LSM data_in.nc LSM_in.nc
+ncrename -h -v LSM,FR_LAND LSM_in.nc
+cdo selname,FR_LAND {cfg.input_files_scratch_extpar_filename} LSM_out_tmp.nc
+
+# -- Add time dimension to LSM_out.nc
+ncecat -O -u time LSM_out_tmp.nc LSM_out_tmp.nc
+ncks -h -A -v time LSM_in.nc LSM_out_tmp.nc
+
+# -- Create two different files for land- and sea-mask
+# --------------------------------------------------
+# -- Comments: 
+# -- setctomoss,0. = setting missing values to 0.
+# -- gtc = greater than constant (o(t,x) = 1 if i(t,x) > const, o(t,x) = 0 else)
+# -- ltc = lower than constant (o(t,x) = 1 if i(t,x) < const, o(t,x) = 0 else)
+# --------------------------------------------------
+cdo -L setctomiss,0. -ltc,0.5  LSM_in.nc oceanmask_in.nc
+cdo -L setctomiss,0. -gec,0.5 LSM_in.nc landmask_in.nc
+cdo -L setctomiss,0. -ltc,0.5 LSM_out_tmp.nc oceanmask_out.nc
+cdo -L setctomiss,0. -gec,0.5 LSM_out_tmp.nc landmask_out.nc
+cdo setrtoc2,0.5,1.0,1,0 LSM_out_tmp.nc LSM_out.nc
+rm LSM_in.nc LSM_out_tmp.nc
+
+# -- Select surface sea variables defined only on sea
+ncks -h -v SST,CI data_in.nc datasea_in.nc
+
+# -- Select surface variables defined on both that must be remapped differently on sea and on land
+ncks -h -v SKT,STL1,STL2,STL3,STL4,ALB_SNOW,W_SNOW,T_SNOW data_in.nc dataland_in.nc
+
+# -----------------------------------------------------------------------------
+# -- Remap land and ocean area differently for variables
+# -----------------------------------------------------------------------------
+
+# -- Ocean part
+# -----------------
+
+# -- Apply the ocean mask (by dividing)
+cdo div dataland_in.nc oceanmask_in.nc tmp1_land.nc
+cdo div datasea_in.nc oceanmask_in.nc tmp1_sea.nc
+
+# -- Set missing values to a distance-weighted average
+cdo setmisstodis tmp1_land.nc tmp2_land.nc
+cdo setmisstodis tmp1_sea.nc tmp2_sea.nc
+
+# -- Remap 
+cdo remap,triangular-grid.nc,weights.nc tmp2_land.nc tmp3_land.nc
+cdo remap,triangular-grid.nc,weights.nc tmp2_sea.nc tmp3_sea.nc
+
+
+# -- Apply the ocean mask to remapped variables (by dividing)
+cdo div tmp3_land.nc oceanmask_out.nc dataland_ocean_out.nc
+cdo div tmp3_sea.nc oceanmask_out.nc datasea_ocean_out.nc
+
+# -- Clean the repository
+rm tmp*.nc oceanmask*.nc
+
+# -- Land part
+# -----------------
+
+cdo div dataland_in.nc landmask_in.nc tmp1.nc
+cdo setmisstodis tmp1.nc tmp2.nc
+cdo remap,triangular-grid.nc,weights.nc tmp2.nc tmp3.nc
+cdo div tmp3.nc landmask_out.nc dataland_land_out.nc
+rm tmp*.nc landmask*.nc dataland_in.nc datasea_in.nc
+
+# -- merge remapped land and ocean part
+# --------------------------------------
+
+cdo ifthenelse LSM_out.nc dataland_land_out.nc dataland_ocean_out.nc dataland_out.nc
+rm dataland_ocean_out.nc dataland_land_out.nc
+
+# remap the rest and merge all files
+# --------------------------------------
+
+# -- Select all variables apart from these ones
+ncks -h -x -v SKT,STL1,STL2,STL3,STL4,ALB_SNOW,W_SNOW,T_SNOW,SST,CI,LSM data_in.nc datarest_in.nc
+# -- Remap
+cdo -s remap,triangular-grid.nc,weights.nc datarest_in.nc era5_final.nc
+rm datarest_in.nc data_in.nc
+
+# -- Fill NaN values for SST and CI
+cdo setmisstodis -selname,SST,CI datasea_ocean_out.nc dataland_ocean_out_filled.nc
+rm datasea_ocean_out.nc
+
+# -- Merge remapped files plus land-sea mask from EXTPAR
+ncks -h -A dataland_out.nc era5_final.nc
+ncks -h -A dataland_ocean_out_filled.nc era5_final.nc
+ncks -h -A -v FR_LAND LSM_out.nc era5_final.nc
+ncrename -h -v FR_LAND,LSM era5_final.nc
+rm LSM_out.nc dataland_out.nc dataland_ocean_out_filled.nc
+
+# ---------------------------------
+# -- Post-processing
+# ---------------------------------
+
+ncrename -h -d cell,ncells era5_final.nc
+ncrename -h -d nv,vertices era5_final.nc
+ncks era5_final.nc {cfg.icon_input_icbc}/{cfg.meteo_prefix}{cfg.startdate_sim_yyyymmddhh}_ic{cfg.inidata_filename_suffix}
+rm era5_final.nc
+
+# -- Clean up
+rm triangular-grid.nc weights.nc 

cases/icon-art-full-chem/icon_era5_lbc.sh

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+#!/bin/bash
+
+cd {cfg.icon_input_icbc}
+
+# -- Loop over file list
+i=0
+for datafilename in {datafile_list_meteo} ; do
+    datafile="${{datafilename##*/}}"  # get filename without path
+	outdatafile=${{datafile%.*}}      # get filename without suffix
+    ((i++))
+
+    # ---------------------------------
+    # -- Pre-processing
+    # ---------------------------------
+
+    rm -f {cfg.icon_input_icbc}/${{outdatafile}}_lbc{cfg.inidata_filename_suffix}
+
+    # -- Convert the GRIB files to NetCDF
+    cdo -t ecmwf -f nc copy $datafilename era5_ori.nc    
+
+    # -- Change variable and coordinates names to be consistent with ICON nomenclature
+    cdo setpartabn,partab_meteo,convert era5_ori.nc tmp.nc
+    # -- Order the variables alphabetically 
+    ncks tmp.nc data_in.nc
+    rm tmp.nc era5_ori.nc
+
+    # ---------------------------------
+    # -- Re-mapping
+    # ---------------------------------
+
+    # -- Retrieve the lateral boundary grid 
+    cdo -s selgrid,2 {cfg.input_files_scratch_lateral_boundary_grid} triangular-grid.nc
+
+    # -- Create the weights for remapping era5 latlon grid onto the triangular grid
+    if [[ $i == "1" ]] ; then
+        echo "creating weights"
+        cdo gendis,triangular-grid.nc data_in.nc weights.nc
+    fi
+
+    # -- Remap
+    cdo -s remap,triangular-grid.nc,weights.nc data_in.nc era5_final.nc
+    rm data_in.nc triangular-grid.nc
+
+    # ---------------------------------
+    # -- Post-processing
+    # ---------------------------------
+
+    ncrename -h -d cell,ncells era5_final.nc
+    ncrename -h -d nv,vertices era5_final.nc
+    ncks era5_final.nc {cfg.icon_input_icbc}/${{outdatafile}}_lbc{cfg.inidata_filename_suffix}
+    rm era5_final.nc
+done
+# -- Clean up
+rm weights.nc